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HHLA3 Gene

protein-coding   GIFtS: 41
GCID: GC01P070820

HERV-H LTR-Associating 3

  Search for HHLA3
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
HERV-H LTR-Associating 31 2
Human Endogenous Retrovirus-H Long Terminal Repeat-Associating Protein 32 3
HERV-H LTR-Associating Protein 32
Human Endogenous Retrovirus-H Long Terminal Repeat-Associating 32

External Ids:    HGNC: 49061   Entrez Gene: 111472   Ensembl: ENSG000001975687   OMIM: 6043725   UniProtKB: Q9XRX53   

Export aliases for HHLA3 gene to outside databases

Previous GC identifers: GC01P070944 GC01P069743 GC01P070205 GC01P070190 GC01P070532 GC01P068931


(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 HHLA3 Gene:
HHLA3 (HERV-H LTR-associating 3) is a protein-coding gene.


(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_000001.11  NC_018912.2  NT_032977.10  
Regulatory elements:
   Regulatory transcription factor binding sites in the HHLA3 gene promoter:
         COUP-TF1   GATA-3   AML1a   COUP   HNF-4alpha2   GATA-2   GATA-1   HNF-4alpha1   HEN1   COUP-TF   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidHHLA3 promoter sequence
   Search Chromatin IP Primers for HHLA3

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat HHLA3


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

Entrez Gene cytogenetic band: 1p31.1   Ensembl cytogenetic band:  1p31.1   HGNC cytogenetic band: 1p31.1

HHLA3 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
HHLA3 gene location

GeneLoc information about chromosome 1         GeneLoc Exon Structure

GeneLoc location for GC01P070820:  view genomic region     (about GC identifiers)

Start:
70,820,488 bp from pter      End:
70,851,022 bp from pter
Size:
30,535 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, 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: HHLA3_HUMAN, Q9XRX5 (See protein sequence)
Recommended Name: HERV-H LTR-associating protein 3  
Size: 114 amino acids; 12913 Da
Sequence caution: Sequence=AAD33288.1; Type=Frameshift; Positions=72;
Secondary accessions: D3DQ74 Q5VZP2 Q96FH5 Q9XRX4
Alternative splicing: 3 isoforms:  Q9XRX5-4   Q9XRX5-2   Q9XRX5-3   

Explore the universe of human proteins at neXtProt for HHLA3: NX_Q9XRX5

Explore proteomics data for HHLA3 at MOPED


See HHLA3 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

REFSEQ proteins (3 alternative transcripts): 
NP_001026863.1  NP_001031722.1  NP_001031723.1  

ENSEMBL proteins: 
 ENSP00000354815   ENSP00000352938   ENSP00000432048   ENSP00000359978   ENSP00000431678  
 ENSP00000434063   ENSP00000395155  

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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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ProtoNet protein and cluster: Q9XRX5


(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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     Gene Ontology (GO): 1 molecular function term:    About this table

GO IDQualified GO termEvidencePubMed IDs
GO:0005515protein binding IPI16189514
     
HHLA3 for ontologies           About GeneDecksing


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 COMPARTMENTS: 

CompartmentConfidence
extracellular2
cytosol1
nucleus1

(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 HHLA3
Interactions:

    Search GeneGlobe Interaction Network for HHLA3

STRING Interaction Network Preview (showing 5 interactants - click image to see 11)

Selected Interacting proteins for HHLA3 (Q9XRX51, 3 ENSP000003599784) via UniProtKB, MINT, STRING, and/or I2D (see all 11)
InteractantInteraction Details
GeneCardExternal ID(s)
NMIQ132871, 3, ENSP000002433464EBI-750554,EBI-372942 I2D: score=5 STRING: ENSP00000243346
CHRM3ENSP000002553804STRING: ENSP00000255380
ENSG00000206379ENSP000003728734STRING: ENSP00000372873
ENSG00000224398ENSP000004130924STRING: ENSP00000413092
ENSG00000225553ENSP000003919014STRING: ENSP00000391901
About this table

(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 drugs & compounds from Enzo Life Sciences
  Browse compounds at ApexBio 

Browse Tocris compounds for HHLA3



(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,
Conferences by KenesGroup, 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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REFSEQ mRNAs for HHLA3 gene (4 alternative transcripts): 
NM_007071.2  NM_001031693.2  NM_001036645.1  NM_001036646.1  

Unigene Cluster for HHLA3:

HERV-H LTR-associating 3
Hs.142245  [show with all ESTs]
Unigene Representative Sequence: NM_001036645
8 Ensembl transcripts including schematic representations, and UCSC links where relevant:
ENST00000361764 ENST00000359875(uc001dfb.3 uc001dfa.3 uc001dfc.3)
ENST00000486110 ENST00000463058(uc010oqp.2) ENST00000370940 ENST00000531950
ENST00000525653 ENST00000432224
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Additional mRNA sequence: 

AF126163.1 BC010922.1 NR_027404.1 

4 DOTS entries:

DT.86855512  DT.40200675  DT.453870  DT.99928763 

Selected AceView cDNA sequences (see all 42):

BQ787849 BU731616 BX105337 BQ673373 CR595442 AA689437 CK429743 AA235113 
BM906004 BU860794 BI868263 BF968417 NM_007071 AF126163 AA600248 N33882 
AI754552 AA283852 AL583502 BG196895 AF126164 BM708957 AI276859 CA395526 

GeneLoc Exon Structure

Selected Alternative Splicing Database (ASD) splice patterns (SP) for HHLA3 (see all 7)    About this scheme

ExUns: 1a · 1b · 1c · 1d · 1e ^ 2a · 2b ^ 3 ^ 4 ^ 5a · 5b · 5c · 5d
SP1:                          -                                                   
SP2:                          -     -     -                                       
SP3:                          -     -     -                                       
SP4:                          -     -     -           -                           
SP5:                                -     -           -                           


ECgene alternative splicing isoforms for HHLA3

(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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HHLA3 expression in normal human tissues (normalized intensities)
See probesets specificity/sensitivity at GeneAnnot
About this imageBioGPS <intensity>2/3
CGAP TAG: TATACATCCA
HHLA3 Expression
About this image

HHLA3 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

HHLA3 Protein Expression

SOURCE GeneReport for Unigene cluster: Hs.142245

UniProtKB/Swiss-Prot: HHLA3_HUMAN, Q9XRX5
Tissue specificity: Expressed in kidney and liver

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In Situ
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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 human and chimp.

Orthologs for HHLA3 gene from 1 species (see representative species )    About this table
Organism Taxonomic
classification
Gene Description Human
Similarity
Orthology
Type
Details
chimpanzee
(Pan troglodytes)
Mammalia HHLA36
HERV-H LTR-associating 3
97(a)
1 ↔ 1
1(70996647-71009476)


ENSEMBL Gene Tree for HHLA3 (if available)
TreeFam Gene Tree for HHLA3 (if available)

(Paralogs according to 1HomoloGene,
2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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  --

(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 HHLA3 (see all 201)    About this table    
Genomic DataTranscription Related DataAllele Frequencies
SNP IDValidClinical
significance
Chr 1 posSequence#AA
Chg
TypeMore#Allele
freq
PopTotal
sample
More
----------
rs1448001841,2
--70822429(+) ATAGTA/CTTTTT 4 -- int10--------
rs1163434781,2
F--70822431(+) AGTCTT/GTTTAG 4 -- int11Minor allele frequency- G:0.03WA 118
rs1920637461,2
C--70822457(+) GAATAC/GCATAA 4 -- int10--------
rs1851078661,2
--70822677(+) GAGGCC/TGAGGC 4 -- int10--------
rs1903531561,2
--70822773(+) ACTTGA/GTCTCA 4 -- int10--------
rs1386434051,2
--70822821(+) CTCATA/GCTTTA 4 -- int10--------
rs1927358661,2
--70822846(+) AAGAAC/GAGAAC 4 -- int10--------
rs1418605531,2
--70822867(+) TATGCA/TGTAAA 4 -- int10--------
rs758250741,2
C--70822876(+) AATCAC/GATGAT 4 -- int10--------
rs1462585751,2
--70823056(+) GGGCTA/GGATTC 4 -- int10--------

HapMap Linkage Disequilibrium report for HHLA3 (70820488 - 70851022 bp)

Structural Variations
     Database of Genomic Variants (DGV) 2 variations for HHLA3:    About this table    
Variant IDTypeSubtypePubMed ID
esv27106CNV Loss19812545
nsv830137CNV Loss17160897

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(in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Conferences by KenesGroup, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
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OMIM gene information: 604372    OMIM disorders: --


HHLA3 for disorders           About GeneDecksing


Export disorders for HHLA3 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 HHLA3 gene integrated from 10 sources:
(articles sorted by number of sources associating them with HHLA3)
    Utopia: connect your pdf to the dynamic
world of online information

  1. Endogenous retroviruses provide the primary polyadenylation signal for two new human genes (HHLA2 and HHLA3). (PubMed id 10444326)1, 2, 3, 9 Mager D.L.... Freeman J.D. (Genomics 1999)
  2. The DNA sequence and biological annotation of human chromosome 1. (PubMed id 16710414)1, 2 Gregory S.G.... Bentley D.R. (Nature 2006)
  3. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PubMed id 15489334)1, 2 Gerhard D.S.... Malek J. (Genome Res. 2004)
  4. hORFeome v3.1: a resource of human open reading frames representing over 10,000 human genes. (PubMed id 17207965)1 Lamesch P.... Vidal M. (Genomics 2007)
  5. Towards a proteome-scale map of the human protein-protein interaction network. (PubMed id 16189514)1 Rual J.F....Vidal M. (Nature 2005)
  6. 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)

(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: 11147 HGNC: 4906 AceView: HHLA3 Ensembl:ENSG00000197568 euGenes: HUgn11147
ECgene: HHLA3 H-InvDB: HHLA3

(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 HHLA3 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 HHLA3 gene:
Search GeneIP for patents involving HHLA3

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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 Custom Antibody / Protein Production Service
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 Browse ProSpec Recombinant Proteins
 Proteins for HHLA3
 Antibodies for HHLA3
 ELISAs for HHLA3
 CLIAs for HHLA3



 Browse ESI BIO Cell Lines and PureStem Progenitors for HHLA3
 Gene Synthesis
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 Variant Library Synthesis
 Codon Optimization
 Protein Production and Purification
 Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for HHLA3
 SwitchGear 3'UTR luciferase reporter plasmids for HHLA3
 SwitchGear Promoter luciferase reporter plasmids for HHLA3
 Search ThermoFisher Antibodies for HHLA3
 Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat HHLA3
 inGenious Targeting Laboratory: Let us create your new Knockout/Knockin mouse model for HHLA3
 inGenious Targeting Laboratory: Contact us about creating complex and humanized mouse models for HHLA3
 LSBio Antibodies in human, mouse, rat for HHLA3
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
       
GeneCards Homepage - Last full update: 7 May 2014 - Incrementals: 9 May 2014 , 2 Jun 2014 , 26 Jun 2014 , 30 Jun 2014

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