Conserved Protein Domain Family

cd12230: RRM1_U2AF65 
Click on image for an interactive view with Cn3D
RNA recognition motif 1 (RRM1) found in U2 large nuclear ribonucleoprotein auxiliary factor U2AF 65 kDa subunit (U2AF65) and similar proteins
The subfamily corresponds to the RRM1 of U2AF65 and dU2AF50. U2AF65, also termed U2AF2, is the large subunit of U2 small nuclear ribonucleoprotein (snRNP) auxiliary factor (U2AF), which has been implicated in the recruitment of U2 snRNP to pre-mRNAs and is a highly conserved heterodimer composed of large and small subunits. U2AF65 specifically recognizes the intron polypyrimidine tract upstream of the 3' splice site and promotes binding of U2 snRNP to the pre-mRNA branchpoint. U2AF65 also plays an important role in the nuclear export of mRNA. It facilitates the formation of a messenger ribonucleoprotein export complex, containing both the NXF1 receptor and the RNA substrate. Moreover, U2AF65 interacts directly and specifically with expanded CAG RNA, and serves as an adaptor to link expanded CAG RNA to NXF1 for RNA export. U2AF65 contains an N-terminal RS domain rich in arginine and serine, followed by a proline-rich segment and three C-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The N-terminal RS domain stabilizes the interaction of U2 snRNP with the branch point (BP) by contacting the branch region, and further promotes base pair interactions between U2 snRNA and the BP. The proline-rich segment mediates protein-protein interactions with the RRM domain of the small U2AF subunit (U2AF35 or U2AF1). The RRM1 and RRM2 are sufficient for specific RNA binding, while RRM3 is responsible for protein-protein interactions. The family also includes Splicing factor U2AF 50 kDa subunit (dU2AF50), the Drosophila ortholog of U2AF65. dU2AF50 functions as an essential pre-mRNA splicing factor in flies. It associates with intronless mRNAs and plays a significant and unexpected role in the nuclear export of a large number of intronless mRNAs.
PSSM-Id: 409677
Aligned: 37 rows
Threshold Bit Score: 108.788
Created: 13-Sep-2011
Updated: 25-Oct-2021
Aligned Rows:
RNA binding
Conserved site includes 11 residues -Click on image for an interactive view with Cn3D
Feature 1:RNA binding site [nucleic acid binding site]

Sequence Alignment
Format: Row Display: Color Bits: Type Selection:
Feature 1           # #  #                                                ### #                   
XP_001349063  650 ARELYVGNIPqhidIQEIVKYLNSCLlilynk-------enenenICLKACIRg-dTHYAFVEFRNIQDTSNCMLL-NGI 720  Plasmodium fa...
XP_001348830  455 QRKLYIGNIPpnskQEDVVDFFNNSIlavikdssldvkigdvqlmPVIKCEIFnsdSRFCFLEFRTVQITWLCLKL-DSI 533  Plasmodium fa...
XP_001447829  149 DRKLYVGNLPpnsqPKELQDFLNQTLlkmgvs--------sehagSICNCWIDs-nGHFGFIEFRSPEEATQGFIL-KDV 218  Paramecium te...
XP_002768233  177 ARELYIGQIPpgisAAHLIDVLNDSLmnmgan--------ampgrPIVHGWLGg-dGLFAFVEFRTAEEASIALERlNGH 247  Perkinsus mar...
CBJ27181      748 MRELHVGGLPhgvsGVQLQDFLNAAMqylkia--------tsagnPVIRIAMGpdgTNFAFIELRTEEETNATLGRmSGI 819  Ectocarpus si...
EGR27170       24 ARRLYIGNIPdsinQEYLSEWLYRSLeaagglv-----dslpnenPIIKCEIDs-kGKFAFIEIRTIEETTTLLQL-DGI 96   Ichthyophthir...
EGD73665       35 TRQLVVENLPegtrDHDLMSFMNDCIasnkli--------tqpgqPVIKCTLSe-dGKSAVLEFRSVDEATNGLVF-DRE 104  Salpingoeca s...
CAK92242       87 AVRLYLGNLPdnvdKDHLHNYIRQQMeshgav--------ldpgdPVIQVQLQp-gQKYCFVQFRSIEETEAALQI-DTI 156  Paramecium te...
CBK24598      150 GKDLYVGNIDegtfPEDVVAFLNRAMhtarln--------lwpgnPVLSCRIL---PKFCFVSLRHEDEATAALNM-DGI 217  Blastocystis ...
Feature 1                  # ###
2G4B_A         74 IFQG--QSLKIRRP 85   human
XP_001349063  721 NFYG--NNLRIGRP 732  Plasmodium falciparum 3D7
XP_001348830  534 PYNN--YCLRIGRP 545  Plasmodium falciparum 3D7
XP_001447829  219 IFKG--HQLKIGRP 230  Paramecium tetraurelia strain d4-2
XP_002768233  248 QLKSygVSIKVGRP 261  Perkinsus marinus ATCC 50983
CBJ27181      820 QCGT--GHLKFGRP 831  Ectocarpus siliculosus
EGR27170       97 ILWH--RQLRIRRP 108  Ichthyophthirius multifiliis
EGD73665      105 RFKG--AQLRVRRP 116  Salpingoeca sp. ATCC50818
CAK92242      157 NYQG--KPLKFKRV 168  Paramecium tetraurelia strain d4-2
CBK24598      218 YFHG--QRLRISIH 229  Blastocystis hominis

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