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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 Transcription-Coupled Nucleotide Excision Repair (TC-NER) and mRNA Splicing - Major Pathway.

UniProtKB/Swiss-Prot for XAB2 Gene

  • Involved in transcription-coupled repair (TCR), transcription and pre-mRNA splicing.

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

Regulatory Elements for XAB2 Gene

Enhancers for XAB2 Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH19H007177 1.5 Ensembl ENCODE dbSUPER 73.6 +448.5 448491 7 HDGF PKNOX1 FEZF1 ZNF121 ZNF302 ZNF143 ZNF207 ATF7 RUNX3 ZNF202 ELAVL1 XAB2 KHSRP ZNF557 MAP2K7 GTF2F1 DENND1C ARHGEF18 GPR108 EVI5L
GH19H008239 1.6 Ensembl ENCODE dbSUPER 65.6 -610.9 -610860 2 HDGF PKNOX1 FOXA2 MLX ARNT ARID4B ZNF2 YY1 CBX5 ZNF416 ZNF558 HNRNPM ELAVL1 ZNF317 XAB2 ENSG00000269300 ZNF414 CERS4 ARHGEF18 MAP2K7
GH19H006718 1 ENCODE 88.8 +911.9 911925 0 HDGF PKNOX1 ATF1 FOXA2 ARNT YBX1 ZNF2 TCF12 GATA2 ZNF207 XAB2 ZNF557 DUS3L KHSRP ENSG00000267571 RANBP3 VMAC GPR108 TRIP10 FLJ25758
GH19H007521 1.7 FANTOM5 ENCODE dbSUPER 49.7 +106.7 106708 2 HDGF MLX ARNT ARID4B SIN3A FEZF1 DMAP1 ZNF2 YY1 ZNF766 HNRNPM ELAVL1 XAB2 ZNF557 ZNF414 MAP2K7 TIMM44 SNAPC2 CD209 EVI5L
GH19H007196 2 FANTOM5 Ensembl ENCODE dbSUPER 41 +430.9 430873 4 HDGF PKNOX1 FOXA2 MLX ARNT ARID4B SIN3A DMAP1 ZNF2 ZBTB7B ELAVL1 XAB2 ZNF557 KHSRP MAP2K7 GTF2F1 ARHGEF18 PSPN GPR108 INSR
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around XAB2 on UCSC Golden Path with GeneCards custom track

Promoters for XAB2 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000106694 -35 1601 PKNOX1 FOXA2 ARNT ARID4B SIN3A ZNF2 YY1 SLC30A9 ZNF143 FOS

Genomic Location for XAB2 Gene

Chromosome:
19
Start:
7,619,525 bp from pter
End:
7,629,565 bp from pter
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. Identified in the spliceosome C complex. Component of the XAB2 complex, a multimeric protein complex composed of XAB2, PRPF19, AQR, ZNF830, ISY1, and PPIE.
    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 Lys174, Lys637, isoforms=654, isoforms=677, and isoforms=708
  • 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

Gene Families for XAB2 Gene

HGNC:
Human Protein Atlas (HPA):
  • Plasma proteins
  • Predicted intracellular proteins

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 transcription-coupled repair (TCR), transcription and pre-mRNA splicing.

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

Clone Products

  • Applied Biological Materials Clones for XAB2
  • Vectors and viruses for ORF, Lenti, Retro, Adenovirus, AAV, and more

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}.

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 IEA,IC 10944529
GO:0005654 nucleoplasm TAS --
GO:0005681 spliceosomal complex IEA --
GO:0016020 membrane IDA 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

Unigene Clusters for XAB2 Gene

XPA binding protein 2:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

Clone Products

  • Applied Biological Materials Clones for XAB2
  • Vectors and viruses for ORF, Lenti, Retro, Adenovirus, AAV, and more

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, PaxDb, 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

Primer Products

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 33 34
  • 99.08 (n)
cow
(Bos Taurus)
Mammalia XAB2 33 34
  • 91.5 (n)
dog
(Canis familiaris)
Mammalia XAB2 33 34
  • 90.72 (n)
oppossum
(Monodelphis domestica)
Mammalia XAB2 34
  • 90 (a)
OneToOne
rat
(Rattus norvegicus)
Mammalia Xab2 33
  • 89.55 (n)
mouse
(Mus musculus)
Mammalia Xab2 33 16 34
  • 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 33 34
  • 74.18 (n)
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 33 34
  • 64.44 (n)
worm
(Caenorhabditis elegans)
Secernentea C50F2.3 33 34
  • 53.65 (n)
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes SYF1 34 36
  • 22 (a)
OneToOne
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
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)

Paralogs for XAB2 Gene

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

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 Sequence Context AA Info Type
rs587777839 Pathogenic 7,629,836(+) GAGAT(C/G)GGGGT nc-transcript-variant, upstream-variant-2KB, reference, missense
rs587779779 Pathogenic 7,631,476(+) AGCTT(C/T)AAGAG intron-variant, nc-transcript-variant, downstream-variant-500B, upstream-variant-2KB, reference, stop-gained
rs4134804 Likely benign 7,630,627(-) CCACT(C/T)GGCCT nc-transcript-variant, upstream-variant-2KB, reference, missense
rs1000498679 -- 7,627,552(+) TGCGG(C/T)GGGAC intron-variant
rs1000550851 -- 7,627,312(+) AGATA(C/T)AGGGG reference, synonymous-codon

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)

Relevant External Links for XAB2 Gene

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

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
  • cockayne's syndrome
- elite association - COSMIC cancer census association via MalaCards
Search XAB2 in MalaCards View complete list of genes associated with diseases

Relevant External Links for XAB2

Genetic Association Database (GAD)
XAB2
Human Genome Epidemiology (HuGE) Navigator
XAB2
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
XAB2
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 60
  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 60
  3. 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 45 60
  4. Cockayne syndrome A and B proteins differentially regulate recruitment of chromatin remodeling and repair factors to stalled RNA polymerase II in vivo. (PMID: 16916636) Fousteri M … Mullenders LH (Molecular cell 2006) 3 22 60
  5. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard DS … MGC Project Team (Genome research 2004) 3 4 60

Products for XAB2 Gene

Sources for XAB2 Gene

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