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Conserved domains on  [gi|1958795452|ref|XP_038937101|]
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5'-3' exoribonuclease 1 isoform X11 [Rattus norvegicus]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
XRN1_D1 super family cl39678
Exoribonuclease Xrn1 D1 domain; This domain can be found in 5' to 3' exoribonuclease 1 (XRN1) ...
 81-266 1.35e-37

Exoribonuclease Xrn1 D1 domain; This domain can be found in 5' to 3' exoribonuclease 1 (XRN1) which belong to a family of conserved enzymes in eukaryotes and have important functions in transcription, RNA metabolism, and RNA interference. Xrn1 in fungi and animals is primarily cytosolic and is involved in degradation of decapped mRNAs, nonsense mediated decay, microRNA decay and is essential for proper development. The Xrn1 homolog in Drosophila, known as Pacman, is required for male fertility. This domain (D1) along with 3 other domains, make up a 510-residue segment following the conserved regions found in XRNs but they are only present in XRN1 and are absent in Rat1/XRN2. The amino acid sequences of these four domains contain an excess of basic residues, suggesting that these domains might help in binding the RNA substrate. Mutational studies carried out in D1 domain show that the mutant forms had dramatically reduced nuclease activity towards ssDNA substrate indicating that domain D1 is required for Xrn1 nuclease activity.


The actual alignment was detected with superfamily member pfam18332:

Pssm-ID: 436418  Cd Length: 192  Bit Score: 139.54  E-value: 1.35e-37
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958795452   81 GFPTLKHIKHKFFLKKSGVQVFQQSSRGENMMleITVNAEPDELSIENIASSVLGKSVFVNWPHLEEARVVAVSDGETKF 160
Cdd:pfam18332   15 GFPSLKTLPFTAQLGFHGVNVFQQDSRNESMV--VTIENKEENRTVEEIAKRKLGKRVFVGWPFLQEAKVVAVSDELFDY 92

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958795452  161 YMEEPPGTQKvylgktappcKVIQ--LSDKEQSNWTKEIQGISEQYLRRKGIMINETSAVVYAQLLTGRRYqvNQNGEvr 238
Cdd:pfam18332   93 ELSEVVDGGK----------KIVSrpHSPREIKQWKKKAERIERNYSKRLGVIIGDVEVLVHVRPLKGLKR--TDDGA-- 158

                          170       180       190
                   ....*....|....*....|....*....|.
gi 1958795452  239 LEKQWSK-QSLPFVY--QTIVKDVRAFDSRF 266
Cdd:pfam18332  159 LVKEYAEiPEYETDYalQLVVDEVVNEDERF 189
SH3_12 pfam18129
Xrn1 SH3-like domain; This is the C-terminal SH3-like domain which can be found in the ...
 524-594 1.13e-25

Xrn1 SH3-like domain; This is the C-terminal SH3-like domain which can be found in the exoribonuclease Xrn1. Xrn1 is a 175 kDa processive exoribonuclease that is conserved from yeast to mammals which targets cytoplasmic RNA substrates marked by a 5' monophosphate for processive 5'-to-3' degradation. The Sh3-like domain in Xrn1 lacks the canonical SH3 residues normally involved in binding proline-rich peptide motifs and instead engages in non-canonical interactions with the catalytic domain. Additionally it is essential in maintaining the structural integrity of Xrn1, since partial truncation of this domain in yeast Xrn1 yields an inactive protein. There is a long loop projecting from the SH3-like domain that contacts the PAZ/Tudor domain, occluding the functional surface that binds RNA or peptide motifs containing methylated arginines, respectively, in canonical PAZ and Tudor domain.


:

Pssm-ID: 465661  Cd Length: 68  Bit Score: 101.10  E-value: 1.13e-25
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1958795452  524 AEFRLFDRVVNVRENFSVPVGLRGTIIGIKGanreaDVLFEVLFDEEFPGGLTI--RCSPGRGYRLPTSALVN 594
Cdd:pfam18129    1 QKFRLGDRVVYVRDSGGVPFGLKGTVVGKGE-----DTLLDVLFDEPFMGGTTLggRCSTYRGLTVPPSALLN 68
XRN1_D2_D3 super family cl39680
Exoribonuclease Xrn1 D2/D3 domain; This domain can be found in 5' to 3' exoribonuclease 1 ...
 276-357 1.37e-04

Exoribonuclease Xrn1 D2/D3 domain; This domain can be found in 5' to 3' exoribonuclease 1 (XRN1) which belong to a family of conserved enzymes in eukaryotes and have important functions in transcription, RNA metabolism, and RNA interference. Xrn1 in fungi and animals is primarily cytosolic, involved in degradation of decapped mRNAs, nonsense mediated decay, microRNA decay and is essential for proper development. The Xrn1 homolog in Drosophila, known as Pacman, is required for male fertility. This entry relates to domain 2 and 3 combined which can be found in the 510-residue C-terminal extension found in XRN1 and not in XRN2/Rat1. Domain D2 is formed by two stretches of Xrn1, residues 915-960 and 1134-1151. The presence of domain (D3) is suggested based on structure. This domain is formed by residues 979-1109, in the insert of domain D2. It is suggested that domains D2-D4 may help maintain domain D1 pfam18332 in the correct conformation, thereby indirectly stabilising the conformation of the N-terminal segment pfam03159.


The actual alignment was detected with superfamily member pfam18334:

Pssm-ID: 436419  Cd Length: 87  Bit Score: 41.68  E-value: 1.37e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958795452  276 FPPRSVVFMLGTPYYGctGEVQDSGDviTEGRIRVV---FSIPCEPNLDALIQNQHKYSIKYNPGYVLAGRLGVSGYLVS 352
Cdd:pfam18334    6 FPEGSRAFFLGEYAYG--RPAQVTGH--SDGKLSVVvskFKSDKEPNFGKKRIVQAERSNRYYPSFAVAKMLGLHPLALS 81


                   ....*
gi 1958795452  353 RFTGS 357
Cdd:pfam18334   82 KITSS 86
DSRM_SF super family cl00054
double-stranded RNA binding motif (DSRM) superfamily; DSRM (also known as dsRBM) is a 65-70 ...
 901-966 4.62e-03

double-stranded RNA binding motif (DSRM) superfamily; DSRM (also known as dsRBM) is a 65-70 amino acid domain that adopts an alpha-beta-beta-beta-alpha fold. It is not sequence specific, but highly specific for double-stranded RNAs (dsRNAs) of various origin and structure. The DSRM domains are found in a variety of proteins including dsRNA dependent protein kinase PKR, RNA helicases, Drosophila Staufen protein, E. coli RNase III, RNase H1, and dsRNA dependent adenosine deaminases. They are involved in numerous cellular mechanisms ranging from localization and transport of messenger RNAs, through maturation and degradation of RNAs, to viral response and signal transduction. Some members harbor tandem DSRMs that act in small RNA biogenesis.


The actual alignment was detected with superfamily member cd19872:

Pssm-ID: 444671  Cd Length: 75  Bit Score: 36.88  E-value: 4.62e-03
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1958795452  901 TPVTELSRICSLVGMPQPDFSFLRTTQT----MTVCQV---KLSNGLLVHGPQ--CHSESEAKERAALFALQQLG 966
Cdd:cd19872      1 NPVQILEEICQKNGWGEPVYQLLSTSSNnevqLFIYKVtipNLPNGRLTFQPDklCRTPEEAKVLAAEFVLAQLG 75
 
Name Accession Description Interval E-value
XRN1_D1 pfam18332
Exoribonuclease Xrn1 D1 domain; This domain can be found in 5' to 3' exoribonuclease 1 (XRN1) ...
 81-266 1.35e-37

Exoribonuclease Xrn1 D1 domain; This domain can be found in 5' to 3' exoribonuclease 1 (XRN1) which belong to a family of conserved enzymes in eukaryotes and have important functions in transcription, RNA metabolism, and RNA interference. Xrn1 in fungi and animals is primarily cytosolic and is involved in degradation of decapped mRNAs, nonsense mediated decay, microRNA decay and is essential for proper development. The Xrn1 homolog in Drosophila, known as Pacman, is required for male fertility. This domain (D1) along with 3 other domains, make up a 510-residue segment following the conserved regions found in XRNs but they are only present in XRN1 and are absent in Rat1/XRN2. The amino acid sequences of these four domains contain an excess of basic residues, suggesting that these domains might help in binding the RNA substrate. Mutational studies carried out in D1 domain show that the mutant forms had dramatically reduced nuclease activity towards ssDNA substrate indicating that domain D1 is required for Xrn1 nuclease activity.


Pssm-ID: 436418  Cd Length: 192  Bit Score: 139.54  E-value: 1.35e-37
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958795452   81 GFPTLKHIKHKFFLKKSGVQVFQQSSRGENMMleITVNAEPDELSIENIASSVLGKSVFVNWPHLEEARVVAVSDGETKF 160
Cdd:pfam18332   15 GFPSLKTLPFTAQLGFHGVNVFQQDSRNESMV--VTIENKEENRTVEEIAKRKLGKRVFVGWPFLQEAKVVAVSDELFDY 92

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958795452  161 YMEEPPGTQKvylgktappcKVIQ--LSDKEQSNWTKEIQGISEQYLRRKGIMINETSAVVYAQLLTGRRYqvNQNGEvr 238
Cdd:pfam18332   93 ELSEVVDGGK----------KIVSrpHSPREIKQWKKKAERIERNYSKRLGVIIGDVEVLVHVRPLKGLKR--TDDGA-- 158

                          170       180       190
                   ....*....|....*....|....*....|.
gi 1958795452  239 LEKQWSK-QSLPFVY--QTIVKDVRAFDSRF 266
Cdd:pfam18332  159 LVKEYAEiPEYETDYalQLVVDEVVNEDERF 189
SH3_12 pfam18129
Xrn1 SH3-like domain; This is the C-terminal SH3-like domain which can be found in the ...
 524-594 1.13e-25

Xrn1 SH3-like domain; This is the C-terminal SH3-like domain which can be found in the exoribonuclease Xrn1. Xrn1 is a 175 kDa processive exoribonuclease that is conserved from yeast to mammals which targets cytoplasmic RNA substrates marked by a 5' monophosphate for processive 5'-to-3' degradation. The Sh3-like domain in Xrn1 lacks the canonical SH3 residues normally involved in binding proline-rich peptide motifs and instead engages in non-canonical interactions with the catalytic domain. Additionally it is essential in maintaining the structural integrity of Xrn1, since partial truncation of this domain in yeast Xrn1 yields an inactive protein. There is a long loop projecting from the SH3-like domain that contacts the PAZ/Tudor domain, occluding the functional surface that binds RNA or peptide motifs containing methylated arginines, respectively, in canonical PAZ and Tudor domain.


Pssm-ID: 465661  Cd Length: 68  Bit Score: 101.10  E-value: 1.13e-25
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1958795452  524 AEFRLFDRVVNVRENFSVPVGLRGTIIGIKGanreaDVLFEVLFDEEFPGGLTI--RCSPGRGYRLPTSALVN 594
Cdd:pfam18129    1 QKFRLGDRVVYVRDSGGVPFGLKGTVVGKGE-----DTLLDVLFDEPFMGGTTLggRCSTYRGLTVPPSALLN 68
XRN1 COG5049
5'-3' exonuclease [Replication, recombination and repair];
8-158 5.99e-05

5'-3' exonuclease [Replication, recombination and repair];


Pssm-ID: 227382 [Multi-domain]  Cd Length: 953  Bit Score: 47.23  E-value: 5.99e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958795452    8 LKKEERKRNQHSECLMcwYDSDTEFTYSSpwpekfpaiercstrykiISLDAWRVDINKNKITRVDQKALY-FCG----- 81
Cdd:COG5049    690 LSEEERKRNLRGLDLL--FSSNKKSDLSE------------------LFKDLYSKCKQKEYITMCSKESPYgLFGtvklg 749

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958795452   82 ----FPTLKHIKHKFFLKKSGVQVFQQSSRGENMMLEITVNAEpdELSIENIASSVLGKSVFVNWPHLEEARVVAVSDGE 157
Cdd:COG5049    750 aeglAPNLLSLCPISFLSYPGLMVFLEYSKNQSARLVIEDPKS--TVTNKSIVLRGFIKPINVLWPYLRESKLVSLTDGS 827


                   .
gi 1958795452  158 T 158
Cdd:COG5049    828 Y 828
XRN1_D2_D3 pfam18334
Exoribonuclease Xrn1 D2/D3 domain; This domain can be found in 5' to 3' exoribonuclease 1 ...
 276-357 1.37e-04

Exoribonuclease Xrn1 D2/D3 domain; This domain can be found in 5' to 3' exoribonuclease 1 (XRN1) which belong to a family of conserved enzymes in eukaryotes and have important functions in transcription, RNA metabolism, and RNA interference. Xrn1 in fungi and animals is primarily cytosolic, involved in degradation of decapped mRNAs, nonsense mediated decay, microRNA decay and is essential for proper development. The Xrn1 homolog in Drosophila, known as Pacman, is required for male fertility. This entry relates to domain 2 and 3 combined which can be found in the 510-residue C-terminal extension found in XRN1 and not in XRN2/Rat1. Domain D2 is formed by two stretches of Xrn1, residues 915-960 and 1134-1151. The presence of domain (D3) is suggested based on structure. This domain is formed by residues 979-1109, in the insert of domain D2. It is suggested that domains D2-D4 may help maintain domain D1 pfam18332 in the correct conformation, thereby indirectly stabilising the conformation of the N-terminal segment pfam03159.


Pssm-ID: 436419  Cd Length: 87  Bit Score: 41.68  E-value: 1.37e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958795452  276 FPPRSVVFMLGTPYYGctGEVQDSGDviTEGRIRVV---FSIPCEPNLDALIQNQHKYSIKYNPGYVLAGRLGVSGYLVS 352
Cdd:pfam18334    6 FPEGSRAFFLGEYAYG--RPAQVTGH--SDGKLSVVvskFKSDKEPNFGKKRIVQAERSNRYYPSFAVAKMLGLHPLALS 81


                   ....*
gi 1958795452  353 RFTGS 357
Cdd:pfam18334   82 KITSS 86
DSRM_A1CF-like cd19872
double-stranded RNA binding motif of APOBEC1 complementation factor (A1CF), RNA-binding ...
 901-966 4.62e-03

double-stranded RNA binding motif of APOBEC1 complementation factor (A1CF), RNA-binding protein 46 (RBM46) and similar proteins; The family includes two dsRNA-binding motif-containing proteins, A1CF and RBM46. A1CF (also known as APOBEC1-stimulating protein) is an essential component of the apolipoprotein B mRNA editing enzyme complex which is responsible for the posttranscriptional editing of a CAA codon for Gln to a UAA codon for stop in APOB mRNA. A1CF binds to APOB mRNA and is probably responsible for docking the catalytic subunit, APOBEC1, to the mRNA to allow it to deaminate its target cytosine. RBM46 (also called cancer/testis antigen 68 (CT68), or RNA-binding motif protein 46) plays a novel role in the regulation of embryonic stem cell (ESC) differentiation by regulating the degradation of beta-catenin mRNA. It also regulates trophectoderm specification by stabilizing Cdx2 mRNA in early mouse embryos. Members of this family contain three RNA recognition motifs (RRMs) and a C-terminal double-stranded RNA binding motif (DSRM) that is not sequence specific, but highly specific for dsRNAs of various origin and structure.


Pssm-ID: 380701  Cd Length: 75  Bit Score: 36.88  E-value: 4.62e-03
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1958795452  901 TPVTELSRICSLVGMPQPDFSFLRTTQT----MTVCQV---KLSNGLLVHGPQ--CHSESEAKERAALFALQQLG 966
Cdd:cd19872      1 NPVQILEEICQKNGWGEPVYQLLSTSSNnevqLFIYKVtipNLPNGRLTFQPDklCRTPEEAKVLAAEFVLAQLG 75
 
Name Accession Description Interval E-value
XRN1_D1 pfam18332
Exoribonuclease Xrn1 D1 domain; This domain can be found in 5' to 3' exoribonuclease 1 (XRN1) ...
 81-266 1.35e-37

Exoribonuclease Xrn1 D1 domain; This domain can be found in 5' to 3' exoribonuclease 1 (XRN1) which belong to a family of conserved enzymes in eukaryotes and have important functions in transcription, RNA metabolism, and RNA interference. Xrn1 in fungi and animals is primarily cytosolic and is involved in degradation of decapped mRNAs, nonsense mediated decay, microRNA decay and is essential for proper development. The Xrn1 homolog in Drosophila, known as Pacman, is required for male fertility. This domain (D1) along with 3 other domains, make up a 510-residue segment following the conserved regions found in XRNs but they are only present in XRN1 and are absent in Rat1/XRN2. The amino acid sequences of these four domains contain an excess of basic residues, suggesting that these domains might help in binding the RNA substrate. Mutational studies carried out in D1 domain show that the mutant forms had dramatically reduced nuclease activity towards ssDNA substrate indicating that domain D1 is required for Xrn1 nuclease activity.


Pssm-ID: 436418  Cd Length: 192  Bit Score: 139.54  E-value: 1.35e-37
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958795452   81 GFPTLKHIKHKFFLKKSGVQVFQQSSRGENMMleITVNAEPDELSIENIASSVLGKSVFVNWPHLEEARVVAVSDGETKF 160
Cdd:pfam18332   15 GFPSLKTLPFTAQLGFHGVNVFQQDSRNESMV--VTIENKEENRTVEEIAKRKLGKRVFVGWPFLQEAKVVAVSDELFDY 92

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958795452  161 YMEEPPGTQKvylgktappcKVIQ--LSDKEQSNWTKEIQGISEQYLRRKGIMINETSAVVYAQLLTGRRYqvNQNGEvr 238
Cdd:pfam18332   93 ELSEVVDGGK----------KIVSrpHSPREIKQWKKKAERIERNYSKRLGVIIGDVEVLVHVRPLKGLKR--TDDGA-- 158

                          170       180       190
                   ....*....|....*....|....*....|.
gi 1958795452  239 LEKQWSK-QSLPFVY--QTIVKDVRAFDSRF 266
Cdd:pfam18332  159 LVKEYAEiPEYETDYalQLVVDEVVNEDERF 189
SH3_12 pfam18129
Xrn1 SH3-like domain; This is the C-terminal SH3-like domain which can be found in the ...
 524-594 1.13e-25

Xrn1 SH3-like domain; This is the C-terminal SH3-like domain which can be found in the exoribonuclease Xrn1. Xrn1 is a 175 kDa processive exoribonuclease that is conserved from yeast to mammals which targets cytoplasmic RNA substrates marked by a 5' monophosphate for processive 5'-to-3' degradation. The Sh3-like domain in Xrn1 lacks the canonical SH3 residues normally involved in binding proline-rich peptide motifs and instead engages in non-canonical interactions with the catalytic domain. Additionally it is essential in maintaining the structural integrity of Xrn1, since partial truncation of this domain in yeast Xrn1 yields an inactive protein. There is a long loop projecting from the SH3-like domain that contacts the PAZ/Tudor domain, occluding the functional surface that binds RNA or peptide motifs containing methylated arginines, respectively, in canonical PAZ and Tudor domain.


Pssm-ID: 465661  Cd Length: 68  Bit Score: 101.10  E-value: 1.13e-25
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1958795452  524 AEFRLFDRVVNVRENFSVPVGLRGTIIGIKGanreaDVLFEVLFDEEFPGGLTI--RCSPGRGYRLPTSALVN 594
Cdd:pfam18129    1 QKFRLGDRVVYVRDSGGVPFGLKGTVVGKGE-----DTLLDVLFDEPFMGGTTLggRCSTYRGLTVPPSALLN 68
XRN1 COG5049
5'-3' exonuclease [Replication, recombination and repair];
8-158 5.99e-05

5'-3' exonuclease [Replication, recombination and repair];


Pssm-ID: 227382 [Multi-domain]  Cd Length: 953  Bit Score: 47.23  E-value: 5.99e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958795452    8 LKKEERKRNQHSECLMcwYDSDTEFTYSSpwpekfpaiercstrykiISLDAWRVDINKNKITRVDQKALY-FCG----- 81
Cdd:COG5049    690 LSEEERKRNLRGLDLL--FSSNKKSDLSE------------------LFKDLYSKCKQKEYITMCSKESPYgLFGtvklg 749

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958795452   82 ----FPTLKHIKHKFFLKKSGVQVFQQSSRGENMMLEITVNAEpdELSIENIASSVLGKSVFVNWPHLEEARVVAVSDGE 157
Cdd:COG5049    750 aeglAPNLLSLCPISFLSYPGLMVFLEYSKNQSARLVIEDPKS--TVTNKSIVLRGFIKPINVLWPYLRESKLVSLTDGS 827


                   .
gi 1958795452  158 T 158
Cdd:COG5049    828 Y 828
XRN1_D2_D3 pfam18334
Exoribonuclease Xrn1 D2/D3 domain; This domain can be found in 5' to 3' exoribonuclease 1 ...
 276-357 1.37e-04

Exoribonuclease Xrn1 D2/D3 domain; This domain can be found in 5' to 3' exoribonuclease 1 (XRN1) which belong to a family of conserved enzymes in eukaryotes and have important functions in transcription, RNA metabolism, and RNA interference. Xrn1 in fungi and animals is primarily cytosolic, involved in degradation of decapped mRNAs, nonsense mediated decay, microRNA decay and is essential for proper development. The Xrn1 homolog in Drosophila, known as Pacman, is required for male fertility. This entry relates to domain 2 and 3 combined which can be found in the 510-residue C-terminal extension found in XRN1 and not in XRN2/Rat1. Domain D2 is formed by two stretches of Xrn1, residues 915-960 and 1134-1151. The presence of domain (D3) is suggested based on structure. This domain is formed by residues 979-1109, in the insert of domain D2. It is suggested that domains D2-D4 may help maintain domain D1 pfam18332 in the correct conformation, thereby indirectly stabilising the conformation of the N-terminal segment pfam03159.


Pssm-ID: 436419  Cd Length: 87  Bit Score: 41.68  E-value: 1.37e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958795452  276 FPPRSVVFMLGTPYYGctGEVQDSGDviTEGRIRVV---FSIPCEPNLDALIQNQHKYSIKYNPGYVLAGRLGVSGYLVS 352
Cdd:pfam18334    6 FPEGSRAFFLGEYAYG--RPAQVTGH--SDGKLSVVvskFKSDKEPNFGKKRIVQAERSNRYYPSFAVAKMLGLHPLALS 81


                   ....*
gi 1958795452  353 RFTGS 357
Cdd:pfam18334   82 KITSS 86
DSRM_A1CF-like cd19872
double-stranded RNA binding motif of APOBEC1 complementation factor (A1CF), RNA-binding ...
 901-966 4.62e-03

double-stranded RNA binding motif of APOBEC1 complementation factor (A1CF), RNA-binding protein 46 (RBM46) and similar proteins; The family includes two dsRNA-binding motif-containing proteins, A1CF and RBM46. A1CF (also known as APOBEC1-stimulating protein) is an essential component of the apolipoprotein B mRNA editing enzyme complex which is responsible for the posttranscriptional editing of a CAA codon for Gln to a UAA codon for stop in APOB mRNA. A1CF binds to APOB mRNA and is probably responsible for docking the catalytic subunit, APOBEC1, to the mRNA to allow it to deaminate its target cytosine. RBM46 (also called cancer/testis antigen 68 (CT68), or RNA-binding motif protein 46) plays a novel role in the regulation of embryonic stem cell (ESC) differentiation by regulating the degradation of beta-catenin mRNA. It also regulates trophectoderm specification by stabilizing Cdx2 mRNA in early mouse embryos. Members of this family contain three RNA recognition motifs (RRMs) and a C-terminal double-stranded RNA binding motif (DSRM) that is not sequence specific, but highly specific for dsRNAs of various origin and structure.


Pssm-ID: 380701  Cd Length: 75  Bit Score: 36.88  E-value: 4.62e-03
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1958795452  901 TPVTELSRICSLVGMPQPDFSFLRTTQT----MTVCQV---KLSNGLLVHGPQ--CHSESEAKERAALFALQQLG 966
Cdd:cd19872      1 NPVQILEEICQKNGWGEPVYQLLSTSSNnevqLFIYKVtipNLPNGRLTFQPDklCRTPEEAKVLAAEFVLAQLG 75
 
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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