SII-SWORD/CoKE huggingface dataset:
PDIP3, RNA recognition motif (PDIP3_RRM)
Type: Domain

This entry represents the RRM of PDIP3.

Polymerase delta-interacting protein 3 (PDIP3), also termed SKAR or 46kDa DNA polymerase delta interaction protein (PDIP46), belongs to the Aly/REF family of RNA binding proteins that have been implicated in coupling transcription with pre-mRNA splicing and nucleo-cytoplasmic mRNA transport . PDIP3 is widely expressed and localizes to the nucleus. It may be a critical player in the function of S6K1 in cell and organism growth control by binding the activated, hyperphosphorylated form of S6K1 but not S6K2 . Furthermore, PDIP3 functions as a protein partner of the p50 subunit of DNA polymerase delta . In addition, PDIP3 may have particular importance in pancreatic beta cell size determination and insulin secretion . PDIP3 contains a well conserved RNA recognition motif (RRM).
Maleylacetate reductase (MAR)
Type: Family

Maleylacetate reductases (MAR) play an important role in the degradation of aromatic compounds in aerobic microbes . In fungi and yeasts, the enzymes are involved in the catabolism of compounds such as phenol, tyrosine, benzoate, 4-hydroxybenzoate and resorcinol. In bacteria, the enzymes contribute to the degradation of resorcinol, 2,4-dihydroxybenzoate ([beta]-resorcylate) and 2,6-dihydroxybenzoate ([gamma]-resorcylate) via hydroxyquinol and maleylacetate . Maleylacetate reductases catalyze NADH- or NADPH-dependent reduction, at the carbon-carbon double bond, of maleylacetate or 2-chloromaleylacetate to 3-oxoadipate . In the case of 2-chloromaleylacetate, maleylacetate reductases initially catalyses the NAD(P)H-dependent dechlorination to maleylacetate, which is then reduced to 3-oxoadipate. This enzyme is a homodimer. It is inhibited by thiol-blocking reagents such as p-chloromercuribenzoate and Hg++, indicating that the cysteine residue is probably necessary for the catalytic activity of maleylacetate reductase .
RBPMS2, RNA recognition motif (RBPMS2_RRM)
Type: Domain

This entry represents the RNA recognition motif (RRM) of RBPMS2, a paralogue of RNA-binding protein with multiple splicing (RBP-MS) . RBPMS2 binds to and regulates mRNA expression of NOGGIN, the major inhibitor of the bone morphogenetic protein (BMP) pathway. It plays a role in the development and plasticity of digestive smooth muscle cells (SMCs) . Like RBP-MS, RBP-MS2 contains an RNA recognition motif (RRM). A particular sequence motif (D-x-K-x-R-E-L-Y-L-L-F: residues 39-51) located in its RRM domain has been shown to be essential for its homodimerization, which is important for its function in the RBPMS2-dependent SMC dedifferentiation process .
Protein couch potato, RNA recognition motif (Cpo_RRM)
Type: Domain

This entry represents the RNA recognition motif (RRM) of Cpo, an RNA-binding protein encoded by Drosophila couch potato (cpo) gene. The gene is named because several partial loss-of-function alleles cause hypoactive behavior in adults. Cpo contains a well conserved RNA recognition motif (RRM). It may control the processing of RNA molecules required for the proper functioning of the peripheral nervous system (PNS) .
Bifunctional aldehyde-alcohol dehydrogenase, C-terminal domain (AAD_C)
Type: Domain

This alcohol dehydrogenase domain is located on the C-terminal part of a bifunctional two-domain protein. The N-terminal part of the protein contains an acetaldehyde-CoA dehydrogenase domain. This protein is involved in pyruvate metabolism. Pyruvate is converted to acetyl-CoA and formate by pyruvate formate-lysase (PFL). Under anaerobic condition, acetyl-CoA is reduced to acetaldehyde and ethanol by this two-domain protein . Acetyl-CoA is first converted into an enzyme-bound thiohemiacetal by the N-terminal acetaldehyde dehydrogenase domain. The enzyme-bound thiohemiacetal is subsequently reduced by the C-terminal NAD+-dependent alcohol dehydrogenase domain. In E. coli, this protein is called AdhE and was shown pyruvate formate-lysase (PFL) deactivase activity, which is involved in the inactivation of PFL, a key enzyme in anaerobic metabolism . In Escherichia coli and Entamoeba histolytica, this enzyme forms homopolymeric peptides composed of more than 20 protomers associated in a helical rod-like structure .
RBM20, RNA recognition motif (RBM20_RRM)
Type: Domain

This entry represent the RNA recognition motif (RRM) of RBM20, an alternative splicing regulator associated with dilated cardiomyopathy (DCM) . It contains only one copy of RNA-recognition motif (RRM).
PTBPH1/PTBPH2, RNA recognition motif 1 (PTBPH1/PTBPH2_RRM1)
Type: Domain

This entry represents the RNA recognition motif 1 (RRM1) of polypyrimidine tract-binding protein homologue 1 (PTBPH1) and 2 from plants (AtPTB1 and AtPTB2 in Arabidopsis respectively).

PTBPH1 and PTBPH2 show significant sequence similarity to polypyrimidine tract binding protein (PTB) that is an important negative regulator of alternative splicing in mammalian cells. They are splicing factors that negatively regulate splicing of a mini-exon splicing reporter and affect alternative splicing of endogenous genes differentially . Both, PTBPH1 and PTBPH2, contain three RNA recognition motifs (RRM).
PTBPH1/PTBPH2, RNA recognition motif 2 (PTBPH1/PTBPH2_RRM2)
Type: Domain

This entry represents the RNA recognition motif 2 (RRM2) of polypyrimidine tract-binding protein homologue 1 (PTBPH1) and 2 from plants (AtPTB1 and AtPTB2 in Arabidopsis respectively).

PTBPH1 and PTBPH2 show significant sequence similarity to polypyrimidine tract binding protein (PTB) that is an important negative regulator of alternative splicing in mammalian cells. They are splicing factors that negatively regulate splicing of a mini-exon splicing reporter and affect alternative splicing of endogenous genes differentially . Both, PTBPH1 and PTBPH2, contain three RNA recognition motifs (RRM).
PTBPH1/PTBPH2, RNA recognition motif 3 (PTBPH1/PTBPH2_RRM3)
Type: Domain

This entry represents the RNA recognition motif 3 (RRM3) of polypyrimidine tract-binding protein homologue 1 (PTBPH1) and 2 from plants (AtPTB1 and AtPTB2 in Arabidopsis respectively).

PTBPH1 and PTBPH2 show significant sequence similarity to polypyrimidine tract binding protein (PTB) that is an important negative regulator of alternative splicing in mammalian cells. They are splicing factors that negatively regulate splicing of a mini-exon splicing reporter and affect alternative splicing of endogenous genes differentially . Both, PTBPH1 and PTBPH2, contain three RNA recognition motifs (RRM).
PTBPH3, RNA recognition motif 1 (PTBPH3_RRM1)
Type: Domain

This entry represents the RNA recognition motif 1 (RRM1) of polypyrimidine tract-binding protein homologue 3 (PTBPH3), also known as AtPTB3 in Arabidopsis.

PTBPH3 shows significant sequence similarity to polypyrimidine tract binding protein (PTB), which is an important negative regulator of alternative splicing in mammalian cells. However, no major alternative splicing regulatory function of AtPTB3 was found . Like PTB, PTBPH3 contains four RNA recognition motifs (RRM).
PTBPH3, RNA recognition motif 2 (PTBPH3_RRM2)
Type: Domain

This entry represents the RNA recognition motif 2 (RRM2) of plant polypyrimidine tract-binding protein homologue 3 (PTBPH3), also known as AtPTB3 in Arabidopsis.

PTBPH3 shows significant sequence similarity to polypyrimidine tract binding protein (PTB), which is an important negative regulator of alternative splicing in mammalian cells. However, no major alternative splicing regulatory function of AtPTB3 was found . Like PTB, PTBPH3 contains four RNA recognition motifs (RRM).
PTBPH3, RNA recognition motif 3 (PTBPH3_RRM3)
Type: Domain

This entry represents the RNA recognition motif 3 (RRM3) of plant polypyrimidine tract-binding protein homologue 3 (PTBPH3), also known as AtPTB3 in Arabidopsis.

PTBPH3 shows significant sequence similarity to polypyrimidine tract binding protein (PTB), which is an important negative regulator of alternative splicing in mammalian cells. However, no major alternative splicing regulatory function of AtPTB3 was found . Like PTB, PTBPH3 contains four RNA recognition motifs (RRM).
PTBP2, RNA recognition motif 3 (PTBP2_RRM3)
Type: Domain

This entry represents the RNA recognition motif 3 (RRM3) of polypyrimidine tract-binding protein 2 (PTBP2).

PTBP2 is a homologue of PTB (PTBP1), a splicing repressor factor implicated in the control of alternative exon selection during mRNA processing of many different transcribed genes, including its own pre-mRNA. PTBP2 is expressed at high levels in adult brain, muscle and testis . PTB and PTBP2 bind to the same RNA sequences and have similar effects on alternative splicing events. However, differential expression of PTB and PTBP2 can lead to the generation of alternatively spliced mRNAs . During neuronal differentiation, microRNA miR-124 downregulates PTB expression, which in turn leads to upregulation of PTBP2. Later in development, the expression of PTBP2 decreases and this leads to a second wave of alternative splicing changes characteristic of adult brain and essential for brain development .
PTBP2, RNA recognition motif 4 (PTBP2_RRM4)
Type: Domain

This entry represents the RNA recognition motif 4 (RRM4) of polypyrimidine tract-binding protein 2 (PTBP2).

PTBP2 is a homologue of PTB (PTBP1), a splicing repressor factor implicated in the control of alternative exon selection during mRNA processing of many different transcribed genes, including its own pre-mRNA. PTBP2 is expressed at high levels in adult brain, muscle and testis . PTB and PTBP2 bind to the same RNA sequences and have similar effects on alternative splicing events. However, differential expression of PTB and PTBP2 can lead to the generation of alternatively spliced mRNAs . During neuronal differentiation, microRNA miR-124 downregulates PTB expression, which in turn leads to upregulation of PTBP2. Later in development, the expression of PTBP2 decreases and this leads to a second wave of alternative splicing changes characteristic of adult brain and essential for brain development .
hnRNP A0, RNA recognition motif 1 (hnRNPA0_RRM1)
Type: Domain

This entry represents the RNA recognition motif 1 (RRM1) of heterogeneous nuclear ribonucleoprotein A0 (hnRNP A0), a low abundance hnRNP protein that has been implicated in mRNA stability in mammalian cells . It has been identified as the substrate for MAPKAP-K2 and may be involved in the lipopolysaccharide (LPS)-induced post-transcriptional regulation of tumor necrosis factor-alpha (TNF-alpha), cyclooxygenase 2 (COX-2) and macrophage inflammatory protein 2 (MIP-2) . hnRNP A0 contains two RNA recognition motifs (RRMs), followed by a long glycine-rich region at the C terminus.
NADPH-dependent butanol dehydrogenase (NADPH_BDH)
Type: Family

NADPH-dependent butanol dehydrogenase (BDH) is involved in the butanol and ethanol formation pathway of some bacteria . The fermentation process is characterised by an acid producing growth phase, followed by a solvent producing phase. The latter phase is associated with the induction of solventogenic enzymes such as butanol dehydrogenase. The activity of the enzymes require NADPH as cofactor, as well as divalent ions zinc or iron.

This family is a member of the iron-containing alcohol dehydrogenase superfamily. Protein structure has a dehydroquinate synthase-like fold. Proteins in this entry also include TBCH5v1_0547 from Thermococcus barophilus, which is a thermostable type III alcohol dehydrogenase .
hnRNP A1, RNA recognition motif 2 (hnRNPA1_RRM2)
Type: Domain

This entry represents the RNA recognition motif 2 (RRM2) of heterogeneous nuclear ribonucleoprotein A1 (hnRNP A1).

hnRNP A1 is an abundant eukaryotic nuclear RNA-binding protein that may modulate splice site selection in pre-mRNA splicing . hnRNP A1 has been characterised as a splicing silencer, often acting in opposition to an activating hnRNP H. It silences exons when bound to exonic elements in the alternatively spliced transcripts of c-src, HIV, GRIN1, and beta-tropomyosin. hnRNP A1 can shuttle between the nucleus and the cytoplasm . Thus, it may be involved in transport of cellular RNAs, including the packaging of pre-mRNA into hnRNP particles and transport of poly A+ mRNA from the nucleus to the cytoplasm .

The cytoplasmic hnRNP A1 has high affinity with AU-rich elements, whereas the nuclear hnRNP A1 has high affinity with a polypyrimidine stretch bordered by AG at the 3' ends of introns. hnRNP A1 is also involved in the replication of an RNA virus, such as mouse hepatitis virus (MHV), through an interaction with the transcription-regulatory region of viral RNA. Moreover, hnRNP A1, together with the scaffold protein septin 6, serves as host proteins to form a complex with NS5b and viral RNA, and further play important roles in the replication of Hepatitis C virus (HCV) .

hnRNP A1 contains two RNA recognition motifs (RRMs) , followed by a long glycine-rich region at the C terminus. The RRMs of hnRNP A1 play an important role in silencing the exon and the glycine-rich domain is responsible for protein-protein interactions.
Fumarate reductase/succinate dehydrogenase, transmembrane subunit (SQR/QFR_C/D)
Type: Homologous_superfamily

Fumarate reductase couples the reduction of fumarate to succinate to the oxidation of quinol to quinone, in a reaction opposite to that catalysed by the related complex II of the respiratory chain (succinate dehydrogenase) . Succinate dehydrogenase (SQR) and fumarate reductase (QFR) share a common subunit arrangement, composed of a flavoprotein catalytic subunit (subunit A), an iron-sulfur protein (subunit B) and one or two hydrophobic transmembrane subunits (subunits C and D) .

This homologous superfamily includes the membrane components of both fumarate reductase and succinate dehydrogenase.
Nop4, RNA recognition motif 1 (Nop4_RRM1)
Type: Domain

This entry represents the RNA recognition motif 1 (RRM1) of Nop4 from fungi.

Nop4 is an essential nucleolar protein involved in processing and maturation of 27S pre-rRNA and biogenesis of 60S ribosomal subunits . Nop4 has four RNA recognition motifs (RRMs).
Nop4, RNA recognition motif 2 (Nop4_RRM2)
Type: Domain

This entry represents the RNA recognition motif 2 (RRM2) of Nop4 from Saccharomyces cerevisiae.

Nop4 is an essential nucleolar protein involved in processing and maturation of 27S pre-rRNA and biogenesis of 60S ribosomal subunits . Nop4 has four RNA recognition motifs (RRMs).
Nop4, RNA recognition motif 3 (Nop4p_RRM3)
Type: Domain

This entry represents the RNA recognition motif 3 (RRM3) of Nop4 from fungi.

Nop4 is an essential nucleolar protein involved in processing and maturation of 27S pre-rRNA and biogenesis of 60S ribosomal subunits . Nop4 has four RNA recognition motifs (RRMs).
Nop4, RNA recognition motif 4 (Nop4_RRM4)
Type: Domain

This entry represents the RNA recognition motif 4 (RRM4) of Nop4 from Saccharomyces cerevisiae.

Nop4 is an essential nucleolar protein involved in processing and maturation of 27S pre-rRNA and biogenesis of 60S ribosomal subunits . Nop4 has four RNA recognition motifs (RRMs).
Psi-factor producing oxygenase-like, N-terminal heme peroxidase domain (Ppo-like_N)
Type: Domain

This entry represents the N-terminal heme peroxidase domain of Psi-factor producing oxygenase and related proteins.

Oxylipins may be synthesized via multi step processes that consist of dioxygenation and isomerization of the intermediately formed hydroperoxy fatty acid. These processes are typically catalyzed by two distinct enzyme classes: dioxygenases and cytochrome P450 enzymes. In fungi both enzymatic activities are combined in a single bifunctional enzyme and are known as are named Psi-factor producing oxygenases (Ppo) . These enzymes consist of an N-terminal heme peroxidase domain and a C-terminal cytochrome P450 domain.

These fungal enzymes, related to animal heme peroxidases, catalyze the oxygenation of linoleate and similar targets. They are responsible for the synthesis of various fatty acid-derived oxylipins. Linoleate diol synthase from Gaeumannomyces graminis catalyzes the dioxygenation of linoleic acid to (8R)-hydroperoxylinoleate and isomerization of the resulting hydroperoxide to (7S,8S)-dihydroxylinoleate . Other members are 5,8-linoleate dioxygenase (ppoA) and linoleate 10R-dioxygenase (ppoC) .
Alpha-dioxygenase (A_dioxygenase)
Type: Family

This is a diverse family of oxygenases related to the animal heme peroxidases, with members from plants, fungi, and bacteria. Plant alpha-dioxygenases 1 (DOX1), also known as pathogen-inducible oxygenase (PIOX), and DOX2 oxygenate fatty acids into 2R-hydroperoxides . PIOX is expressed during the hypersensitive reaction, which is characterised by rapid and localised cell death induced by infection with pathogens, and the rapidly induced expression of PIOX may be caused by the oxidative burst that occurs in the process of cell death . PIOX may protect plant tissues from oxidative stress and cell death .
hnRNP-L, RNA recognition motif 3 (hnRNP-L_RRM3)
Type: Domain

This entry represents the RNA recognition motif 3 (RRM3) of heterogeneous nuclear ribonucleoprotein L (hnRNP-L).

hnRNP-L is a subunit of the KMT3a (also known as HYPB or hSet2) complex required for histone H3 Lys-36 trimethylation activity and which is found only in higher eukaryotes . It plays both nuclear and cytoplasmic roles in pre-mRNA processing, mRNA export of intronless genes, internal ribosomal entry site-mediated translation, and chromatin modification . hnRNP-L is an RNA-binding protein with four RNA recognition motifs (RRMs) .
hnRNP-L, RNA recognition motif 4 (hnRNPL_RRM4)
Type: Domain

This entry represents the RNA recognition motif 4 (RRM4) of heterogeneous nuclear ribonucleoprotein L (hnRNP-L) from vertebrates.

hnRNP-L is a subunit of the KMT3a (also known as HYPB or hSet2) complex required for histone H3 Lys-36 trimethylation activity and which is found only in higher eukaryotes . It plays both nuclear and cytoplasmic roles in pre-mRNA processing, mRNA export of intronless genes, internal ribosomal entry site-mediated translation, and chromatin modification . hnRNP-L is an RNA-binding protein with four RNA recognition motifs (RRMs) .
Cytoplasmic polyadenylation element-binding protein (CPEB)
Type: Family

CPEB family members are RNA-binding proteins that are essential regulators of post-transcriptional gene expression. CPEBs target mRNAs defined by a cis-acting sequence in their 3' untranslated region (UTR), known as cytoplasmic polyadenylation element (CPE; with a consensus sequence of UUUUUAU). They are indirectly responsible for both translational repression and translational activation by polyadenylation . They are involved in may biological processes such as cell proliferation, senescence, cell polarity, and synaptic plasticity . They regulate the translation of maternal mRNAs controlling meiotic cell cycle progression. Mammals have four CPEBs, CPEB1-4, among which CPEB1/2/4 are essential to successful mitotic cell division . All four paralogues have two RNA recognition motifs (RRMs) and a zinc-binding domain (ZZ domain).

Drosophila CPEB homologue is known as Orb2, which may have a role in long-term memory formation .
Dual oxidase, peroxidase domain (DUOX_peroxidase)
Type: Domain

Animal heme peroxidases of the dual-oxidase like subfamily play vital roles in the innate mucosal immunity of gut epithelia. They provide reactive oxygen species which help control infection .
One innate immune mechanism is ROS (reactive oxygen species) production by NADPH oxidases of the NOX/DUOX (NADPH oxidase/dual oxidase) family. NOX enzymes consist of one NADPH oxidase domain and most often produce O2- (superoxide). Dual oxidases (DUOX) are enzymes that contain an NADPH oxidase domain that produces hydrogen peroxide (H2O2) and a peroxidase domain that can utilize H2O2 to carry out a variety of reactions .
CID8-like protein, RNA recognition motif 1 (CID8-like_RRM1)
Type: Domain

This entry represents the RNA recognition motif 1 (RRM1) domains found in A. thaliana CID8, CID9, CID10, CID11, CID12, CID 13 and mainly their plant homologues . These highly related RNA-binding proteins contain an N-terminal PAM2 domain (PABP-interacting motif 2), two RNA recognition motifs (RRMs) and a basic region that resembles a bipartite nuclear localization signal. The biological role of this family remains unclear.
Peroxidasin, peroxidase domain (Peroxidasin_peroxidase)
Type: Domain

Peroxidasin is a secreted heme peroxidase which is involved in hydrogen peroxide metabolism and peroxidative reactions in the cardiovascular system . It is a multidomain peroxidase that contain a signal peptide, several (e.g., five in Drosophila or one in Homo sapiens) leucine-rich regions, followed by four immunoglobulin-like domains, a linking region, the peroxidase domain, and a carboxy terminal Willebrand type C protein-protein interaction domain .

This entry represents the peroxidase domain of peroxidasin and related proteins. The domain co-occurs with extracellular matrix domains and may play a role in the formation of the extracellular matrix .

This entry also includes the human peroxidasin-like protein (PDXNL), a probable oxidoreductase that lacks peroxidase activity. It inhibits the peroxidase activity of PXDN through its interaction .
CID8-like protein, RNA recognition motif 2 (CID8-like_RRM2)
Type: Domain

This entry represents the RNA recognition motif 2 (RRM2) domain found in A. thaliana CID8, CID9, CID10, CID11, CID12, CID13 and mainly their plant homologues . These highly related RNA-binding proteins contain an N-terminal PAM2 domain (PABP-interacting motif 2), two RNA recognition motifs (RRMs) and a basic region that resembles a bipartite nuclear localization signal. The biological role of this family remains unclear.
TIA-1, RNA recognition motif 1 (TIA-1_RRM1)
Type: Domain

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

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 . Under conditions of rapid oxygen decline and extreme hypoxia, TIA-1 can aggregate with TIAR and suppress the HIF-1alpha pathway . TIA-1 binds Zn, which is involved in formation and recruitment to stress granules .

TIA-1 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. It interacts with RNAs containing short stretches of uridylates and its RRM2 can mediate the specific binding to uridylate-rich RNAs .
Peroxidasin, Ig-like domain 4 (Peroxidasin_Ig-like4)
Type: Domain

Peroxidasin is a secreted heme peroxidase which is involved in hydrogen peroxide metabolism and peroxidative reactions in the cardiovascular system . It is a multidomain peroxidase that contain a signal peptide, several (e.g., five in Drosophila or one in Homo sapiens) leucine-rich regions, followed by four immunoglobulin-like domains, a linking region, the peroxidase domain, and a carboxy terminal Willebrand type C protein-protein interaction domain .

This entry represents the fourth immunoglobulin (Ig)-like domain of vertebrate peroxidasin.
DnaD-like domain superfamily (DnaD-like_sf)
Type: Homologous_superfamily

This superfamily represents a domain found in several bacterial replication initiation and membrane attachment proteins, DnaD.

The DnaD protein is a component of the PriA primosome. The PriA primosome functions to recruit the replication fork helicase onto the DNA . Members, both chromosomal or phage-associated, are found in the Bacillus/Clostridium group of Gram-positive bacteria . DnaD consists of two domains with distinct activities: an N-terminal domain with oligomerisation activity and a C-terminal domain with DNA-binding activity and a second DNA-induced oligomerisation activity .