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HIGD2B Gene

protein-coding   GIFtS: 33
GCID: GC15M072968

HIG1 Hypoxia Inducible Domain Family, Member 2B

(Previous names: HIG1 hypoxia inducible domain family, member 2B (pseudogene))
(Previous symbol: HIGD2BP)
  See related disease
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
HIG1 Hypoxia Inducible Domain Family, Member 2B1 2
HIGD2BP1 2 3
HIG1 Hypoxia Inducible Domain Family, Member 2B (Pseudogene)1
HIG1 Domain Family Member 2B Pseudogene3

External Ids:    HGNC: 269841   Entrez Gene: 1233462   Ensembl: ENSG000001752027   UniProtKB: Q4VC393   

Export aliases for HIGD2B gene to outside databases

Previous GC identifers: GC15M070758 GC15M049798


(According to Entrez Gene, GeneCards, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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GeneCards Summary for HIGD2B Gene:
HIGD2B (HIG1 hypoxia inducible domain family, member 2B) is a protein-coding gene. Diseases associated with HIGD2B include hypoxia. An important paralog of this gene is HIGD2A.


(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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RefSeq DNA sequence:
NC_000015.10  NC_018926.2  NT_010194.18  
Regulatory elements:
   Regulatory transcription factor binding sites in the HIGD2B gene promoter:
         AP-2rep   STAT1   Brachyury   Nkx2-5   NF-AT   HEN1   NF-AT4   NF-AT2   NF-AT3   NF-AT1   
         Other transcription factors

Browse SwitchGear Promoter luciferase reporter plasmids
   Search Chromatin IP Primers for HIGD2B

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat HIGD2B


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

Entrez Gene cytogenetic band: 15q24.1   Ensembl cytogenetic band:  15q24.1   HGNC cytogenetic band: 15q24.1

HIGD2B Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
HIGD2B gene location

GeneLoc information about chromosome 15         GeneLoc Exon Structure

GeneLoc location for GC15M072968:  view genomic region     (about GC identifiers)

Start:
72,968,123 bp from pter      End:
72,978,490 bp from pter
Size:
10,368 bases      Orientation:
minus 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, and/or Cloud-Clone Corp.,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Cloud-Clone Corp., 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/Swiss-Prot: HIG2B_HUMAN, Q4VC39 (See protein sequence)
Recommended Name: Putative HIG1 domain family member 2B  
Size: 106 amino acids; 11405 Da
Caution: Could be the product of a pseudogene

Explore the universe of human proteins at neXtProt for HIGD2B: NX_Q4VC39


ENSEMBL proteins: 
 ENSP00000307951  

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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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1 InterPro protein domain:
 IPR007667 Hypoxia_induced_domain

Graphical View of Domain Structure for InterPro Entry Q4VC39

ProtoNet protein and cluster: Q4VC39

UniProtKB/Swiss-Prot: HIG2B_HUMAN, Q4VC39
Similarity: Contains 1 HIG1 domain


HIGD2B for domains           About GeneDecksing


(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, and Vector BioLabs, Cell Lines from GenScript, ESI BIO, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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Animal Models:
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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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Subcellular locations from UniProtKB/Swiss-Prot
HIG2B_HUMAN, Q4VC39: Membrane; Multi-pass membrane protein (Potential)
Subcellular locations from COMPARTMENTS: 

CompartmentConfidence
cytosol3
mitochondrion3
plasma membrane2
endoplasmic reticulum1
extracellular1
golgi apparatus1
lysosome1
nucleus1

Gene Ontology (GO): 1 cellular component term:    About this table

GO IDQualified GO termEvidencePubMed IDs
GO:0016021integral component of membrane IEA--

HIGD2B for ontologies           About GeneDecksing


(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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    Custom Pathway & Disease-focused RT2 Profiler PCR Arrays for HIGD2B
Interactions:

    Search GeneGlobe Interaction Network for HIGD2B

STRING Interaction Network Preview (showing 5 interactants - click image to see 20)

Selected Interacting proteins for HIGD2B (ENSP000003079514) via UniProtKB, MINT, STRING, and/or I2D (see all 20)
InteractantInteraction Details
GeneCardExternal ID(s)
COX5BENSP000002584244STRING: ENSP00000258424
CYC1ENSP000003171594STRING: ENSP00000317159
FIP1L1ENSP000003367524STRING: ENSP00000336752
MT-CO1ENSP000003544994STRING: ENSP00000354499
MT-CO2ENSP000003548764STRING: ENSP00000354876
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(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 Small Molecules at EMD Millipore
   Browse drugs & compounds from Enzo Life Sciences
  Browse compounds at ApexBio 

Browse Tocris compounds for HIGD2B (HIG2B)



(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, Primers from OriGene, and/or QIAGEN )
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Unigene Cluster for HIGD2B:

HIG1 hypoxia inducible domain family, member 2B
Hs.434111
Unigene Representative Sequence: NR_002780
1 Ensembl transcript including schematic representation, and UCSC links where relevant:
ENST00000311755(uc002ava.3)
miRNA
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Additional mRNA sequence: 

BC040890.1 NR_002780.1 

1 DOTS entry:

DT.97785300 

2 AceView cDNA sequences:

BC040890 BM564128 

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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HIGD2B expression in normal human tissues (normalized intensities)
See probesets specificity/sensitivity at GeneAnnot
About this imageBioGPS <intensity>2/3
CGAP TAG: GGACTTACTC
HIGD2B Expression
About this image

HIGD2B Protein expression data from MOPED1, PaxDb2 and MaxQB3 --

SOURCE GeneReport for Unigene cluster: Hs.434111
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In Situ
Assay Products:
 

 
Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for HIGD2B

(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.

Orthologs for HIGD2B gene from Selected species (see all 10)    About this table
Organism Taxonomic
classification
Gene Description Human
Similarity
Orthology
Type
Details
chicken
(Gallus gallus)
Aves --
Uncharacterized protein
46(a)
1 → many
13(9736142-9736742)
lizard
(Anolis carolinensis)
Reptilia --
Uncharacterized protein
48(a)
1 → many
GL343548.1(335362-337136)
zebrafish
(Danio rerio)
Actinopterygii higd2a6
HIG1 hypoxia inducible domain family, member 2A
43(a)
1 → many
14(47694540-47697522) ENSDARG00000052371
fruit fly
(Drosophila melanogaster)
Insecta CG99216
--
42(a)
1 → many
X(16225292-16227427)
        Species with no ortholog for HIGD2B

ENSEMBL Gene Tree for HIGD2B (if available)
TreeFam Gene Tree for HIGD2B (if available)

(Paralogs according to 1HomoloGene,
2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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Paralogs for HIGD2B gene
HIGD2A2  
4 SIMAP similar genes for HIGD2B using alignment to 1 protein entry:     HIG2B_HUMAN:
HIGD2A    HIGD1B    HIGD1C    HIGD1A

HIGD2B for paralogs           About GeneDecksing



(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 HIGD2B (see all 152)    About this table    
Genomic DataTranscription Related DataAllele Frequencies
SNP IDValidClinical
significance
Chr 15 posSequence#AA
Chg
TypeMore#Allele
freq
PopTotal
sample
More
----------
rs1914867221,2
--72967736(+) CTGGCC/TAGGTG 1 -- int10--------
rs1450965731,2
--72967742(+) AGGTGC/GGGTGG 1 -- int10--------
rs1389383411,2
C--72967885(+) GGCGCA/GTATCT 1 -- int10--------
rs1829111171,2
--72967906(+) CTACTC/TGGGAG 1 -- int10--------
rs2010448921,2
--72967995(+) GCAAC-/AAGGGC 1 -- int10--------
rs1420514921,2
--72968001(+) AGGGCC/TGAAGT 1 -- int10--------
rs1463180571,2
--72968075(+) CCATAC/TAAATA 1 -- int10--------
rs1872615961,2
--72968331(+) CCCATC/GGTAGG 1 -- nc-transcript-variant0--------
rs761778581,2
C--72968438(+) GCAAGA/GTGGCT 1 -- nc-transcript-variant1Minor allele frequency- G:0.00EU 593
rs615284291,2
C,F--72968522(+) AGCAGT/CAGAGG 1 -- nc-transcript-variant4Minor allele frequency- C:0.06CSA WA EA EU 832

HapMap Linkage Disequilibrium report for HIGD2B (72968123 - 72978490 bp)

Structural Variations
     Database of Genomic Variants (DGV) 3 variations for HIGD2B:    About this table    
Variant IDTypeSubtypePubMed ID
nsv483057CNV Loss15286789
nsv428307CNV Gain18775914
dgv755e1CNV Complex17122850

Site Specific Mutation Identification with PCR Assays
Search QIAGEN SeqTarget long-range PCR primers for resequencing HIGD2B
DNA2.0 Custom Variant and Variant Library Synthesis for HIGD2B

(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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1 disease for HIGD2B:    
About MalaCards
hypoxia


HIGD2B for disorders           About GeneDecksing


Export disorders for HIGD2B gene to outside databases

(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 HIGD2B gene integrated from 10 sources:
(articles sorted by number of sources associating them with HIGD2B)
    Utopia: connect your pdf to the dynamic
world of online information

  1. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PubMed id 15489334)2 Gerhard D.S.... Malek J. (Genome Res. 2004)
  2. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. (PubMed id 12477932)1 Strausberg R.L....Marra M.A. (Proc. Natl. Acad. Sci. U.S.A. 2002)
  3. (PubMed id )2 

(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: 123346 HGNC: 26984 AceView: LOC123346 Ensembl:ENSG00000175202 euGenes: HUgn123346
ECgene: HIGD2B H-InvDB: HIGD2B

(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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NameDescription
PharmGKB entry for HIGD2B Pharmacogenomics, SNPs, Pathways

(Patent information from GeneIP,
Licensable technologies from WIS Yeda, Salk, Tufts,
IP news from LifeMap Sciences, Inc.)
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Patent Information for HIGD2B gene:
Search GeneIP for patents involving HIGD2B

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, Gene Editing from DNA2.0. Clones from OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Cell lines from GenScript, and ESI BIO, 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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Developed at the Crown Human Genome Center, Department of Molecular Genetics, the Weizmann Institute of Science

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