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HHLA3 Gene

protein-coding GIFtS: 41
GCID: GC01P070820

HERV-H LTR-Associating 3

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(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 at NCBI GenBank:

NC_000001.10 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 plasmid: HHLA3 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, Cloud-Clone Corp., eBioscience, and/or antibodies-online,
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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, 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): 1 molecular function term: About this table

GO ID	Qualified GO term	Evidence	PubMed IDs
GO:0005515	protein binding	IPI	16189514

Find genes that share ontologies with HHLA3 About GenesLikeMe

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:

Compartment	Confidence
extracellular	2
cytosol	1
nucleus	1

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(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 (Q9XRX5^{1, 3} ENSP00000359978⁴) via UniProtKB, MINT, STRING, and/or I2D (see all 11)

Interactant		Interaction Details
GeneCard	External ID(s)	Interaction Details
NMI	Q13287¹^,³, ENSP00000243346⁴	EBI-750554,EBI-372942 I2D: score=5 STRING: ENSP00000243346
CHRM3	ENSP00000255380⁴	STRING: ENSP00000255380
ENSG00000206379	ENSP00000372873⁴	STRING: ENSP00000372873
ENSG00000224398	ENSP00000413092⁴	STRING: ENSP00000413092
ENSG00000225553	ENSP00000391901⁴	STRING: ENSP00000391901

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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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(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 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

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HHLA3 Protein expression data from MOPED¹, PaxDb² and MaxQB³:

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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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(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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SNP ID	Valid	Clinical significance	Chr 1 pos	Sequence	#	AA Chg	Type	More	#	Allele freq	Pop	Total sample	More
Genomic Data					Transcription Related Data				Allele Frequencies
				--	--	--		--	--
rs144800184^1,2		--	70822429(+)	`ATAGTA/CTTTTT`	4	--	int¹		0	--	--	--	--
rs116343478^1,2	F	--	70822431(+)	`AGTCTT/GTTTAG`	4	--	int¹		1		WA	118
rs192063746^1,2	C	--	70822457(+)	`GAATAC/GCATAA`	4	--	int¹		0	--	--	--	--
rs185107866^1,2		--	70822677(+)	`GAGGCC/TGAGGC`	4	--	int¹		0	--	--	--	--
rs190353156^1,2		--	70822773(+)	`ACTTGA/GTCTCA`	4	--	int¹		0	--	--	--	--
rs138643405^1,2		--	70822821(+)	`CTCATA/GCTTTA`	4	--	int¹		0	--	--	--	--
rs192735866^1,2		--	70822846(+)	`AAGAAC/GAGAAC`	4	--	int¹		0	--	--	--	--
rs141860553^1,2		--	70822867(+)	`TATGCA/TGTAAA`	4	--	int¹		0	--	--	--	--
rs75825074^1,2	C	--	70822876(+)	`AATCAC/GATGAT`	4	--	int¹		0	--	--	--	--
rs146258575^1,2		--	70823056(+)	`GGGCTA/GGATTC`	4	--	int¹		0	--	--	--	--

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

Structural Variations
Database of Genomic Variants (DGV) 2 variations for HHLA3: About this table

Variant ID	Type	Subtype	PubMed ID
esv27106	CNV	Loss	19812545
nsv830137	CNV	Loss	17160897

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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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OMIM gene information: 604372 OMIM disorders: --

Find genes that share disorders with HHLA3 About GenesLikeMe

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

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)
The DNA sequence and biological annotation of human chromosome 1. (PubMed id 16710414)^{1, 2} Gregory S.G.... Bentley D.R. (Nature 2006)
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)
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)
Towards a proteome-scale map of the human protein-protein interaction network. (PubMed id 16189514)¹ Rual J.F....Vidal M. (Nature 2005)
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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		AND	OR
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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Name	Description
PharmGKB entry for HHLA3	Pharmacogenomics, SNPs, Pathways

Intellectual Property for HHLA3 gene
(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

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Advanced Cell Diagnostics, Animal models from genOway)
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Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for HHLA3

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Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat HHLA3

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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 , 2 Nov 2014 , 8 Jan 2015

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Hot genes Disease genes HHLA3 gene at Home site.

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HHLA3 Gene

HERV-H LTR-Associating 3

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HHLA3 Gene

HERV-H LTR-Associating 3

Aliasesfor HHLA3 gene

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Genomic Viewsfor HHLA3 gene

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HHLA3 Human Recombinant Protein Products:

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Genome Databases showing HHLA3 gene

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Specialized Databases showing HHLA3 gene

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for HHLA3 gene

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for HHLA3 gene

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for HHLA3 gene

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for HHLA3 gene

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for HHLA3 gene

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for HHLA3 gene

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for HHLA3 gene

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for HHLA3 gene

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for HHLA3 gene

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for HHLA3 gene

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for HHLA3 gene