XAB2 XPA binding protein 2 [Homo sapiens (human)] - Gene

Summary

Official Symbol: XAB2provided by HGNC
Official Full Name: XPA binding protein 2provided by HGNC
Primary source: HGNC:HGNC:14089
See related: Ensembl:ENSG00000076924 MIM:610850; AllianceGenome:HGNC:14089
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as: HCNP; HCRN; SYF1; NTC90
Summary: Involved in mRNA splicing, via spliceosome; transcription, DNA-templated; and transcription-coupled nucleotide-excision repair. Located in nucleoplasm. Part of U2-type catalytic step 2 spliceosome. [provided by Alliance of Genome Resources, Apr 2022]
Expression: Ubiquitous expression in testis (RPKM 21.5), ovary (RPKM 19.8) and 25 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 19p13.2

Exon count:: 19

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	19	NC_000019.10 (7619525..7629545, complement)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	19	NC_060943.1 (7620408..7630428, complement)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	19	NC_000019.9 (7684411..7694431, complement)

Chromosome 19 - NC_000019.10 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: HPA RNA-seq normal tissues
Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
BioProject: PRJEB4337
Publication: PMID 24309898
Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

XAB2 promotes Ku eviction from single-ended DNA double-strand breaks independently of the ATM kinase.
Title: XAB2 promotes Ku eviction from single-ended DNA double-strand breaks independently of the ATM kinase.
XAB2 TagSNP Is Associated with the Risk of Gastric Cancer in Chinese Population: A Case-Control Study.
Title: XAB2 TagSNP Is Associated with the Risk of Gastric Cancer in Chinese Population: A Case-Control Study.
Data suggest that XPA-binding protein 2 (XAB2) serves as a guardian of RNA polymerase II subunit A (POLR2A) expression to ensure global gene expression and antagonize cell senescence.
Title: XAB2 depletion induces intron retention in POLR2A to impair global transcription and promote cellular senescence.
these results support a novel function of XAB2 in mitotic cell cycle regulation, which is partially mediated by transcription regulation on CENPE.
Title: XAB2 functions in mitotic cell cycle progression via transcriptional regulation of CENPE.
we suggest that the XAB2 complex mediates DNA damage response events important for the end resection step of homologous recombination , and speculate that its adjacent-localization relative to double-strand break marked by gH2AX is important for this function
Title: Tetratricopeptide repeat factor XAB2 mediates the end resection step of homologous recombination.
Study identifies XAB2 tagSNPs (rs794078 and rs4134816) significantly associated with the risk of non-small cell lung cancer (NSCLC) in Chinese population, which supports XAB2 playing significant role in the development of NSCLC.
Title: XAB2 tagSNPs contribute to non-small cell lung cancer susceptibility in Chinese population.
Results of protein-protein interaction between human Dbr1 and factors found in the Intron Large complex identify Xab2 and a novel protein CWF19L1 as specific interactors of DBR1.
Title: Identification of the specific interactors of the human lariat RNA debranching enzyme 1 protein.
Hematopoietic myeloid cell differentiation diminishes nucleotide excision repair and XAB2 expression.
Title: Hematopoietic myeloid cell differentiation diminishes nucleotide excision repair.
Observational study of gene-disease association. (HuGE Navigator)
Title: Variation within DNA repair pathway genes and risk of multiple sclerosis.
XAB2 complex is a multifunctional factor involved in pre-mRNA splicing, transcription, and transcription-coupled DNA repair.
Title: Isolation of XAB2 complex involved in pre-mRNA splicing, transcription, and transcription-coupled repair.

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Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

HIV-1 interactions

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Replication interactions

Interaction	Pubs
Knockdown of XPA binding protein 2 (XAB2) by siRNA inhibits the early stages of HIV-1 replication in 293T cells infected with VSV-G pseudotyped HIV-1	PubMed

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Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
involved_in DNA-templated transcription	IDA Inferred from Direct Assay more info	PubMed
involved_in blastocyst development	IEA Inferred from Electronic Annotation more info
involved_in generation of catalytic spliceosome for first transesterification step	IBA Inferred from Biological aspect of Ancestor more info
involved_in mRNA splicing, via spliceosome	IBA Inferred from Biological aspect of Ancestor more info
involved_in mRNA splicing, via spliceosome	IC Inferred by Curator more info	PubMed
involved_in mRNA splicing, via spliceosome	IDA Inferred from Direct Assay more info	PubMed
involved_in transcription-coupled nucleotide-excision repair	IDA Inferred from Direct Assay more info	PubMed

Component	Evidence Code	Pubs
part_of Prp19 complex	IBA Inferred from Biological aspect of Ancestor more info
part_of U2-type catalytic step 2 spliceosome	IBA Inferred from Biological aspect of Ancestor more info
part_of U2-type catalytic step 2 spliceosome	IDA Inferred from Direct Assay more info	PubMed
part_of catalytic step 2 spliceosome	IDA Inferred from Direct Assay more info	PubMed
located_in intracellular membrane-bounded organelle	IDA Inferred from Direct Assay more info
located_in membrane	HDA more info	PubMed
located_in nucleoplasm	IDA Inferred from Direct Assay more info
located_in nucleoplasm	TAS Traceable Author Statement more info
located_in nucleus	IC Inferred by Curator more info	PubMed
located_in nucleus	IDA Inferred from Direct Assay more info	PubMed
part_of post-mRNA release spliceosomal complex	IBA Inferred from Biological aspect of Ancestor more info

General protein information

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Preferred Names: pre-mRNA-splicing factor SYF1

Names: SYF1 homolog, RNA splicing factor; SYF1 pre-mRNA-splicing factor; crn-related protein kim1

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

NM_020196.3 → NP_064581.2 pre-mRNA-splicing factor SYF1

See identical proteins and their annotated locations for NP_064581.2

Status: VALIDATED

Source sequence(s)

AF226051, BC007208

Consensus CDS

CCDS32892.1

UniProtKB/Swiss-Prot

Q8TET6, Q96HB0, Q96IW0, Q9HCS7, Q9NRG6, Q9ULP3

UniProtKB/TrEMBL

Q71SV8

Related

ENSP00000351137.3, ENST00000358368.5

Conserved Domains (3) summary

COG0457
Location:272 → 549

TPR; Tetratricopeptide (TPR) repeat [General function prediction only]

sd00006
Location:389 → 424

TPR; TPR repeat [structural motif]

pfam13424
Location:396 → 462

TPR_12; Tetratricopeptide repeat