SII-SWORD/CoKE huggingface dataset:
Probable RNA-binding protein 19, RNA recognition motif 4 (RBM19_RRM4)
Type: Domain

This entry represents the RNA recognition motif 4 (RRM4) 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).
Probable RNA-binding protein 19, RNA recognition motif 6 (RBM19_RRM6)
Type: Domain

This entry represents the RNA recognition motif 6 (RRM6) 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).
HydE/PylB-like (HydE/PylB-like)
Type: Family

This family includes 3-methylornithine synthase (also known as pylB), which catalyzes a step in the biosynthesis pathway of pyrrolysine (isomerization of L-lysine to (2R,3R)-3-methylornithine via a radical-based mechanism) and [FeFe] hydrogenase maturase subunit HydE, which is required for the maturation of the [FeFe]-hydrogenase HydA .
Probable RNA-binding protein 19, RNA recognition motif 5 (RBM19_RRM5)
Type: Domain

This entry represents the RNA recognition motif 1 (RRM1) 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).
GRSF-1, RNA recognition motif 2 (GRSF-1_RRM2)
Type: Domain

This entry represents the RNA recognition motif 2 (RRM2) of G-rich sequence factor 1 (GRSF-1).

GRSF-1 is a cytoplasmic poly(A)+ mRNA binding protein which interacts with RNA in a G-rich element-dependent manner . It regulates RNA processing in mitochondrial RNA granules . It also mediates vial mRNA translation in infected cells . GRSF-1 contains three potential RNA recognition motifs (RRMs), which are responsible for the RNA binding. In addition, GRSF-1 has two auxiliary domains, an acidic α-helical domain and an N-terminal alanine-rich region, that may play a role in protein-protein interactions and provide binding specificity .
GRSF-1, RNA recognition motif 1 (GRSF1_RRM1)
Type: Domain

This entry represents the RNA recognition motif 1 (RRM1) of G-rich sequence factor 1 (GRSF-1).

GRSF-1 is a cytoplasmic poly(A)+ mRNA binding protein which interacts with RNA in a G-rich element-dependent manner . It regulates RNA processing in mitochondrial RNA granules . It also mediates vial mRNA translation in infected cells . GRSF-1 contains three potential RNA recognition motifs (RRMs), which are responsible for the RNA binding. In addition, GRSF-1 has two auxiliary domains, an acidic α-helical domain and an N-terminal alanine-rich region, that may play a role in protein-protein interactions and provide binding specificity .
GRSF-1, RNA recognition motif 3 (GRSF1_RRM3)
Type: Domain

This entry represents the RNA recognition motif 3 (RRM3) of G-rich sequence factor 1 (GRSF-1).

GRSF-1 is a cytoplasmic poly(A)+ mRNA binding protein which interacts with RNA in a G-rich element-dependent manner . It regulates RNA processing in mitochondrial RNA granules . It also mediates vial mRNA translation in infected cells . GRSF-1 contains three potential RNA recognition motifs (RRMs), which are responsible for the RNA binding. In addition, GRSF-1 has two auxiliary domains, an acidic α-helical domain and an N-terminal alanine-rich region, that may play a role in protein-protein interactions and provide binding specificity .
ESRP1, RNA recognition motif 1 (ESRP1_RRM1)
Type: Domain

This entry represents the RNA recognition motif 1 (RRM1) of epithelial splicing regulatory protein 1 (ESRP1).

ESRP1 has been identified as an epithelial cell type-specific regulator of fibroblast growth factor receptor 2 (FGFR2) splicing . It is required for expression of epithelial FGFR2-IIIb and the regulation of CD44, CTNND1 (p120-Catenin) and ENAH (hMena) splicing. It enhances epithelial-specific exons of CD44 and ENAH, silences mesenchymal exons of CTNND1, or both within FGFR2 . ESRP1 has been shown to function as a tumour suppressor in colon cancer cells, due to its ability to bind to the 5' UTR of several cancer-related genes and regulate their translation . However, high ESRP1 expression has been linked to colorectal cancer progression . ESRP1 contains three RNA recognition motifs (RRMs).
ThiH/NocL/HydG-like (ThiH/NoCL/HydG-like)
Type: Family

These proteins homolytically cleave the C-alpha--C-beta bond of aromatic amino acids (such as tyrosine in ThiH and HydG or tryptophan in the MIA synthase family) using the 5'-deoxyadenosyl radical formed by the Radical SAM enzymes .
Protein PSY (PSY)
Type: Family

PSY1 is a tyrosine-sulfated peptide isolated from Arabidopsis which promotes cellular proliferation and expansion . Another two tyrosine-sulfated proteins compose this family: PSY2 and PSY3. Their function is not known.
Nucleoporin nup60 (Nup60)
Type: Family

This family represents nucleoporin Nup60, a component of the yeast nuclear pore complex (NPC). Yeast NPCs are shaped as an octagonal ring . A subset of nucleoporins (Nups) form filaments that extend into the cytoplasm and a different subset form a basket structure that extends into the nucleoplasm. All other Nups are distributed symmetrically about a central axis in the NPC forming a ringed scaffold with a central transporter that serves as the conduit for macromolecular transport . The nucleoporins Nup60, Nup2, and Nup1 form part of the nuclear basket structure . Nup60 and Nup1 are the only two Nups in S. cerevisiae that localize exclusively to the nucleoplasmic side of the NPC .

The translocation of macromolecules between the nucleus and cytosol of eukaryotic cells occurs through the NPC and is facilitated by karyopherins (Kaps, importins, exportins, or transportins). Nups that contain FG peptide repeats (FG Nups) are proposed to function as binding sites for karyopherins. Nup60 is a FG Nup that also contains a putative RNA-binding RRM motif . Nup60 binds to Nup2 and serves as a docking site for Kap95p-Kap60p (karyopherin α-β) and Kap123p . Nup60 is required for the nuclear and cytoplasmic localization of some transcripts, such as ASH1 mRNA .
Vomeromodulin (Vomeromodulin)
Type: Family

Vomeromodulin is a putative pheromone and odorant transporter. It is a glycoprotein mainly found in the lateral nasal glands, with a high concentration in the mucus of the vomeronasal organ of Jacobson. Its distribution suggests that it may function in olfactory and vomeronasal perireceptor processes as a transporter for pheromones and odorants .
Probable RNA-binding protein 46, RNA recognition motif 1 (RBM46_RRM1)
Type: Domain

This entry represents the RNA recognition motif 1 (RRM1) of RBM46.

RNA-binding motif protein 46 (RBM46), also known as cancer/testis antigen 68 (CT68), is a germ cell-specific RNA-binding protein that is essential for spermatogenesis and male fertility. It is involved in the regulation of gene expression during meiosis . It has been shown to bind to and stabilise Cdx2 mRNA in early mouse embryos . RBM46 contains two well-defined and one degenerated RNA recognition motifs (RRMs) and a C-terminal double-stranded RNA binding motif (DSRM) .
Probable RNA-binding protein 46, RNA recognition motif 2 (RBM46_RRM2)
Type: Domain

This entry represents the RNA recognition motif 2 (RRM2) of RBM46.

RNA-binding motif protein 46 (RBM46), also known as cancer/testis antigen 68 (CT68), is a germ cell-specific RNA-binding protein that is essential for spermatogenesis and male fertility. It is involved in the regulation of gene expression during meiosis . It has been shown to bind to and stabilise Cdx2 mRNA in early mouse embryos . RBM46 contains two well-defined and one degenerated RNA recognition motifs (RRMs) and a C-terminal double-stranded RNA binding motif (DSRM) .
3-Methyl-2-indolic acid methyltransferase, NocN/NosN-like (NocN/NosN-like)
Type: Family

NocN shares 75% sequence identity with NosN and thus is thought to have a very similar function. NosN shares high sequence similarity to various putative methyltransferases with a radical S-AdoMet-dependent manner, including Tlm-Orf11 (32% identity) in tallysomycin biosynthesis. Experimental characterization shows that NosN functions as a methyltransferase and acts on the 3-methylindolyl group (product of the NosL enzyme's reaction) at the C-4 position for furnishing the 3,4-dimethylindolyl moiety .
4-Hydroxyphenylacetate decarboxylase activase (4-hPhe_decarboxylase_activase)
Type: Family

This family of enzymes is responsible for the creation of a glycyl radical in the ground state of the enzyme 4-hydroxyphenylacetate decarboxylase. This enzyme is unique amongst the glycyl radical enzymes in having a small subunit and being a functional hetero-octamer (made up of four large subunits and four small subunits) in the biologically active state . The small subunit is responsible for metal binding and is also involved in the regulation of the enzymes' oligomeric state and activity, which are triggered by reversible serine phosphorylation of the glycyl radical subunits . These enzymes differ from their PFL-AE and Nrd counterparts in that they contain up to two iron-sulfur centres, in addition to the characteristic SAM cluster, these extra clusters are thought to be involved in the electron transfer to the SAM cluster but do not directly participate in the reductive cleavage of SAM .
Diuretic hormone class 2-like (DH2-like)
Type: Family

DH31 is a diuretic hormone that increases cAMP production and fluid secretion in Malpighian tubules of several insect species. DH31 is similar to the calcitonin family . In Drosophila, it has also been linked to a neuropeptide relay mechanism for circadian control of sleep , and peristalsis in the junction region of the larval midgut . Drosophila neuropeptide DH31 is a ligand for orphan GPCR named CG17415 .

This entry also includes venom protein 55.1 and U-limacoditoxin(8)-Dv66 (also known as Vulnericin) , which belong to the diuretic hormone class 2 family. U-scoloptoxin(21)-Sm1/2a are uncharacterised proteins related to DH31.
RNA-binding protein 47, RNA recognition motif 2 (RBM47_RRM2)
Type: Domain

This entry represents the RNA recognition motif 2 (RRM2) of RBM47.

RBM47 is a putative RNA-binding protein that shows high sequence homology with heterogeneous nuclear ribonucleoprotein R (hnRNP R) and heterogeneous nuclear ribonucleoprotein Q (hnRNP Q). Like hnRNP R and hnRNP Q, RBM47 contains two well-defined and one degenerated RNA recognition motifs (RRMs). RBM47 is necessary for Cytidine to Uridine RNA editing .
Bursicon subunit beta (Bursicon_suB)
Type: Family

Bursicon is a neurohormone released at the end of the molting cycle, involved in the sclerotization (tanning) of the insect cuticle and wing spreading. Bursicon as a heterodimer made of two cystine knot polypeptides: burs-alpha and burs-beta. Bursicon is the natural agonist of the orphan G protein-coupled receptor DLGR2 .

Burs α-α and burs β-β homodimers are also formed; they act via an unknown receptor and influence expression of additional genes acting after the molt. Burs β-β and bursicon appear to regulate the expression of cuticular protein and chitin metabolizing related genes .

This entry represents burs-beta.
Meiotically up-regulated protein PB1A10.08 (PB1A10.08)
Type: Family

The function of PB1A10.08 is not known. In a fission yeast study, it was identified as belonging to a group of late genes that are induced after meiotic divisions and whose expression remains high until the completion of sporulation .
NADH-ubiquinone oxidoreductase 17.8kDa subunit (Nuo17.8)
Type: Family

NADH:ubiquinone oxidoreductase of the mitochondrial respiratory chain (complex I;

) is a complicated assembly of at least 25 proteins. This family includes the 17.8kDa subunit from mitochondrial NADH-ubiquinone oxidoreductase from Neurospora crassa and yeast homologues .
RNA-binding protein 47, RNA recognition motif 3 (RBM47_RRM3)
Type: Domain

This entry represents the RNA recognition motif 3 (RRM3) of RBM47.

RBM47 is a putative RNA-binding protein that shows high sequence homology with heterogeneous nuclear ribonucleoprotein R (hnRNP R) and heterogeneous nuclear ribonucleoprotein Q (hnRNP Q). Like hnRNP R and hnRNP Q, RBM47 contains two well-defined and one degenerated RNA recognition motifs (RRMs). RBM47 is necessary for Cytidine to Uridine RNA editing .
Fibronectin type III domain-containing protein 10 (Fndc10)
Type: Family

The function of this Fibronectin type III domain-containing protein is not known.
Serine/arginine-rich splicing factor 11, RRM (RRM_SRSF11)
Type: Domain

SRSF11, also known as SRp54 or p54, belongs to the SR proteins family. It is involved in bridge-complex formation and splicing by mediating protein-protein interactions across either introns or exons. SRSF11 has been identified as a tau exon 10 splicing repressor. It interacts with a purine-rich element in exon 10, and suppresses exon 10 inclusion by antagonizing Tra2beta, an SR-domain-containing protein that enhances exon 10 inclusion . SRSF11 has also been shown to associate with active telomerase through the interaction with TERC and directs it to nuclear speckles specifically during S phase .
Adipogenesis regulatory factor (ADIRF)
Type: Family

APM2 (adipose specific 2 or adipose most abundant 2), also known as adipogenesis regulatory factor, was so named because it was originally identified as the second most abundant transcript in adipose tissue . It up-regulates the levels of CCAAT/enhancer binding protein alpha (C/EBP-alpha) and PPAR-gamma, and promotes adipogenic differentiation starting from the early stage of adipogenesis. It is thought to be an adipocyte lineage-specific nuclear factor that can modulate the master adipogenesis transcription factors early during differentiation . It is also involved in regulating glucose transport in adipocytes, as well as regulating the number of preadipocytes .

APM2 it is widely dysregulated in various cancers .
RNA-binding protein 27, RNA recognition motif (RBM27_RRM)
Type: Domain

This entry represents the RNA recognition motif (RRM) of human RNA-binding protein 27 (RBM27). Although the specific function of the RRM in RBM27 remains unclear, it shows high sequence similarity with RRM1 of RBM26, which functions as a cutaneous lymphoma (CL)-associated antigen .
Transmembrane protein PVRIG (TM_PVRIG)
Type: Family

The human transmembrane protein (PVRIG) is a cell surface receptor for NECTIN2. It may act as a coinhibitory receptor that suppresses T-cell receptor-mediated signals . It competes with CD226 to bind to CD112
MEI2-like, RNA recognition motif 1 (MEI2-like_RRM1)
Type: Domain

This entry represents the RNA recognition motif 1 (RRM1) of Mei2-like proteins.

Mei2-like proteins represent an ancient eukaryotic RNA-binding proteins family . Their corresponding Mei2-like genes appear to have arisen early in eukaryote evolution, been lost from some lineages such as Saccharomyces cerevisiae and metazoans, and diversified in the plant lineage . The plant Mei2-like genes may function in cell fate specification during development, rather than as stimulators of meiosis . Members of the Mei2-like family contain three RNA recognition motifs (RRMs). The C-terminal RRM (RRM3) is unique to Mei2-like proteins and it is highly conserved between plants and fungi .
MEI2-like, RNA recognition motif 3 (MEI2-like_RRM3)
Type: Domain

This entry represents the RNA recognition motif 3 (RRM3) of Mei2-like proteins.

Mei2-like proteins represent an ancient eukaryotic RNA-binding proteins family . Their corresponding Mei2-like genes appear to have arisen early in eukaryote evolution, been lost from some lineages such as Saccharomyces cerevisiae and metazoans, and diversified in the plant lineage . The plant Mei2-like genes may function in cell fate specification during development, rather than as stimulators of meiosis . Members of the Mei2-like family contain three RNA recognition motifs (RRMs). The C-terminal RRM (RRM3) is unique to Mei2-like proteins and it is highly conserved between plants and fungi .
Biogenesis of lysosome-related organelles complex 1, subunit CNL1 (CNL1)
Type: Family

CNL1 (CNO-like protein 1) is a component of the yeast biogenesis of lysosome-related organelles complex-1 (BLOC-1), a complex that is involved in sorting cargo to lysosome-related organelles and endosomes . The yeast BLOC-1 consists of six subunits. BLOC-1 functions as an endosomal Rab-GAP (GTPase-activating protein) adapter complex in yeast. It controls the lifetime of active Rab5/Vps21 and thus is involved in endosomal maturation along the endocytic pathway .
Mediator of RNA polymerase II transcription subunit 28 (MED28)
Type: Family

Med28 is a subunit of the large protein complex Mediator, a central coregulator of transcription in eukaryotes. In plants, Med28 mutants are affected in root development and senescence, phenotypes that are possibly associated to redox changes .
Organic radical-activating enzymes (Organic_radical-activating)
Type: Family

Enzymes in this family all create a glycyl radical in the substrate protein .
Terminal EAR1-like, RNA recognition motif 3 (EAR1-like_RRM3)
Type: Domain

This entry represents the RNA recognition motif 3 (RRM3) of terminal EAR1-like proteins, including terminal EAR1-like protein 1 and 2 (TEL1 and TEL2) found in land plants . They may play a role in the regulation of leaf initiation . The terminal EAR1-like proteins are putative RNA-binding proteins carrying three RNA recognition motifs (RRMs), and TEL characteristic motifs that allow sequence and putative functional discrimination between the terminal EAR1-like proteins and Mei2-like proteins .
Adropin (Adropin)
Type: Family

Adropin is a peptide hormone that plays an important role in the regulation of lipid and glucose homeostasis . It is involved in carbohydrate-lipid metabolism, metabolic diseases, central nervous system function, endothelial function and cardiovascular disease . Some potential therapeutic benefits derived from adropin include enhancing glucose tolerance , ameliorating insulin resistance and lipid metabolism , and protecting against endothelial barrier dysfunction .
Benzylsuccinate synthase activase (Benzylsuc_synthase_activase)
Type: Family

Proteins in this entry are thought to be radical SAM benzylsuccinate synthase-activating enzymes. These are a glycyl radical active site-creating enzyme related to pyruvate formate lyase-activating enzyme and additional uncharacterised homologues which activate additional glycyl radical-containing enzymes .
PARP-10, RNA recognition motif 1 and 2 (PAR10_RRM1_2)
Type: Domain

This entry represents the RNA recognition motif 1 and 2 (RRM1 and 2) of PARP-10, a novel oncoprotein c-Myc-interacting protein with poly(ADP-ribose) polymerase activity. It is localized to the nuclear and cytoplasmic compartments. In addition to the PARP activity, PARP-10 is also involved in the control of cell proliferation by inhibiting c-Myc- and E1A-mediated cotransformation of primary cells .

It contains two N-terminal RNA recognition motifs (RRMs), two overlapping C-terminal domains composed of a glycine-rich region and a region with homology to catalytic domains of PARP enzymes (PARP domain). In addition, PARP-10 contains two ubiquitin-interacting motifs (UIM).
Pyruvate formate-lyase activase (Pyruvate_for-lyase_activase)
Type: Family

Pyruvate formate lyase activating enzyme (PFL-AE) is a member of the Radical SAM superfamily that functions by catalyzing the formation of the Gly734 radical of PFL .
Methyltransferase, class B (Methyltransferase_Class_B)
Type: Family

These enzymes all belong to the Class B Radical SAM Methyltransferases, i.e. they are all B12-dependent methyltransferases that utilise two SAM moieties, the first to generate the 5'-deoxyadenosyl radical and the second to regenerate the methylcobalamin cofactor .
Set1A, RNA recognition motif (Set1A_RRM)
Type: Domain

This entry represents the RNA recognition motif (RRM) of Setd1A (also known as Set1A), a ubiquitously expressed vertebrates histone methyltransferase that exhibits high homology to yeast Set1. Set1A is localized to euchromatic nuclear speckles and associates with a complex containing six human homologs of the yeast Set1/COMPASS complex, including CXXC finger protein 1 (CFP1; homologous to yeast Spp1), Rbbp5 (homologous to yeast Swd1), Ash2 (homologous to yeast Bre2), Wdr5 (homologous to yeast Swd3), and Wdr82 (homologous to yeast Swd2) .
Set1B, RNA recognition motif (Set1B_RRM)
Type: Domain

This entry represents the RNA recognition motif (RRM) of Setd1B (also known as Set1B), a ubiquitously expressed vertebrates histone methyltransferase that exhibits high homology to yeast Set1. Set1B is localised to euchromatic nuclear speckles and associates with a complex containing six human homologues of the yeast Set1/COMPASS complex, including CXXC finger protein 1 (CFP1; homologous to yeast Spp1), Rbbp5 (homologous to yeast Swd1), Ash2 (homologous to yeast Bre2), Wdr5 (homologous to yeast Swd3), and Wdr82 (homologous to yeast Swd2). Set1B complex is a histone methyltransferase that produces trimethylated histone H3 at Lys4 .
Ribosome biogenesis protein 15, RNA recognition motif (Nop15_RRM)
Type: Domain

This entry represents the RNA recognition motif (RRM) of Nop15. Nop15 has been identified as a component of a pre-60S particle. It interacts with RNA components of the early pre-60S particles. Furthermore, Nop15 binds directly to a pre-rRNA transcript in vitro and is required for pre-rRNA processing. It functions as a ribosome synthesis factor required for the 5' to 3' exonuclease digestion that generates the 5' end of the major, short form of the 5.8S rRNA as well as for processing of 27SB to 7S pre-rRNA. Nop15p also play a specific role in cell cycle progression . Nop15p contains an RNA recognition motif (RRM).
RBM15, RNA recognition motif 1 (RBM15_RRM1)
Type: Domain

This entry represents the RNA recognition motif 1 (RRM1) 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) .
GDGT/MA synthase (GDGT/MA_synthase)
Type: Family

This entry includes GDGT/MA synthase (MJ0619, formerly known as 7,8-dihydro-6-hydroxymethylpterin dimethyltransferase) and its homologues mostly from archaea. This is the pioneer enzyme of class D radical S-adenosylmethionine methylases (RSMT) subclass.

The MJ0619 protein from Methanocaldococcus jannaschii was first thought to be responsible for catalysing the methylation at both C-7 and C-9 of the 7,8-dihydro-6-hydroxymethylpterin substrate . However, this could not be corroborated and the X-ray structure of MJ0619 revealed that this enzyme is, actually, involved in isoprenoid-based ether-linked membrane lipids synthesis and catalyses the biphytanyl chain formation between the termini of two lipid tails within one glycerophospholipid to generate the macrocyclic archaeol or between the termini of two lipid tails from two glycerophospholipids to generate the macrocycle glycerol dibiphytanyl glycerol tetraether (GDGT). These lipids enable archaea to resist extreme environmental conditions. Therefore, MJ0619 has been renamed GDGT/MA synthase or GDGT/MAS. It contains three Fe4-S4 clusters and a mononuclear rubredoxin-type Fe2/3 cofactor .
RBM15, RNA recognition motif 2 (RBM15_RRM2)
Type: Domain

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