SII-SWORD/CoKE huggingface dataset:
MTHFSD, RNA recognition motif (MTHFSD_RRM)
Type: Domain

This entry represents the RNA recognition motif found in the methenyltetrahydrofolate synthase domain-containing protein (MTHFSD), a putative RNA-binding protein found in various vertebrate species. It contains an N-terminal 5-formyltetrahydrofolate cyclo-ligase domain and a C-terminal RNA recognition motif (RRM). The biological role of MTHFSD remains unclear.
Vip1-like, RNA recognition motif, plant (Vip1-like_RRM_plant)
Type: Domain

This entry represents the Vip1-like, uncharacterised proteins found in plants. Although their biological roles remain unclear, these proteins show high sequence similarity to the fission yeast Vip1. Similar to the Vip1 protein, members in this family contain an N-terminal RNA recognition motif (RRM).
PHIP1, RNA recognition motif 1 (PHIP1_RRM1)
Type: Domain

This entry represents the RNA recognition motif 1 (RRM1) of PHIP1. A. thaliana PHIP1 and its homologues represent a novel class of plant-specific RNA-binding proteins that may play a unique role in the polarized mRNA transport to the vicinity of the cell plate . PHIP1 is a peripheral membrane protein and is localized at the cell plate during cytokinesis in plants. In addition to phragmoplastin, PHIP1 interacts with two Arabidopsis small GTP-binding proteins, Rop1 and Ran2. However, PHIP1 interacted only with the GTP-bound form of Rop1 but not the GDP-bound form. It also binds specifically to Ran2 mRNA . This group of proteins consist of multiple functional domains, including a lysine-rich domain (KRD domain) that contains three nuclear localization motifs (KKKR/NK), two RNA recognition motifs (RRMs), and three CCHC-type zinc fingers.
PHIP1, RNA recognition motif 2 (PHIP1_RRM2)
Type: Domain

This entry represents the RNA recognition motif 2 (RRM2) of PHIP1. A. thaliana PHIP1 and its homologues represent a novel class of plant-specific RNA-binding proteins that may play a unique role in the polarized mRNA transport to the vicinity of the cell plate . PHIP1 is a peripheral membrane protein and is localized at the cell plate during cytokinesis in plants. In addition to phragmoplastin, PHIP1 interacts with two Arabidopsis small GTP-binding proteins, Rop1 and Ran2. However, PHIP1 interacted only with the GTP-bound form of Rop1 but not the GDP-bound form. It also binds specifically to Ran2 mRNA . This group of proteins consist of multiple functional domains, including a lysine-rich domain (KRD domain) that contains three nuclear localization motifs (KKKR/NK), two RNA recognition motifs (RRMs), and three CCHC-type zinc fingers.
eIF3B, RNA recognition motif (eIF3B_RRM)
Type: Domain

This entry represents the RNA recognition motif (RRM) found in eukaryotic translation initiation factor 3 (eIF-3), 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.
AtC3H46-like, RNA recognition motif (AtC3H46-like_RRM)
Type: Domain

This entry represents the RNA recognition motif
(RRM) found in AtC3H46, a putative RNA-binding protein that contains an RNA recognition motif (RRM) and a CCCH class of zinc finger, typically C-X8-C-X5-C-X3-H. It may possess ribonuclease activity .
Protein xmas, RNA recognition motif (XMAS_RRM)
Type: Domain

This entry represents the RNA recognition motif (RRM) found in Xmas, the Drosophila homologue of yeast Sac3p protein. Together with E(y)2, the Drosophila homologue of yeast Sus1p protein, Xmas is part of the nuclear pore complex (NPC)-associated TREX-2/AMEX complex that is required in the regulation of mRNA transport and also involved in the efficient transcription regulation of the heat-shock protein 70 (hsp70) loci . This group of proteins are found in insects and contain an N-terminal RNA recognition motif (RRM), followed by a PCI domain.
SCAF4, RNA recognition motif (SCAF4_RRM)
Type: Domain

This entry represents the RNA recognition motif (RRM) of SCAF4 (also known as Splicing factor, arginine/serine-rich 15) that belongs to a new class of SCAFs (SR-like CTD-associated factors). Although its biological function remains unclear, SCAF4 shows high sequence similarity to SCAF8 that interacts specifically with a highly serine-phosphorylated form of the carboxy-terminal domain (CTD) of the largest subunit of RNA polymerase II (pol II) and may play a direct role in coupling with both, transcription and pre-mRNA processing, processes . SCAF4 and SCAF8 both contain a conserved N-terminal CTD-interacting domain (CID), an atypical RNA recognition motif (RRM) and serine/arginine-rich motifs.
SCAF8, RNA recognition motif (SCAF8_RRM)
Type: Domain

This entry represents the RNA recognition motif (RRM) of SCAF8, a nuclear matrix protein that interacts specifically with a highly serine-phosphorylated form of the carboxy-terminal domain (CTD) of the largest subunit of RNA polymerase II (pol II) . The pol II CTD plays a role in coupling transcription and pre-mRNA processing . SCAF8 co-localizes primarily with transcription sites that are enriched in nuclear matrix fraction, which is known to contain proteins involved in pre-mRNA processing . Thus, SCAF8 may play a direct role in coupling with both, transcription and pre-mRNA processing, processes. SCAF8, together with SCAF4, represents a new class of SCAFs (SR-like CTD-associated factors). They contain a conserved N-terminal CTD-interacting domain (CID), an atypical RNA recognition motif (RRM) and serine/arginine-rich motifs.
UHMK1, RNA recognition motif (UHMK1_RRM)
Type: Domain

This entry represents the RNA recognition motif (RRM) of UHMK1. UHMK1, also termed kinase interacting with stathmin (KIS) or P-CIP2, is a serine/threonine protein kinase functionally related to RNA metabolism and neurite outgrowth. It contains an N-terminal kinase domain and a C-terminal RNA recognition motif (RRM), with high homology to the corresponding motif of the mammalian U2 small nuclear ribonucleoprotein auxiliary factor U2AF 65kDa subunit (U2AF65 or U2AF2) .
Serine/threonine-protein kinase Kist (UHMK1)
Type: Family

UHMK1, also termed kinase interacting with stathmin (KIS), Kist or P-CIP2, is a serine/threonine protein kinase functionally related to RNA metabolism and neurite outgrowth. It contains an N-terminal kinase domain and a C-terminal RNA recognition motif (RRM), with high homology to the corresponding motif of the mammalian U2 small nuclear ribonucleoprotein auxiliary factor U2AF 65kDa subunit (U2AF65 or U2AF2) .
G3BP1, RNA recognition motif (G3BP1_RRM)
Type: Domain

This entry represents the RNA recognition motif (RRM) of G3BP1, which has been identified as a phosphorylation-dependent endoribonuclease that interacts with the SH3 domain of RasGAP . However, this interaction has been questioned . G3BP1 binds to and cleaves the 3'-untranslated region (3'-UTR) of the c-myc mRNA in a phosphorylation-dependent manner . G3BP1 has been linked to the formation of stress granules (SGs), membrane-less structures consisting of mRNA and protein aggregates form rapidly in response to a wide range of stresses and viral infections . G3BP1 is targeted by many viruses and may be involved in innate immune response . Its activities can be regulated through post-translational modifications .

It has also been shown that G3BP1 is a novel Dishevelled-associated protein that is methylated upon Wnt3a stimulation and that arginine methylation of G3BP1 regulates both Ctnnb1 mRNA and canonical Wnt/beta-catenin signaling . Furthermore, G3BP1 can be associated with the 3'-UTR of beta-F1 mRNA in cytoplasmic RNA-granules, demonstrating that G3BP1 may specifically repress the translation of the transcript .

G3BP1 contains an N-terminal nuclear transfer factor 2 (NTF2)-like domain, an RNA recognition motif (RRM domain), and an Arg-Gly-rich region (RGG-rich region, or arginine methylation motif). The RRM domain and RGG-rich region are canonically associated with RNA binding .
G3BP2, RNA recognition motif (G3BP2_RRM)
Type: Domain

This entry represents the RNA recognition motif (RRM) of G3BP2, a cytoplasmic protein that interacts with both IkappaBalpha and IkappaBalpha/NF-kappaB complexes, indicating that G3BP2 may play a role in the control of nucleocytoplasmic distribution of IkappaBalpha and cytoplasmic anchoring of the IkappaBalpha/NF-kappaB complex . It also contributes to stress granule formation .
3,6-anhydro-alpha-L-galactonate cycloisomerase (AHGA_cycloisomerase)
Type: Family

3,6-anhydro-alpha-L-galactonate (AHGA) cycloisomerase catalyzes the conversion of 3,6-anhydro-alpha-L-galactonate to 2-dehydro-3-deoxy-D-galactonate, as part of the breakdown of 3,6-anhydro-L-galactose, the major monomeric sugar of red macroalgae .
2-Deoxy-scyllo-inosamine dehydrogenase (BtrN-like) (BtrN-like)
Type: Family

BtrN catalyses an unusual radical mediated dehydrogenation during aminoglycoside biosynthesis: oxidation of 2-deoxy-scyllo-inosamine (DOIA) to amino-dideoxy-scyllo-inosose (amino-DOI) in the biosynthetic pathway of butirosin . Butirosin is an amino cyclitol glycoside antibiotic produced by
Bacillus circulans
, and bears a unique (S)-4-amino-2-hydroxybutyrate (AHBA) side chain. BtrN contains two [4Fe-4S] clusters, the first is the canonical radical SAM cluster, the second is implicated in substrate-radical oxidation (oxidises a secondary alcohol to a ketone). This family of proteins has a non-canonical structural architecture with a β5/α4 motif .
Star-PAP, RNA recognition motif (Star-PAP_RRM)
Type: Domain

This entry represents the RNA recognition motif (RRM) of Star-PAP (Speckle targeted PIPKIalpha regulated poly (A) polymerase), which is a nuclear non-canonical PAP (Poly(A) polymerase) regulated by lipid second messenger phosphatidyl-inositol-4,5-bisphosphate (PI4,5P2) . As its name suggests, Star-PAP interacts and is regulated by the enzyme phosphatidyl-inositol-4-phosphate-5-kinase type I alpha (PIPKIalpha) that synthesises nuclear PI4,5P2. Star-PAP polyadenylates select subset of mRNAs in the cell involved in oxidative stress response, apoptosis and cancer
. Although it belongs to the well-characterised poly(A) polymerase protein superfamily, Star-PAP is highly divergent from both the poly(A) polymerase (PAP) and the terminal uridylyl transferase (TUTase), identified within the editing complexes of trypanosomes.
Cmo-like SPASM domain containing protein (Cmo-like_SPASM_containing)
Type: Family

This entry contains non-canonical members of the SPASM/twitch domain containing family, including Cmo, also known as tungsten-containing aldehyde ferredoxin oxidoreductase cofactor-modifying protein and AdoMet-dependent heme synthase (ahbD) involved in the siroheme-dependent heme b biosynthesis, catalysing the conversion of Fe-coproporphyrin III into heme by the oxidative decarboxylation of two propionate side chains .
TatSF1-like, RNA recognition motif 1 (TatSF1-like_RRM1)
Type: Domain

This entry represents the RNA recognition motif 1 (RRM1) of Tat-SF1, which interacts with components of both the transcription and splicing machineries . It has been shown to be a cofactor for human immunodeficiency virus-type 1 (HIV-1) Tat, which stimulates transcription elongation of HIV-1 through a series of events termed Tat transactivation . It contains two RNA recognition motifs (RRMs) and a highly acidic carboxyl-terminal half.
TatSF1-like (TatSF1-like)
Type: Family

Tat-SF1 (HIV Tat-specific factor 1, also known as 17S U2 SnRNP complex component HTATSF1) interacts with components of both the transcription and splicing machineries. It is required to stabilize the branchpoint-interacting stem loop . It has been shown to be a cofactor for human immunodeficiency virus-type 1 (HIV-1) Tat, which stimulates transcription elongation of HIV-1 through a series of events termed Tat transactivation . It contains two RNA recognition motifs (RRMs) and a highly acidic carboxyl-terminal half.
MAN1, RNA recognition motif (Man1_RRM)
Type: Domain

This entry represents the RNA recognition motif 1 (RRM1) of Man1, an integral protein of the inner nuclear membrane that binds to nuclear lamins and emerin, thus playing a role in nuclear organization . It is part of a protein complex essential for chromatin organization and cell division. It also functions as an important negative regulator for the transforming growth factor (TGF) beta/activin/Nodal signaling pathway by directly interacting with chromatin-associated proteins and transcriptional regulators, including the R-Smads, Smad1, Smad2, and Smad3 . Moreover, Man1 is a unique type of left-right (LR) signaling regulator that acts on the inner nuclear membrane. Man1 plays a crucial role in angiogenesis. The vascular remodeling can be regulated at the inner nuclear membrane through the interaction between Man1 and Smads .
Yra2, RNA recognition motif (Yra2_RRM)
Type: Domain

This entry represents the RNA recognition motif (RRM) of Yra2. Yra2 consists of two highly conserved N- and C-terminal boxes, referred as the REF-N and REF-C, and a central RNA recognition motif (RRM), also termed RBD (RNA binding domain) . The REF motifs are necessary to interact with RNA and the RBD/RRM domain is involved in both RNA and RNAPII CTD binding .
Prp24, RNA recognition motif1 (Prp24_RRM1)
Type: Domain

This entry represents the RNA recognition motif 1 (RRM1) of Prp24.

Prp24 is an RNA-binding protein with four well conserved RNA recognition motifs (RRMs). It facilitates U6 RNA base-pairing with U4 RNA during spliceosome assembly . Prp24 specifically binds free U6 RNA primarily with RRM 1 and 2 and facilitates pairing of U6 RNA bases with U4 RNA bases .
Prp24, RNA recognition motif2 (Prp24_RRM2)
Type: Domain

This entry represents the RNA recognition motif 2 (RRM2) of Prp24.

Prp24 is an RNA-binding protein with four well conserved RNA recognition motifs (RRMs). It facilitates U6 RNA base-pairing with U4 RNA during spliceosome assembly . Prp24 specifically binds free U6 RNA primarily with RRM 1 and 2 and facilitates pairing of U6 RNA bases with U4 RNA bases .
Srp1, RNA recognition motif (Srp1p_RRM)
Type: Domain

This entry represents the RNA recognition motif (RRM) found in Srp1 from Schizosaccharomyces pombe. It plays a role in the pre-mRNA splicing process, but not essential for growth. Srp1 is closely related to the SR protein family found in metazoa . It contains an N-terminal RNA recognition motif (RRM), a glycine hinge and a RS domain in the middle, and a C-terminal domain. Some family members also contain another RRM domain.
MSSP-1, RNA recognition motif 1 (MSSP1_RRM1)
Type: Domain

This entry represents the RNA recognition motif 1 (RRM1) of MSSP-1 (also known as RBMS1), a double- and single-stranded DNA binding protein that belongs to the c-myc single-strand binding proteins (MSSP) family . It specifically recognizes the sequence CT(A/T)(A/T)T, and stimulates DNA replication in the system using SV40 DNA . MSSP-1 is identical with Scr2, a human protein which complements the defect of cdc2 kinase in Schizosaccharomyces pombe . MSSP-1 has been implied in regulating DNA replication, transcription, apoptosis induction, and cell-cycle movement, via the interaction with C-MYC, the product of protooncogene c-myc .
F420, menaquinone cofactor biosynthesis (F420)
Type: Family

In micro-organisms such as
Chlamydomonas
, DNA that has been damaged by ultraviolet light can be repaired by blue light-dependent DNA photolyases in a process known as photoreactivation. Two noncovalently bound chromophores are required. FAD is the catalytic chromophore for all photolyases and is essential for photoreactivation. The identity of the second chromophore is often 7,8-didemethyl-8-hydroxy-5-deazariboflavin (FO) .

This family contains the proteins that form part of the biosynthetic pathways of Factor420 (F420) in the form of FO synthase, and menaquinone (vitamin K2). Both perform complex ring formations and are members of the radical S-adenosylmethionine (AdoMet) superfamily of proteins. In the case of the menaquinone synthase enzymes, both the mechanisms of the two enzymes and role of the SAM moiety have been proposed. In mqnC, SAM is stoichiometric, and generates methionine and deoxyadenosine. In mqnE, the deoxyadeonsine moiety is added to the chorismate substrate. Thus, in both cases SAM is stoichometric .
RBMS3, RNA recognition motif 2 (RBMS3_RRM2)
Type: Domain

This entry represents the RNA recognition motif 2 (RRM2) of RBMS3 (RNA-binding motif, single-stranded-interacting protein 3). RBMS3 contains two RNA binding motifs and is closely related to the structure of the c-myc gene single-strand binding proteins (MSSPs). RBMS3 has been shown to exhibit tumour suppressor function via regulation of c-Myc and to bind/stabilize RNA in vitro . It may posttranscriptionally regulate the transforming growth factor beta receptor pathway . RBMS3 regulates the expression of Ptf1a (pancreas transcription factor 1 alpha subunit) .
U1 small nuclear ribonucleoprotein A, RNA recognition motif 1 (U1A_RRM1)
Type: Domain

This entry represents the RNA recognition motif 1 (RRM1) of U1A (also termed U1 snRNP A), an RNA-binding protein associated with the U1 snRNP .

U1A binds with high affinity and specificity to stem-loop II (SLII) of U1 snRNA. When U1A is not associated with the U1 snRNP, it functions as a modulator of polyadenylation .

U1A contains two RNA recognition motifs (RRMs); the N-terminal RRM (RRM1) binds tightly and specifically to the U1 snRNA SLII and its own 3'-UTR, while in contrast, the C-terminal RRM (RRM2) does not appear to associate with any RNA and may be free to bind other proteins. U1A also contains a proline-rich region, and a nuclear localization signal (NLS) in the central domain that is responsible for its nuclear import .
Sulphate/thiosulphate-binding site (Sulphate/thiosulphate_BS)
Type: Binding_site

Sulphate-binding protein (gene sbp or sbpA) and thiosulphate-binding protein (gene cysP) are two structurally related periplasmic bacterial proteins which specifically bind sulphate and thiosulphate and are involved in the transport systems for these nutrients . There are two conserved regions in the protein, one located in the N-terminal region and the other in the central part of these proteins. The second region includes two adjacent amino acids (Ser-Gly) that, in sbp, are known to be essential for sulphate binding .

This entry represents the second conserved region that includes two adjacent amino acids (Ser-Gly) known to be essential for sulfate binding .
U1 small nuclear ribonucleoprotein A, RNA recognition motif 2 (U1A_RRM2)
Type: Domain

This entry represents the RNA recognition motif 2 (RRM2) of U1A (also termed U1 snRNP A), an RNA-binding protein associated with the U1 snRNP .

U1A binds with high affinity and specificity to stem-loop II (SLII) of U1 snRNA. When U1A is not associated with the U1 snRNP, it functions as a modulator of polyadenylation .

U1A contains two RNA recognition motifs (RRMs); the N-terminal RRM (RRM1) binds tightly and specifically to the U1 snRNA SLII and its own 3'-UTR, while in contrast, the C-terminal RRM (RRM2) does not appear to associate with any RNA and may be free to bind other proteins. U1A also contains a proline-rich region, and a nuclear localization signal (NLS) in the central domain that is responsible for its nuclear import .
Heterogeneous nuclear ribonucleoprotein R, RNA recognition motif 1 (hnRNPR_RRM1)
Type: Domain

This entry represents the RNA recognition motif 1 (RRM1) of heterogeneous nuclear ribonucleoprotein R (hnRNP R).

hnRNP R is an ubiquitously expressed RNA-binding protein. hnRNP R has been implicated in transcription regulation and AANAT mRNA translation . It is predominantly located in axons of motor neurons and to a much lower degree in sensory axons . In axons of motor neurons, it also functions as a cytosolic protein and interacts with wild type of survival motor neuron (SMN) proteins directly, further providing a molecular link between SMN and the spliceosome . Moreover, hnRNP R plays an important role in neural differentiation and development, and in retinal development and light-elicited cellular activities .

hnRNP R contains an acidic auxiliary N-terminal region, followed by two well defined and one degenerated RNA recognition motifs (RRMs), and a C-terminal RGG motif; it binds RNA through its RRM domains.
Heterogeneous nuclear ribonucleoprotein R, RNA recognition motif 2 (hnRNPR_RRM2)
Type: Domain

This entry represents the RNA recognition motif 2 (RRM2) of heterogeneous nuclear ribonucleoprotein R (hnRNP R).

hnRNP R is an ubiquitously expressed RNA-binding protein. hnRNP R has been implicated in transcription regulation and AANAT mRNA translation . It is predominantly located in axons of motor neurons and to a much lower degree in sensory axons . In axons of motor neurons, it also functions as a cytosolic protein and interacts with wild type of survival motor neuron (SMN) proteins directly, further providing a molecular link between SMN and the spliceosome . Moreover, hnRNP R plays an important role in neural differentiation and development, and in retinal development and light-elicited cellular activities .

hnRNP R contains an acidic auxiliary N-terminal region, followed by two well defined and one degenerated RNA recognition motifs (RRMs), and a C-terminal RGG motif; it binds RNA through its RRM domains.
Dead end protein 1, RNA recognition motif 1 (DND1_RRM1)
Type: Domain

This entry represents the RNA recognition motif 1 (RRM1) of DND1, an RNA-binding protein that is essential for maintaining viable germ cells in vertebrates . It interacts with the 3'-untranslated region (3'-UTR) of multiple messenger RNAs (mRNAs) and prevents micro-RNA (miRNA) mediated repression of mRNA . For instance, DND1 binds cell cycle inhibitor, P27 (p27Kip1, CDKN1B), and cell cycle regulator and tumor suppressor, LATS2 (large tumor suppressor, homologue 2 of Drosophila) . It helps maintain their protein expression through blocking the inhibitory function of microRNAs (miRNA) from these transcripts.
CsdA, RNA recognition motif (CsdA_RRM)
Type: Domain

This entry represents the C-terminal RRM homology domain of E. coli CsdA (also knwon as DeaD or W2), a member of the DbpA subfamily of prokaryotic DEAD-box rRNA helicases that have been implicated in translational regulation, ribosome biogenesis and the regulation of mRNA stability and degradation . In vitro, CsdA exhibits helicase activities which unwind RNA duplexes, provided they have a 5' or 3' single-stranded extension or a hairpin structure attached to them .

It contains two N-terminal ATPase catalytic domains and a C-terminal RNA binding domain, an atypical RNA recognition motif (RRM). The catalytic domains bind to nearby regions of RNA to stimulate ATP hydrolysis and disrupt RNA structures. The C-terminal domain is responsible for the high-affinity RNA binding .
Probable RNA-binding protein 19, RNA recognition motif 2 (RMB19_RRM2)
Type: Domain

This entry represents the RNA recognition motif 2 (RRM2) of RNA-binding protein 19 (RBM19).

RBM19 (also known as RBD-1), a nucleolar protein conserved in eukaryotes. It is involved in ribosome biogenesis by processing rRNA and is also essential for preimplantation development in mice . RBM19 has a unique domain organization containing 6 conserved RNA recognition motifs (RRMs).
Probable RNA-binding protein 19, RNA recognition motif 1 (RMB19_RRM1)
Type: Domain

This entry represents the RNA recognition motif 1 (RRM1) of RNA-binding protein 19 (RBM19).

RBM19 (also known as RBD-1), a nucleolar protein conserved in eukaryotes. It is involved in ribosome biogenesis by processing rRNA and is also essential for preimplantation development in mice . RBM19 has a unique domain organization containing 6 conserved RNA recognition motifs (RRMs).
Probable RNA-binding protein 19, RNA recognition motif 3 (RBM19_RRM3)
Type: Domain

This entry represents the RNA recognition motif 3 (RRM3) of RBM19.

RBM19 (also known as RBD-1), a nucleolar protein conserved in eukaryotes. It is involved in ribosome biogenesis by processing rRNA and is also essential for preimplantation development in mice . RBM19 has a unique domain organization containing 6 conserved RNA recognition motifs (RRMs).