InterPro : IPR000504

Name  RNA recognition motif domain Short Name  RRM_dom
Type  Domain Description  Many eukaryotic proteins containing one or more copies of a putative RNA-binding domain of about 90 amino acids are known to bind single-stranded RNAs [, , ]. The largest group of single strand RNA-binding proteins is the eukaryotic RNA recognition motif (RRM) family that contains an eight amino acid RNP-1 consensus sequence [, ]. RRM proteins have a variety of RNA binding preferences and functions, and include heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing (SR, U2AF, Sxl), protein components of small nuclear ribonucleoproteins (U1 and U2 snRNPs), and proteins that regulate RNA stability and translation (PABP, La, Hu) [, , ]. The RRM in heterodimeric splicing factor U2 snRNP auxiliary factor (U2AF) appears to have two RRM-like domains with specialised features for protein recognition []. The motif also appears in a few single stranded DNA binding proteins.The typical RRM consists of four anti-parallel beta-strands and two alpha-helices arranged in a beta-alpha-beta-beta-alpha-beta fold with side chains that stack with RNA bases. Specificity of RNA binding is determined by multiple contacts with surrounding amino acids. A third helix is present during RNA binding in some cases []. The RRM is reviewed in a number of publications [, , ].

Sequence Features

GO Displayer


InterPro protein domain ID --> Contigs



1 Child Features

Id Name Short Name Type
IPR003954 RNA recognition motif domain, eukaryote RRM_dom_euk Domain

0 Contains

20 Found In

Id Name Short Name Type
IPR012677 Nucleotide-binding alpha-beta plait domain Nucleotide-bd_a/b_plait Domain
IPR009145 U2 auxiliary factor small subunit U2_small Family
IPR017334 Eukaryotic translation initiation factor 3 subunit G eIF3_g Family
IPR008111 RNA-binding motif protein 8 RNA-bd_8 Family
IPR011400 Eukaryotic translation initiation factor 3 subunit B EIF3B Family
IPR002343 Paraneoplastic encephalomyelitis antigen Hud_Sxl_RNA Family
IPR006548 Splicing factor ELAV/HuD ELAD_HUD_SF Family
IPR006515 Polyadenylate binding protein, human types 1, 2, 3, 4 PABP_1234 Family
IPR006536 HnRNP-L/PTB/hephaestus splicing factor HnRNP-L_PTB Family
IPR002344 Lupus La protein Lupus_La Family
IPR006535 HnRNP R/Q splicing factor HnRNP_R/Q_splicing_fac Family
IPR006529 U2 snRNP auxilliary factor, large subunit, splicing factor U2AF_lg Family
IPR006509 Splicing factor, RBM39-like RBM39_SF Family
IPR006546 Sex-lethal splicing factor Sxl Family
IPR006532 Poly-U binding splicing factor, half-pint PolyU-bd Family
IPR016304 Cyclophilin-type peptidyl-prolyl cis-trans isomerase E Cyclophilin-type_PPIase_E Family
IPR016967 Splicing factor, SPF45 Splicing_factor_SPF45 Family
IPR017111 Histone H3-K4 methyltransferase Set1, fungal Hist_H3-K4_MeTrfase_1_fun Family
IPR017325 RNA binding protein Fox-1 RNA-bd_Fox-1 Family
IPR017347 Heterogeneous nuclear ribonucleoprotein C, Raly hnRNP_C_Raly Family

1 Parent Features

Id Name Short Name Type
IPR012677 Nucleotide-binding alpha-beta plait domain Nucleotide-bd_a/b_plait Domain

10 Publications

First Author Title Year Journal Volume Pages
Bandziulis RJ RNA-binding proteins as developmental regulators. 1989 Genes Dev 3 431-7
Birney E Analysis of the RNA-recognition motif and RS and RGG domains: conservation in metazoan pre-mRNA splicing factors. 1993 Nucleic Acids Res 21 5803-16
Dreyfuss G Heterogeneous nuclear ribonucleoprotein particles and the pathway of mRNA formation. 1988 Trends Biochem Sci 13 86-91
Kielkopf CL U2AF homology motifs: protein recognition in the RRM world. 2004 Genes Dev 18 1513-26
Chambers JC Genomic structure and amino acid sequence domains of the human La autoantigen. 1988 J Biol Chem 263 18043-51
Sachs AB A single domain of yeast poly(A)-binding protein is necessary and sufficient for RNA binding and cell viability. 1987 Mol Cell Biol 7 3268-76
Query CC A common RNA recognition motif identified within a defined U1 RNA binding domain of the 70K U1 snRNP protein. 1989 Cell 57 89-101
Kenan DJ RNA recognition: towards identifying determinants of specificity. 1991 Trends Biochem Sci 16 214-20
Maris C The RNA recognition motif, a plastic RNA-binding platform to regulate post-transcriptional gene expression. 2005 FEBS J 272 2118-31
Teplova M Structural basis for recognition and sequestration of UUU(OH) 3' temini of nascent RNA polymerase III transcripts by La, a rheumatic disease autoantigen. 2006 Mol Cell 21 75-85

To cite PlanMine, please refer to the following publication:

Rozanski, A., Moon, H., Brandl, H., Martín-Durán, J. M., Grohme, M., Hüttner, K., Bartscherer, K., Henry, I., & Rink, J. C.
PlanMine 3.0—improvements to a mineable resource of flatworm biology and biodiversity
Nucleic Acids Research, gky1070. doi:10.1093/nar/gky1070 (2018)