SII-SWORD/CoKE huggingface dataset:
Testin, LIM domain 1 (LIM1_Testin)
Type: Domain

Testin contains three C-terminal LIM domains and a PET protein-protein interaction domain at the N terminus. Testin is a cytoskeleton associated focal adhesion protein that localizes along actin stress fibres, at cell-cell-contact areas, and at focal adhesion plaques. Testin interacts with a variety of cytoskeletal proteins, including zyxin, mena, VASP, talin, and actin and it is involved in cell motility and adhesion events . Knockout mice experiments reveal the tumour repressor function of Testin .

LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes .

This is the first LIM domain of Testin.
Testin, LIM domain 2 (LIM2_Testin)
Type: Domain

Testin contains three C-terminal LIM domains and a PET protein-protein interaction domain at the N terminus. Testin is a cytoskeleton associated focal adhesion protein that localizes along actin stress fibres, at cell-cell-contact areas, and at focal adhesion plaques. Testin interacts with a variety of cytoskeletal proteins, including zyxin, mena, VASP, talin, and actin and it is involved in cell motility and adhesion events . Knockout mice experiments reveal the tumour repressor function of Testin .

LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes .

This is the second LIM domain of Testin.
Testin, LIM domain 3 (LIM3_Testin)
Type: Domain

Testin contains three C-terminal LIM domains and a PET protein-protein interaction domain at the N terminus. Testin is a cytoskeleton associated focal adhesion protein that localizes along actin stress fibres, at cell-cell-contact areas, and at focal adhesion plaques. Testin interacts with a variety of cytoskeletal proteins, including zyxin, mena, VASP, talin, and actin and it is involved in cell motility and adhesion events . Knockout mice experiments reveal the tumour repressor function of Testin .

LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes .

This is the third LIM domain of Testin.
Lumazine synthase (LS)
Type: Family

Riboflavin is biosynthesized in plants, fungi and certain microorganisms; as animals lack the necessary enzymes to produce this vitamin, they acquire it from dietary sources. The penultimate step in the biosynthesis of riboflavin (vitamin B2) involves the condensation of 3,4-dihydroxy-2-butanone 4-phosphate with 5-amino-6-ribitylamino-2,4(1H,3H)-pyrimidinedione, which is catalyzed by 6,7-dimethyl-8-ribityllumazine synthase (lumazine synthase) .

The biosynthesis of one riboflavin molecule requires one molecule of GTP and two molecules of ribulose 5-phosphate as substrates. The final step in the biosynthesis of the vitamin involves the dismutation of 6,7-dimethyl-8-ribityllumazine catalyzed by riboflavin synthase (RS) .
Nocturnin, deadenylase domain (Deadenylase_nocturnin)
Type: Domain

This entry represents the C-terminal catalytic domain of the deadenylase nocturnin, and related domains. Nocturnin is a poly(A)-specific 3' exonuclease that specifically degrades the 3' poly(A) tail of RNA in a process known as deadenylation. This nuclease activity is manganese dependent. Nocturnin is expressed in the cytoplasm of Xenopus laevis retinal photoreceptor cells in a rhythmic fashion, and it has been proposed that it participates in posttranscriptional regulation of the circadian clock or its outputs, and that the mRNA target(s) of this deadenylase are circadian clock-related . In mouse, the nocturnin gene, mNoc, is expressed in a circadian pattern in a range of tissues including retina, spleen, heart, kidney, and liver. It is highly expressed in bone-marrow stromal cells, adipocytes and hepatocytes . In mammals, nocturnin plays a role in regulating mesenchymal stem-cell lineage allocation, perhaps through regulating PPAR-gamma (peroxisome proliferator-activated receptor-gamma) nuclear translocation .
CCR4-NOT transcription complex subunit 6 (Cnot6)
Type: Domain

This entry represents the C-terminal catalytic domain of the deadenylase CCR4a, also known as CCR4-NOT transcription complex subunit 6 (CNOT6). CCR4 belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. In S. cerevisiae, Ccr4 is the major deadenylase subunit of the CCR4-NOT transcription complex, which contains two deadenylase subunits and several noncatalytic subunits .

There are two vertebrate CCR4 proteins, CCR4a and CCR4b (also called CNOT6-like or CNOT6L). CCR4a associates with other components, such as CNOT1-3 and Caf1, to form a CCR4-NOT multisubunit complex, which regulates transcription and mRNA degradation . CCR4a is a component of P-bodies and is necessary for foci formation of various P-body components . It also plays a role in cellular responses to DNA damage, by regulating Chk2 activity .
CCR4-NOT transcription complex subunit 6-like (Deadenylase_CCR4b)
Type: Domain

This entry represents the C-terminal catalytic domain of the deadenylase CCR4b, also known as CCR4-NOT transcription complex subunit 6-like (CNOT6L). CCR4 belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. In S. cerevisiae, CCR4 is the major deadenylase subunit of the CCR4-NOT transcription complex, which contains two deadenylase subunits and several noncatalytic subunits .

There are two vertebrate CCR4 proteins, CCR4a (also called CCR4-NOT transcription complex subunit 6 or CNOT6) and CCR4b. CCR4b associates with other components, such as CNOT1-3 and Caf1, to form a CCR4-NOT multisubunit complex, which regulates transcription and mRNA degradation . The nuclease domain of CCR4b exhibits Mg2+-dependent deadenylase activity with strict specificity for poly (A) RNA as substrate . CCR4b is mainly localized in the cytoplasm. It regulates cell growth and influences cell cycle progression by regulating p27/Kip1 mRNA levels . It contributes to the prevention of cell death by regulating insulin-like growth factor-binding protein 5 .
Reelin (Reelin)
Type: Family

Reelin is an extracellular matrix serine protease that regulates neuronal migration during embryonic development and acts as a modulator of synaptic transmission in the adult brain . Reelin acts on its receptors, VLDLR and ApoER2, acting on cytoskeleton, controlling migration and subsequently positioning and stabilizing the cortical neurons . In the adult brain, reelin stabilizes the actin cytoskeleton by inducing cofilin phosphorylation. Decreased Reelin expression causes destabilization of neurons, which could have implications for brain disorders, such as epilepsy and schizophrenia .
hnRNPH3, RNA recognition motif 3 (hnRNPH3_RRM3)
Type: Domain

This entry represents the RNA recognition motif 3 (RRM3) of heterogeneous nuclear ribonucleoprotein H3 (hnRNP H3).

hnRNP H3 (also termed hnRNP 2H9) is a nuclear RNA binding protein that belongs to the hnRNP H protein family that also includes hnRNP H, hnRNP H2, and hnRNP F. This family is involved in mRNA processing and exhibit extensive sequence homology. Little is known about the functions of hnRNP H3 except for its role in the splicing arrest induced by heat shock .
hnRNPH3, RNA recognition motif 2 (hnRNPH3_RRM2)
Type: Domain

This entry represents the RNA recognition motif 2 (RRM2) of heterogeneous nuclear ribonucleoprotein H3 (hnRNP H3).

hnRNP H3 (also termed hnRNP 2H9) is a nuclear RNA binding protein that belongs to the hnRNP H protein family that also includes hnRNP H, hnRNP H2, and hnRNP F. This family is involved in mRNA processing and exhibit extensive sequence homology. Little is known about the functions of hnRNP H3 except for its role in the splicing arrest induced by heat shock .
Synaptojanin-1, RNA recognition motif (SYNJ1_RRM)
Type: Domain

This entry represents the RNA recognition motif (RRM) of synaptojanin-1.

Synaptojanin-1 was originally identified as one of the major Grb2-binding proteins that may participate in synaptic vesicle endocytosis . It also acts as an Src homology 3 (SH3) domain-binding brain-specific inositol 5-phosphatase, with a putative role in clathrin-mediated endocytosis . Synaptojanin-1 contains an N-terminal domain homologous to the cytoplasmic portion of the yeast protein Sac1p , a central inositol 5-phosphatase domain followed by a putative RNA recognition motif (RRM), and a C-terminal proline-rich region mediating the binding of synaptojanin-1 to various SH3 domain-containing proteins including amphiphysin, SH3p4, SH3p8, SH3p13, and Grb2 .
Synaptojanin-2, RNA recognition motif (SYNJ2_RRM)
Type: Domain

This entry represents the RNA recognition motif (RRM) of synaptojanin-2.

Synaptojanin-2 is a ubiquitously expressed central regulatory enzyme in the phosphoinositide-signaling cascade . As a novel Rac1 effector regulating an early step of clathrin-mediated endocytosis, synaptojanin-2 acts as a polyphosphoinositide phosphatase, directly and specifically interacting with Rac1 in a GTP-dependent manner. It mediates the inhibitory effect of Rac1 on endocytosis and plays an important role in the Rac1-mediated control of cell growth . Synaptojanin-2 shows high sequence homology to the N-terminal Sac1p homology domain , the central inositol 5-phosphatase domain, and the putative RNA recognition motif (RRM) of synaptojanin-1, but differs in the proline-rich region.
Somatotropin (Somatotropin)
Type: Family

Somatotropin, also known as growth hormone (GH), plays an important role in growth control. In addition to the growth-stimulating effect, GH is able to exert both insulin-like and insulin-antagonistic effects in adipose tissue and skeletal muscle . The 3D structure of bovine somatotropin has been predicted using a combination of heuristics and energy minimisation .
CPEB-1, RNA recognition motif 1 (CPEB1_RRM1)
Type: Domain

This entry represents the RNA recognition motif 1 (RRM1) of CPEB-1, an RNA-binding protein that interacts with the cytoplasmic polyadenylation element (CPE), a short U-rich motif in the 3' untranslated regions (UTRs) of certain mRNAs. It functions as a translational regulator that plays a major role in the control of maternal CPE-containing mRNA in oocytes , as well as of subsynaptic CPE-containing mRNA in neurons . Once phosphorylated and recruiting the polyadenylation complex, CPEB-1 may function as a translational activator stimulating polyadenylation and translation . Otherwise, it may function as a translational inhibitor when dephosphorylated and bound to a protein such as maskin or neuroguidin, which blocks translation initiation through interfering with the assembly of eIF-4E and eIF-4G . Although CPEB-1 is mainly located in cytoplasm, it can shuttle between nucleus and cytoplasm .

CPEB-1 contains an N-terminal unstructured region, two RNA recognition motifs (RRMs) and a Zn-finger motif. Both of the RRMs and the Zn finger are required for CPEB-1 to bind CPE. The N-terminal regulatory region may be responsible for CPEB-1 interacting with other proteins. This entry includes CPB3 from C. elegans which is the orthologue of human CPEB-1.
UPF3B, RNA recognition motif-like domain (UPF3B_RRM-like)
Type: Domain

This entry represents the RNA recognition motif (RRM)-like domain in Upf3B (also known as Regulator of nonsense transcripts 3B), a human orthologue of yeast Upf3p and Caenorhabditis elegans SMG-4 . It derives from X-linked gene UPF3B and is required for nonsense-mediated mRNA decay (NMD) in human . Upf3B is a nucleocytoplasmic shuttling protein that associates selectively with spliced beta-globin mRNA in vivo . Like other Upf3 proteins, Upf3B contains nuclear import and export signals, and a conserved domain with some similarity to an RNA recognition motif (RRM), indicating that it may be an RNA binding protein.
RNA-binding protein fusilli, RNA recognition motif 2 (Fusilli_RRM2)
Type: Domain

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

Fusilli is encoded by Drosophila fusilli (fus) gene. Loss of Fusilli activity causes lethality during embryogenesis in flies. Drosophila Fusilli can regulate endogenous fibroblast growth factor receptor 2 (FGFR2) splicing and functions as a splicing factor . Fusilli contains three RNA recognition motifs (RRMs), an N-terminal domain with unknown function and a C-terminal domain particularly rich in alanine, glutamine, and serine.
EfeO/Algp7, imelysin-like domain (Imelysin-like_EfeO/Algp7)
Type: Domain

EfeO is an essential component of the EfeUOB operon which is highly conserved in bacteria. However, its biochemical function is unknown. EfeO contains an N-terminal cupredoxin (CUP)-like domain and C-terminal imelysin-like domain that may bind iron . Algp7 (

), a member of the EfeO family of proteins from Sphingomonas sp. A1, is found to bind alginate at neutral pH, but does not contain the CUP domain, thus having a role that does not seem to be related to iron uptake . Some members of this group are fused to an N-terminal putative EfeU ion permease domain. The imelysin-like domain of this family also contains the GxHxxE sequence motif and a highly conserved functional site, suggesting a similar role to other imelysin family proteins containing the same motif .
Iron-regulated protein A, imelysin-like domain (Imelysin-like_IrpA)
Type: Domain

Putative iron-regulated protein A (IrpA), found mainly in Bacteriodes, proteobacteria and cyanobacteria, contains a domain similar to insulin-cleaving membrane protease (imelysin, ICMP) protein . IrpA has been shown to be essential for growth under iron-deficient conditions in the cyanobacteria Synechococcus sp . The conserved GxHxxE motif is similar to other known imelysin-like proteins that are regulated by iron, such as ICMP and EfeO.
hnRPLL, RNA recognition motif 3 (hnRPLL_RRM3)
Type: Domain

This entry represents the RNA recognition motif 3 (RRM3) of hnRNP-LL.

hnRNP-LL plays a critical and unique role in the signal-induced regulation of CD45 and acts as a global regulator of alternative splicing in activated T cells . It is closely related in domain structure and sequence to heterogeneous nuclear ribonucleoprotein L (hnRNP-L), which is an abundant nuclear, multifunctional RNA-binding protein with three RNA-recognition motifs (RRMs).
IPPA , imelysin-like domain (Imelysin-like_IPPA)
Type: Domain

This family includes insulin-cleaving membrane protease (imelysin, ICMP)-like protein (IPPA from Psychrobacter arcticus), the Pseudomonas aeruginosa PA4372 and Vibrio cholera VC1266 Fur-regulated imelysin-like protein. They share the overall fold and a similar functional site as the insulin-cleaving membrane protease (ICMP) . However, IPPA adopts a structure distinctive from the known HxxE metallopeptidases or iron-binding proteins, suggesting this protein may not be a peptidase; the histidine in the GxHxxE motif region is no longer conserved (GxxxxE), indicating a possible loss of enzymatic function or a change in substrate preference. A putative functional site for this non-peptidase homologue is located at the domain interface. The tertiary structure shows a fold consisting of two domains, each of which consists of a bundle of four helices that are similar to each other, implying an ancient gene duplication and fusion event .
hnRPLL, RNA recognition motif 1 (hnRPLL_RRM1)
Type: Domain

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

hnRNP-LL plays a critical and unique role in the signal-induced regulation of CD45 and acts as a global regulator of alternative splicing in activated T cells . It is closely related in domain structure and sequence to heterogeneous nuclear ribonucleoprotein L (hnRNP-L), which is an abundant nuclear, multifunctional RNA-binding protein with three RNA-recognition motifs (RRMs).
hnRPLL, RNA recognition motif 2 (hnRPLL_RRM2)
Type: Domain

This entry represents the RNA recognition motif 2 (RRM2) of hnRNP-LL.

hnRNP-LL plays a critical and unique role in the signal-induced regulation of CD45 and acts as a global regulator of alternative splicing in activated T cells . It is closely related in domain structure and sequence to heterogeneous nuclear ribonucleoprotein L (hnRNP-L), which is an abundant nuclear, multifunctional RNA-binding protein with three RNA-recognition motifs (RRMs).
hnRPLL, RNA recognition motif 4 (hnRPLL_RRM4)
Type: Domain

This entry represents the RNA recognition motif 4 (RRM4) of hnRNP-LL.

hnRNP-LL plays a critical and unique role in the signal-induced regulation of CD45 and acts as a global regulator of alternative splicing in activated T cells . It is closely related in domain structure and sequence to heterogeneous nuclear ribonucleoprotein L (hnRNP-L), which is an abundant nuclear, multifunctional RNA-binding protein with three RNA-recognition motifs (RRMs).
DAZ/BOULE, RNA recognition motif (DAZ_BOULE_RRM)
Type: Domain

This entry represents the RNA recognition motif (RRM) domain of Deleted in AZoospermia (DAZ) homologues from invertebrates. Invertebrates contain a single DAZ homologue, known as BOULE in Drosophila, while vertebrates, other than catarrhine primates, possess both BOULE and DAZL (DAZ-like) genes. The catarrhine primates possess BOULE, DAZL, and DAZ genes .
Emerin, LEM domain (LEM_emerin)
Type: Domain

Emerin is an inner nuclear membrane protein with roles in nuclear "lamina" structure, nuclear assembly, chromatin tethering, gene regulation, mitosis, development and signaling . Emerin is absent from the inner nuclear membrane in most patients with X-linked muscular dystrophy . BAF recruits emerin to chromatin and regulates higher-order chromatin structure during nuclear assembly . Emerin interacts with A-type lamins . It contains an N-terminal LEM domain followed by a poly-serine segment, a region rich in hydrophobic amino acids comprising the nuclear localization signal (NLS) followed by another poly-serine segment, and a C-terminal transmembrane region .

The LEM domain of Emerin is involved in interaction with the DNA binding protein barrier-to-autointegration factor (BAF) .
hnRNPM, RNA recognition motif 3 (hnRNPM_RRM3)
Type: Domain

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

Heterogeneous nuclear ribonucleoproteins (hnRNPs) bind directly to nascent RNA polymerase II transcripts and play an important role in both transcript-specific packaging and alternative splicing of pre-mRNAs . hnRNP M proteins are an abundant group of hnRNPs that have been shown to bind avidly to poly(G) and poly(U) RNA homopolymers .
hnRNP M family members are able to induce exon skipping and promote exon inclusion, suggesting that the proteins may broadly contribute to the fidelity of splice site recognition and alternative splicing regulation .
RNA-binding protein 5, RNA recognition motif 1 (RBM5_RRM1)
Type: Domain

This entry represents the RNA recognition motif 1 (RRM1) of RNA-binding protein 5.

RNA-binding protein 5 (RBM5), also known as LUCA15, is a component of complexes involved in 3' splice site recognition and regulates alternative splicing of apoptosis-related genes, including the Fas receptor, c-FLIP and caspase 2 . In the case of FAS, it promotes exclusion of exon 6 thereby producing a soluble form of FAS that inhibits apoptosis . In the case of CASP2/caspase-2, it promotes exclusion of exon 9 thereby producing a catalytically active form of CASP2/Caspase-2 that induces apoptosis .
RNA-binding protein 10, RNA recognition motif 2 (RBM10_RRM2)
Type: Domain

This entry represents the RNA recognition motif 2 (RRM2) of RNA-binding protein 10.

RBM10, also known as S1-1, is a nuclear RNA-binding protein with domains characteristic of RNA processing proteins. Similar to RBM5, it promotes exon skipping of Fas pre-mRNA as well as selection of an internal 5'-splice site in Bcl-x pre-mRNA . It preferentially binds to G- and U-rich RNA sequences .
RNA-binding protein 5, RNA recognition motif 2 (RBM5_RRM2)
Type: Domain

This entry represents the RNA recognition motif 2 (RRM2) of RNA-binding protein 5.

RNA-binding protein 5 (RBM5), also known as LUCA15, is a component of complexes involved in 3' splice site recognition and regulates alternative splicing of apoptosis-related genes, including the Fas receptor, c-FLIP and caspase 2 . In the case of FAS, it promotes exclusion of exon 6 thereby producing a soluble form of FAS that inhibits apoptosis . In the case of CASP2/caspase-2, it promotes exclusion of exon 9 thereby producing a catalytically active form of CASP2/Caspase-2 that induces apoptosis .
SRSF9, RNA recognition motif 2 (SRSF9_RRM2)
Type: Domain

This entry represents the RNA recognition motif 2 (RRM2) of SRSF9 (also known as SRp30c), an essential splicing regulatory serine/arginine (SR) protein that has been implicated in the activity of many elements that control splice site selection . SRSF9 can also interact with other proteins implicated in alternative splicing, such as YB-1 . It represses the splicing of Tau exon 10 . SRSF9 contains two N-terminal RNA recognition motifs (RRMs), followed by an unusually short C-terminal RS domains rich in serine-arginine dipeptides.
HuR, RNA recognition motif 2 (HuR_RRM2)
Type: Domain

This entry represents the RNA recognition motif 2 (RRM2) of HuR, also known as ELAV-like protein 1 (ELAV-1), the ubiquitously expressed Hu family member . HuR binds to AU-rich RNA element (ARE) in target mRNAs and stabilizes them against degradation. It also regulates the nuclear import of proteins . It has a variety of biological functions mostly related to the regulation of cellular response to DNA damage and other types of stress. HuR has an anti-apoptotic function during early cell stress response . HuR may be important in muscle differentiation, adipogenesis, suppression of inflammatory response and modulation of gene expression in response to chronic ethanol exposure and amino acid starvation .

Like other Hu proteins, HuR contains three RNA recognition motifs (RRMs). RRM1 and RRM2 may cooperate in binding to an AU-rich RNA element (ARE). RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions .
Ankyrin repeat and LEM domain-containing protein 1 (ANKLE1)
Type: Family

ANKLE1 is a LEM protein with a GIY-YIG-type endonuclease activity and unknown function . Although most characterised LEM proteins are components of the inner nuclear membrane, ectopic Ankle1 shuttles between cytoplasm and nucleus. In mammals, ANKLE1 is predominantly expressed in hematopoietic tissues.
HuB, RNA recognition motif 2 (HuB_RRM2)
Type: Domain

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

HuB (also known as ELAV-like protein 2 or Hel-N1) is one of the neuronal members of the Hu family . The neuronal Hu proteins play important roles in neuronal differentiation, plasticity and memory. HuB is also expressed in gonads. It is up-regulated during neuronal differentiation of embryonic carcinoma P19 cells . Like other Hu proteins, HuB contains three RNA recognition motifs (RRMs). RRM1 and RRM2 may cooperate in binding to an AU-rich RNA element (ARE). RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions .