SII-SWORD/CoKE huggingface dataset:
Far upstream element-binding protein 2, first type I K homology domain (KH-I_FUBP2_rpt1)
Type: Domain

This entry represents the first type I KH domain of FUBP2.

FUBP2, also called FUSE-binding protein 2, or KH type-splicing regulatory protein (KSRP), is a single-strand nucleic acid binding protein implicated in a variety of cellular processes, including splicing in the nucleus, mRNA decay, maturation of miRNA, and transcriptional control of proto-oncogenes such as c-myc. It regulates the stability and/or translatability of many mRNA species, encoding immune-relevant proteins, either by binding to AU-rich elements (AREs) of mRNA 3'UTR or by facilitating miRNA biogenesis to target mRNA . FUBP2 contains four K-homology (KH) RNA-binding domains .
Mask-like, type I K homology (KH-I_MASK)
Type: Domain

This entry represents the type I KH domain of Mask and similar proteins mainly found in arthropods and nematodes.

Mask, also called multiple ankyrin repeat single KH domain-containing protein, is a large ankyrin repeat and KH domain-containing protein involved in Drosophila receptor tyrosine kinase signalling. It acts as a mediator of receptor tyrosine kinase (RTK) signalling and may act either downstream of MAPK or transduce signalling through a parallel branch of the RTK pathway. Mask is required for the development and organisation of indirect flight muscle sarcomeres by regulating the formation of M line and H zone and the correct assembly of thick and thin filaments in the sarcomere .
Ankyrin repeat and KH domain-containing protein 1, type I K homology domain (KH-I_ANKHD1)
Type: Domain

This entry represents the type I KH domain of ANKHD1 and similar animal proteins.

ANKHD1, also called HIV-1 Vpr-binding ankyrin repeat protein, or multiple ankyrin repeats single KH domain, or Hmask, is highly expressed in various cancer tissues and is involved in cancer progression, including proliferation and invasion . It acts as a scaffolding protein that may be associated with the abnormal phenotype of leukaemia cells. It may play a role in multiple myeloma cell proliferation and cell cycle progression by regulating expression of p21 . ANKHD1 is a component of Hippo signalling pathway. It functions as a positive regulator of YAP1 and promotes cell growth and cell cycle progression through Cyclin A upregulation in prostate cancer cells .
Ankyrin repeat domain-containing protein 17, type I K homology domain (KH-I_ANKRD17)
Type: Domain

This entry represents the type I K homology (KH) RNA-binding domain found at the C-terminal of ANKRD17 and similar proteins from animals. They contain ankyrin repeats at the N-terminal.

ANKRD17, also called ankyrin repeat protein 17, or gene trap ankyrin repeat protein (GTAR), or serologically defined breast cancer antigen NY-BR-16, is a ubiquitously expressed ankyrin factor essential for the vascular integrity during embryogenesis. It may be directly involved in the DNA replication process and play pivotal roles in cell cycle and DNA regulation . It is also involved in innate immune defence against bacteria and viruses .
Tudor domain-containing protein 1, first Tudor domain (Tudor_TDRD1_rpt1)
Type: Domain

This entry represents the first Tudor domain of TDRD1 and similar proteins found in vertebrates. The Tudor domain binds to proteins with dimethylated arginine or lysine residues, and may also bind methylated histone tails to facilitate protein-protein interactions.

TDRD1, also called cancer/testis antigen 41.1 (CT41.1), plays a central role during spermatogenesis by participating in the repression transposable elements and preventing their mobilization, which is essential for germline integrity . It acts via the piRNA metabolic process, which mediates the repression of transposable elements during meiosis by forming complexes composed of piRNAs and Piwi proteins, and governs the methylation and subsequent repression of transposons . TDRD1 might play an important role in human prostate cancer development and, therefore, it has been suggested as a prostate cancer biomarker. As a cancer/testis antigen, TDRD1 might have long-term potential to be a therapeutic target for prostate cancer immunotherapy . TDRD1 contains four Tudor domains.
Tudor domain-containing protein 1, second Tudor domain (Tudor_TDRD1_rpt2)
Type: Domain

This entry represents the second Tudor domain of TDRD1 and similar proteins found in vertebrates. The Tudor domain binds to proteins with dimethylated arginine or lysine residues, and may also bind methylated histone tails to facilitate protein-protein interactions.

TDRD1, also called cancer/testis antigen 41.1 (CT41.1), plays a central role during spermatogenesis by participating in the repression transposable elements and preventing their mobilization, which is essential for germline integrity . It acts via the piRNA metabolic process, which mediates the repression of transposable elements during meiosis by forming complexes composed of piRNAs and Piwi proteins, and governs the methylation and subsequent repression of transposons . TDRD1 might play an important role in human prostate cancer development and, therefore, it has been suggested as a prostate cancer biomarker. As a cancer/testis antigen, TDRD1 might have long-term potential to be a therapeutic target for prostate cancer immunotherapy . TDRD1 contains four Tudor domains.
Tudor domain-containing protein 1, third Tudor domain (Tudor_TDRD1_rpt3)
Type: Domain

This entry represents the third Tudor domain of TDRD1 and similar proteins found in vertebrates. The Tudor domain binds to proteins with dimethylated arginine or lysine residues, and may also bind methylated histone tails to facilitate protein-protein interactions.

TDRD1, also called cancer/testis antigen 41.1 (CT41.1), plays a central role during spermatogenesis by participating in the repression transposable elements and preventing their mobilization, which is essential for germline integrity . It acts via the piRNA metabolic process, which mediates the repression of transposable elements during meiosis by forming complexes composed of piRNAs and Piwi proteins, and governs the methylation and subsequent repression of transposons . TDRD1 might play an important role in human prostate cancer development and, therefore, it has been suggested as a prostate cancer biomarker. As a cancer/testis antigen, TDRD1 might have long-term potential to be a therapeutic target for prostate cancer immunotherapy . TDRD1 contains four Tudor domains.
Tudor domain-containing protein 3, Tudor domain (Tudor_TDRD3)
Type: Domain

This entry represents the Tudor domain of TDRD3 and similar proteins from animals.

TDRD3 is a scaffolding protein that specifically recognises and binds dimethylarginine-containing proteins . In the nucleus, it acts as a coactivator; it recognizes and binds asymmetric dimethylation on the core histone tails associated with transcriptional activation (H3R17me2a and H4R3me2a) and recruits proteins at these arginine-methylated loci. In the cytoplasm, it may play a role in the assembly and/or disassembly of mRNA stress granules and in the regulation of translation of target mRNAs by binding Arg/Gly-rich motifs (GAR) in dimethylarginine-containing proteins

]. TDRD3 can interact with methylated RNA-binding proteins, such as fragile X messenger ribonucleoprotein 1 (FMRP) and DEAD/H box-3 (also known as DDX3X/Y, DBX/Y, HLP2 and DDX14) which is implicated in human genetic diseases . At this point, TDRD3 may play a central role in RNA processing regulatory pathways involving arginine methylation. TDRD3 contains a Tudor domain, a DUF/OB-fold motif and a ubiquitin-associated (UBA) domain .
Tudor domain-containing protein 2-like, tudor domain (TDRD2-like_tudor)
Type: Domain

This entry represents the Tudor domain of TDRD2/PAPI, which binds to proteins with dimethylated arginine or lysine residues, and may also bind methylated histone tails to facilitate protein-protein interactions.

TDRD2, also called Tudor and KH domain-containing protein (TDRKH), is a mitochondria-anchored RNA-binding protein that is required for spermatogenesis and participates in the primary piwi-interacting RNA (piRNA) biogenesis pathway. It specifically recruits MIWI, but not MILI, to engage the piRNA pathway . It is required during spermatogenesis to repress transposable elements and prevent their mobilization, which is essential for germline integrity . This entry also includes the TDRD2 homologue from Drosophila melanogaster (dTDRKH), which is also called partner of PIWIs protein, or PAPI, and is involved in Zucchini-mediated piRNA 3'-end maturation . These proteins contain two KH domains and one Tudor domain .
Tudor and KH domain-containing protein, second type I K homology domain (KH-I_TDRKH_rpt2)
Type: Domain

KH domains are involved in binding to RNA or single-strand DNA. This entry represents the second KH RNA-binding domain of TDRD2 and similar proteins from chordates.

TDRD2, also called Tudor and KH domain-containing protein (TDRKH), is a mitochondria-anchored RNA-binding protein that is required for spermatogenesis and participates in the primary piwi-interacting RNA (piRNA) biogenesis pathway. It specifically recruits MIWI, but not MILI, to engage the piRNA pathway . It is required during spermatogenesis to repress transposable elements and prevent their mobilization, which is essential for germline integrity . These proteins contain two KH domains and one Tudor domain .
Tudor and KH domain-containing protein, first type I K homology domain (KH-I_TDRKH_rpt1)
Type: Domain

KH domains are involved in binding to RNA or single-strand DNA. This entry represents the first KH RNA-binding domain of TDRD2 and similar proteins from chordates.

TDRD2, also called Tudor and KH domain-containing protein (TDRKH), is a mitochondria-anchored RNA-binding protein that is required for spermatogenesis and participates in the primary piwi-interacting RNA (piRNA) biogenesis pathway. It specifically recruits MIWI, but not MILI, to engage the piRNA pathway . It is required during spermatogenesis to repress transposable elements and prevent their mobilization, which is essential for germline integrity . These proteins contain two KH domains and one Tudor domain .
Tudor domain-containing protein 8, Tudor domain (Tudor_TDRD8)
Type: Domain

This entry represents the Tudor domain of TDRD8 and similar proteins mainly found in chordates, which binds to proteins with dimethylated arginine or lysine residues, and may also bind methylated histone tails to facilitate protein-protein interactions.

TDRD8, also called serine/threonine-protein kinase (

) 31 (STK31), serine/threonine-protein kinase NYD-SPK, or Sugen kinase 396 (SgK396), is a germ cell-specific factor expressed in embryonic gonocytes of both sexes, and in postnatal spermatocytes and round spermatids in males . It acts as a cell-cycle regulated protein that contributes to the tumorigenicity of epithelial cancer cells . TDRD8 contains a Tudor domain and a serine/threonine kinase domain.
Tudor domain-containing protein 9, Tudor domain (Tudor_TDRD9)
Type: Domain

This entry represents the Tudor domain of TDRD9 ans similar proteins from chordates.

TDRD9 is an ATP-dependent DEAD-like RNA helicase required during spermatogenesis. It is involved in the biosynthesis of PIWI-interacting RNAs (piRNAs). A recessive deleterious mutation mutation in TDRD9 causes non-obstructive azoospermia in infertile men . TDRD9 contains an N-terminal HrpA-like RNA helicase module and a Tudor domain.
Tudor domain-containing protein 10, RNA recognition motif (RRM_TDRD10)
Type: Domain

This entry represents the RNA recognition motif of TDRD10 and similar proteins from chordates.

TDRD10 is widely expressed and localized both to the nucleus and cytoplasm and may play general roles like regulation of RNA metabolism. It contains a Tudor domain and a RNA recognition motif (RRM) .
Tudor domain-containing protein 11, Tudor domain (Tudor_TDRD11)
Type: Domain

This entry represents the Tudor domain of TDRD11 and similar proteins from animals.

TDRD11, also called Staphylococcal nuclease domain-containing protein 1 (SND1), 100 kDa coactivator, EBNA2 coactivator p100, or p100 co-activator, is a multifunctional protein that is reportedly associated with different types of RNA molecules, including mRNA, miRNA, pre-miRNA, and dsRNA . It has been implicated in a number of biological processes in eukaryotic cells, including the cell cycle, DNA damage repair, proliferation, and apoptosis. TDRD11 is overexpressed in multiple cancers and functions as an oncogene . It contains multiple Staphylococcal nuclease (SN) domains and a C-terminal Tudor domain.
Bifunctional UDP-N-acetylglucosamine transferase and deubiquitinase ALG13, OTU domain (OTU_ALG13)
Type: Domain

This entry represents the OTU domain of the bifunctional UDP-N-acetylglucosamine transferase and deubiquitinase ALG13 and similar sequences from vertebrates.

Bifunctional UDP-N-acetylglucosamine transferase and deubiquitinase ALG13 is also called asparagine-linked glycosylation 13 homologue, glycosyltransferase 28 domain-containing protein 1 (GLT28D1), or UDP-N-acetylglucosamine transferase subunit ALG13 homologue. It displays both glycosyltransferase (

) and deubiquitinase (DUB)/ubiquitin thioesterase (

) activities. With ALG14, it forms a UDP-N-acetylglucosamine transferase that catalyses the second step of eukaryotic N-linked glycosylation in the endoplasmic reticulum . ALG13 variants cause a form of early infantile epileptic encephalopathy known as EIEE36 refractory seizures , neurodevelopmental impairment, and poor prognosis . Given the essential role of ALG13 in glycosylation, it is also considered a congenital disorder of glycosylation (CDG). ALG13 belongs to the OTU family of cysteine proteases that use a conserved cysteine, histidine, and an aspartate, as the catalytic triad.
Protein fork head-like, forkhead domain (FH-like_dFKH)
Type: Domain

This entry represents the forkhead (FH) domain of FKH from Drosophila melanogaster and similar proteins predominantly found in invertebrates, including the homologue Silk gland factor 1 (SGF-1) from the silk moth Bombyx mori . The FH domain is a winged helix DNA-binding domain.

Drosophila melanogaster protein fork head (dFKH) promotes terminal as opposed to segmental development. In the absence of dFKH, this developmental switch does not occur . FOX transcription factors recognize the core sequence 5'-(A/C)AA(C/T)A-3'.
Forkhead box protein B1/B2, forkhead domain (FOXB1_B2_FH)
Type: Domain

This entry represents the forkhead (FH) domain of human FOXB1/B2 and similar sequences predominantly found in vertebrates. The FH domain is a winged helix DNA-binding domain.

Forkhead box protein B1 (FOXB1) is a transcription factor expressed by neural progenitor cells in specific regions of the embryonic neuroepithelium. It is essential for the mammillary nuclei maintenance. FOXB1 negatively regulates the proliferation of oligodendrocyte progenitors and promotes oligodendrocyte maturation .

Forkhead box protein B2 (FOXB2) may act as a transcription factor. It may also act as a tumour suppressor. It has been found to inhibit the malignant characteristics of the pancreatic cancer cell line Panc-1 in vitro .
Tudor domain-containing protein 12, first Tudor domain (Tudor_TDRD12_rpt1)
Type: Domain

This entry represents the first Tudor domain of Tudor domain-containing protein 12 and similar proteins from chordates.

Tudor domain-containing protein 12 (TDRD12), also called ES cell-associated transcript 8 protein (ECAT8), is a putative ATP-dependent DEAD-like RNA helicase that is essential for germ cell development and maintenance. It acts as a unique piRNA biogenesis factor essential for secondary PIWI interacting RNA (piRNA) biogenesis . TDRD12 contains two Tudor domains, one at the N-terminal and the other at the C-terminal end.
Forkhead box protein C1/C2-like, forkhead domain (FOXC1/C2-like_FH)
Type: Domain

This entry represents the forkhead (FH) domain of human FOXC1/C2 and similar sequences predominantly found in vertebrates. The FH domain is a winged helix DNA-binding domain.

Forkhead box protein C1 (FOXC1) is a DNA-binding transcriptional factor that plays a role in a broad range of cellular and developmental processes such as the development of the eyes, bones, cardiovascular system, kidneys, and skin . It plays a role in the gene regulatory network essential for epidermal keratinocyte terminal differentiation . FOX1 may function as a tumour suppressor. It is associated with Axenfeld-Rieger syndrome 3 . FOXC1 has been identified as a potential prognostic candidate and also a potential molecular therapeutic target, as elevated FOXC1 expression predicted poor overall survival in basal-like breast cancer (BLBC) .

Forkhead box protein C2 (FOXC2) is a transcriptional activator that might be involved in the formation of special mesenchymal tissues . It is associated with the rare disorder lymphedema-distichiasis syndrome .
Forkhead box protein D3, forkhead domain (FH_FOXD3)
Type: Domain

This entry represents the forkhead (FH) domain of human FOXD3 and similar sequences predominantly found in vertebrates. The FH domain is a winged helix DNA-binding domain .

Forkhead box protein D3 (FOXD3) acts as a transcriptional repressor that binds to the consensus sequence 5'-A[AT]]T[AG]]TTTGTTT-3'. It also acts as a transcriptional activator. It promotes development of neural crest cells from neural tube progenitors and restricts neural progenitor cells to the neural crest lineage while suppressing interneuron differentiation . FOXD3 is required for maintenance of pluripotent cells in the pre-implantation and peri-implantation stages of embryogenesis .
Forkhead box protein J2, forkhead domain (FH_FOXJ2)
Type: Domain

This entry represents the forkhead (FH) domain of human FOXJ2 and similar sequences from vertebrates. The FH domain is a winged helix DNA-binding domain.

Forkhead box protein J2 (FOXJ2) plays an important role in tumourigenesis, progression, and metastasis of certain cancers . It acts as a transcriptional activator that can bind to two different type of DNA binding sites . It is specifically expressed in meiotic spermatocytes in adult mouse testes and appears to promote meiotic progression during spermatogenesis . FOXJ2 may play a role in maintenance and survival of developing and adult neurons and it is important in inflammatory response .
Forkhead box protein K1, forkhead domain (FH_FOXK1)
Type: Domain

This entry represents the forkhead (FH) domain of human FOXK1 and similar sequences predominantly found in vertebrates. The FH domain is a winged helix DNA-binding domain.

Forkhead box protein K1 (FOXK1) is a transcriptional regulator involved in different processes such as glucose metabolism, aerobic glycolysis, muscle cell differentiation and autophagy . It recognizes the core sequence 5'-(A/C)AA(C/T)A-3' that can both act as a transcription activator or repressor, depending on the context . It acts as a transcriptional regulator that binds to the upstream enhancer region (CCAC box) of myoglobin genes and thus regulates the myogenic progenitor cell population . It positively regulates Wnt/beta-catenin signalling by translocating dishevelled (DVL) proteins into the nucleus . It also reduces virus replication, probably by binding the interferon stimulated response element (ISRE) to promote antiviral gene expression . In addition, FOXK1 plays important roles in multiple human cancers .
Ribonuclease Tudor 1/2, Tudor domain (Tudor_AtTudor1-like)
Type: Domain

The entry represents the Tudor domain found in plant ribonucleases, including Tudor1 (also called Tudor-SN protein 1) and Tudor2 (also called Tudor-SN protein 2 or 100 kDa coactivator-like protein) proteins from Arabidopsis thaliana. They are cytoprotective ribonucleases (RNases) required for resistance to abiotic stresses, acting as positive regulators of mRNA decapping during stress .
Protein vreteno, second Tudor domain (Tudor_vreteno-like_rpt2)
Type: Domain

This entry represents the second Tudor domain of Protein vreteno from Drosophila and similar sequences from insects.

Protein vreteno from Drosophila is a gonad-specific protein, essential for germline development to repress transposable elements and preventing their mobilization, which is essential for germline integrity. It acts via the piRNA metabolic process in both germline and somatic gonadal tissues by mediating the repression of transposable elements during meiosis . Vreteno contains two Tudor domains.
Forkhead box protein K2, forkhead domain (FH_FOXK2)
Type: Domain

This entry represents the forkhead (FH) domain of human FOXK2 and similar sequences predominantly found in vertebrates. The FH domain is a winged helix DNA-binding domain .

Forkhead box protein K2 (FOXK2) is a transcriptional regulator that recognises the core sequence 5'-TAAACA-3'. It binds to NFAT-like motifs (purine-rich) in the IL2 promoter . FOXK2 is required for cell proliferation and survival . It functions as a chromatin-targeting factor for BAP1 (BRCA1-associated protein 1) that recruits BAP1 via its FHA domain in a phosphorylation-dependent manner. BAP1 functions as a corepressor at FOXK2 target genes . FOXK2 is a key regulator of metabolic reprogramming towards aerobic glycolysis playing a role in gluconeogenesis during overnight fasting, when lactate from white adipose tissue and muscle is the main substrate . It also binds to the HIV-1 long terminal repeat . FOXK2 may be involved in both, positive and negative regulation of important viral and cellular promoter elements . In addition, FOXK2 plays a critical role in suppressing tumourigenesis .
Forkhead box protein K2, forkhead associated domain (FHA_FOXK2)
Type: Domain

This entry represents the forkhead associated (FHA) domain of human FOXK2 and similar sequences predominantly found in vertebrates. The FHA domain is a small phosphopeptide recognition module.

Forkhead box protein K2 (FOXK2) is a transcriptional regulator that recognises the core sequence 5'-TAAACA-3'. It binds to NFAT-like motifs (purine-rich) in the IL2 promoter . FOXK2 is required for cell proliferation and survival . It functions as a chromatin-targeting factor for BAP1 (BRCA1-associated protein 1) that recruits BAP1 via its FHA domain in a phosphorylation-dependent manner. BAP1 functions as a corepressor at FOXK2 target genes . FOXK2 is a key regulator of metabolic reprogramming towards aerobic glycolysis playing a role in gluconeogenesis during overnight fasting, when lactate from white adipose tissue and muscle is the main substrate . It also binds to the HIV-1 long terminal repeat . FOXK2 may be involved in both, positive and negative regulation of important viral and cellular promoter elements . In addition, FOXK2 plays a critical role in suppressing tumourigenesis .
PHD finger protein 1, Tudor domain (Tudor_PHF1)
Type: Domain

This entry represents the Tudor domain of PHF1, which selectively binds to histone H3K36me3 .

PHF1, also called Polycomb-like protein 1 (PCL1), together with JARID2 and AEBP2, associates with the Polycomb repressive complex 2 (PRC2), which is the major H3K27 methyltransferase that regulates pluripotency, differentiation, and tumourigenesis, through catalysis of histone H3 lysine 27 trimethylation (H3K27me3) on chromatin . PHF1 is essential in epigenetic regulation and genome maintenance . It acts as a dual reader of lysine trimethylation at lysine 36 of histone H3 and lysine 27 of histone variant H3t . Moreover, PHF1 is required for efficient H3-K27 trimethylation (H3K27me3) and Hox gene silencing . It can mediate deposition of the repressive H3K27me3 mark and acts as a cofactor in early DNA-damage response.