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BIVM-ERCC5 Gene

protein-coding   GIFtS: 23
GCID: GC13P103461

BIVM-ERCC5 Readthrough

  Search for BIVM-ERCC5
at  

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, 10fRNAdb, 12H-InvDB, 13NCBI, 14NONCODE, and/or 15RNAdb)
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Aliases
BIVM-ERCC5 Readthrough1 2
BIVM-ERCC5 Protein2

External Ids:    HGNC: 436901   Entrez Gene: 1005334672   Ensembl: ENSG000002701817   UniProtKB: R4GMW84   

Export aliases for BIVM-ERCC5 gene to outside databases

Previous GC identifers: GC13U900839 GC13P103460


(According to Entrez Gene, GeneCards, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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Entrez Gene summary for BIVM-ERCC5 Gene:
This locus represents naturally occurring read-through transcription between the neighboring BIVM (basic,
immunoglobulin-like variable motif containing) and ERCC5 (excision repair cross-complementing rodent repair
deficiency, complementation group 5) genes on chromosome 13. The read-through transcript encodes a fusion protein
that shares sequence identity with the products of each individual gene. (provided by RefSeq, Feb 2011)

GeneCards Summary for BIVM-ERCC5 Gene:
BIVM-ERCC5 (BIVM-ERCC5 readthrough) is a protein-coding gene. An important paralog of this gene is ERCC5.




(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 37),
and/or miRBase,
Genomic Views according to UCSC (hg19) and Ensembl (release 75), Regulatory elements and Epigenetics data according to QIAGEN, and/or SwitchGear Genomics)
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Regulatory elements:
   Search for regulatory transcription factor binding sites for BIVM-ERCC5
         Other transcription factors

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Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat BIVM-ERCC5


Genomic Location:
Genomic View: UCSC Golden Path with GeneCards custom track

Entrez Gene cytogenetic band: 13q   Ensembl cytogenetic band:  13q33.1   HGNC cytogenetic band: 13q33.1

BIVM-ERCC5 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
BIVM-ERCC5 gene location

GeneLoc information about chromosome 13         GeneLoc Exon Structure

GeneLoc location for GC13P103461:  view genomic region     (about GC identifiers)

Start:
103,459,496 bp from pter      End:
103,528,351 bp from pter
Size:
68,856 bases      Orientation:
plus strand

(According to 1UniProtKB, HORDE, 2neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from EMD Millipore, R&D Systems, GenScript, Enzo Life Sciences, OriGene, Novus Biologicals, Sino Biological, ProSpec, Cloud-Clone Corp., and/or eBioscience,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, Cloud-Clone Corp., and/or eBioscience, Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, Cloud-Clone Corp, and/or others.)
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UniProtKB/TrEMBL: R4GMW8 (See protein sequence)
Recommended Name: Protein BIVM-ERCC5  
Size: 1385 amino acids; 156070 Da
Caution: The sequence shown here is derived from an Ensembl automatic analysis pipeline and should be considered
as preliminary data

REFSEQ proteins: NP_001191354.1  
ENSEMBL proteins: 
 ENSP00000473384  

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(According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
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Selected InterPro protein domains (see all 7):
 IPR006084 XPG/Rad2
 IPR006086 XPG-I_dom
 IPR006085 XPG_DNA_repair_N
 IPR001044 XPG/Rad2_eukaryotes
 IPR019974 XPG_CS

Graphical View of Domain Structure for InterPro Entry R4GMW8

ProtoNet protein and cluster: R4GMW8


Find genes that share domains with BIVM-ERCC5           About GenesLikeMe


(According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, inGenious Targeting Laboratory, genOway,
transcription factor targeting from QIAGEN and/or HOMER, miRNA Gene Targets from miRTarBase, shRNA from OriGene, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, SwitchGear Genomics, Gene Editing from DNA2.0, Clones from OriGene, GenScript, Sino Biological, DNA2.0, Vector BioLabs and/or Addgene, Cell Lines from GenScript, ESI BIO, In Situ Hybridization Assays from Advanced Cell Diagnostics, Flow cytometry from eBioscience, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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     Gene Ontology (GO): 5 molecular function terms:    About this table

GO IDQualified GO termEvidencePubMed IDs
GO:0003677DNA binding ----
GO:0003697single-stranded DNA binding ----
GO:0003824catalytic activity ----
GO:0004518nuclease activity ----
GO:0004519endonuclease activity ----
     
Find genes that share ontologies with BIVM-ERCC5           About GenesLikeMe


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(According to UniProtKB, COMPARTMENTS Subcellular localization database, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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Gene Ontology (GO): 1 cellular component term:    About this table

GO IDQualified GO termEvidencePubMed IDs
GO:0005634nucleus ----

Find genes that share ontologies with BIVM-ERCC5           About GenesLikeMe


(SuperPaths according to PathCards, Pathways according to R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Sino Biological, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to QIAGEN, and/or STRING, Interactions according to 1UniProtKB, 2MINT, 3I2D, and/or 4STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene).
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SuperPaths for BIVM-ERCC5 About    
See pathways by source

SuperPathContained pathways About
1Global Genomic NER (GG-NER)
Nucleotide excision repair0.69


Find genes that share SuperPaths with BIVM-ERCC5           About GenesLikeMe

Pathways by source                                                                                                                                                                 See SuperPaths
Show all pathways



1 Kegg Pathway  (Kegg details for BIVM-ERCC5):
    Nucleotide excision repair

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Interactions:

    Search GeneGlobe Interaction Network for BIVM-ERCC5

Gene Ontology (GO): 2 biological process terms:    About this table

GO IDQualified GO termEvidencePubMed IDs
GO:0006281DNA repair ----
GO:0006289nucleotide-excision repair ----

Find genes that share ontologies with BIVM-ERCC5           About GenesLikeMe



(Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience, ApexBio, HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB)
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Browse Tocris compounds for BIVM-ERCC5



(Secondary structures according to fRNAdb,
GenBank/EMBL/DDBJ Accessions according to
Unigene (Build 236 Homo sapiens; Apr 25 2013) or GenBank,
RefSeq according to Entrez Gene,
DOTS (version 10), and/or AceView, transcript ids from Ensembl with links to UCSC,
exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN, SwitchGear Genomics,
Tagged/untagged cDNA clones from OriGene, GenScript, DNA2.0, Vector BioLabs, and/or Addgene, Primers from OriGene, and/or QIAGEN, Flow cytometry from eBioscience )
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REFSEQ mRNAs for BIVM-ERCC5 gene: 
NM_001204425.1  

1 Ensembl transcript including schematic representation, and UCSC links where relevant:
ENST00000602836
miRNA
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GeneLoc Exon Structure


(RNA expression data according to H-InvDB, NONCODE, miRBase, and RNAdb, Expression images according to data from BioGPS, Illumina Human BodyMap, and CGAP SAGE, Sets of similar genes according to GeneDecks, in vivo and in vitro expression data from LifeMap Discovery™, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MaxQB, plus additional links to SOURCE, and/or BioGPS, and/or UniProtKB,
PCR Arrays from QIAGEN, Primers from OriGene, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
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See probesets specificity/sensitivity at GeneAnnot
CGAP TAG: --

BIVM-ERCC5 Protein expression data from MOPED1, PaxDb2 and MaxQB3 --
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(Orthologs according to 1,2HomoloGene (2older version, for species not in 1newer version), 3euGenes, 4SGD , 5MGI Mar 06 2013, with possible further links to Flybase and/or WormBase, and/or 6Ensembl pan taxonomic compara , Gene Trees according to Ensembl and TreeFam)
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This gene was present in the common ancestor of animals and fungi.

Orthologs for BIVM-ERCC5 gene from Selected species (see all 12)    About this table
Organism Taxonomic
classification
Gene Description Human
Similarity
Orthology
Type
Details
chicken
(Gallus gallus)
Aves ERCC56
Gallus gallus excision repair cross-complementing ...
45(a)
1 → many
1(142008009-142023348)
lizard
(Anolis carolinensis)
Reptilia --
--
47(a)
1 → many
3(101065875-101099416)
zebrafish
(Danio rerio)
Actinopterygii ercc56
excision repair cross-complementing rodent repair ...
38(a)
1 → many
1(348782-368977) ENSDARG00000023678
fruit fly
(Drosophila melanogaster)
Insecta mus2016
mutagen-sensitive 201
21(a)
1 → many
2L(8437411-8442352)
worm
(Caenorhabditis elegans)
Secernentea gen-16
xpg-16
Protein XPG-1 (xpg-1) mRNA, complete cds
21(a)
20(a)
many ↔ many
many ↔ many
III(6245924-6248234) WBGene00020442
I(6558700-6562392) WBGene00019004
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes RAD26
Single-stranded DNA endonuclease, cleaves single-s...
21(a)
1 → many
VII(1007671-1010766) YGR258C
        Species with no ortholog for BIVM-ERCC5

ENSEMBL Gene Tree for BIVM-ERCC5 (if available)
TreeFam Gene Tree for BIVM-ERCC5 (if available)

(Paralogs according to 1HomoloGene,
2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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Paralogs for BIVM-ERCC5 gene
ERCC52  
3 SIMAP similar genes for BIVM-ERCC5 using alignment to 1 protein entry:     R4GMW8_HUMAN:
ERCC5    BIVM    GEN1

Find genes that share paralogs with BIVM-ERCC5           About GenesLikeMe



(SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, 4UniProtKB, and DNA2.0, Linkage Disequilibrium by HapMap, Structural Variations(CNVs/InDels/Inversions) from the Database of Genomic Variants, Mutations from the Human Gene Mutation Database (HGMD), the Human Cytochrome P450 Allele Nomenclature Database, and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers, Cancer Mutation PCR Arrays and Assays, and Copy Number PCR Arrays from QIAGEN)
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Selected SNPs for BIVM-ERCC5 (see all 30)    About this table                                 

Genomic DataTranscription Related DataAllele Frequencies
SNP IDValidClinical
significance
Chr 13 posSequence#AA
Chg
TypeMore#Allele
freq
PopTotal
sample
More
----------
rs1176256691,2
C,F--103494557(+) GTGATA/GTAGGC 1 -- int11Minor allele frequency- G:0.04EA 120
rs73169631,2
C,F,A,H--103494644(+) AATTTC/GAAGAA 1 -- int116Minor allele frequency- G:0.36NS EA NA WA CSA 795
rs1492730751,2
--103494706(+) ATTTAA/GGAGCT 1 -- int10--------
rs1892018981,2
--103494735(+) TGTGAA/CTTTTA 1 -- int10--------
rs44009161,2
H--103494771(+) CTTTAG/TATAGC 1 -- int14Minor allele frequency- T:0.00NS EA 420
rs1818474741,2
--103494871(+) TTATTC/TTTTTG 1 -- int10--------
rs1865813711,2
--103494930(+) TGCAAC/TCTCCG 1 -- int10--------
rs1894112251,2
--103494931(+) GCAACC/TTCCGC 1 -- int10--------
rs1806972961,2
--103494949(+) GTTCAA/GGTGGT 1 -- int10--------
rs1434267591,2
--103495004(+) CCACCA/TTGCCC 1 -- int10--------

HapMap Linkage Disequilibrium report for BIVM-ERCC5 (103459496 - 103528351 bp)

Structural Variations
     Database of Genomic Variants (DGV) 2 variations for BIVM-ERCC5:    About this table    
Variant IDTypeSubtypePubMed ID
esv2661939CNV Deletion23128226
nsv900972CNV Loss21882294

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(in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
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  --

(in PubMed. Associations of this gene to articles via 1Entrez Gene, 2UniProtKB/Swiss-Prot, 3HGNC, 4GAD, 5PharmGKB, 6HMDB, 7DrugBank, 8UniProtKB/TrEMBL, 9 Novoseek, and/or 10fRNAdb)
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PubMed articles for BIVM-ERCC5 gene integrated from 10 sources:
(articles sorted by number of sources associating them with BIVM-ERCC5)
    Utopia: connect your pdf to the dynamic
world of online information

  1. Systems-wide analysis of ubiquitylation dynamics reveals a key role for PAF15 ubiquitylation in DNA-damage bypass. (PubMed id 23000965)1 Povlsen L.K....Choudhary C. (Nat. Cell Biol. 2012)
  2. A proteome-wide, quantitative survey of in vivo ubiquitylation sites reveals widespread regulatory roles. (PubMed id 21890473)1 Wagner S.A....Choudhary C. (amp 2011)
  3. Global identification of modular cullin-RING ligase substrates. (PubMed id 21963094)1 Emanuele M.J....Elledge S.J. (Cell 2011)
  4. Expression of conjoined genes: another mechanism for gene regulation in eukaryotes. (PubMed id 20967262)1 Prakash T....Taylor T.D. (PLoS ONE 2010)

(in PubMed, OMIM, and NCBI Bookshelf)
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 ANDOR
Aliases
Free Text  

  Query String
PubMed
OMIM
NCBI Bookshelf
  (Note: In FireFox, select the above section and copy using Ctrl-C)

(According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
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Entrez Gene: 100533467 HGNC: 43690 Ensembl:ENSG00000270181 euGenes: HUgn100533467 ECgene: BIVM-ERCC5 Kegg: 100533467
H-InvDB: BIVM-ERCC5

(According to HUGE)
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  --

(According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL, and/or others, e.g. Wikipedia and GeneReviews, via UniProtKB/Swiss-Prot)
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  --

(Patent information from GeneIP,
Licensable technologies from WIS Yeda, Salk, Tufts,
IP news from LifeMap Sciences, Inc.)
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Patent Information for BIVM-ERCC5 gene:
Search GeneIP for patents involving BIVM-ERCC5

GeneCards and IP:
Japan Patent Office Licenses GeneCards     European Patent Office Licenses GeneCards     Improving the IP Search



(Antibodies, recombinant proteins, and assays from EMD Millipore, R&D Systems, OriGene, QIAGEN, GenScript, Cell Signaling Technology, Novus Biologicals, Sino Biological, Enzo Life Sciences, Abcam, ProSpec, Cloud-Clone Corp., Thermo Fisher Scientific, LSBio, eBioscience, and/or others, Gene Editing from DNA2.0. Clones from OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Addgene, Cell lines from GenScript, and ESI BIO, Flow cytometery from eBioscience, PCR Arrays from QIAGEN, Drugs and/or compounds from EMD Millipore, Tocris Bioscience, Enzo Life Sciences, and/or ApexBio, In Situ Hybridization Assays from
Advanced Cell Diagnostics, Animal models from inGenious Targeting Laboratory, genOway)
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 Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for BIVM-ERCC5
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 Browse SwitchGear Promoter luciferase reporter plasmids for BIVM-ERCC5
 Search ThermoFisher Antibodies for BIVM-ERCC5
 Search Vector BioLabs for ready-to-use adenovirus/AAV for human, mouse, rat BIVM-ERCC5
 inGenious Targeting Laboratory: Let us create your new Knockout/Knockin mouse model for BIVM-ERCC5
 inGenious Targeting Laboratory: Contact us about creating complex and humanized mouse models for BIVM-ERCC5
 Search LSBio for Antibodies for BIVM-ERCC5
Customized transgenic rodents for:
 Humanization
 Biomarker expression
 Off-target effect monitoring
 Translational medicine
 Tissue-specific gene expresssion
 Time-controlled gene expresssion
 Browse compounds at ApexBio
 Search Addgene for plasmids for BIVM-ERCC5
  Search eBioscience for proteins for BIVM-ERCC5
  Search eBioscience for elisas for BIVM-ERCC5
  eBioscience FlowRNA Probe Sets
       
GeneCards Homepage - Last full update: 7 May 2014 - Incrementals: 9 May 2014 , 2 Jun 2014 , 26 Jun 2014 , 30 Jun 2014 , 21 Aug 2014 , 8 Sep 2014

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