RNA recognition motif 2 (RRM2) found in vertebrate RNA-binding protein 10 (RBM10); This subgroup corresponds to the RRM2 of RBM10, also termed G patch domain-containing protein 9, or RNA-binding protein S1-1 (S1-1), a paralog of putative tumor suppressor RNA-binding protein 5 (RBM5 or LUCA15 or H37). It may play an important role in mRNA generation, processing and degradation in several cell types. The rat homolog of human RBM10 is protein S1-1, a hypothetical RNA binding protein with poly(G) and poly(U) binding capabilities. RBM10 is structurally related to RBM5 and RNA-binding protein 6 (RBM6 or NY-LU-12 or g16 or DEF-3). It contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), two C2H2-type zinc fingers, and a G-patch/D111 domain.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 325120986 363 ANDTIILRNLNPHSTMDSILGALAPYAVLSSSNVRVIKDKQTQLNRGFAFIQLSTIVEAAQLLQILQALHPPLTIDGKTI 442
Cdd:cd12754    1 ANDTIILRNLNPHSTMDSILSALAPYAVLSSSNVRVIKDKQTQLNRGFAFIQLSTIVEAAQLLQILQALHPPLTIDGKTI 80

                 ....*..
gi 325120986 443 NVEFAKG 449
Cdd:cd12754   81 NVEFAKG 87

OCRE domain found in RNA-binding protein 10 (RBM10) and similar proteins; RBM10, also called G patch domain-containing protein 9, or RNA-binding protein S1-1 (S1-1), is a paralogue of putative tumor suppressor RNA-binding protein 5 (RBM5 or LUCA15 or H37). It may play an important role in mRNA generation, processing and degradation in several cell types. The rat homolog of human RBM10 is protein S1-1, a hypothetical RNA binding protein with poly(G) and poly(U) binding capabilities. RBM10 contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), an OCtamer REpeat (OCRE) domain, two C2H2-type zinc fingers, and a G-patch/D111 domain.

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 325120986 629 YPVPDVSTYQYDETSGYYYDPQTGLYYDPNSQYYYNAQSQQYLYWDGERRTYVPALEQSADGHK 692
Cdd:cd16167    1 YPVPDVSTYQYDETSGYYYDPQTGLYYDPNSQYYYNAQTQQYLYWDGERRTYVPASEQGADGHK 64

Zinc finger domain; Zinc finger domain in Ran-binding proteins (RanBPs), and other proteins. In RanBPs, this domain binds RanGDP.

                           10        20
                   ....*....|....*....|....*
gi 325120986   280 EDWLCNKCGVQNFKRREKCFKCGVP 304
Cdd:smart00547   1 GDWECPACTFLNFASRSKCFACGAP 25

RNA recognition motif 2 (RRM2) found in vertebrate RNA-binding protein 10 (RBM10); This subgroup corresponds to the RRM2 of RBM10, also termed G patch domain-containing protein 9, or RNA-binding protein S1-1 (S1-1), a paralog of putative tumor suppressor RNA-binding protein 5 (RBM5 or LUCA15 or H37). It may play an important role in mRNA generation, processing and degradation in several cell types. The rat homolog of human RBM10 is protein S1-1, a hypothetical RNA binding protein with poly(G) and poly(U) binding capabilities. RBM10 is structurally related to RBM5 and RNA-binding protein 6 (RBM6 or NY-LU-12 or g16 or DEF-3). It contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), two C2H2-type zinc fingers, and a G-patch/D111 domain.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 325120986 363 ANDTIILRNLNPHSTMDSILGALAPYAVLSSSNVRVIKDKQTQLNRGFAFIQLSTIVEAAQLLQILQALHPPLTIDGKTI 442
Cdd:cd12754    1 ANDTIILRNLNPHSTMDSILSALAPYAVLSSSNVRVIKDKQTQLNRGFAFIQLSTIVEAAQLLQILQALHPPLTIDGKTI 80

                 ....*..
gi 325120986 443 NVEFAKG 449
Cdd:cd12754   81 NVEFAKG 87

OCRE domain found in RNA-binding protein 10 (RBM10) and similar proteins; RBM10, also called G patch domain-containing protein 9, or RNA-binding protein S1-1 (S1-1), is a paralogue of putative tumor suppressor RNA-binding protein 5 (RBM5 or LUCA15 or H37). It may play an important role in mRNA generation, processing and degradation in several cell types. The rat homolog of human RBM10 is protein S1-1, a hypothetical RNA binding protein with poly(G) and poly(U) binding capabilities. RBM10 contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), an OCtamer REpeat (OCRE) domain, two C2H2-type zinc fingers, and a G-patch/D111 domain.

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 325120986 629 YPVPDVSTYQYDETSGYYYDPQTGLYYDPNSQYYYNAQSQQYLYWDGERRTYVPALEQSADGHK 692
Cdd:cd16167    1 YPVPDVSTYQYDETSGYYYDPQTGLYYDPNSQYYYNAQTQQYLYWDGERRTYVPASEQGADGHK 64

G-patch domain; This domain is found in a number of RNA binding proteins, and is also found in proteins that contain RNA binding domains. This suggests that this domain may have an RNA binding function. This domain has seven highly conserved glycines.

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 325120986  923 SDNIGSRMLQAMGWKEGSGLGRKKQGIVTPIEAQTRVRGSGLGAR 967
Cdd:pfam01585   1 TSNIGFKLLQKMGWKEGQGLGKNEQGIAEPIEAKIKKDRRGLGAE 45

RNA recognition motif;

                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 325120986   196 VMLRMLPQAATEDDIRGQLQSHGvQAREVRLMRNKSSGQSRGFAFVEFSHLQDATRWMEANqHSLNILGQKV 267
Cdd:smart00360   2 LFVGNLPPDTTEEELRELFSKFG-KVESVRLVRDKETGKSKGFAFVEFESEEDAEKALEAL-NGKELDGRPL 71

RNA recognition motif;

                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 325120986   366 TIILRNLNPHSTMDSILGALAPYAVLSSsnVRVIKDKQTQLNRGFAFIQLSTIVEAAQLLQILQAlhppLTIDGKTINV 444
Cdd:smart00360   1 TLFVGNLPPDTTEEELRELFSKFGKVES--VRLVRDKETGKSKGFAFVEFESEEDAEKALEALNG----KELDGRPLKV 73

RNA recognition motif (RRM) domain [Translation, ribosomal structure and biogenesis];

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 325120986 366 TIILRNLNPHSTMDSILGALAPY-AVLSssnVRVIKDKQTQLNRGFAFIQLSTIVEAAqllQILQALHpPLTIDGKTINV 444
Cdd:COG0724    3 KIYVGNLPYSVTEEDLRELFSEYgEVTS---VKLITDRETGRSRGFGFVEMPDDEEAQ---AAIEALN-GAELMGRTLKV 75

                 ....
gi 325120986 445 EFAK 448
Cdd:COG0724   76 NEAR 79

ELAV/HuD family splicing factor; This model describes the ELAV/HuD subfamily of splicing factors found in metazoa. HuD stands for the human paraneoplastic encephalomyelitis antigen D of which there are 4 variants in human. ELAV stnds for the Drosophila Embryonic lethal abnormal visual protein. ELAV-like splicing factors are also known in human as HuB (ELAV-like protein 2), HuC (ELAV-like protein 3, Paraneoplastic cerebellar degeneration-associated antigen) and HuR (ELAV-like protein 1). These genes are most closely related to the sex-lethal subfamily of splicing factors found in Dipteran insects (TIGR01659). These proteins contain 3 RNA-recognition motifs (rrm: pfam00076).

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 325120986  201 LPQAATEDDIRGQLQSHGvQAREVRLMRNKSSGQSRGFAFVEFSHLQDATRWMEAnQHSLNILGQKVSMHYSDPK----- 275
Cdd:TIGR01661  11 LPQTMTQEEIRSLFTSIG-EIESCKLVRDKVTGQSLGYGFVNYVRPEDAEKAVNS-LNGLRLQNKTIKVSYARPSsdsik 88

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 325120986  276 ---------PK-----------------INEDWLCNK-------CGVQNFKRRE------KCFKCGVPKSEAEQ------ 310
Cdd:TIGR01661  89 ganlyvsglPKtmtqhelesifspfgqiITSRILSDNvtglskgVGFIRFDKRDeadraiKTLNGTTPSGCTEPitvkfa 168

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 325120986  311 ---------------------KLPLGTRLDQQTLPLGG---------------------RELSQGLLPLPQPYQAQGVLA 348
Cdd:TIGR01661 169 nnpsssnskgllsqleavqnpQTTRVPLSTILTAAGIGpmhhaaarfrpsagdftavlaHQQQQHAVAQQHAAQRASPPA 248

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 325120986  349 SQA----LSQGSE-PSSENANDTIILRNLNPhSTMDSILGAL-APYAVLssSNVRVIKDKQTQLNRGFAFIQLSTIVEAA 422
Cdd:TIGR01661 249 TDGqtagLAAGAQiSASDGAGYCIFVYNLSP-DTDETVLWQLfGPFGAV--QNVKIIRDLTTNQCKGYGFVSMTNYDEAA 325

                         330       340
                  ....*....|....*....|....
gi 325120986  423 QLLQILQAlhppLTIDGKTINVEF 446
Cdd:TIGR01661 326 MAILSLNG----YTLGNRVLQVSF 345

RNA recognition motif 2 (RRM2) found in vertebrate RNA-binding protein 10 (RBM10); This subgroup corresponds to the RRM2 of RBM10, also termed G patch domain-containing protein 9, or RNA-binding protein S1-1 (S1-1), a paralog of putative tumor suppressor RNA-binding protein 5 (RBM5 or LUCA15 or H37). It may play an important role in mRNA generation, processing and degradation in several cell types. The rat homolog of human RBM10 is protein S1-1, a hypothetical RNA binding protein with poly(G) and poly(U) binding capabilities. RBM10 is structurally related to RBM5 and RNA-binding protein 6 (RBM6 or NY-LU-12 or g16 or DEF-3). It contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), two C2H2-type zinc fingers, and a G-patch/D111 domain.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 325120986 363 ANDTIILRNLNPHSTMDSILGALAPYAVLSSSNVRVIKDKQTQLNRGFAFIQLSTIVEAAQLLQILQALHPPLTIDGKTI 442
Cdd:cd12754    1 ANDTIILRNLNPHSTMDSILSALAPYAVLSSSNVRVIKDKQTQLNRGFAFIQLSTIVEAAQLLQILQALHPPLTIDGKTI 80

                 ....*..
gi 325120986 443 NVEFAKG 449
Cdd:cd12754   81 NVEFAKG 87

RNA recognition motif 2 (RRM2) found in RNA-binding protein 5 (RBM5) and similar proteins; This subgroup corresponds to the RRM2 of RNA-binding protein 5 (RBM5 or LUCA15 or H37), RNA-binding protein 10 (RBM10 or S1-1) and similar proteins. RBM5 is a known modulator of apoptosis. It may also act as a tumor suppressor or an RNA splicing factor; it specifically binds poly(G) RNA. RBM10, a paralog of RBM5, may play an important role in mRNA generation, processing and degradation in several cell types. The rat homolog of human RBM10 is protein S1-1, a hypothetical RNA binding protein with poly(G) and poly(U) binding capabilities. Both, RBM5 and RBM10, contain two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), two C2H2-type zinc fingers, and a G-patch/D111 domain.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 325120986 363 ANDTIILRNLNPHSTMDSILGALAPYAVLSSSNVRVIKDKQTQLNRGFAFIQLSTIVEAAQLLQILQALHPPLTIDGKTI 442
Cdd:cd12562    1 ANDTIILRNINPHTTVDSILGALAPYAVLSSSNVRLIKDKQTQLNRGFAFVQLSSPIEASQLLQILQSLHPPLTIDGKTI 80

                 ....*.
gi 325120986 443 NVEFAK 448
Cdd:cd12562   81 NVDFAK 86

RNA recognition motif 2 (RRM2) found in vertebrate RNA-binding protein 5 (RBM5); This subgroup corresponds to the RRM2 of RBM5, also termed protein G15, or putative tumor suppressor LUCA15, or renal carcinoma antigen NY-REN-9, a known modulator of apoptosis. It may also act as a tumor suppressor or an RNA splicing factor. RBM5 shows high sequence similarity to RNA-binding protein 6 (RBM6 or NY-LU-12 or g16 or DEF-3). Both, RBM5 and RBM6, specifically bind poly(G) RNA. They contain two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), two C2H2-type zinc fingers, a nuclear localization signal, and a G-patch/D111 domain.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 325120986 365 DTIILRNLNPHSTMDSILGALAPYAVLSSSNVRVIKDKQTQLNRGFAFIQLSTIVEAAQLLQILQALHPPLTIDGKTINV 444
Cdd:cd12755    3 DTIILRNIAPHTVVDSIMTALSPYASLAVNNIRLIKDKQTQQNRGFAFVQLSSALEASQLLQILQSLHPPLKIDGKTIGV 82

                 ....
gi 325120986 445 EFAK 448
Cdd:cd12755   83 DFAK 86

OCRE domain found in RNA-binding protein 5 (RBM5) and similar proteins; RBM5 is also called protein G15, H37, putative tumor suppressor LUCA15, or renal carcinoma antigen NY-REN-9. It is a known modulator of apoptosis. It acts as a tumor suppressor or an RNA splicing factor. RBM5 shows high sequence similarity to RNA-binding protein 6 (RBM6 or NY-LU-12 or g16 or DEF-3). Both of them specifically binds poly(G) RNA. RBM5 contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), an OCtamer REpeat (OCRE) domain, two C2H2-type zinc fingers, a nuclear localization signal, and a G-patch/D111 domain.

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 325120986 631 VPDVSTYQYDETSGYYYDPQTGLYYDPNSQYYYNAQSQQYLYWDGERRTYVPALE 685
Cdd:cd16168    2 VPDTSTYQYDESSGYYYDPITGLYYDPNSQYYYNSLTQQYLYWDGEKQTYLPAAE 56

RNA recognition motif 1 (RRM1) and 2 (RRM2) found in RNA-binding protein 5 (RBM5) and similar proteins; This subfamily includes the RRM1 and RRM2 of RNA-binding protein 5 (RBM5 or LUCA15 or H37) and RNA-binding protein 10 (RBM10 or S1-1), and the RRM2 of RNA-binding protein 6 (RBM6 or NY-LU-12 or g16 or DEF-3). These RBMs share high sequence homology and may play an important role in regulating apoptosis. RBM5 is a known modulator of apoptosis. It may also act as a tumor suppressor or an RNA splicing factor. RBM6 has been predicted to be a nuclear factor based on its nuclear localization signal. Both, RBM6 and RBM5, specifically bind poly(G) RNA. RBM10 is a paralog of RBM5. It may play an important role in mRNA generation, processing and degradation in several cell types. The rat homolog of human RBM10 is protein S1-1, a hypothetical RNA binding protein with poly(G) and poly(U) binding capabilities. All family members contain two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), two C2H2-type zinc fingers, and a G-patch/D111 domain.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 325120986 364 NDTIILRNLNPHSTMDSILGALAPYAVLSSSNVRVIKDKQTQLNRGFAFIQLSTIVEAAQLLQILQALHPPLTIDGKTIN 443
Cdd:cd12313    2 TNVLILRGLDVLTTEEDILSALQAHADLPIKDVRLIRDKLTGTSRGFAFVEFSSLEDATQVMDALQNLLPPFKIDGRVVS 81

                 ....
gi 325120986 444 VEFA 447
Cdd:cd12313   82 VSYA 85

RNA recognition motif 1 (RRM1) found in vertebrate RNA-binding protein 5 (RBM5); This subgroup corresponds to the RRM1 of RBM5, also termed protein G15, or putative tumor suppressor LUCA15, or renal carcinoma antigen NY-REN-9, a known modulator of apoptosis. It may also act as a tumor suppressor or an RNA splicing factor. RBM5 shows high sequence similarity to RNA-binding protein 6 (RBM6 or NY-LU-12 or g16 or DEF-3). Both, RBM5 and RBM6, specifically bind poly(G) RNA. They contain two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), two C2H2-type zinc fingers, a nuclear localization signal, and a G-patch/D111 domain.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 325120986 191 KASNIVMLRMLPQAATEDDIRGQLQS-HGVQAREVRLMRNKSsGQSRGFAFVEFSHLQDATRWMEANQHSLNILGQKVSM 269
Cdd:cd12752    3 KESKTIMLRGLPINITENDIRELIESfEGPQPADVRLMKRKT-GVSRGFAFVEFYHLQDATSWMEANQKKLVIQGKTIAM 81

                 ....*.
gi 325120986 270 HYSDPK 275
Cdd:cd12752   82 HYSNPR 87

OCRE domain; The OCRE (OCtamer REpeat) domain contains 5 repeats of an 8-residue motif, which were shown to form beta-strands. Based on the architectures of proteins containing OCRE domains, a role in RNA metabolism and/or signalling has been proposed.

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|.
gi 325120986 632 PDVSTYQYDETSGYYYDPQTGLYYDPNSQYYYNAQSQQYLYWDGERRTYVP 682
Cdd:cd16074    3 PDPSGFVFDPNSGYYYDPSTGLYYDPNTGYYYDPTSGTYYIWDDELGAYVP 53

G-patch domain; This domain is found in a number of RNA binding proteins, and is also found in proteins that contain RNA binding domains. This suggests that this domain may have an RNA binding function. This domain has seven highly conserved glycines.

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 325120986  923 SDNIGSRMLQAMGWKEGSGLGRKKQGIVTPIEAQTRVRGSGLGAR 967
Cdd:pfam01585   1 TSNIGFKLLQKMGWKEGQGLGKNEQGIAEPIEAKIKKDRRGLGAE 45

OCRE domain found in Suppressor of ABI3-5 (SUA) and similar proteins; SUA is an RNA-binding protein located in the nucleus and expressed in all plant tissues. It functions as a splicing factor that influences seed maturation by controlling alternative splicing of ABI3. The suppression of the cryptic ABI3 intron indicates a role of SUA in mRNA processing. SUA also interacts with the prespliceosomal component U2AF65, the larger subunit of the conserved pre-mRNA splicing factor U2AF. SUA contains two RNA recognition motifs surrounding a zinc finger domain, an OCtamer REpeat (OCRE) domain, and a Gly-rich domain close to the C-terminus.

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|
gi 325120986 634 VSTYQYDETSGYYYDPQTGLYYDPNSQYYYNAQSQQYLYWDGERRTYVPA 683
Cdd:cd16166    5 PSGFVYDPASGYYYDASSGYYYDANTGLYYDAASGRWYSYDEETGQYVEV 54

OCRE domain found in RNA-binding protein 6 (RBM6) and similar proteins; RBM6, also called lung cancer antigen NY-LU-12, or protein G16, or RNA-binding protein DEF-3, has been predicted to be a nuclear factor based on its nuclear localization signal. It shows high sequence similarity to RNA-binding protein 5 (RBM5 or LUCA15 or NY-REN-9). Both specifically binds poly(G) RNA. RBM6 contain two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), an OCtamer REpeat (OCRE) domain, two C2H2-type zinc fingers, a nuclear localization signal, and a G-patch/D111 domain. In contrast to RBM5, RBM6 has an additional unique domain, the POZ (poxvirus and zinc finger) domain, which may be involved in protein-protein interactions and inhibit binding of target sequences by zinc fingers.

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|
gi 325120986 634 VSTYQYDETSGYYYDPQTGLYYDPNSQYYYNAQSQQYLYWDGERRTYVPA 683
Cdd:cd16163    6 APTYRSDPDSGYIYDPETGYYYDPVTGLYYDPATGEYVDPDTGTLPYDPS 55

RNA recognition motif 1 (RRM1) found in vertebrate RNA-binding protein 6 (RBM6); This subfamily corresponds to the RRM1 of RBM6, also termed lung cancer antigen NY-LU-12, or protein G16, or RNA-binding protein DEF-3, which has been predicted to be a nuclear factor based on its nuclear localization signal. It shows high sequence similarity to RNA-binding protein 5 (RBM5 or LUCA15 or NY-REN-9). Both, RBM6 and RBM5, specifically bind poly(G) RNA. They contain two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), two C2H2-type zinc fingers, a nuclear localization signal, and a G-patch/D111 domain. In contrast to RBM5, RBM6 has two additional unique domains: the decamer repeat occurring more than 20 times, and the POZ (poxvirus and zinc finger) domain. The POZ domain may be involved in protein-protein interactions and inhibit binding of target sequences by zinc fingers.

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 325120986 194 NIVMLRMLPQAATEDDIRGQLQS-HGVQAREVRLmRNKSSGQSRGFAFVEFSHLQDATRWMEANQHSLNILGQKVSMHY 271
Cdd:cd12314    1 NLIRLIGVPETATKEQILNAFRVpDGMPVKNLKL-KNYVPGYDYDYVCVEFSLLEDAIGCMEANQGTLKIGTKEVTLEY 78

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).

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 325120986 196 VMLRMLPQAATEDDIRGQLQSHGvQAREVRLMRNKSsGQSRGFAFVEFSHLQDATRWMEANQHSLnILGQKV 267
Cdd:cd00590    1 LFVGNLPPDTTEEDLRELFSKFG-EVVSVRIVRDRD-GKSKGFAFVEFESPEDAEKALEALNGTE-LGGRPL 69

RNA recognition motif (RRM) domain [Translation, ribosomal structure and biogenesis];

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 325120986 201 LPQAATEDDIRGQLQSHGvQAREVRLMRNKSSGQSRGFAFVEFSHLQDATRWMEA 255
Cdd:COG0724    9 LPYSVTEEDLRELFSEYG-EVTSVKLITDRETGRSRGFGFVEMPDDEEAQAAIEA 62

G-patch domain; Yeast Spp2, a G-patch protein and spliceosome component, interacts with the ATP-dependent DExH-box splicing factor Prp2. As this interaction involves the G-patch sequence in Spp2 and is required for the recruitment of Prp2 to the spliceosome before the first catalytic step of splicing, it is proposed that Spp2 might be an accessory factor that confers spliceosome specificity on Prp2.

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 325120986  924 DNIGSRMLQAMGWKEGSGLGRKKQGIVTPIEAQTRVRGSGLGARGSS 970
Cdd:pfam12656  15 EEFGAAMLRGMGWKPGQGIGKNKKGDVKPKEYKRRPGGLGLGAKPAE 61

RNA recognition motif 1 (RRM1) and 2 (RRM2) found in CELF/Bruno-like family of RNA binding proteins and plant flowering time control protein FCA; This subfamily corresponds to the RRM1 and RRM2 domains of the CUGBP1 and ETR-3-like factors (CELF) as well as plant flowering time control protein FCA. CELF, also termed BRUNOL (Bruno-like) proteins, is a family of structurally related RNA-binding proteins involved in regulation of pre-mRNA splicing in the nucleus, and control of mRNA translation and deadenylation in the cytoplasm. The family contains six members: CELF-1 (also known as BRUNOL-2, CUG-BP1, NAPOR, EDEN-BP), CELF-2 (also known as BRUNOL-3, ETR-3, CUG-BP2, NAPOR-2), CELF-3 (also known as BRUNOL-1, TNRC4, ETR-1, CAGH4, ER DA4), CELF-4 (BRUNOL-4), CELF-5 (BRUNOL-5) and CELF-6 (BRUNOL-6). They all contain three highly conserved RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains): two consecutive RRMs (RRM1 and RRM2) situated in the N-terminal region followed by a linker region and the third RRM (RRM3) close to the C-terminus of the protein. The low sequence conservation of the linker region is highly suggestive of a large variety in the co-factors that associate with the various CELF family members. Based on both, sequence similarity and function, the CELF family can be divided into two subfamilies, the first containing CELFs 1 and 2, and the second containing CELFs 3, 4, 5, and 6. The different CELF proteins may act through different sites on at least some substrates. Furthermore, CELF proteins may interact with each other in varying combinations to influence alternative splicing in different contexts. This subfamily also includes plant flowering time control protein FCA that functions in the posttranscriptional regulation of transcripts involved in the flowering process. FCA contains two RRMs, and a WW protein interaction domain.

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 325120986 200 MLPQAATEDDIRGQLQSHGVqAREVRLMRNKSSGQSRGFAFVEFSHLQDATRWMEA 255
Cdd:cd12361    6 MIPKTASEEDVRPLFEQFGN-IEEVQILRDKQTGQSKGCAFVTFSTREEALRAIEA 60

RNA recognition motif 2 (RRM2) found in yeast protein gar2 and similar proteins; This subfamily corresponds to the RRM2 of yeast protein gar2, a novel nucleolar protein required for 18S rRNA and 40S ribosomal subunit accumulation. It shares similar domain architecture with nucleolin from vertebrates and NSR1 from Saccharomyces cerevisiae. The highly phosphorylated N-terminal domain of gar2 is made up of highly acidic regions separated from each other by basic sequences, and contains multiple phosphorylation sites. The central domain of gar2 contains two closely adjacent N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The C-terminal RGG (or GAR) domain of gar2 is rich in glycine, arginine and phenylalanine residues.

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 325120986 201 LPQAATEDDIRGQLQSHGvQAREVRLMRNKSSGQSRGFAFVEFSHLQDATRWMEANQH 258
Cdd:cd12448    6 LPFSATQDALYEAFSQHG-SIVSVRLPTDRETGQPKGFGYVDFSTIDSAEAAIDALGG 62

RNA recognition motif 1 (RRM1) found in RNA-binding protein 5 (RBM5) and similar proteins; This subgroup corresponds to the RRM1 of RNA-binding protein 5 (RBM5 or LUCA15 or H37), RNA-binding protein 10 (RBM10 or S1-1) and similar proteins. RBM5 is a known modulator of apoptosis. It may also act as a tumor suppressor or an RNA splicing factor; it specifically binds poly(G) RNA. RBM10, a paralog of RBM5, may play an important role in mRNA generation, processing and degradation in several cell types. The rat homolog of human RBM10 is protein S1-1, a hypothetical RNA binding protein with poly(G) and poly(U) binding capabilities. Both, RBM5 and RBM10, contain two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), two C2H2-type zinc fingers, and a G-patch/D111 domain.

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 325120986 363 ANDTIILRNLNPHSTMDSILGALAPYAVlSSSNVRVIKDKQTQLNRGFAFIQLSTIVEA 421
Cdd:cd12561    1 PNNTIMLRGLPLSVTEEDIRNALVSHGV-QPKDVRLMRRKTTGASRGFAFVEFMSLEEA 58

OCRE domain found in Zinc-finger and OCRE domain-containing Protein 1 (ZOP1) and similar proteins found in plant; ZOP1 is a novel plant-specific nucleic acid-binding protein required for both RNA-directed DNA methylation (RdDM) and pre-mRNA splicing. It promotes RNA polymerase IV (Pol IV)-dependent siRNA accumulation, DNA methylation, and transcriptional silencing. As a pre-mRNA splicing factor, ZOP1 associates with several typical splicing proteins as well as with RNA polymerase II (RNAP II and Pol II). It also shows both RdDM-dependent and -independent roles in transcriptional silencing. ZOP1 contains an N-terminal C2H2-type ZnF domain and an OCtamer REpeat (OCRE) domain that is usually related to RNA processing.

                         10        20        30
                 ....*....|....*....|....*....|.
gi 325120986 634 VSTYQYDETSGYYYDPQTGLYYDPNSQYYYN 664
Cdd:cd16165    5 AGDWVLDSKSGYYYNAATRYYYDPKTGMYYS 35

RNA recognition motif (RRM) found in eukaryotic translation initiation factor 3 subunit G (eIF-3G) and similar proteins; This subfamily corresponds to the RRM of eIF-3G and similar proteins. eIF-3G, also termed eIF-3 subunit 4, or eIF-3-delta, or eIF3-p42, or eIF3-p44, is the RNA-binding subunit of eIF3, a large multisubunit complex that plays a central role in the initiation of translation by binding to the 40 S ribosomal subunit and promoting the binding of methionyl-tRNAi and mRNA. eIF-3G binds 18 S rRNA and beta-globin mRNA, and therefore appears to be a nonspecific RNA-binding protein. eIF-3G is one of the cytosolic targets and interacts with mature apoptosis-inducing factor (AIF). eIF-3G contains one RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). This family also includes yeast eIF3-p33, a homolog of vertebrate eIF-3G, plays an important role in the initiation phase of protein synthesis in yeast. It binds both, mRNA and rRNA, fragments due to an RRM near its C-terminus.

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 325120986 201 LPQAATEDDIRGQLQSHGVQAReVRLMRNKSSGQSRGFAFVEFSHLQDATRWMEA 255
Cdd:cd12408    7 LSEDATEEDLRELFRPFGPISR-VYLAKDKETGQSKGFAFVTFETREDAERAIEK 60

RNA recognition motif 5 (RRM5) found in yeast multiple RNA-binding domain-containing protein 1 (MRD1) and similar proteins; This subgroup corresponds to the RRM5 of MRD1 which is encoded by a novel yeast gene MRD1 (multiple RNA-binding domain). It is well-conserved in yeast and its homologs exist in all eukaryotes. MRD1 is present in the nucleolus and the nucleoplasm. It interacts with the 35 S precursor rRNA (pre-rRNA) and U3 small nucleolar RNAs (snoRNAs). MRD1 is essential for the initial processing at the A0-A2 cleavage sites in the 35 S pre-rRNA. It contains 5 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which may play an important structural role in organizing specific rRNA processing events.

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 325120986 196 VMLRMLPQAATEDDIRGQLQSHGvQAREVRLMRnKSSGQSRGFAFVEFSHLQDATRWMEANQHSlNILGQKVSMHYS 272
Cdd:cd12570    3 ILVKNLPFEATKKDVRTLFSSYG-QLKSVRVPK-KFDQSARGFAFVEFSTAKEALNAMNALKDT-HLLGRRLVLQYA 76

RNA recognition motif 1 (RRM1) found in plant flowering time control protein FCA and similar proteins; This subgroup corresponds to the RRM1 of FCA, a gene controlling flowering time in Arabidopsis, encoding a flowering time control protein that functions in the posttranscriptional regulation of transcripts involved in the flowering process. FCA contains two RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNP (ribonucleoprotein domains), and a WW protein interaction domain.

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 325120986 201 LPQAATEDDIRGQLQSHGvQAREVRLMRNKSSGQSRGFAFVEFSHLQDATRWMEA--NQHSLNILGQKVSMHYSD 273
Cdd:cd12633    7 VPRTITEQEVRPMFEEHG-NVLEVAIIKDKRTGHQQGCCFVKYSTRDEADRAIRAlhNQRTLPGGASPVQVRYAD 80

RNA recognition motif 3 (RRM3) found in RNA-binding protein 19 (RBM19) and RNA recognition motif 2 found in multiple RNA-binding domain-containing protein 1 (MRD1); This subfamily corresponds to the RRM3 of RBM19 and RRM2 of MRD1. RBM19, also termed RNA-binding domain-1 (RBD-1), is a nucleolar protein conserved in eukaryotes involved in ribosome biogenesis by processing rRNA and is essential for preimplantation development. It has a unique domain organization containing 6 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). MRD1 is encoded by a novel yeast gene MRD1 (multiple RNA-binding domain). It is well conserved in yeast and its homologs exist in all eukaryotes. MRD1 is present in the nucleolus and the nucleoplasm. It interacts with the 35 S precursor rRNA (pre-rRNA) and U3 small nucleolar RNAs (snoRNAs). It is essential for the initial processing at the A0-A2 cleavage sites in the 35 S pre-rRNA. MRD1 contains 5 conserved RRMs, which may play an important structural role in organizing specific rRNA processing events.

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 325120986 198 LRMLPQAATEDDIRGQLQSHGVQArEVRLMRNKSSGQSRGFAFVEFSHLQDATRWMEA 255
Cdd:cd12316    4 VRNLPFTATEDELRELFEAFGKIS-EVHIPLDKQTKRSKGFAFVLFVIPEDAVKAYQE 60

RNA recognition motif 2 (RRM2) found in yeast nucleolar protein 13 (Nop13p) and similar proteins; This subfamily corresponds to the RRM2 of Nop13p encoded by YNL175c from Saccharomyces cerevisiae. It shares high sequence similarity with nucleolar protein 12 (Nop12p). Both Nop12p and Nop13p are not essential for growth. However, unlike Nop12p that is localized to the nucleolus, Nop13p localizes primarily to the nucleolus but is also present in the nucleoplasm to a lesser extent. Nop13p contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains).

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 325120986 201 LPQAATEDDIRGQLQSHGvQAREVRLMRNKSSGQSRGFAFVEFSHLQDATRWMEaNQHSLNILGQKVSMHY 271
Cdd:cd12397    6 LSFETTEEDLRKHFAPAG-KIRKVRMATFEDSGKCKGFAFVDFKEIESATNAVK-GPINHSLNGRDLRVEY 74

RNA recognition motif 2 (RRM2) found in vertebrate RNA-binding protein 10 (RBM10); This subgroup corresponds to the RRM2 of RBM10, also termed G patch domain-containing protein 9, or RNA-binding protein S1-1 (S1-1), a paralog of putative tumor suppressor RNA-binding protein 5 (RBM5 or LUCA15 or H37). It may play an important role in mRNA generation, processing and degradation in several cell types. The rat homolog of human RBM10 is protein S1-1, a hypothetical RNA binding protein with poly(G) and poly(U) binding capabilities. RBM10 is structurally related to RBM5 and RNA-binding protein 6 (RBM6 or NY-LU-12 or g16 or DEF-3). It contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), two C2H2-type zinc fingers, and a G-patch/D111 domain.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 325120986 192 ASNIVMLRMLPQAATEDDIRGQLQSHGV-QAREVRLMRNKSSGQSRGFAFVEFSHLQDATRW---MEANQHSLNILGQKV 267
Cdd:cd12754    1 ANDTIILRNLNPHSTMDSILSALAPYAVlSSSNVRVIKDKQTQLNRGFAFIQLSTIVEAAQLlqiLQALHPPLTIDGKTI 80

                 ....*
gi 325120986 268 SMHYS 272
Cdd:cd12754   81 NVEFA 85

RNA recognition motif (RRM) found in pre-mRNA cleavage factor Im 68 kDa subunit (CFIm68 or CPSF6), pre-mRNA cleavage factor Im 59 kDa subunit (CFIm59 or CPSF7), and similar proteins; This subfamily corresponds to the RRM of cleavage factor Im (CFIm) subunits. Cleavage factor Im (CFIm) is a highly conserved component of the eukaryotic mRNA 3' processing machinery that functions in UGUA-mediated poly(A) site recognition, the regulation of alternative poly(A) site selection, mRNA export, and mRNA splicing. It is a complex composed of a small 25 kDa (CFIm25) subunit and a larger 59/68/72 kDa subunit. Two separate genes, CPSF6 and CPSF7, code for two isoforms of the large subunit, CFIm68 and CFIm59. Structurally related CFIm68 and CFIm59, also termed cleavage and polyadenylation specificity factor subunit 6 (CPSF7), or cleavage and polyadenylation specificity factor 59 kDa subunit (CPSF59), are functionally redundant. Both contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a central proline-rich region, and a C-terminal RS-like domain. Their N-terminal RRM mediates the interaction with CFIm25, and also serves to enhance RNA binding and facilitate RNA looping.

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 325120986 206 TEDDIRGQLQSHGV-QAREVRLMRNKSSGQSRGFAFVEFSHLQDATRWMEA-NQHSLNilGQKVSMHY 271
Cdd:cd12372   11 TDEDLEGACASFGVvDVKEIKFFEHKANGKSKGYAYVEFASPAAAAAVKEKlEKREFN--GRPCVVTP 76

RNA recognition motif 1 (RRM1) found in the Hu proteins family; This subfamily corresponds to the RRM1 of the Hu proteins family which represents a group of RNA-binding proteins involved in diverse biological processes. Since the Hu proteins share high homology with the Drosophila embryonic lethal abnormal vision (ELAV) protein, the Hu family is sometimes referred to as the ELAV family. Drosophila ELAV is exclusively expressed in neurons and is required for the correct differentiation and survival of neurons in flies. The neuronal members of the Hu family include Hu-antigen B (HuB or ELAV-2 or Hel-N1), Hu-antigen C (HuC or ELAV-3 or PLE21), and Hu-antigen D (HuD or ELAV-4), which play important roles in neuronal differentiation, plasticity and memory. HuB is also expressed in gonads. Hu-antigen R (HuR or ELAV-1 or HuA) is the ubiquitously expressed Hu family member. It has a variety of biological functions mostly related to the regulation of cellular response to DNA damage and other types of stress. HuR has an anti-apoptotic function during early cell stress response. It binds to mRNAs and enhances the expression of several anti-apoptotic proteins, such as p21waf1, p53, and prothymosin alpha. HuR also has pro-apoptotic function by promoting apoptosis when cell death is unavoidable. Furthermore, HuR may be important in muscle differentiation, adipogenesis, suppression of inflammatory response and modulation of gene expression in response to chronic ethanol exposure and amino acid starvation. Hu proteins perform their cytoplasmic and nuclear molecular functions by coordinately regulating functionally related mRNAs. In the cytoplasm, Hu proteins recognize and bind to AU-rich RNA elements (AREs) in the 3' untranslated regions (UTRs) of certain target mRNAs, such as GAP-43, vascular epithelial growth factor (VEGF), the glucose transporter GLUT1, eotaxin and c-fos, and stabilize those ARE-containing mRNAs. They also bind and regulate the translation of some target mRNAs, such as neurofilament M, GLUT1, and p27. In the nucleus, Hu proteins function as regulators of polyadenylation and alternative splicing. Each Hu protein contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an ARE. RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions.

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|.
gi 325120986 201 LPQAATEDDIRGQLQSHGvQAREVRLMRNKSSGQSRGFAFVEFSHLQDATR 251
Cdd:cd12650    8 LPQNMTQDEIRSLFSSIG-EIESCKLIRDKVTGQSLGYGFVNYVDPSDAEK 57

RNA recognition motif 4 (RRM4) found in RNA-binding protein RBM12, RBM12B and similar proteins; This subfamily corresponds to the RRM4 of RBM12 and RBM12B. RBM12, also termed SH3/WW domain anchor protein in the nucleus (SWAN), is ubiquitously expressed. It contains five distinct RNA binding motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), two proline-rich regions, and several putative transmembrane domains. RBM12B show high sequence semilarity with RBM12. It contains five distinct RRMs as well. The biological roles of both RBM12 and RBM12B remain unclear.

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 325120986 196 VMLRMLPQAATEDDIRGQLQSHGVQAREVRLMRNKsSGQSRGFAFVEFSHLQDATRWMEANQHSLN 261
Cdd:cd12514    2 IRITNLPYDATPVDIQRFFEDHGVRPEDVHLLRNK-KGRGNGEALVTFKSEGDAREVLKLNGKKLG 66

RNA recognition motif 1 (RRM1) found in Drosophila sex-lethal (SXL) and similar proteins; This subfamily corresponds to the RRM1 of SXL which governs sexual differentiation and X chromosome dosage compensation in Drosophila melanogaster. It induces female-specific alternative splicing of the transformer (tra) pre-mRNA by binding to the tra uridine-rich polypyrimidine tract at the non-sex-specific 3' splice site during the sex-determination process. SXL binds also to its own pre-mRNA and promotes female-specific alternative splicing. SXL contains an N-terminal Gly/Asn-rich domain that may be responsible for the protein-protein interaction, and tandem RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), that show high preference to bind single-stranded, uridine-rich target RNA transcripts.

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|.
gi 325120986 201 LPQAATEDDIRGQLQSHGvQAREVRLMRNKSSGQSRGFAFVEFSHLQDATR 251
Cdd:cd12649    8 LPQDLTDREFRALFRAIG-PVNTCKIVRDKKTGYSYGFGFVDFTSEEDAQR 57

ELAV/HuD family splicing factor; This model describes the ELAV/HuD subfamily of splicing factors found in metazoa. HuD stands for the human paraneoplastic encephalomyelitis antigen D of which there are 4 variants in human. ELAV stnds for the Drosophila Embryonic lethal abnormal visual protein. ELAV-like splicing factors are also known in human as HuB (ELAV-like protein 2), HuC (ELAV-like protein 3, Paraneoplastic cerebellar degeneration-associated antigen) and HuR (ELAV-like protein 1). These genes are most closely related to the sex-lethal subfamily of splicing factors found in Dipteran insects (TIGR01659). These proteins contain 3 RNA-recognition motifs (rrm: pfam00076).

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 325120986  201 LPQAATEDDIRGQLQSHGvQAREVRLMRNKSSGQSRGFAFVEFSHLQDATRWMEAnQHSLNILGQKVSMHYSDPK----- 275
Cdd:TIGR01661  11 LPQTMTQEEIRSLFTSIG-EIESCKLVRDKVTGQSLGYGFVNYVRPEDAEKAVNS-LNGLRLQNKTIKVSYARPSsdsik 88

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 325120986  276 ---------PK-----------------INEDWLCNK-------CGVQNFKRRE------KCFKCGVPKSEAEQ------ 310
Cdd:TIGR01661  89 ganlyvsglPKtmtqhelesifspfgqiITSRILSDNvtglskgVGFIRFDKRDeadraiKTLNGTTPSGCTEPitvkfa 168

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 325120986  311 ---------------------KLPLGTRLDQQTLPLGG---------------------RELSQGLLPLPQPYQAQGVLA 348
Cdd:TIGR01661 169 nnpsssnskgllsqleavqnpQTTRVPLSTILTAAGIGpmhhaaarfrpsagdftavlaHQQQQHAVAQQHAAQRASPPA 248

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 325120986  349 SQA----LSQGSE-PSSENANDTIILRNLNPhSTMDSILGAL-APYAVLssSNVRVIKDKQTQLNRGFAFIQLSTIVEAA 422
Cdd:TIGR01661 249 TDGqtagLAAGAQiSASDGAGYCIFVYNLSP-DTDETVLWQLfGPFGAV--QNVKIIRDLTTNQCKGYGFVSMTNYDEAA 325

                         330       340
                  ....*....|....*....|....
gi 325120986  423 QLLQILQAlhppLTIDGKTINVEF 446
Cdd:TIGR01661 326 MAILSLNG----YTLGNRVLQVSF 345

RNA recognition motif 2 (RRM2) found in Nicotiana sylvestris chloroplastic 33 kDa ribonucleoprotein (NsCP33) and similar proteins; The family includes NsCP33, Arabidopsis thaliana chloroplastic 31 kDa ribonucleoprotein (CP31A) and mitochondrial glycine-rich RNA-binding protein 2 (AtGR-RBP2). NsCP33 may be involved in splicing and/or processing of chloroplast RNA's. AtCP31A, also called RNA-binding protein 1/2/3 (AtRBP33), or RNA-binding protein CP31A, or RNA-binding protein RNP-T, or RNA-binding protein cp31, is required for specific RNA editing events in chloroplasts and stabilizes specific chloroplast mRNAs, as well as for normal chloroplast development under cold stress conditions by stabilizing transcripts of numerous mRNAs under these conditions. CP31A may modulate telomere replication through RNA binding domains. AtGR-RBP2, also called AtRBG2, or glycine-rich protein 2 (AtGRP2), or mitochondrial RNA-binding protein 1a (At-mRBP1a), plays a role in RNA transcription or processing during stress. It binds RNAs and DNAs sequence with a preference to single-stranded nucleic acids. AtGR-RBP2 displays strong affinity to poly(U) sequence. It exerts cold and freezing tolerance, probably by exhibiting an RNA chaperone activity during the cold and freezing adaptation process. Some members in this family contain two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The model corresponds to the second RRM motif.

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 325120986 371 NLNPHSTMDSILGALAPY-AVLSssnVRVIKDKQTQLNRGFAFIQLSTIVEAAQLLQILQAlhppLTIDGKTINVEFA 447
Cdd:cd21608    6 NLSWDTTEDDLRDLFSEFgEVES---AKVITDRETGRSRGFGFVTFSTAEAAEAAIDALNG----KELDGRSIVVNEA 76

RNA recognition motif (RRM) found in U11/U12 small nuclear ribonucleoprotein 35 kDa protein (U11/U12-35K) and similar proteins; This subfamily corresponds to the RRM of U11/U12-35K, also termed protein HM-1, or U1 snRNP-binding protein homolog, and is one of the components of the U11/U12 snRNP, which is a subunit of the minor (U12-dependent) spliceosome required for splicing U12-type nuclear pre-mRNA introns. U11/U12-35K is highly conserved among bilateria and plants, but lacks in some organisms, such as Saccharomyces cerevisiae and Caenorhabditis elegans. Moreover, U11/U12-35K shows significant sequence homology to U1 snRNP-specific 70 kDa protein (U1-70K or snRNP70). It contains a conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), followed by an adjacent glycine-rich region, and Arg-Asp and Arg-Glu dipeptide repeats rich domain, making U11/U12-35K a possible functional analog of U1-70K. It may facilitate 5' splice site recognition in the minor spliceosome and play a role in exon bridging, interacting with components of the major spliceosome bound to the pyrimidine tract of an upstream U2-type intron. The family corresponds to the RRM of U11/U12-35K that may directly contact the U11 or U12 snRNA through the RRM domain.

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 325120986 199 RMLPQAaTEDDIRGQLQSHGvQAREVRLMRNKSSGQSRGFAFVEFSHLQDATRWMEANQHSL 260
Cdd:cd12237   11 RLSLQT-TEEKLKEVFSRYG-DIRRLRLVRDIVTGFSKRYAFIEYKEERDALHAYRDAKKLV 70

RNA recognition motif 4 (RRM4) found in RNA-binding protein 28 (RBM28) and similar proteins; This subfamily corresponds to the RRM4 of RBM28 and Nop4p. RBM28 is a specific nucleolar component of the spliceosomal small nuclear ribonucleoproteins (snRNPs), possibly coordinating their transition through the nucleolus. It specifically associates with U1, U2, U4, U5, and U6 small nuclear RNAs (snRNAs), and may play a role in the maturation of both small nuclear and ribosomal RNAs. RBM28 has four RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an extremely acidic region between RRM2 and RRM3. The family also includes nucleolar protein 4 (Nop4p or Nop77p) encoded by YPL043W from Saccharomyces cerevisiae. It is an essential nucleolar protein involved in processing and maturation of 27S pre-rRNA and biogenesis of 60S ribosomal subunits. Nop4p also contains four RRMs.

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 325120986 198 LRMLPQAATEDDIRGQLQSH--------GVQAREVRLMRNK------SSGQSRGFAFVEFSHLQDA 249
Cdd:cd12416    5 VRNLPKSVDDKKLKKLFLKAvkerakkkGVKIKEVKVMRDKkrlnsdGKGRSKGYGFVEFTEHEHA 70

RNA recognition motif 1 (RRM1) found in yeast multiple RNA-binding domain-containing protein 1 (MRD1) and similar proteins; This subgroup corresponds to the RRM1 of MRD1 which is encoded by a novel yeast gene MRD1 (multiple RNA-binding domain). It is well-conserved in yeast and its homologs exist in all eukaryotes. MRD1 is present in the nucleolus and the nucleoplasm. It interacts with the 35 S precursor rRNA (pre-rRNA) and U3 small nucleolar RNAs (snoRNAs). MRD1 is essential for the initial processing at the A0-A2 cleavage sites in the 35 S pre-rRNA. It contains 5 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which may play an important structural role in organizing specific rRNA processing events.

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|.
gi 325120986 201 LPQAATEDDIRGQLQSHGvQAREVRLMRNKSsGQSRGFAFVEFSHLQDATR 251
Cdd:cd12565    8 LPKYVTEKRLKEHFSKKG-EITDVKVMRTKD-GKSRRFGFIGFKSEEEAQK 56