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Conserved domains on  [gi|1907829357|ref|NP_001373993|]
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cytoplasmic polyadenylation element-binding protein 1 isoform 5 [Homo sapiens]

Protein Classification

cytoplasmic polyadenylation element-binding protein 1( domain architecture ID 11242593)

cytoplasmic polyadenylation element-binding protein 1 (CPEB-1) is a sequence-specific RNA-binding protein that regulates mRNA cytoplasmic polyadenylation and translation initiation during oocyte maturation, early development and at postsynapse sites of neurons

CATH:  3.30.70.330
Gene Symbol:  CPEB1
SCOP:  3000110

Graphical summary

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List of domain hits

Name Accession Description Interval E-value
CEBP1_N pfam16368
Cytoplasmic polyadenylation element-binding protein 1 N-terminus; This is the N-terminal ...
31-334 3.94e-154

Cytoplasmic polyadenylation element-binding protein 1 N-terminus; This is the N-terminal domain of cytoplasmic polyadenylation element-binding protein 1.


:

Pssm-ID: 465107  Cd Length: 307  Bit Score: 444.35  E-value: 3.94e-154
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907829357  31 PLEEEAGRIKDCWDNQEAPALSTCSNANIFRRINAILDNSLDFSRVCTTPINRGIHDHLPDFQDSEETVTSRMLFPTSAQ 110
Cdd:pfam16368   4 SLVRSIKRCWDSPDAPELPALSTCSNADIFRRMNTMLGNSLDFTGVCTTPSKKDKLDDLQDSEDSVAAVMSRMLFPSESQ 83
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907829357 111 ESSRGLPDANDLCLGLQSLSLTGWDRPWSTQDSDSSAQSSTHSVLSMLHNPLGNVLGKPPLSFLPLDPLGSDLVDKFPAP 190
Cdd:pfam16368  84 RSSRGLPDVNDLGLGLQSLSLSGWDRPWSTQDAEQSSQQSVPSMLGNLLSPLLGKLGKGPLGLLPIDSDGPDFLEKFPLR 163
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907829357 191 SVRGSRLDTRPILDSRSSSPSDSDTSGFSSGSDHLSDLISSLRISPPLPFLSLSGGGPRDPLKMGVGSRMDQEQAALAAV 270
Cdd:pfam16368 164 ASRSSRLDSRSLLDSRSSSPDDSETSGFSSGSDHLSDLLSSLRISPPLPFSGLMSRDPKDPLKLSQGSRLDAASAALTSS 243
                         250       260       270       280       290       300
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1907829357 271 TPSPTSASKRWPGASVWPSWDLLEAPKDPFSIEREARLHRQAAAVNEATCTWSGQLPPRNYKNP 334
Cdd:pfam16368 244 PASASSLSPRWPGASVWPSWDLLEDPFSPFSIEREARLHRQAAAVNEATFTWSGQLPPRNYKNP 307
RRM1_CPEB1 cd12723
RNA recognition motif 1 (RRM1) found in cytoplasmic polyadenylation element-binding protein 1 ...
336-438 2.20e-68

RNA recognition motif 1 (RRM1) found in cytoplasmic polyadenylation element-binding protein 1 (CPEB-1) and similar proteins; This subgroup corresponds to the RRM2 of CPEB-1 (also termed CPE-BP1 or CEBP), an RNA-binding protein that interacts with the cytoplasmic polyadenylation element (CPE), a short U-rich motif in the 3' untranslated regions (UTRs) of certain mRNAs. It functions as a translational regulator that plays a major role in the control of maternal CPE-containing mRNA in oocytes, as well as of subsynaptic CPE-containing mRNA in neurons. Once phosphorylated and recruiting the polyadenylation complex, CPEB-1 may function as a translational activator stimulating polyadenylation and translation. Otherwise, it may function as a translational inhibitor when dephosphorylated and bound to a protein such as maskin or neuroguidin, which blocks translation initiation through interfering with the assembly of eIF-4E and eIF-4G. Although CPEB-1 is mainly located in cytoplasm, it can shuttle between nucleus and cytoplasm. CPEB-1 contains an N-terminal unstructured region, two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a Zn-finger motif. Both of the RRMs and the Zn finger are required for CPEB-1 to bind CPE. The N-terminal regulatory region may be responsible for CPEB-1 interacting with other proteins.


:

Pssm-ID: 410122 [Multi-domain]  Cd Length: 101  Bit Score: 216.40  E-value: 2.20e-68
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907829357 336 YSCKVFLGGVPWDITEAGLVNTFRVFGSLSVEWPGKDGKHPR-CPPKGYVYLVFELEKSVRSLLQACSHDplsPDGLSEY 414
Cdd:cd12723     1 YSCKVFLGGVPWDITEAGLQNAFKPFGSLSVEWPGKDGKHPRgHPPKGYVYLIFESEKSVKALLQACTHD---FLGGGEY 77
                          90       100
                  ....*....|....*....|....
gi 1907829357 415 YFKMSSRRMRCKEVQVIPWVLADS 438
Cdd:cd12723    78 YFKISSRRMRSKEVQVIPWVLSDS 101
RRM2_CPEB1 cd12725
RNA recognition motif 2 (RRM2) found in cytoplasmic polyadenylation element-binding protein 1 ...
449-532 1.51e-59

RNA recognition motif 2 (RRM2) found in cytoplasmic polyadenylation element-binding protein 1 (CPEB-1) and similar proteins; This subgroup corresponds to the RRM2 of CPEB-1 (also termed CPE-BP1 or CEBP), an RNA-binding protein that interacts with the cytoplasmic polyadenylation element (CPE), a short U-rich motif in the 3' untranslated regions (UTRs) of certain mRNAs. It functions as a translational regulator that plays a major role in the control of maternal CPE-containing mRNA in oocytes, as well as of subsynaptic CPE-containing mRNA in neurons. Once phosphorylated and recruiting the polyadenylation complex, CPEB-1 may function as a translational activator stimulating polyadenylation and translation. Otherwise, it may function as a translational inhibitor when dephosphorylated and bound to a protein such as maskin or neuroguidin, which blocks translation initiation through interfering with the assembly of eIF-4E and eIF-4G. Although CPEB-1 is mainly located in cytoplasm, it can shuttle between nucleus and cytoplasm. CPEB-1 contains an N-terminal unstructured region, two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a Zn-finger motif. Both of the RRMs and the Zn finger are required for CPEB-1 to bind CPE. The N-terminal regulatory region may be responsible for CPEB-1 interacting with other proteins.


:

Pssm-ID: 410124 [Multi-domain]  Cd Length: 84  Bit Score: 192.55  E-value: 1.51e-59
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907829357 449 DPSRTVFVGALHGMLNAEALAAILNDLFGGVVYAGIDTDKHKYPIGSGRVTFNNQRSYLKAVSAAFVEIKTTKFTKKVQI 528
Cdd:cd12725     1 DPSKTVFVGALHGMLNAEGLANIMNDLFGGVVYAGIDTDKHKYPIGSGRVTFNNQRSYMKAVNAAFVEIKTPKFTKKVQI 80

                  ....
gi 1907829357 529 DPYL 532
Cdd:cd12725    81 DPYL 84
CEBP_ZZ pfam16366
Cytoplasmic polyadenylation element-binding protein ZZ domain; This ZZ-type zinc finger domain ...
526-581 1.90e-34

Cytoplasmic polyadenylation element-binding protein ZZ domain; This ZZ-type zinc finger domain binds zinc via two conserved histidines in the C-terminal part of the domain.


:

Pssm-ID: 465105  Cd Length: 56  Bit Score: 124.30  E-value: 1.90e-34
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1907829357 526 VQIDPYLEDSLCHICSSQPGPFFCRDQVCFKYFCRSCWHWRHSMEGLRHHSPLMRN 581
Cdd:pfam16366   1 VQIDPYLEDSLCSECNGQPGPYFCRDLSCFKYYCRSCWQWQHSRDRLRNHKPLVRN 56
 
Name Accession Description Interval E-value
CEBP1_N pfam16368
Cytoplasmic polyadenylation element-binding protein 1 N-terminus; This is the N-terminal ...
31-334 3.94e-154

Cytoplasmic polyadenylation element-binding protein 1 N-terminus; This is the N-terminal domain of cytoplasmic polyadenylation element-binding protein 1.


Pssm-ID: 465107  Cd Length: 307  Bit Score: 444.35  E-value: 3.94e-154
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907829357  31 PLEEEAGRIKDCWDNQEAPALSTCSNANIFRRINAILDNSLDFSRVCTTPINRGIHDHLPDFQDSEETVTSRMLFPTSAQ 110
Cdd:pfam16368   4 SLVRSIKRCWDSPDAPELPALSTCSNADIFRRMNTMLGNSLDFTGVCTTPSKKDKLDDLQDSEDSVAAVMSRMLFPSESQ 83
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907829357 111 ESSRGLPDANDLCLGLQSLSLTGWDRPWSTQDSDSSAQSSTHSVLSMLHNPLGNVLGKPPLSFLPLDPLGSDLVDKFPAP 190
Cdd:pfam16368  84 RSSRGLPDVNDLGLGLQSLSLSGWDRPWSTQDAEQSSQQSVPSMLGNLLSPLLGKLGKGPLGLLPIDSDGPDFLEKFPLR 163
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907829357 191 SVRGSRLDTRPILDSRSSSPSDSDTSGFSSGSDHLSDLISSLRISPPLPFLSLSGGGPRDPLKMGVGSRMDQEQAALAAV 270
Cdd:pfam16368 164 ASRSSRLDSRSLLDSRSSSPDDSETSGFSSGSDHLSDLLSSLRISPPLPFSGLMSRDPKDPLKLSQGSRLDAASAALTSS 243
                         250       260       270       280       290       300
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1907829357 271 TPSPTSASKRWPGASVWPSWDLLEAPKDPFSIEREARLHRQAAAVNEATCTWSGQLPPRNYKNP 334
Cdd:pfam16368 244 PASASSLSPRWPGASVWPSWDLLEDPFSPFSIEREARLHRQAAAVNEATFTWSGQLPPRNYKNP 307
RRM1_CPEB1 cd12723
RNA recognition motif 1 (RRM1) found in cytoplasmic polyadenylation element-binding protein 1 ...
336-438 2.20e-68

RNA recognition motif 1 (RRM1) found in cytoplasmic polyadenylation element-binding protein 1 (CPEB-1) and similar proteins; This subgroup corresponds to the RRM2 of CPEB-1 (also termed CPE-BP1 or CEBP), an RNA-binding protein that interacts with the cytoplasmic polyadenylation element (CPE), a short U-rich motif in the 3' untranslated regions (UTRs) of certain mRNAs. It functions as a translational regulator that plays a major role in the control of maternal CPE-containing mRNA in oocytes, as well as of subsynaptic CPE-containing mRNA in neurons. Once phosphorylated and recruiting the polyadenylation complex, CPEB-1 may function as a translational activator stimulating polyadenylation and translation. Otherwise, it may function as a translational inhibitor when dephosphorylated and bound to a protein such as maskin or neuroguidin, which blocks translation initiation through interfering with the assembly of eIF-4E and eIF-4G. Although CPEB-1 is mainly located in cytoplasm, it can shuttle between nucleus and cytoplasm. CPEB-1 contains an N-terminal unstructured region, two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a Zn-finger motif. Both of the RRMs and the Zn finger are required for CPEB-1 to bind CPE. The N-terminal regulatory region may be responsible for CPEB-1 interacting with other proteins.


Pssm-ID: 410122 [Multi-domain]  Cd Length: 101  Bit Score: 216.40  E-value: 2.20e-68
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907829357 336 YSCKVFLGGVPWDITEAGLVNTFRVFGSLSVEWPGKDGKHPR-CPPKGYVYLVFELEKSVRSLLQACSHDplsPDGLSEY 414
Cdd:cd12723     1 YSCKVFLGGVPWDITEAGLQNAFKPFGSLSVEWPGKDGKHPRgHPPKGYVYLIFESEKSVKALLQACTHD---FLGGGEY 77
                          90       100
                  ....*....|....*....|....
gi 1907829357 415 YFKMSSRRMRCKEVQVIPWVLADS 438
Cdd:cd12723    78 YFKISSRRMRSKEVQVIPWVLSDS 101
RRM2_CPEB1 cd12725
RNA recognition motif 2 (RRM2) found in cytoplasmic polyadenylation element-binding protein 1 ...
449-532 1.51e-59

RNA recognition motif 2 (RRM2) found in cytoplasmic polyadenylation element-binding protein 1 (CPEB-1) and similar proteins; This subgroup corresponds to the RRM2 of CPEB-1 (also termed CPE-BP1 or CEBP), an RNA-binding protein that interacts with the cytoplasmic polyadenylation element (CPE), a short U-rich motif in the 3' untranslated regions (UTRs) of certain mRNAs. It functions as a translational regulator that plays a major role in the control of maternal CPE-containing mRNA in oocytes, as well as of subsynaptic CPE-containing mRNA in neurons. Once phosphorylated and recruiting the polyadenylation complex, CPEB-1 may function as a translational activator stimulating polyadenylation and translation. Otherwise, it may function as a translational inhibitor when dephosphorylated and bound to a protein such as maskin or neuroguidin, which blocks translation initiation through interfering with the assembly of eIF-4E and eIF-4G. Although CPEB-1 is mainly located in cytoplasm, it can shuttle between nucleus and cytoplasm. CPEB-1 contains an N-terminal unstructured region, two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a Zn-finger motif. Both of the RRMs and the Zn finger are required for CPEB-1 to bind CPE. The N-terminal regulatory region may be responsible for CPEB-1 interacting with other proteins.


Pssm-ID: 410124 [Multi-domain]  Cd Length: 84  Bit Score: 192.55  E-value: 1.51e-59
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907829357 449 DPSRTVFVGALHGMLNAEALAAILNDLFGGVVYAGIDTDKHKYPIGSGRVTFNNQRSYLKAVSAAFVEIKTTKFTKKVQI 528
Cdd:cd12725     1 DPSKTVFVGALHGMLNAEGLANIMNDLFGGVVYAGIDTDKHKYPIGSGRVTFNNQRSYMKAVNAAFVEIKTPKFTKKVQI 80

                  ....
gi 1907829357 529 DPYL 532
Cdd:cd12725    81 DPYL 84
RRM_7 pfam16367
RNA recognition motif;
337-432 5.98e-45

RNA recognition motif;


Pssm-ID: 465106 [Multi-domain]  Cd Length: 91  Bit Score: 154.06  E-value: 5.98e-45
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907829357 337 SCKVFLGGVPWDITEAGLVNTFRVFGSLSVEWPGKdGKHPRCPP--KGYVYLVFELEKSVRSLLQACSHDPlspdglSEY 414
Cdd:pfam16367   1 SRKVFVGGLPWDITEAELTATFGRFGPLLVDWPGK-PESPSYFPdvKGYVFLVFEDEKSVQALLDACTQED------GKY 73
                          90
                  ....*....|....*...
gi 1907829357 415 YFKMSSRRMRCKEVQVIP 432
Cdd:pfam16367  74 YLKLSSPRMKDKPVQIRP 91
CEBP_ZZ pfam16366
Cytoplasmic polyadenylation element-binding protein ZZ domain; This ZZ-type zinc finger domain ...
526-581 1.90e-34

Cytoplasmic polyadenylation element-binding protein ZZ domain; This ZZ-type zinc finger domain binds zinc via two conserved histidines in the C-terminal part of the domain.


Pssm-ID: 465105  Cd Length: 56  Bit Score: 124.30  E-value: 1.90e-34
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1907829357 526 VQIDPYLEDSLCHICSSQPGPFFCRDQVCFKYFCRSCWHWRHSMEGLRHHSPLMRN 581
Cdd:pfam16366   1 VQIDPYLEDSLCSECNGQPGPYFCRDLSCFKYYCRSCWQWQHSRDRLRNHKPLVRN 56
Bbox1 cd19757
B-box-type 1 zinc finger (Bbox1); The B-box-type zinc finger is a short zinc binding domain of ...
536-575 1.37e-05

B-box-type 1 zinc finger (Bbox1); The B-box-type zinc finger is a short zinc binding domain of around 40 amino acid residues in length. It has been found in transcription factors, ribonucleoproteins and proto-oncoproteins, such as in TRIM (tripartite motif) proteins that consist of an N-terminal RING finger (originally called an A-box), followed by 1-2 B-box domains and a coiled-coil domain (also called RBCC for Ring, B-box, Coiled-Coil). The B-box-type zinc finger often presents in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain, in functionally unrelated proteins, most likely mediating protein-protein interactions. Based on different consensus sequences and the spacing of the 7-8 zinc-binding residues, the B-box-type zinc fingers can be divided into two groups, type 1 (Bbox1: C6H2) and type 2 (Bbox2: CHC3H2). This family corresponds to the type 1 B-box (Bbox1).


Pssm-ID: 380815 [Multi-domain]  Cd Length: 44  Bit Score: 42.48  E-value: 1.37e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|.
gi 1907829357 536 LCHICSSQPGPFFCRDqvCFKYFCRSCWHWRHS-MEGLRHH 575
Cdd:cd19757     1 LCDECEEREATVYCLE--CEEFLCDDCSDAIHRrGKLTRSH 39
RRM smart00360
RNA recognition motif;
339-401 3.08e-04

RNA recognition motif;


Pssm-ID: 214636 [Multi-domain]  Cd Length: 73  Bit Score: 39.50  E-value: 3.08e-04
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1907829357  339 KVFLGGVPWDITEAGLVNTFRVFGSL-SVEWPgKDGKHPRcpPKGYVYLVFELEKSVRSLLQAC 401
Cdd:smart00360   1 TLFVGNLPPDTTEEELRELFSKFGKVeSVRLV-RDKETGK--SKGFAFVEFESEEDAEKALEAL 61
 
Name Accession Description Interval E-value
CEBP1_N pfam16368
Cytoplasmic polyadenylation element-binding protein 1 N-terminus; This is the N-terminal ...
31-334 3.94e-154

Cytoplasmic polyadenylation element-binding protein 1 N-terminus; This is the N-terminal domain of cytoplasmic polyadenylation element-binding protein 1.


Pssm-ID: 465107  Cd Length: 307  Bit Score: 444.35  E-value: 3.94e-154
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907829357  31 PLEEEAGRIKDCWDNQEAPALSTCSNANIFRRINAILDNSLDFSRVCTTPINRGIHDHLPDFQDSEETVTSRMLFPTSAQ 110
Cdd:pfam16368   4 SLVRSIKRCWDSPDAPELPALSTCSNADIFRRMNTMLGNSLDFTGVCTTPSKKDKLDDLQDSEDSVAAVMSRMLFPSESQ 83
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907829357 111 ESSRGLPDANDLCLGLQSLSLTGWDRPWSTQDSDSSAQSSTHSVLSMLHNPLGNVLGKPPLSFLPLDPLGSDLVDKFPAP 190
Cdd:pfam16368  84 RSSRGLPDVNDLGLGLQSLSLSGWDRPWSTQDAEQSSQQSVPSMLGNLLSPLLGKLGKGPLGLLPIDSDGPDFLEKFPLR 163
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907829357 191 SVRGSRLDTRPILDSRSSSPSDSDTSGFSSGSDHLSDLISSLRISPPLPFLSLSGGGPRDPLKMGVGSRMDQEQAALAAV 270
Cdd:pfam16368 164 ASRSSRLDSRSLLDSRSSSPDDSETSGFSSGSDHLSDLLSSLRISPPLPFSGLMSRDPKDPLKLSQGSRLDAASAALTSS 243
                         250       260       270       280       290       300
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1907829357 271 TPSPTSASKRWPGASVWPSWDLLEAPKDPFSIEREARLHRQAAAVNEATCTWSGQLPPRNYKNP 334
Cdd:pfam16368 244 PASASSLSPRWPGASVWPSWDLLEDPFSPFSIEREARLHRQAAAVNEATFTWSGQLPPRNYKNP 307
RRM1_CPEB1 cd12723
RNA recognition motif 1 (RRM1) found in cytoplasmic polyadenylation element-binding protein 1 ...
336-438 2.20e-68

RNA recognition motif 1 (RRM1) found in cytoplasmic polyadenylation element-binding protein 1 (CPEB-1) and similar proteins; This subgroup corresponds to the RRM2 of CPEB-1 (also termed CPE-BP1 or CEBP), an RNA-binding protein that interacts with the cytoplasmic polyadenylation element (CPE), a short U-rich motif in the 3' untranslated regions (UTRs) of certain mRNAs. It functions as a translational regulator that plays a major role in the control of maternal CPE-containing mRNA in oocytes, as well as of subsynaptic CPE-containing mRNA in neurons. Once phosphorylated and recruiting the polyadenylation complex, CPEB-1 may function as a translational activator stimulating polyadenylation and translation. Otherwise, it may function as a translational inhibitor when dephosphorylated and bound to a protein such as maskin or neuroguidin, which blocks translation initiation through interfering with the assembly of eIF-4E and eIF-4G. Although CPEB-1 is mainly located in cytoplasm, it can shuttle between nucleus and cytoplasm. CPEB-1 contains an N-terminal unstructured region, two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a Zn-finger motif. Both of the RRMs and the Zn finger are required for CPEB-1 to bind CPE. The N-terminal regulatory region may be responsible for CPEB-1 interacting with other proteins.


Pssm-ID: 410122 [Multi-domain]  Cd Length: 101  Bit Score: 216.40  E-value: 2.20e-68
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907829357 336 YSCKVFLGGVPWDITEAGLVNTFRVFGSLSVEWPGKDGKHPR-CPPKGYVYLVFELEKSVRSLLQACSHDplsPDGLSEY 414
Cdd:cd12723     1 YSCKVFLGGVPWDITEAGLQNAFKPFGSLSVEWPGKDGKHPRgHPPKGYVYLIFESEKSVKALLQACTHD---FLGGGEY 77
                          90       100
                  ....*....|....*....|....
gi 1907829357 415 YFKMSSRRMRCKEVQVIPWVLADS 438
Cdd:cd12723    78 YFKISSRRMRSKEVQVIPWVLSDS 101
RRM1_CPEBs cd12444
RNA recognition motif 1 (RRM1) found in cytoplasmic polyadenylation element-binding protein ...
338-435 9.44e-61

RNA recognition motif 1 (RRM1) found in cytoplasmic polyadenylation element-binding protein CPEB-1, CPEB-2, CPEB-3, CPEB-4 and similar protiens; This subfamily corresponds to the RRM1 of the CPEB family of proteins that bind to defined groups of mRNAs and act as either translational repressors or activators to regulate their translation. CPEB proteins are well conserved in both, vertebrates and invertebrates. Based on sequence similarity, RNA-binding specificity, and functional regulation of translation, the CPEB proteins have been classified into two subfamilies. The first subfamily includes CPEB-1 and related proteins. CPEB-1 is an RNA-binding protein that interacts with the cytoplasmic polyadenylation element (CPE), a short U-rich motif in the 3' untranslated regions (UTRs) of certain mRNAs. It functions as a translational regulator that plays a major role in the control of maternal CPE-containing mRNA in oocytes, as well as of subsynaptic CPE-containing mRNA in neurons. Once phosphorylated and recruiting the polyadenylation complex, CPEB-1 may function as a translational activator stimulating polyadenylation and translation. Otherwise, it may function as a translational inhibitor when dephosphorylated and bind to a protein such as maskin or neuroguidin, which blocks translation initiation through interfering with the assembly of eIF-4E and eIF-4G. Although CPEB-1 is mainly located in cytoplasm, it can shuttle between nucleus and cytoplasm. The second subfamily includes CPEB-2, CPEB-3, CPEB-4, and related protiens. Due to high sequence similarity, members in this subfamily may share similar expression patterns and functions. CPEB-2 is an RNA-binding protein that is abundantly expressed in testis and localized in cytoplasm in transfected HeLa cells. It preferentially binds to poly(U) RNA oligomers and may regulate the translation of stored mRNAs during spermiogenesis. CPEB-2 impedes target RNA translation at elongation; it directly interacts with the elongation factor, eEF2, to reduce eEF2/ribosome-activated GTP hydrolysis in vitro and inhibit peptide elongation of CPEB2-bound RNA in vivo. CPEB-3 is a sequence-specific translational regulatory protein that regulates translation in a polyadenylation-independent manner. It functions as a translational repressor that governs the synthesis of the AMPA receptor GluR2 through binding GluR2 mRNA. It also represses translation of a reporter RNA in transfected neurons and stimulates translation in response to NMDA. CPEB-4 is an RNA-binding protein that mediates meiotic mRNA cytoplasmic polyadenylation and translation. It is essential for neuron survival and present on the endoplasmic reticulum (ER). It is accumulated in the nucleus upon ischemia or the depletion of ER calcium. CPEB-4 is overexpressed in a large variety of tumors and is associated with many mRNAs in cancer cells. All CPEB proteins are nucleus-cytoplasm shuttling proteins. They contain an N-terminal unstructured region, followed by two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a Zn-finger motif. CPEB-2, -3, and -4 have conserved nuclear export signals that are not present in CPEB-1.


Pssm-ID: 409878 [Multi-domain]  Cd Length: 95  Bit Score: 196.29  E-value: 9.44e-61
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907829357 338 CKVFLGGVPWDITEAGLVNTFRVFGSLSVEWPGKDGKHPRCPPKGYVYLVFELEKSVRSLLQACSHDplsPDGLSEYYFK 417
Cdd:cd12444     1 RKVFLGGVPWDITEAELTASFRRFGSLSVDWPGKDESKSYFPPKGYVYLLFESEKSVQALLQACTHD---DDKLYEYYFK 77
                          90
                  ....*....|....*...
gi 1907829357 418 MSSRRMRCKEVQVIPWVL 435
Cdd:cd12444    78 VSSRTMKDKEVQVIPWVL 95
RRM2_CPEB1 cd12725
RNA recognition motif 2 (RRM2) found in cytoplasmic polyadenylation element-binding protein 1 ...
449-532 1.51e-59

RNA recognition motif 2 (RRM2) found in cytoplasmic polyadenylation element-binding protein 1 (CPEB-1) and similar proteins; This subgroup corresponds to the RRM2 of CPEB-1 (also termed CPE-BP1 or CEBP), an RNA-binding protein that interacts with the cytoplasmic polyadenylation element (CPE), a short U-rich motif in the 3' untranslated regions (UTRs) of certain mRNAs. It functions as a translational regulator that plays a major role in the control of maternal CPE-containing mRNA in oocytes, as well as of subsynaptic CPE-containing mRNA in neurons. Once phosphorylated and recruiting the polyadenylation complex, CPEB-1 may function as a translational activator stimulating polyadenylation and translation. Otherwise, it may function as a translational inhibitor when dephosphorylated and bound to a protein such as maskin or neuroguidin, which blocks translation initiation through interfering with the assembly of eIF-4E and eIF-4G. Although CPEB-1 is mainly located in cytoplasm, it can shuttle between nucleus and cytoplasm. CPEB-1 contains an N-terminal unstructured region, two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a Zn-finger motif. Both of the RRMs and the Zn finger are required for CPEB-1 to bind CPE. The N-terminal regulatory region may be responsible for CPEB-1 interacting with other proteins.


Pssm-ID: 410124 [Multi-domain]  Cd Length: 84  Bit Score: 192.55  E-value: 1.51e-59
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907829357 449 DPSRTVFVGALHGMLNAEALAAILNDLFGGVVYAGIDTDKHKYPIGSGRVTFNNQRSYLKAVSAAFVEIKTTKFTKKVQI 528
Cdd:cd12725     1 DPSKTVFVGALHGMLNAEGLANIMNDLFGGVVYAGIDTDKHKYPIGSGRVTFNNQRSYMKAVNAAFVEIKTPKFTKKVQI 80

                  ....
gi 1907829357 529 DPYL 532
Cdd:cd12725    81 DPYL 84
RRM_7 pfam16367
RNA recognition motif;
337-432 5.98e-45

RNA recognition motif;


Pssm-ID: 465106 [Multi-domain]  Cd Length: 91  Bit Score: 154.06  E-value: 5.98e-45
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907829357 337 SCKVFLGGVPWDITEAGLVNTFRVFGSLSVEWPGKdGKHPRCPP--KGYVYLVFELEKSVRSLLQACSHDPlspdglSEY 414
Cdd:pfam16367   1 SRKVFVGGLPWDITEAELTATFGRFGPLLVDWPGK-PESPSYFPdvKGYVFLVFEDEKSVQALLDACTQED------GKY 73
                          90
                  ....*....|....*...
gi 1907829357 415 YFKMSSRRMRCKEVQVIP 432
Cdd:pfam16367  74 YLKLSSPRMKDKPVQIRP 91
RRM2_CPEBs cd12445
RNA recognition motif 2 (RRM2) found in cytoplasmic polyadenylation element-binding protein ...
452-531 4.99e-36

RNA recognition motif 2 (RRM2) found in cytoplasmic polyadenylation element-binding protein CPEB-1, CPEB-2, CPEB-3, CPEB-4 and similar protiens; This subfamily corresponds to the RRM2 of CPEB family of proteins that bind to defined groups of mRNAs and act as either translational repressors or activators to regulate their translation. CPEB proteins are well conserved in both, vertebrates and invertebrates. Based on sequence similarity, RNA-binding specificity, and functional regulation of translation, the CPEB proteins has been classified into two subfamilies. The first subfamily includes CPEB-1 and related proteins. CPEB-1 is an RNA-binding protein that interacts with the cytoplasmic polyadenylation element (CPE), a short U-rich motif in the 3' untranslated regions (UTRs) of certain mRNAs. It functions as a translational regulator that plays a major role in the control of maternal CPE-containing mRNA in oocytes, as well as of subsynaptic CPE-containing mRNA in neurons. Once phosphorylated and recruiting the polyadenylation complex, CPEB-1 may function as a translational activator stimulating polyadenylation and translation. Otherwise, it may function as a translational inhibitor when dephosphorylated and bound to a protein such as maskin or neuroguidin, which blocks translation initiation through interfering with the assembly of eIF-4E and eIF-4G. Although CPEB-1 is mainly located in cytoplasm, it can shuttle between nucleus and cytoplasm. The second subfamily includes CPEB-2, CPEB-3, CPEB-4, and related protiens. Due to the high sequence similarity, members in this subfamily may share similar expression patterns and functions. CPEB-2 is an RNA-binding protein that is abundantly expressed in testis and localized in cytoplasm in transfected HeLa cells. It preferentially binds to poly(U) RNA oligomers and may regulate the translation of stored mRNAs during spermiogenesis. Moreover, CPEB-2 impedes target RNA translation at elongation. It directly interacts with the elongation factor, eEF2, to reduce eEF2/ribosome-activated GTP hydrolysis in vitro and inhibit peptide elongation of CPEB2-bound RNA in vivo. CPEB-3 is a sequence-specific translational regulatory protein that regulates translation in a polyadenylation-independent manner. It functions as a translational repressor that governs the synthesis of the AMPA receptor GluR2 through binding GluR2 mRNA. It also represses translation of a reporter RNA in transfected neurons and stimulates translation in response to NMDA. CPEB-4 is an RNA-binding protein that mediates meiotic mRNA cytoplasmic polyadenylation and translation. It is essential for neuron survival and present on the endoplasmic reticulum (ER). It is accumulated in the nucleus upon ischemia or the depletion of ER calcium. CPEB-4 is overexpressed in a large variety of tumors and is associated with many mRNAs in cancer cells. All CPEB proteins are nucleus-cytoplasm shuttling proteins. They contain an N-terminal unstructured region, followed by two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a Zn-finger motif. CPEB-2, -3, and -4 have conserved nuclear export signals that are not present in CPEB-1.


Pssm-ID: 409879 [Multi-domain]  Cd Length: 81  Bit Score: 129.40  E-value: 4.99e-36
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907829357 452 RTVFVGALHGMLNAEALAAILNDLFGGVVYAGIDTDKHK-YPIGSGRVTFNNQRSYLKAVSAAFVEIKTTKFTKKVQIDP 530
Cdd:cd12445     1 RTVFVGGLPLPLTAAELAAILERLYGGVCYVEIDTDEFYlYPTGCARVTFNNEQSYIKAVSEVFVELPFGTINKRVRIRP 80

                  .
gi 1907829357 531 Y 531
Cdd:cd12445    81 Y 81
CEBP_ZZ pfam16366
Cytoplasmic polyadenylation element-binding protein ZZ domain; This ZZ-type zinc finger domain ...
526-581 1.90e-34

Cytoplasmic polyadenylation element-binding protein ZZ domain; This ZZ-type zinc finger domain binds zinc via two conserved histidines in the C-terminal part of the domain.


Pssm-ID: 465105  Cd Length: 56  Bit Score: 124.30  E-value: 1.90e-34
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1907829357 526 VQIDPYLEDSLCHICSSQPGPFFCRDQVCFKYFCRSCWHWRHSMEGLRHHSPLMRN 581
Cdd:pfam16366   1 VQIDPYLEDSLCSECNGQPGPYFCRDLSCFKYYCRSCWQWQHSRDRLRNHKPLVRN 56
RRM2_CPEB2_like cd12726
RNA recognition motif 2 (RRM2) found in cytoplasmic polyadenylation element-binding protein ...
452-531 6.62e-24

RNA recognition motif 2 (RRM2) found in cytoplasmic polyadenylation element-binding protein CPEB-2, CPEB-3, CPEB-4 and similar protiens; This subgroup corresponds to the RRM2 of the paralog proteins CPEB-2, CPEB-3 and CPEB-4, all well conserved in both, vertebrates and invertebrates. Due to the high sequence similarity, members in this family may share similar expression patterns and functions. CPEB-2 is an RNA-binding protein that is abundantly expressed in testis and localized in cytoplasm in transfected HeLa cells. It preferentially binds to poly(U) RNA oligomers and may regulate the translation of stored mRNAs during spermiogenesis. Moreover, CPEB-2 impedes target RNA translation at elongation; it directly interacts with the elongation factor, eEF2, to reduce eEF2/ribosome-activated GTP hydrolysis in vitro and inhibit peptide elongation of CPEB2-bound RNA in vivo. CPEB-3 is a sequence-specific translational regulatory protein that regulates translation in a polyadenylation-independent manner. It functions as a translational repressor that governs the synthesis of the AMPA receptor GluR2 through binding GluR2 mRNA. It also represses translation of a reporter RNA in transfected neurons and stimulates translation in response to NMDA. CPEB-4 is an RNA-binding protein that mediates meiotic mRNA cytoplasmic polyadenylation and translation. It is essential for neuron survival and present on the endoplasmic reticulum (ER). It is accumulated in the nucleus upon ischemia or the depletion of ER calcium. CPEB-4 is overexpressed in a large variety of tumors and is associated with many mRNAs in cancer cells. All family members contain an N-terminal unstructured region, two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a Zn-finger motif. In addition, they do have conserved nuclear export signals that are not present in CPEB-1.


Pssm-ID: 410125 [Multi-domain]  Cd Length: 81  Bit Score: 95.57  E-value: 6.62e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907829357 452 RTVFVGALHGMLNAEALAAILNDLFGGVVYAGIDTD-KHKYPIGSGRVTFNNQRSYLKAVSAAFVEIKTTKFTKKVQIDP 530
Cdd:cd12726     1 KTIFVGGVPRPLRAVELAMIMDRLYGGVCYAGIDTDpELKYPKGAGRVAFSNQQSYIAAISARFVQLQHGDIDKRVEVKP 80

                  .
gi 1907829357 531 Y 531
Cdd:cd12726    81 Y 81
RRM1_CPEB2_like cd12724
RNA recognition motif 1 (RRM1) found in cytoplasmic polyadenylation element-binding protein ...
339-435 3.08e-23

RNA recognition motif 1 (RRM1) found in cytoplasmic polyadenylation element-binding protein CPEB-2, CPEB-3, CPEB-4 and similar protiens; This subgroup corresponds to the RRM1 of the paralog proteins CPEB-2, CPEB-3 and CPEB-4, all well-conserved in both, vertebrates and invertebrates. Due to the high sequence similarity, members in this family may share similar expression patterns and functions. CPEB-2 is an RNA-binding protein that is abundantly expressed in testis and localized in cytoplasm in transfected HeLa cells. It preferentially binds to poly(U) RNA oligomers and may regulate the translation of stored mRNAs during spermiogenesis. Moreover, CPEB-2 impedes target RNA translation at elongation; it directly interacts with the elongation factor, eEF2, to reduce eEF2/ribosome-activated GTP hydrolysis in vitro and inhibit peptide elongation of CPEB2-bound RNA in vivo. CPEB-3 is a sequence-specific translational regulatory protein that regulates translation in a polyadenylation-independent manner. It functions as a translational repressor that governs the synthesis of the AMPA receptor GluR2 through binding GluR2 mRNA. It also represses translation of a reporter RNA in transfected neurons and stimulates translation in response to NMDA. CPEB-4 is an RNA-binding protein that mediates meiotic mRNA cytoplasmic polyadenylation and translation. It is essential for neuron survival and present on the endoplasmic reticulum (ER). It is accumulated in the nucleus upon ischemia or the depletion of ER calcium. CPEB-4 is overexpressed in a large variety of tumors and is associated with many mRNAs in cancer cells. All family members contain an N-terminal unstructured region, two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a Zn-finger motif. In addition, they do have conserved nuclear export signals that are not present in CPEB-1.


Pssm-ID: 410123 [Multi-domain]  Cd Length: 92  Bit Score: 93.99  E-value: 3.08e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907829357 339 KVFLGGVPWDITEAGLVNTFRVFGSLSVEWPGKDGKHPRCPPKGYVYLVFELEKSVRSLLQACSHDPlspdglSEYYFKM 418
Cdd:cd12724     2 KVFVGGLPPDIDEDEITASFRRFGPLVVDWPHKAESKSYFPPKGYAFLLFQDERSVQALIDACIEED------DKLYLCV 75
                          90
                  ....*....|....*..
gi 1907829357 419 SSRRMRCKEVQVIPWVL 435
Cdd:cd12724    76 SSPTIKDKPVQIRPWNL 92
Bbox1 cd19757
B-box-type 1 zinc finger (Bbox1); The B-box-type zinc finger is a short zinc binding domain of ...
536-575 1.37e-05

B-box-type 1 zinc finger (Bbox1); The B-box-type zinc finger is a short zinc binding domain of around 40 amino acid residues in length. It has been found in transcription factors, ribonucleoproteins and proto-oncoproteins, such as in TRIM (tripartite motif) proteins that consist of an N-terminal RING finger (originally called an A-box), followed by 1-2 B-box domains and a coiled-coil domain (also called RBCC for Ring, B-box, Coiled-Coil). The B-box-type zinc finger often presents in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain, in functionally unrelated proteins, most likely mediating protein-protein interactions. Based on different consensus sequences and the spacing of the 7-8 zinc-binding residues, the B-box-type zinc fingers can be divided into two groups, type 1 (Bbox1: C6H2) and type 2 (Bbox2: CHC3H2). This family corresponds to the type 1 B-box (Bbox1).


Pssm-ID: 380815 [Multi-domain]  Cd Length: 44  Bit Score: 42.48  E-value: 1.37e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|.
gi 1907829357 536 LCHICSSQPGPFFCRDqvCFKYFCRSCWHWRHS-MEGLRHH 575
Cdd:cd19757     1 LCDECEEREATVYCLE--CEEFLCDDCSDAIHRrGKLTRSH 39
RRM2_DAZAP1 cd12327
RNA recognition motif 2 (RRM2) found in Deleted in azoospermia-associated protein 1 (DAZAP1) ...
337-429 6.92e-05

RNA recognition motif 2 (RRM2) found in Deleted in azoospermia-associated protein 1 (DAZAP1) and similar proteins; This subfamily corresponds to the RRM2 of DAZAP1 or DAZ-associated protein 1, also termed proline-rich RNA binding protein (Prrp), a multi-functional ubiquitous RNA-binding protein expressed most abundantly in the testis and essential for normal cell growth, development, and spermatogenesis. DAZAP1 is a shuttling protein whose acetylated is predominantly nuclear and the nonacetylated form is in cytoplasm. DAZAP1 also functions as a translational regulator that activates translation in an mRNA-specific manner. DAZAP1 was initially identified as a binding partner of Deleted in Azoospermia (DAZ). It also interacts with numerous hnRNPs, including hnRNP U, hnRNP U like-1, hnRNPA1, hnRNPA/B, and hnRNP D, suggesting DAZAP1 might associate and cooperate with hnRNP particles to regulate adenylate-uridylate-rich elements (AU-rich element or ARE)-containing mRNAs. DAZAP1 contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal proline-rich domain.


Pssm-ID: 409765 [Multi-domain]  Cd Length: 80  Bit Score: 41.33  E-value: 6.92e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907829357 337 SCKVFLGGVPWDITEAGLVNTFRVFGSLSVEWPGKDGKHPRcpPKGYVYLVFELEKSVRsllQACshdplspdglSEYYF 416
Cdd:cd12327     2 SKKVFVGGIPHNCGETELRDYFKRYGVVTEVVMMYDAEKQR--SRGFGFITFEDEQSVD---QAV----------NMHFH 66
                          90
                  ....*....|...
gi 1907829357 417 KMSSRRMRCKEVQ 429
Cdd:cd12327    67 DIMGKKVEVKRAE 79
RRM_SF cd00590
RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP ...
340-403 1.29e-04

RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs).


Pssm-ID: 409669 [Multi-domain]  Cd Length: 72  Bit Score: 40.34  E-value: 1.29e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1907829357 340 VFLGGVPWDITEAGLVNTFRVFGS-LSVEWPgkdgKHPRCPPKGYVYLVFELEKSVRSLLQACSH 403
Cdd:cd00590     1 LFVGNLPPDTTEEDLRELFSKFGEvVSVRIV----RDRDGKSKGFAFVEFESPEDAEKALEALNG 61
RRM smart00360
RNA recognition motif;
339-401 3.08e-04

RNA recognition motif;


Pssm-ID: 214636 [Multi-domain]  Cd Length: 73  Bit Score: 39.50  E-value: 3.08e-04
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1907829357  339 KVFLGGVPWDITEAGLVNTFRVFGSL-SVEWPgKDGKHPRcpPKGYVYLVFELEKSVRSLLQAC 401
Cdd:smart00360   1 TLFVGNLPPDTTEEELRELFSKFGKVeSVRLV-RDKETGK--SKGFAFVEFESEEDAEKALEAL 61
RRM2_hnRPDL cd12585
RNA recognition motif 2 (RRM2) found in heterogeneous nuclear ribonucleoprotein D-like (hnRNP ...
339-403 5.37e-04

RNA recognition motif 2 (RRM2) found in heterogeneous nuclear ribonucleoprotein D-like (hnRNP DL) and similar proteins; This subgroup corresponds to the RRM2 of hnRNP DL (or hnRNP D-like), also termed AU-rich element RNA-binding factor, or JKT41-binding protein (protein laAUF1 or JKTBP), is a dual functional protein that possesses DNA- and RNA-binding properties. It has been implicated in mRNA biogenesis at the transcriptional and post-transcriptional levels. hnRNP DL binds single-stranded DNA (ssDNA) or double-stranded DNA (dsDNA) in a non-sequencespecific manner, and interacts with poly(G) and poly(A) tenaciously. It contains two putative two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glycine- and tyrosine-rich C-terminus.


Pssm-ID: 409998 [Multi-domain]  Cd Length: 75  Bit Score: 38.83  E-value: 5.37e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1907829357 339 KVFLGGVPWDITEAGLVNTFRVFGSL-SVEWPGKDGKHPRcppKGYVYLVFELEKSVRSLLQACSH 403
Cdd:cd12585     1 KVFVGGLSPDTSEEQIKEYFGAFGEIeNIELPMDTKTNER---RGFCFITYTDEEPVQKLLESRYH 63
RRM2_Hrp1p cd12330
RNA recognition motif 2 (RRM2) found in yeast nuclear polyadenylated RNA-binding protein 4 ...
339-404 1.32e-03

RNA recognition motif 2 (RRM2) found in yeast nuclear polyadenylated RNA-binding protein 4 (Hrp1p or Nab4p) and similar proteins; This subfamily corresponds to the RRM1 of Hrp1p and similar proteins. Hrp1p or Nab4p, also termed cleavage factor IB (CFIB), is a sequence-specific trans-acting factor that is essential for mRNA 3'-end formation in yeast Saccharomyces cerevisiae. It can be UV cross-linked to RNA and specifically recognizes the (UA)6 RNA element required for both, the cleavage and poly(A) addition steps. Moreover, Hrp1p can shuttle between the nucleus and the cytoplasm, and play an additional role in the export of mRNAs to the cytoplasm. Hrp1p also interacts with Rna15p and Rna14p, two components of CF1A. In addition, Hrp1p functions as a factor directly involved in modulating the activity of the nonsense-mediated mRNA decay (NMD) pathway; it binds specifically to a downstream sequence element (DSE)-containing RNA and interacts with Upf1p, a component of the surveillance complex, further triggering the NMD pathway. Hrp1p contains two central RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an arginine-glycine-rich region harboring repeats of the sequence RGGF/Y.


Pssm-ID: 409767 [Multi-domain]  Cd Length: 78  Bit Score: 37.69  E-value: 1.32e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1907829357 339 KVFLGGVPWDITEAGLVNTFRVFGSL--SVEWPGKDGKHPRcppkGYVYLVFELEKSVRSLLQACSHD 404
Cdd:cd12330     1 KIFVGGLAPDVTEEEFKEYFEQFGTVvdAVVMLDHDTGRSR----GFGFVTFDSESAVEKVLSKGFHE 64
RRM2_hnRNPD_like cd12329
RNA recognition motif 2 (RRM2) found in heterogeneous nuclear ribonucleoprotein hnRNP D0, ...
339-403 2.15e-03

RNA recognition motif 2 (RRM2) found in heterogeneous nuclear ribonucleoprotein hnRNP D0, hnRNP A/B, hnRNP DL and similar proteins; This subfamily corresponds to the RRM2 of hnRNP D0, hnRNP A/B, hnRNP DL and similar proteins. hnRNP D0, a UUAG-specific nuclear RNA binding protein that may be involved in pre-mRNA splicing and telomere elongation. hnRNP A/B is an RNA unwinding protein with a high affinity for G- followed by U-rich regions. It has also been identified as an APOBEC1-binding protein that interacts with apolipoprotein B (apoB) mRNA transcripts around the editing site and thus plays an important role in apoB mRNA editing. hnRNP DL (or hnRNP D-like) is a dual functional protein that possesses DNA- and RNA-binding properties. It has been implicated in mRNA biogenesis at the transcriptional and post-transcriptional levels. All memembers in this family contain two putative RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glycine- and tyrosine-rich C-terminus.


Pssm-ID: 240775 [Multi-domain]  Cd Length: 75  Bit Score: 36.96  E-value: 2.15e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1907829357 339 KVFLGGVPWDITEAGLVNTFRVFGSL-SVEWPGKDGKHPRcppKGYVYLVFELEKSVRSLLQACSH 403
Cdd:cd12329     1 KIFVGGLSPETTEEKIREYFGKFGNIvEIELPMDKKTNKR---RGFCFITFDSEEPVKKILETQFH 63
RRM1_PUF60 cd12370
RNA recognition motif 1 (RRM1) found in (U)-binding-splicing factor PUF60 and similar proteins; ...
338-390 2.15e-03

RNA recognition motif 1 (RRM1) found in (U)-binding-splicing factor PUF60 and similar proteins; This subfamily corresponds to the RRM1 of PUF60, also termed FUSE-binding protein-interacting repressor (FBP-interacting repressor or FIR), or Ro-binding protein 1 (RoBP1), or Siah-binding protein 1 (Siah-BP1). PUF60 is an essential splicing factor that functions as a poly-U RNA-binding protein required to reconstitute splicing in depleted nuclear extracts. Its function is enhanced through interaction with U2 auxiliary factor U2AF65. PUF60 also controls human c-myc gene expression by binding and inhibiting the transcription factor far upstream sequence element (FUSE)-binding-protein (FBP), an activator of c-myc promoters. PUF60 contains two central RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal U2AF (U2 auxiliary factor) homology motifs (UHM) that harbors another RRM and binds to tryptophan-containing linear peptide motifs (UHM ligand motifs, ULMs) in several nuclear proteins. Research indicates that PUF60 binds FUSE as a dimer, and only the first two RRM domains participate in the single-stranded DNA recognition.


Pssm-ID: 409805 [Multi-domain]  Cd Length: 76  Bit Score: 37.01  E-value: 2.15e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1907829357 338 CKVFLGGVPWDITEAGLVNTFRVFG---SLSVEWPGKDGKHprcppKGYVYLVFEL 390
Cdd:cd12370     1 CRVYVGSIYFELGEDTIRQAFAPFGpikSIDMSWDPVTMKH-----KGFAFVEYEV 51
RRM_SF cd00590
RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP ...
454-512 5.33e-03

RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs).


Pssm-ID: 409669 [Multi-domain]  Cd Length: 72  Bit Score: 35.72  E-value: 5.33e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1907829357 454 VFVGALHGMLNAEALAAILNDlFGGVVYAGIDTDKHKYPIGSGRVTFNNQRSYLKAVSA 512
Cdd:cd00590     1 LFVGNLPPDTTEEDLRELFSK-FGEVVSVRIVRDRDGKSKGFAFVEFESPEDAEKALEA 58
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
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