SII-SWORD/CoKE huggingface dataset:
RBM15, RNA recognition motif 3 (RBM15_RRM3)
Type: Domain

This entry represents the RNA recognition motif 3 (RRM3) of RBM15.

RNA-binding motif protein 15 (RBM15), also termed one-twenty two protein 1 (OTT1), is a novel mRNA export factor and component of the NXF1 pathway. It binds to NXF1 and serves as receptor for the RNA export element RTE . It also possesses mRNA export activity and can facilitate the access of DEAD-box protein DBP5 to mRNA at the nuclear pore complex (NPC) .
Methyltransferase, class D (Methyltransferase_Class_D)
Type: Family

This group of radical S-adenosylmethionine enzymes are found in archaea and bacteria and have been classified as class D RS methylases (RSMT) subclass , whose pioneer member is MJ0619 protein from Methanocaldococcus jannaschii, recently designated GDGT/MA synthase or GDGT/MAS (formerly known as 7,8-dihydro-6-hydroxymethylpterin dimethyltransferase) .
RBM15B, RNA recognition motif 1 (RBM15B_RRM1)
Type: Domain

This entry represents the RNA recognition motif 1 (RRM1) of RBM15B.

RNA binding motif protein 15B (RBM15B, also known as OTT3) is a paralogue of RBM15. Like RBM15, RBM15B has post-transcriptional regulatory activity. It is a nuclear protein sharing with RBM15 the association with the splicing factor compartment and the nuclear envelope as well as the binding to mRNA export factors NXF1 and Aly/REF .

RBM15B belongs to the Spen (split end) protein family, which shares a domain architecture comprising three N-terminal RNA recognition motifs (RRMs) and a C-terminal SPOC (Spen paralog and ortholog C-terminal) domain.
Alternative heme biosynthesis C (AhbC-like) (AhbC-like)
Type: Family

Fe-coproporphyrin III synthase (encoded by the gene ahbC) (

) is known to transform didecarboxysirohaem into Fe-coproporphyrin III via homolytic cleavage of the C-C bond connecting the acetate group to the macrocycle, resulting in a double bond in the macrocycle and an acetate radical. It is thought that the acetate radical is transformed into acetate by providing a further electron and proton, which could come from the second Fe-S cluster present in the protein. Two molecules of SAM are consumed for each catalytic turnover, however it is unclear whether these are used stoichiometrically or catalytically .
Heme carboxy lyase-like (Heme_carboxy_lyase-like)
Type: Family

This subgroup is named after the two known reaction types in this set of proteins.
Mrd1, RNA recognition motif 3 (Mrd1_RRM3)
Type: Domain

This entry represents the RNA recognition motif 3 (RRM3) of Mrd1. It is well-conserved in yeast, and its homologues 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), which may play an important structural role in organizing specific rRNA processing events.
Regulator of G-protein signalling Egl-10, RGS domain (RGS_Egl-10)
Type: Domain

Egl-10 regulates G protein signalling in the C. elegans nervous system. It is related to regulator of G protein signaling R7 subfamily of proteins, orthologue of human RGS7 .
Anaerobic Cys-type sulfatase-maturating enzyme (Anaerobic_Cys-type_sulfatase-m)
Type: Family

To be active, all sulfatases require a maturation process, this is the group of proteins that perform this maturation. The proteins in this family are thought to favour the Cys-type sulfatases . The Cys residue is covalently attached to one of the [4Fe-4S] clusters and the C-beta proton is abstracted by the 5'-deoxyadenosyl radical. The Cys-SH group is first reduced to Cys=S and then hydrolysed to the formylglycyl C=O group .
hnRNP A2/B1, RNA recognition motif 1 (hnRNPA2B1_RRM1)
Type: Domain

This entry represents the RNA recognition motif 1 (RRM1) of hnRNP A2/B1.

Heterogeneous nuclear ribonucleoprotein (hnRNP) A2/B1 is an RNA trafficking response element-binding protein that interacts with the hnRNP A2 response element (A2RE), a cis-acting signal present in certain trafficked mRNAs, including those encoding myelin basic protein (MBP), CaMKII, neurogranin, and Arc .
Anaerobic Ser-type sulfatase-maturating enzyme (Anaerob_Ser_sulfatase-maturase)
Type: Family

To be active, all sulfatases require a maturation process, this is the group of proteins that perform this maturation. The proteins in this family are thought to favour the Ser-type sulfatases. It is not clear in the literature how the SAM moiety is used, whether it is catalytic or stoichiometric .
TIAR, RNA recognition motif 1 (TIAR_RRM1)
Type: Domain

This entry represents the RNA recognition motif 1 (RRM1) of nucleolysin TIAR (TIA-1-related protein).

TIAR is a cytotoxic granule-associated RNA-binding protein that shows high sequence similarity with TIA-1 . TIAR plays a critical role in transcriptional and posttranscriptional regulation of gene expression . It binds to target mRNA and DNA via its RNA recognition motif (RRM) domains and is involved in both splicing regulation and translational repression via the formation of stress granules . TIAR is composed of three N-terminal highly homologous RNA recognition motifs (RRMs) and a glutamine-rich C-terminal auxiliary domain containing a lysosome-targeting motif. Its RRMs are involved in binding to U-rich RNA, but with unequal contributions. RRM2 of TIAR is the major RNA- and DNA-binding domain .
TIAR, RNA recognition motif 2 (TIAR_RRM2)
Type: Domain

This entry represents the RNA recognition motif 2 (RRM2) of nucleolysin TIAR (TIA-1-related protein).

TIAR is a cytotoxic granule-associated RNA-binding protein that shows high sequence similarity with TIA-1 . TIAR plays a critical role in transcriptional and posttranscriptional regulation of gene expression . It binds to target mRNA and DNA via its RNA recognition motif (RRM) domains and is involved in both splicing regulation and translational repression via the formation of stress granules . TIAR is composed of three N-terminal highly homologous RNA recognition motifs (RRMs) and a glutamine-rich C-terminal auxiliary domain containing a lysosome-targeting motif. Its RRMs are involved in binding to U-rich RNA, but with unequal contributions. RRM2 of TIAR is the major RNA- and DNA-binding domain .
TIAR, RNA recognition motif 3 (TIAR_RRM3)
Type: Domain

This entry represents the RNA recognition motif 3 (RRM3) of TIA-1 and nucleolysin TIAR (TIA-1-related protein), proteins that share high sequence similarity.

TIA-1 is the 40kDa isoform of T-cell-restricted intracellular antigen-1 (TIA-1, also known as Cytotoxic granule associated RNA binding protein TIA1), a cytotoxic granule-associated RNA-binding protein mainly found in the granules of cytotoxic lymphocytes . TIA-1 regulate alternative pre-mRNA splicing by promoting the use of suboptimal 5' splice sites followed by uridine-rich intronic enhancer sequences. It can be phosphorylated by a serine/threonine kinase that is activated during Fas-mediated apoptosis, and functions as the granule component responsible for inducing apoptosis in cytolytic lymphocyte (CTL) targets .

TIAR is a cytotoxic granule-associated RNA-binding protein that shows high sequence similarity with TIA-1 . TIAR plays a critical role in transcriptional and posttranscriptional regulation of gene expression . It binds to target mRNA and DNA via its RNA recognition motif (RRM) domains and is involved in both splicing regulation and translational repression via the formation of stress granules . TIAR is composed of three N-terminal highly homologous RNA recognition motifs (RRMs) and a glutamine-rich C-terminal auxiliary domain containing a lysosome-targeting motif. Its RRMs are involved in binding to U-rich RNA, but with unequal contributions. RRM2 of TIAR is the major RNA- and DNA-binding domain .
Bacteriochlorophyll C12 methyltransferase (Bacteriochlorophyll_C12_MT)
Type: Family

Bacteriochlorophyllide d C-12(1)-methyltransferase (bchR, EC 2.1.1.331) catalyses the transfer of a methyl groups to C-12 methyl carbon in the biosynthesis of certain bacteriochlorophylls in
Chlorobium tepidum
, and has the sequence motifs that tentatively assigns it to the cobalamin-dependent P-methylase subfamily .
Bacteriochlorophyll C8 methyltransferase (Bacteriochlorophyll_C8_MT)
Type: Family

The enzyme in this family, bacteriochlorophyllide d C-8(2)-methyltransferase (bchQ, EC 2.1.1.332), catalyses the transfer of a methyl group to the C-8 ethyl carbon in the biosynthesis of certain bacteriochlorophylls in
Chlorobium tepidum
, and has the sequence motif that tentatively assigns it to the cobalamin-dependent P-methylase subfamily .
RBM7, RNA recognition motif (RBM7_RRM)
Type: Domain

This entry represents the RNA recognition motif (RRM) of RNA-binding motif protein 7 (RBM7), a ubiquitously expressed pre-mRNA splicing factor that enhances messenger RNA (mRNA) splicing in a cell-specific manner or in a certain developmental process, such as spermatogenesis. RBM7 interacts with splicing factors SAP145 (the spliceosomal splicing factor 3b subunit 2) and SRp20. It may play a more specific role in meiosis entry and progression. Together with additional testis-specific RNA-binding proteins, RBM7 may regulate the splicing of specific pre-mRNA species that are important in the meiotic cell cycle . RBM7 contains an N-terminal RNA recognition motif (RRM) and a region lacking known homology at the C terminus.
RBM11, RNA recognition motif (RBM11_RRM)
Type: Domain

This entry represents the RNA recognition motif (RRM) of RBM11, a novel tissue-specific splicing regulator that is selectively expressed in brain, cerebellum and testis, and to a lower extent in kidney. RBM11 is localized in the nucleoplasm and enriched in SRSF2-containing splicing speckles. It may play a role in the modulation of alternative splicing during neuron and germ cell differentiation. RBM11 contains an N-terminal RNA recognition motif (RRM), and a region lacking known homology at the C terminus. The RRM of RBM11 is responsible for RNA binding, whereas the C-terminal region permits nuclear localization and homodimerization .
Raly, RNA recognition motif (RALY_RRM)
Type: Domain

This entry represents the RNA recognition motif (RRM) of Raly, an RNA-binding protein that may play a critical role in embryonic development. It is encoded by raly, a ubiquitously expressed gene of unknown function . Raly shows a high degree of identity with the 5' sequences of p542 gene encoding autoantigen, which can cross-react with EBNA-1 of the Epstein Barr virus . Raly contains two distinct domains, an N-terminal RNA recognition motif (RRM), and a C-terminal auxiliary domain that includes a unique glycine/serine-rich stretch.
SRSF9, RNA recognition motif 1 (SRSF9_RRM1)
Type: Domain

This entry represents the RNA recognition motif 1 (RRM1) of SRSF9 (also known as SRp30C). SRSF9 is a member of the SR (serine/arginine) protein family of splicing regulators. It interacts with Y-box protein 1 (YB-1) and is involved in the alternative splice site selection. Besides stimulating the mRNA splicing , it also functions as a repressor of 3' splice site utilization and has been shown to promote skipping of exon 7B in the hnRNP A1 pre-mRNA .
Anaerobic coproporphyrinogen-III oxidase (Coproporphyrinogen-III_oxidase)
Type: Family

Biosynthesis of heme and chlorophyll requires coproporphyrinogen III to be converted to protoporphyrinogen IX by oxidatively decarboxylating the propionate side chains of rings A and B to the corresponding vinyl group .

This entry includes HemN, HemW, HemZ from bacteria, and Rsad1 from animals. HemN catalyzes the anaerobic oxidative decarboxylation of propionate groups of rings A and B of coproporphyrinogen III to yield the vinyl groups in protoporphyrinogen IX . HemW may act as a heme chaperone, transferring heme to an unknown acceptor . HemZ is involved in the biosynthesis of porphyrin-containing compound .
RBM14, RNA recognition motif 1 (RBM14_RRM1)
Type: Domain

This entry represents the RNA recognition motif 1 (RRM1) of RBM14.

RBM14 (also known as CoAA) is a heterogeneous nuclear ribonucleoprotein (hnRNP)-like protein identified as an activator of the receptor coactivator TRBP (thyroid-hormone-receptor-binding protein) . It also regulates mRNA splicing and transcription . RBM14 is a suppressor of ectopic assembly of centriolar protein complexes . It contains two N-terminal RNA recognition motifs (RRMs) and a TRBP-interacting domain.
RBM14, RNA recognition motif 2 (RBM14_RRM2)
Type: Domain

This entry represents the RNA recognition motif 2 (RRM2) of RBM14.

RBM14 (also known as CoAA) is a heterogeneous nuclear ribonucleoprotein (hnRNP)-like protein identified as an activator of the receptor coactivator TRBP (thyroid-hormone-receptor-binding protein) . It also regulates mRNA splicing and transcription . RBM14 is a suppressor of ectopic assembly of centriolar protein complexes . It contains two N-terminal RNA recognition motifs (RRMs) and a TRBP-interacting domain.
Spectinomycin biosynthesis (Spectinomycin_biosynthesis)
Type: Family

Proteins in this family are involved in spectinomycin biosynthesis and are thought to play a role in generating TDP-actinospectose. Although the reaction is somewhat similar to that of DesII, these proteins are not detectably similar .
SECp43, RNA recognition motif 2 (SECp43_RRM2)
Type: Domain

This entry represents the RNA recognition motif 2 (RRM2) of SECp43, an RNA-binding protein associated specifically with eukaryotic selenocysteine tRNA [tRNA(Sec)] . It may play an adaptor role in the mechanism of selenocysteine insertion . SECp43 is located primarily in the nucleus and contains two N-terminal RNA recognition motifs (RRMs) and a C-terminal polar/acidic region.
SRSF6, RNA recognition motif 1 (SRSF6_RRM1)
Type: Domain

This entry represents the RNA recognition motif 1 (RRM1) of SRSF6, also termed pre-mRNA-splicing factor SRp55, which is an essential splicing regulatory serine/arginine (SR) protein that preferentially interacts with a number of purine-rich splicing enhancers (ESEs) to activate splicing of the ESE-containing exon . It is the only protein from HeLa nuclear extract or purified SR proteins that specifically binds B element RNA after UV irradiation. SRSF6 may also recognize different types of RNA sites. For instance, it does not bind to the purine-rich sequence in the calcitonin-specific ESE, but binds to a region adjacent to the purine tract . Moreover, cellular levels of SRSF6 may control tissue-specific alternative splicing of the calcitonin/ calcitonin gene-related peptide (CGRP) pre-mRNA .
Carbapenem intermediate methyltransferase ThnK-like (ThnK-like)
Type: Family

This entry includes the 2-(S-pantetheinyl)-carbapenam-3-carboxylate methyltransferase ThnK from S. cattleyicolor and Cobalamin-dependent radical SAM methyltransferase TokK from S. tokunonensis. ThnK is involved in the biosynthesis of the beta-lactam carbapenem antibiotic thienamycin . This enzyme catalyses two consecutive S-adenosyl-L-methionine-dependent methylations to build out the C6-ethyl side chain in a stereocontrolled manner . TokK is involved in the biosynthesis of the beta-lactam carbapenem antibiotic asparenomycin . It catalyses three consecutive S-adenosyl-L-methionine-dependent methylations to build out the C6-isopropyl side chain in a stereocontrolled manner .
Carbapenem intermediate methyltransferase, ThnL-like (ThnL-like)
Type: Family

The enzyme in this family is responsible for the vitamin B12 dependent methylation of the beta-lactam ring in the thienamycin (thn) gene cluster. It is currently not known what the methyl donor is, but in keeping with the other B12-dependent methyltransferases, it is likely to be methylcobalamin, which is regenerated by a second SAM molecule .
hnRNP A1/3, RNA recognition motif 2 (hnRNPA1/3_RRM2)
Type: Domain

This entry represents the RNA recognition motif 2 (RRM2) of heterogeneous nuclear ribonucleoprotein (hnRNP) A1/3).
PARP-14, RNA recognition motif 2 (PAR14_RRM2)
Type: Domain

This entry represents the RNA recognition motif 2 (RRM2) of poly [ADP-ribose] polymerase 14 (PARP-14), also termed aggressive lymphoma protein 2, a member of the B aggressive lymphoma (BAL) family of macrodomain-containing PARPs . It is expressed in B lymphocytes and interacts with the IL-4-induced transcription factor Stat6. It plays a fundamental role in the regulation of IL-4-induced B-cell protection against apoptosis after irradiation or growth factor withdrawal. It mediates IL-4 effects on the levels of gene products that regulate cell survival, proliferation, and lymphomagenesis. PARP-14 acts as a transcriptional switch for Stat6-dependent gene activation. In the presence of IL-4, PARP-14 activates transcription by facilitating the binding of Stat6 to the promoter and release of HDACs from the promoter with an IL-4 signal. In contrast, in the absence of a signal, PARP-14 acts as a transcriptional repressor by recruiting HDACs . Absence of PARP-14 protects against Myc-induced developmental block and lymphoma. Thus, PARP-14 may play an important role in Myc-induced oncogenesis . Additional research indicates that PARP-14 is also a binding partner with phosphoglucose isomerase (PGI)/autocrine motility factor (AMF). It can inhibit PGI/AMF ubiquitination, thus contributing to its stabilization and secretion .

PARP-14 contains two N-terminal RNA recognition motifs (RRMs), three tandem macro domains, and C-terminal region with sequence homology to PARP catalytic domain.
UDP-N-acetyl-tunicamine-uracil synthase TunB-like (TunB-like)
Type: Family

Radical SAM domain protein TunB is involved in the biosynthesis of tunicamycins. It catalyses the radical coupling reaction in which a 5'-uridyl radical undergoes radical addition at C6 of N-acetyl-galactoseamine-5,6-ene to yield an alpha-alkoxyalkyl radical. Subsequent hydrogen atom abstraction from 5'-deoxyadenosine could lead to UDP-N-acetyl-tunicamine-uracil and the regeneration of SAM .
SRSF1, RNA recognition motif 1 (SRSF1_RRM1)
Type: Domain

This entry represents the RNA recognition motif 1 (RRM1) of SRSF1 (also knwon as ASF/SF2). SRSF1 is a member of the SR (serine/arginine) protein family of splicing regulators. Besides mRNA splicing, it is also involved in regulating mRNA transcription, stability and nuclear export, NMD, and translation, as well as protein sumoylation. It has been identified as a proto-oncogene. SRSF1 contains two RRMs, which are required for efficient RNA binding and splicing .
PSP1, RNA recognition motif 1 (PSP1_RRM1)
Type: Domain

This entry represents the RNA recognition motif 1 (RRM1) of paraspeckle component 1 (PSP1).

PSP1 (also known as PSPC1) is a novel nucleolar factor that accumulates within a new nucleoplasmic compartment, termed paraspeckles, and diffusely distributes in the nucleoplasm . PSP1 belongs to the DBHS (Drosophila behavior human splicing) family. It is ubiquitously expressed and highly conserved in vertebrates. Its cellular function remains unknown currently; however, PSPC1 forms a novel heterodimer with the nuclear protein p54nrb, also known as non-POU domain-containing octamer-binding protein (NonO), which localizes to paraspeckles in an RNA-dependent manner . PSPC1 contains two conserved RNA recognition motifs (RRMs) at the N terminus.

DBHS (Drosophila behavior human splicing) family are characterised by a core domain arrangement consisting of tandem RNA recognition motifs (RRMs), a ~100 amino acid coiled-coil domain, and a conserved intervening sequence referred to as a NONA/ParaSpeckle (NOPS) domain. Its members include p54nrb (also known as NONO), PTB-associated splicing factor/splicing factor proline-glutamine rich (PSF or SFPQ) and PSPC1 (paraspeckle protein component 1). They are found in the nucleoplasm and can be triggered by binding to local high concentrations of various nucleic acids to form microscopically visible nuclear bodies, paraspeckles or large complexes such as DNA repair foci. They may also function cytoplasmically and on the cell surface in defined cell types. All three DBHS proteins are conserved throughout vertebrate species, while flies, worms, and yeast express a single DBHS protein .
PSP1, RNA recognition motif 2 (PSP1_RRM2)
Type: Domain

This entry represents the RNA recognition motif 2 (RRM2) of paraspeckle component 1 (PSP1).

PSP1 (also known as PSPC1) is a novel nucleolar factor that accumulates within a new nucleoplasmic compartment, termed paraspeckles, and diffusely distributes in the nucleoplasm . PSP1 belongs to the DBHS (Drosophila behavior human splicing) family. It is ubiquitously expressed and highly conserved in vertebrates. Its cellular function remains unknown currently; however, PSPC1 forms a novel heterodimer with the nuclear protein p54nrb, also known as non-POU domain-containing octamer-binding protein (NonO), which localizes to paraspeckles in an RNA-dependent manner . PSPC1 contains two conserved RNA recognition motifs (RRMs) at the N terminus.

DBHS (Drosophila behavior human splicing) family are characterised by a core domain arrangement consisting of tandem RNA recognition motifs (RRMs), a ~100 amino acid coiled-coil domain, and a conserved intervening sequence referred to as a NONA/ParaSpeckle (NOPS) domain. Its members include p54nrb (also known as NONO), PTB-associated splicing factor/splicing factor proline-glutamine rich (PSF or SFPQ) and PSPC1 (paraspeckle protein component 1). They are found in the nucleoplasm and can be triggered by binding to local high concentrations of various nucleic acids to form microscopically visible nuclear bodies, paraspeckles or large complexes such as DNA repair foci. They may also function cytoplasmically and on the cell surface in defined cell types. All three DBHS proteins are conserved throughout vertebrate species, while flies, worms, and yeast express a single DBHS protein .
PSF, RNA recognition motif 1 (PSF_RRM1)
Type: Domain

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

PSF is a member of the DBHS (Drosophila behavior human splicing) family. It participates in a wide range of gene regulatory processes and cellular response pathways. It has been shown to affect the alternative splicing of CD45 and Tau and regulate the 3' polyadenylation of mRNAs. It is often localised in the paraspeckles and may be involved in the nuclear retention of mRNAs. It is involved in translation and transcription. It can bind directly to DSBs and play a role in DNA repair. PSF can also be utilized as an essential host factor for viral RNA multiplication and replication . In addition to the common DHBS core, which encompasses RRM1 and RRM2, the protein-protein interaction NOPS domain and the coiled-coil domain, PSF features additional domains, such as a RGG motif and a proline-rich region in its N terminus .

DBHS (Drosophila behavior human splicing) family are characterised by a core domain arrangement consisting of tandem RNA recognition motifs (RRMs), a conserved intervening sequence referred to as a NONA/ParaSpeckle (NOPS) domain, and a ~100 amino acid coiled-coil domain. Its members include p54nrb (also known as NONO), PTB-associated splicing factor/splicing factor proline-glutamine rich (PSF or SFPQ) and PSPC1 (paraspeckle protein component 1). They are found in the nucleoplasm and can be triggered by binding to local high concentrations of various nucleic acids to form microscopically visible nuclear bodies, paraspeckles or large complexes such as DNA repair foci. They may also function cytoplasmically and on the cell surface in defined cell types. All three DBHS proteins are conserved throughout vertebrate species, while flies, worms, and yeast express a single DBHS protein .