XAB2 (XPA binding protein 2)

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Gene miRNA Gene ontology Other IDs Protein Pathways Associated diseases Related genes Diseases linked via similar genes

Gene

• Entrez ID: 56949
• Gene name: XPA binding protein 2
• Gene symbol: XAB2
• Synonyms (NCBI Gene): HCNP, HCRN, NTC90, SYF1
• Chromosome: 19
• Chromosome location: 19p13.2

miRNA 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

Gene ontology (GO) 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

Other IDs

• MIM: 610850
• HGNC: 14089
• e!Ensembl: ENSG00000076924

Protein

• UniProt ID: 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

Pathways

KEGG Pathway	Reactome Pathway
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

Associated diseases

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)

Unknown / Other Associations
Phenotype Name	Clinical Significance	Source	Reference	Evidence Score
PERIPHERAL ARTERIAL DISEASE	—	GWAS catalog	27082954	★★☆☆☆ Found in Text Mining + Unknown/Other Associations

Associations from Text Mining Show/Hide Text Mining Associations (15)
Disease Name	Disease (Merged)	Source	PMID	Relationship Type	Evidence Score
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

Related Genes

Sort by: Blended Diseases Pathways Evidence source

ISY1-RAB43 6 shared pathwaysSpliceosome, 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 Related via 6 shared pathways including Spliceosome, Formation of TC-NER Pre-Incision Complex. PPIE 6 shared pathwaysSpliceosome, 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 Related via 6 shared pathways including Spliceosome, Formation of TC-NER Pre-Incision Complex. ISY1 6 shared pathwaysSpliceosome, 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 Related via 6 shared pathways including Spliceosome, Formation of TC-NER Pre-Incision Complex. AQR 6 shared pathwaysSpliceosome, 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 Related via 6 shared pathways including Spliceosome, Formation of TC-NER Pre-Incision Complex. PRPF19 6 shared pathwaysSpliceosome, 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 Related via 6 shared pathways including Spliceosome, Formation of TC-NER Pre-Incision Complex.

Related Gene	Shared Diseases	Shared Disease Names	Shared Pathways	Shared Pathway Names	Shared Evidence Sources	Shared Evidence Names
ISY1-RAB43	0	[]	6	["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"]	0	[]
PPIE	0	[]	6	["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"]	0	[]
ISY1	0	[]	6	["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"]	0	[]
AQR	0	[]	6	["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"]	0	[]
PRPF19	0	[]	6	["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"]	0	[]

Diseases Linked via Similar Genes

Non-immune hydrops fetalis Linked via 1 of 5 related genesPRPF19 Stomach neoplasms Linked via 1 of 5 related genesPRPF19

Disease	Linked Via (Gene Count)	Linked Via (Gene Names)
Non-immune hydrops fetalis	1	["PRPF19"]
Stomach neoplasms	1	["PRPF19"]