Gene Details | GeDiPNet - Complete Gene Info, Disease Associations & Pathways

Gene Gene information from NCBI Gene database. Gene miRNA Gene ontology Other IDs Protein Pathways Associated diseases
Entrez ID	56949
Gene name	XPA binding protein 2
Gene symbol	XAB2
Synonyms (NCBI Gene)	HCNPHCRNNTC90SYF1
Chromosome	19
Chromosome location	19p13.2

Show/Hide all (35)

miRTarBase ID	miRNA	Experiments	Reference
MIRT439281	hsa-miR-544a	HITS-CLIP	24374217
MIRT439281	hsa-miR-544a	HITS-CLIP	24374217
MIRT1495085	hsa-miR-2110	CLIP-seq
MIRT1495086	hsa-miR-3150a-3p	CLIP-seq
MIRT1495087	hsa-miR-3175	CLIP-seq
MIRT1495088	hsa-miR-4728-5p	CLIP-seq
MIRT1495089	hsa-miR-4742-3p	CLIP-seq
MIRT1495090	hsa-miR-939	CLIP-seq
MIRT1495085	hsa-miR-2110	CLIP-seq
MIRT1495086	hsa-miR-3150a-3p	CLIP-seq
MIRT1495087	hsa-miR-3175	CLIP-seq
MIRT2149144	hsa-miR-4651	CLIP-seq
MIRT1495088	hsa-miR-4728-5p	CLIP-seq
MIRT1495089	hsa-miR-4742-3p	CLIP-seq
MIRT2149145	hsa-miR-491-5p	CLIP-seq
MIRT2149146	hsa-miR-608	CLIP-seq
MIRT1495090	hsa-miR-939	CLIP-seq
MIRT1495085	hsa-miR-2110	CLIP-seq
MIRT1495086	hsa-miR-3150a-3p	CLIP-seq
MIRT1495087	hsa-miR-3175	CLIP-seq
MIRT2149144	hsa-miR-4651	CLIP-seq
MIRT1495088	hsa-miR-4728-5p	CLIP-seq
MIRT1495089	hsa-miR-4742-3p	CLIP-seq
MIRT2149145	hsa-miR-491-5p	CLIP-seq
MIRT2149146	hsa-miR-608	CLIP-seq
MIRT1495090	hsa-miR-939	CLIP-seq
MIRT1495085	hsa-miR-2110	CLIP-seq
MIRT1495086	hsa-miR-3150a-3p	CLIP-seq
MIRT1495087	hsa-miR-3175	CLIP-seq
MIRT2149144	hsa-miR-4651	CLIP-seq
MIRT1495088	hsa-miR-4728-5p	CLIP-seq
MIRT1495089	hsa-miR-4742-3p	CLIP-seq
MIRT2149145	hsa-miR-491-5p	CLIP-seq
MIRT2149146	hsa-miR-608	CLIP-seq
MIRT1495090	hsa-miR-939	CLIP-seq

Show/Hide all (27)

GO ID	Ontology	Definition	Evidence	Reference
GO:0000349	Process	Generation of catalytic spliceosome for first transesterification step	IBA
GO:0000398	Process	MRNA splicing, via spliceosome	IBA
GO:0000398	Process	MRNA splicing, via spliceosome	IC	11991638
GO:0000398	Process	MRNA splicing, via spliceosome	IDA	28076346
GO:0000398	Process	MRNA splicing, via spliceosome	IEA
GO:0000974	Component	Prp19 complex	IBA
GO:0001824	Process	Blastocyst development	IEA
GO:0005515	Function	Protein binding	IPI	10944529, 16189514, 22365833, 24981860, 25416956, 25599396, 28502770, 28514442, 32296183, 32814053, 33961781
GO:0005634	Component	Nucleus	IC	10944529
GO:0005634	Component	Nucleus	IDA	28076346
GO:0005634	Component	Nucleus	IEA
GO:0005654	Component	Nucleoplasm	IDA
GO:0005654	Component	Nucleoplasm	TAS
GO:0005681	Component	Spliceosomal complex	IEA
GO:0006281	Process	DNA repair	IEA
GO:0006283	Process	Transcription-coupled nucleotide-excision repair	IDA	10944529
GO:0006351	Process	DNA-templated transcription	IDA	10944529
GO:0006396	Process	RNA processing	IEA
GO:0006397	Process	MRNA processing	IEA
GO:0006974	Process	DNA damage response	IEA
GO:0008380	Process	RNA splicing	IEA
GO:0016020	Component	Membrane	HDA	19946888
GO:0021987	Process	Cerebral cortex development	IEA
GO:0071007	Component	U2-type catalytic step 2 spliceosome	IBA
GO:0071007	Component	U2-type catalytic step 2 spliceosome	IDA	28076346
GO:0071013	Component	Catalytic step 2 spliceosome	IDA	11991638
GO:0071014	Component	Post-mRNA release spliceosomal complex	IBA

MIM	HGNC	e!Ensembl
610850	14089	ENSG00000076924

Q9HCS7

Protein name

Pre-mRNA-splicing factor SYF1 (Protein HCNP) (XPA-binding protein 2)

Protein function

Involved in pre-mRNA splicing as component of the spliceosome (PubMed:11991638, PubMed:28076346, PubMed:28502770). Involved in transcription-coupled repair (TCR), transcription and pre-mRNA splicing (PubMed:10944529, PubMed:17981804). {ECO:00002

PDB

5MQF , 5XJC , 5YZG , 5Z56 , 5Z57 , 6FF7 , 6ICZ , 6ID0 , 6ID1 , 6QDV , 7A5P , 7ABI , 7W59 , 7W5A , 7W5B , 8C6J , 8CH6 , 8I0P , 8I0R , 8I0S , 8I0T , 8I0U , 8I0V , 8I0W , 8RO2 , 9FMD

Family and domains

Pfam

Accession	ID	Position in sequence	Description	Type
PF13181	TPR_8	256 → 285	Tetratricopeptide repeat	Repeat
PF13181	TPR_8	395 → 428	Tetratricopeptide repeat	Repeat

Sequence

MVVMARLSRPERPDLVFEEEDLPYEEEIMRNQFSVKCWLRYIEFKQGAPKPRLNQLYERA
LKLLPCSYKLWYRYLKARRAQVKHRCVTDPAYEDVNNCHERAFVFMHKMPRLWLDYCQFL
MDQGRVTHTRRTFDRALRALPITQHSRIWPLYLRFLRSHPLPETAVRGYRRFLKLSPESA
EEYIEYLKSSDRLDEAAQRLATVVNDERFVSKAGKSNYQLWHELCDLISQNPDKVQSLNV
DAIIRGGLTRFTDQLGKLWCSLADYYIRSGHFEKARDVYEEAIRTVMTVRDFTQVFDSYA
QFEESMIAAKMETASELGREEEDDVDLELRLARFEQLISRRPLLLNSVLLRQNPHHVHEW
HKRVALHQGRPREIINTYTEAVQTVDPFKATGKPHTLWVAFAKFYEDNGQLDDARVILEK
ATKVNFKQVDDLASVWCQCGELELRHENYDEALRLLRKATALPARRAEYFDGSEPVQNRV
YKSLKVWSMLADLEESLGTFQSTKAVYDRILDLRIATPQIVINYAMFLEEHKYFEESFKA
YERGISLFKWPNVSDIWSTYLTKFIARYGGRKLERARDLFEQALDGCPPKYAKTLYLLYA
QLEEEWGLARHAMAVYERATRAVEPAQQYDMFNIYIKRAAEIYGVTHTRGIYQKAIEVLS
DEHAREMCLRFADMECKLGEIDRARAIYSFCSQICDPRTTGAFWQTWKDFEVRHGNEDTI
KEMLRIRRSVQATYNTQVNFMASQMLKVSGSATGTVSDLAPGQSGMDDMKLLEQRAEQLA
AEAERDQPLRAQSKILFVRSDASREELAELAQQVNPEEIQLGEDEDEDEMDLEPNEVRLE
QQSVPAAVFGSLKED

Sequence length

855

Interactions

View interactions

	KEGG		Reactome
	Spliceosome		Formation of TC-NER Pre-Incision Complex Transcription-Coupled Nucleotide Excision Repair (TC-NER) Dual incision in TC-NER Gap-filling DNA repair synthesis and ligation in TC-NER mRNA Splicing - Major Pathway

Evidence Score: ★☆☆☆☆ Gene-disease association found in Text Mining only ★★☆☆☆ Found in Text Mining and Unknown/Other Associations ★★★☆☆ Reported in Unknown/Other Associations across ≥2 Sources ★★★★☆ ClinVar: Pathogenic/Likely Pathogenic (<5 Variants) ★★★★★ ClinVar: Pathogenic/Likely Pathogenic (≥5 Variants)

Show/Hide Unknown Diseases (1)

Phenotype Name	Clinical Significance	Source	Evidence Score
Unknown / Other Associations ClinVar entries with uncertain/conflicting evidence, and associations from other databases (OMIM, Orphanet, GWAS, etc.) where the gene is not established as causal.
PERIPHERAL ARTERIAL DISEASE	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations

Show/Hide Text Mining Associations (15)

Disease Name	Disease (Merged)	Source	PMID	Relationship Type	Evidence Score
Associations from Text Mining Disease associations identified through text mining
Acute Promyelocytic Leukemia	Promyelocytic Leukemia	BEFREE	17283134, 25027282		★★★★★ ★☆☆☆☆ Found in Text Mining only
Chromosomal Instability	Chromosomal instability	Pubtator	34500463	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Cockayne Syndrome	Cockayne Syndrome	BEFREE	26228655		★★★★★ ★☆☆☆☆ Found in Text Mining only
Cockayne Syndrome	Cockayne syndrome	Pubtator	26228655	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Cockayne Syndrome, Type I	Cockayne Syndrome	BEFREE	17283134, 17981804		★★★★★ ★☆☆☆☆ Found in Text Mining only
Diabetes Gestational	Gestational diabetes	Pubtator	39777224	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Liver Diseases	Liver disease	Pubtator	40065360	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Malignant Neoplasms	Malignant Neoplasm	BEFREE	17283134		★★★★★ ★☆☆☆☆ Found in Text Mining only
Mosaic variegated aneuploidy syndrome	Mosaic variegated aneuploidy	Pubtator	27735937	Inhibit	★★★★★ ★☆☆☆☆ Found in Text Mining only
Neuroblastoma	Neuroblastoma	BEFREE	17283134		★★★★★ ★☆☆☆☆ Found in Text Mining only
Non-Small Cell Lung Carcinoma	Lung carcinoma	BEFREE	26228655		★★★★★ ★☆☆☆☆ Found in Text Mining only
Rhabdomyosarcoma	Rhabdomyosarcoma	BEFREE	17283134		★★★★★ ★☆☆☆☆ Found in Text Mining only
Stomach Neoplasms	Stomach neoplasms	Pubtator	33557438	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Uterine Cervical Dysplasia	Uterine disease	Pubtator	37932662	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Xeroderma pigmentosum, group A	Xeroderma Pigmentosum	BEFREE	17283134		★★★★★ ★☆☆☆☆ Found in Text Mining only

XAB2 (XPA binding protein 2)