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Aliases for XAB2 Gene

Aliases for XAB2 Gene

  • XPA Binding Protein 2 2 3 5
  • SYF1 Pre-MRNA-Splicing Factor 2 3
  • HCNP 3 4
  • SYF1 3 4
  • SYF1 Homolog, RNA Splicing Factor (S. Cerevisiae) 2
  • SYF1 Homolog, RNA Splicing Factor 3
  • Pre-MRNA-Splicing Factor SYF1 3
  • Crn-Related Protein Kim1 3
  • XPA-Binding Protein 2 4
  • Protein HCNP 4
  • KIAA1177 4
  • NTC90 3
  • HCRN 3

External Ids for XAB2 Gene

Previous GeneCards Identifiers for XAB2 Gene

  • GC00U913006
  • GC19M007590
  • GC19M007354
  • GC19M007684

Summaries for XAB2 Gene

GeneCards Summary for XAB2 Gene

XAB2 (XPA Binding Protein 2) is a Protein Coding gene. Diseases associated with XAB2 include Cockayne Syndrome. Among its related pathways are mRNA Splicing - Major Pathway and Transcription-Coupled Nucleotide Excision Repair (TC-NER).

UniProtKB/Swiss-Prot for XAB2 Gene

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

Gene Wiki entry for XAB2 Gene

Additional gene information for XAB2 Gene

No data available for Entrez Gene Summary , CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for XAB2 Gene

Genomics for XAB2 Gene

GeneHancer (GH) Regulatory Elements for XAB2 Gene

Promoters and enhancers for XAB2 Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH19J007628 Promoter/Enhancer 2 EPDnew Ensembl ENCODE 690.6 0.0 -22 2.7 PKNOX1 FOXA2 SMAD1 ARNT ARID4B SIN3A ZNF2 YY1 SLC30A9 POLR2B XAB2 PET100 ENSG00000268400 ELAVL1 HNRNPM TRIP10 ZNF557 ENSG00000269680 RETN PCP2
GH19J008361 Promoter/Enhancer 2.4 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 61.4 -733.8 -733844 3.6 FOXA2 PKNOX1 ARNT ZFP64 ARID4B SIN3A YY1 FOS DEK ZC3H11A ANGPTL4 HNRNPM ZNF317 XAB2 ZNF699 ZNF558 MAP2K7 ELAVL1 ZNF559 ZNF414
GH19J008388 Promoter/Enhancer 2.5 EPDnew Ensembl ENCODE dbSUPER 58.5 -763.3 -763279 10.3 MLX IRF4 YY1 ZNF213 E2F8 ZNF143 ZNF548 SP3 NFYC GLIS1 RAB11B HNRNPM ELAVL1 ZNF699 ZNF558 XAB2 ZNF317 MAP2K7 ZNF559 ENSG00000269300
GH19J007521 Promoter/Enhancer 2.6 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 51.6 +106.7 106708 2 MLX FEZF1 DMAP1 IRF4 YY1 ZNF213 ZNF143 ZNF548 SP3 NFYC MCOLN1 GC19M007510 HNRNPM ELAVL1 XAB2 ZNF557 MAP2K7 ZNF414 TIMM44 SNAPC2
GH19J008319 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE 55.4 -691.9 -691891 3.6 HDGF HNRNPUL1 PKNOX1 SMAD1 ZFP64 ARID4B SIN3A DMAP1 ZNF2 YY1 RPS28 GC19P008321 NDUFA7 ENSG00000167774 HNRNPM XAB2 ZNF317 ZNF699 ZNF558 MAP2K7
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around XAB2 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the XAB2 gene promoter:
  • Nkx2-5
  • SEF-1 (1)
  • GR-alpha
  • GR
  • Sp1
  • GCNF
  • STAT3
  • Lmo2
  • GCNF-1

Genomic Locations for XAB2 Gene

Genomic Locations for XAB2 Gene
chr19:7,619,525-7,629,565
(GRCh38/hg38)
Size:
10,041 bases
Orientation:
Minus strand
chr19:7,684,411-7,694,451
(GRCh37/hg19)
Size:
10,041 bases
Orientation:
Minus strand

Genomic View for XAB2 Gene

Genes around XAB2 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
XAB2 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for XAB2 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for XAB2 Gene

Proteins for XAB2 Gene

  • Protein details for XAB2 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9HCS7-SYF1_HUMAN
    Recommended name:
    Pre-mRNA-splicing factor SYF1
    Protein Accession:
    Q9HCS7
    Secondary Accessions:
    • Q8TET6
    • Q96HB0
    • Q96IW0
    • Q9NRG6
    • Q9ULP3

    Protein attributes for XAB2 Gene

    Size:
    855 amino acids
    Molecular mass:
    100010 Da
    Quaternary structure:
    • Associates with RNA polymerase II, the TCR-specific proteins CKN1/CSA and ERCC6/CSB, and XPA (PubMed:10944529). Identified in the spliceosome C complex (PubMed:11991638, PubMed:28502770, PubMed:28076346). Component of the XAB2 complex, a multimeric protein complex composed of XAB2, PRPF19, AQR, ZNF830, ISY1, and PPIE (PubMed:17981804). Identified in a pentameric intron-binding (IB) complex composed of AQR, XAB2, ISY1, ZNF830 and PPIE that is incorporated into the spliceosome as a preassembled complex (PubMed:25599396). The IB complex does not contain PRPF19 (PubMed:25599396).
    SequenceCaution:
    • Sequence=AAF86951.1; Type=Frameshift; Positions=314, 411, 426, 429, 468; Evidence={ECO:0000305}; Sequence=AAH08778.1; Type=Erroneous initiation; Note=Translation N-terminally shortened.; Evidence={ECO:0000305}; Sequence=BAB84861.1; Type=Miscellaneous discrepancy; Note=Alternative splicing. Incomplete sequence.; Evidence={ECO:0000305};

    Three dimensional structures from OCA and Proteopedia for XAB2 Gene

neXtProt entry for XAB2 Gene

Post-translational modifications for XAB2 Gene

  • Ubiquitination at posLast=708708, isoforms=677, posLast=654654, isoforms=637, and isoforms=174
  • Modification sites at PhosphoSitePlus

Other Protein References for XAB2 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for XAB2 Gene

Domains & Families for XAB2 Gene

Protein Domains for XAB2 Gene

Suggested Antigen Peptide Sequences for XAB2 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

Q9HCS7

UniProtKB/Swiss-Prot:

SYF1_HUMAN :
  • Belongs to the crooked-neck family.
Family:
  • Belongs to the crooked-neck family.
genes like me logo Genes that share domains with XAB2: view

Function for XAB2 Gene

Molecular function for XAB2 Gene

UniProtKB/Swiss-Prot Function:
Involved in pre-mRNA splicing as component of the spliceosome (PubMed:11991638, PubMed:28502770, PubMed:28076346). Involved in transcription-coupled repair (TCR), transcription and pre-mRNA splicing (PubMed:10944529, PubMed:17981804).

Phenotypes From GWAS Catalog for XAB2 Gene

Gene Ontology (GO) - Molecular Function for XAB2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IPI 10944529
genes like me logo Genes that share ontologies with XAB2: view
genes like me logo Genes that share phenotypes with XAB2: view

Animal Models for XAB2 Gene

MGI Knock Outs for XAB2:

Animal Model Products

CRISPR Products

miRNA for XAB2 Gene

miRTarBase miRNAs that target XAB2

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for XAB2

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for XAB2 Gene

Localization for XAB2 Gene

Subcellular locations from UniProtKB/Swiss-Prot for XAB2 Gene

Nucleus. Note=Detected in the splicing complex carrying pre-mRNA. {ECO:0000250 UniProtKB:Q99PK0}.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for XAB2 gene
Compartment Confidence
nucleus 5
cytosol 3
extracellular 1
peroxisome 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Nucleus (2)
  • Vesicles (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for XAB2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000974 Prp19 complex IBA --
GO:0005634 nucleus IDA,IEA 28076346
GO:0005654 nucleoplasm TAS --
GO:0005681 spliceosomal complex IEA --
GO:0016020 membrane HDA 19946888
genes like me logo Genes that share ontologies with XAB2: view

Pathways & Interactions for XAB2 Gene

genes like me logo Genes that share pathways with XAB2: view

Pathways by source for XAB2 Gene

Gene Ontology (GO) - Biological Process for XAB2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000349 generation of catalytic spliceosome for first transesterification step IBA --
GO:0000398 mRNA splicing, via spliceosome TAS --
GO:0001824 blastocyst development IEA --
GO:0006281 DNA repair IEA --
GO:0006283 transcription-coupled nucleotide-excision repair TAS,IDA --
genes like me logo Genes that share ontologies with XAB2: view

No data available for SIGNOR curated interactions for XAB2 Gene

Drugs & Compounds for XAB2 Gene

No Compound Related Data Available

Transcripts for XAB2 Gene

mRNA/cDNA for XAB2 Gene

(1) REFSEQ mRNAs :
(10) Additional mRNA sequences :
(272) Selected AceView cDNA sequences:
(4) Ensembl transcripts including schematic representations, and UCSC links where relevant :

Unigene Clusters for XAB2 Gene

XPA binding protein 2:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for XAB2

Alternative Splicing Database (ASD) splice patterns (SP) for XAB2 Gene

ExUns: 1 ^ 2a · 2b ^ 3 ^ 4 ^ 5 ^ 6 ^ 7 ^ 8 ^ 9 ^ 10 ^ 11 ^ 12 ^ 13a · 13b ^ 14a · 14b ^ 15a · 15b ^ 16 ^ 17 ^ 18 ^ 19a · 19b
SP1: -
SP2:
SP3:
SP4:

Relevant External Links for XAB2 Gene

GeneLoc Exon Structure for
XAB2
ECgene alternative splicing isoforms for
XAB2

Expression for XAB2 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for XAB2 Gene

Protein differential expression in normal tissues from HIPED for XAB2 Gene

This gene is overexpressed in Peripheral blood mononuclear cells (19.0) and CD8 Tcells (7.9).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for XAB2 Gene



Protein tissue co-expression partners for XAB2 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of XAB2 Gene:

XAB2

SOURCE GeneReport for Unigene cluster for XAB2 Gene:

Hs.9822

Evidence on tissue expression from TISSUES for XAB2 Gene

  • Nervous system(4.6)
  • Adrenal gland(4.2)
  • Liver(4.2)
  • Lung(4.2)
  • Spleen(4.2)
genes like me logo Genes that share expression patterns with XAB2: view

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for XAB2 Gene

Orthologs for XAB2 Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for XAB2 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia XAB2 34 33
  • 99.08 (n)
OneToOne
cow
(Bos Taurus)
Mammalia XAB2 34 33
  • 91.5 (n)
OneToOne
dog
(Canis familiaris)
Mammalia XAB2 34 33
  • 90.72 (n)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia XAB2 34
  • 90 (a)
OneToOne
rat
(Rattus norvegicus)
Mammalia Xab2 33
  • 89.55 (n)
mouse
(Mus musculus)
Mammalia Xab2 16 34 33
  • 89.04 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia -- 34
  • 86 (a)
OneToMany
-- 34
  • 74 (a)
OneToMany
lizard
(Anolis carolinensis)
Reptilia XAB2 34
  • 78 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia xab2 33
  • 70.77 (n)
African clawed frog
(Xenopus laevis)
Amphibia Xl.1969 33
zebrafish
(Danio rerio)
Actinopterygii xab2 34 33 33
  • 74.18 (n)
OneToOne
rainbow trout
(Oncorhynchus mykiss)
Actinopterygii Omy.4228 33
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP012369 33
  • 70.75 (n)
fruit fly
(Drosophila melanogaster)
Insecta CG6197 34 33
  • 64.44 (n)
OneToOne
worm
(Caenorhabditis elegans)
Secernentea C50F2.3 34 33
  • 53.65 (n)
OneToOne
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes SYF1 36 34
  • 22 (a)
thale cress
(Arabidopsis thaliana)
eudicotyledons AT5G28740 33
  • 55.39 (n)
rice
(Oryza sativa)
Liliopsida Os07g0644300 33
  • 57.35 (n)
Os.33176 33
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 65 (a)
OneToOne
Cin.6158 33
bread mold
(Neurospora crassa)
Ascomycetes NCU08036 33
  • 59.44 (n)
fission yeast
(Schizosaccharomyces pombe)
Schizosaccharomycetes cwf3 33
  • 49.45 (n)
sea squirt
(Ciona intestinalis)
Ascidiacea Cin.6158 33
Species where no ortholog for XAB2 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • chicken (Gallus gallus)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for XAB2 Gene

ENSEMBL:
Gene Tree for XAB2 (if available)
TreeFam:
Gene Tree for XAB2 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for XAB2: view image

Paralogs for XAB2 Gene

(1) SIMAP similar genes for XAB2 Gene using alignment to 2 proteins:

  • SYF1_HUMAN
  • F5H315_HUMAN
genes like me logo Genes that share paralogs with XAB2: view

No data available for Paralogs for XAB2 Gene

Variants for XAB2 Gene

Sequence variations from dbSNP and Humsavar for XAB2 Gene

SNP ID Clin Chr 19 pos Variation AA Info Type
rs587777839 pathogenic, Hepatic failure, early-onset, and neurologic disorder due to cytochrome C oxidase deficiency, not provided 7,629,836(-) G/C upstream_transcript_variant
rs587779779 pathogenic, Congenital lactic acidosis, Hepatic failure, early-onset, and neurologic disorder due to cytochrome C oxidase deficiency 7,631,476(-) C/T upstream_transcript_variant
rs4134804 likely-benign, not provided 7,630,627(-) G/A/T upstream_transcript_variant
rs1057522294 likely-benign, not specified 7,631,458(-) C/G/T upstream_transcript_variant
rs1057522682 likely-benign, not specified 7,629,815(-) G/C upstream_transcript_variant

Structural Variations from Database of Genomic Variants (DGV) for XAB2 Gene

Variant ID Type Subtype PubMed ID
esv2751809 CNV gain 17911159
esv993190 CNV deletion 20482838
nsv1060887 CNV gain 25217958
nsv833730 CNV loss 17160897
nsv833731 CNV loss 17160897
nsv953958 CNV deletion 24416366

Variation tolerance for XAB2 Gene

Residual Variation Intolerance Score: 4.24% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 2.38; 42.15% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for XAB2 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
XAB2

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for XAB2 Gene

Disorders for XAB2 Gene

MalaCards: The human disease database

(1) MalaCards diseases for XAB2 Gene - From: DISEASES and GeneCards

Disorder Aliases PubMed IDs
cockayne syndrome
  • cs
- elite association - COSMIC cancer census association via MalaCards
Search XAB2 in MalaCards View complete list of genes associated with diseases

Additional Disease Information for XAB2

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
genes like me logo Genes that share disorders with XAB2: view

No data available for UniProtKB/Swiss-Prot and Genatlas for XAB2 Gene

Publications for XAB2 Gene

  1. XAB2, a novel tetratricopeptide repeat protein involved in transcription-coupled DNA repair and transcription. (PMID: 10944529) Nakatsu Y … Tanaka K (The Journal of biological chemistry 2000) 2 3 4 22 58
  2. Isolation of XAB2 complex involved in pre-mRNA splicing, transcription, and transcription-coupled repair. (PMID: 17981804) Kuraoka I … Tanaka K (The Journal of biological chemistry 2008) 3 4 22 58
  3. Cryo-EM structure of a human spliceosome activated for step 2 of splicing. (PMID: 28076346) Bertram K … Lührmann R (Nature 2017) 3 4 58
  4. The RNA helicase Aquarius exhibits structural adaptations mediating its recruitment to spliceosomes. (PMID: 25599396) De I … Pena V (Nature structural & molecular biology 2015) 3 4 58
  5. Variation within DNA repair pathway genes and risk of multiple sclerosis. (PMID: 20522537) Briggs FB … International Multiple Sclerosis Genetics Consortium (American journal of epidemiology 2010) 3 44 58

Products for XAB2 Gene

Sources for XAB2 Gene

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