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Category Symbol Source: HGNC EntrezGene Ensembl GeneCards RNA genes CroW21

GIFtS
-

HIGD1A Gene

protein-coding GIFtS: 48
GCID: GC03M042801

HIG1 hypoxia inducible domain family, member 1A

(Previous names: HIG1 domain family, member 1A )

Explore 5 diseases affiliated with
HIGD1A via

MalaCards

our new
Human Malady Compendium

(According to ¹HGNC, ²Entrez Gene,
³UniProtKB/Swiss-Prot, ⁴UniProtKB/TrEMBL, ⁵OMIM, ⁶GeneLoc, ⁷Ensembl, ⁸DME, ⁹miRBase, and/or ¹⁰fRNAdb)
About This Section

Aliases
HIG1 Hypoxia Inducible Domain Family, Member 1A¹ ²		RCF1 Homolog A² ³
HIG1¹ ² ³		DKFZP564K247¹
HIG1 Domain Family, Member 1A¹ ²		HIG1 Domain Family Member 1A, Mitochondrial²
Hypoxia-Inducible Gene 1 Protein² ³		Hypoxia Inducible Gene 1²
RCF1a² ³

External Ids:	HGNC: 29527¹	Entrez Gene: 25994²	Ensembl: ENSG00000181061⁷	UniProtKB: Q9Y241³

Export aliases for HIGD1A gene to outside databases

(According to Entrez Gene, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
About This Section

UniProtKB/Swiss-Prot: HIG1A_HUMAN, Q9Y241

Function: Proposed subunit of cytochrome c oxidase (COX, complex IV), which is the terminal component of the

mitochondrial respiratory chain that catalyzes the reduction of oxygen to water. May play a role in the assembly of

respiratory supercomplexes

Gene Wiki entry for HIGD1A

(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 69), Regulatory elements and Epigenetics data according to QIAGEN, SABiosciences, and/or SwitchGear Genomics)
About This Section

RefSeq DNA sequence:

NC_000003.11 NC_018914.1 NT_022517.18

Regulatory elements:

SABiosciences Regulatory transcription factor binding sites in the HIGD1A gene promoter:
HOXA9B HOXA9 LyF-1 Meis-1 Meis-1b
Other transcription factors

SwitchGear Promoter luciferase reporter plasmid: HIGD1A promoter sequence

Search SABiosciences Chromatin IP Primers for HIGD1A

Epigenetics:

QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat HIGD1A

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

Entrez Gene cytogenetic band: 3p22.1 Ensembl cytogenetic band: 3p22.1 HGNC cytogenetic band: 3p22.1

HIGD1A Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
HIGD1A gene location

GeneLoc information about chromosome 3 GeneLoc Exon Structure

GeneLoc location for GC03M042801: view genomic region (about GC identifiers)

Start:	42,798,669 bp from pter	End:	42,846,027 bp from pter
Size:	47,359 bases	Orientation:	minus strand

(According to ¹UniProtKB, HORDE, neXtProt, Ensembl, and/or Reactome, Modification sites according to ²PhosphoSitePlus, Specific Peptides from DME, Protein expression images according to data from SPIRE MOPED and PaxDb, 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 Uscn,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Uscn, Ontologies according to Gene Ontology Consortium 01 Mar 2013 and Entrez Gene, Antibodies by EMD Millipore, R&D Systems, GenScript, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, Abcam, and/or Uscn)
About This Section

UniProtKB/Swiss-Prot: HIG1A_HUMAN, Q9Y241 (See protein sequence)

Recommended Name: HIG1 domain family member 1A, mitochondrial

Size: 93 amino acids; 10143 Da

Subunit: Associates with cytochrome c oxidase (COX, complex IV); proposed complex component. Also associates with

respratory chain supercomplexes

Subcellular location: Mitochondrion membrane; Multi-pass membrane protein. Mitochondrion inner membrane (Probable)

Sequence caution: Sequence=BG400624; Type=Frameshift; Positions=32;

1 PDB 3D structure from and Proteopedia for HIGD1A:

2LOM (3D)

Secondary accessions: Q9UFZ2

Alternative splicing: 2 isoforms: Q9Y241-1 Q9Y241-2

Explore the universe of human proteins at neXtProt for HIGD1A: NX_Q9Y241

Post-translational modifications:

View modification sites using PhosphoSitePlus²

View neXtProt modification sites for NX_Q9Y241

HIGD1A Protein expression data from MOPED and PaxDb: About this image

REFSEQ proteins (3 alternative transcripts):

NP_001093138.1 NP_001093139.1 NP_054775.2

ENSEMBL proteins:

ENSP00000406044 ENSP00000319393 ENSP00000402160 ENSP00000408289 ENSP00000398064

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	Uscn Proteins for HIGD1A

Gene Ontology (GO): 4 cellular component terms (GO ID links to tree view): About this table

GO ID	Qualified GO term	Evidence	PubMed IDs
GO:0005743	mitochondrial inner membrane	IEA	--
GO:0016021	integral to membrane	IEA	--
GO:0043234	protein complex	IDA	--
GO:0070469	respiratory chain	IEA	--

HIGD1A for ontologies About GeneDecksing

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	Uscn ELISAs and CLIAs for HIGD1A

(According to InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
About This Section

HIGD1A for domains About GeneDecksing

1 InterPro domain/family:

IPR007667 Hypoxia_induced_domain

Graphical View of Domain Structure for InterPro Entry Q9Y241

ProtoNet protein and cluster: Q9Y241

UniProtKB/Swiss-Prot: HIG1A_HUMAN, Q9Y241

Similarity: Contains 1 HIG1 domain

(According to ¹UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or ²DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013,
bound targets from SABiosciences, miRNA Gene Targets from miRTarBase shRNA from OriGene, RNAi from EMD Millipore, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, Gene Editing from DNA2.0, Clones from EMD Millipore, OriGene, SwitchGear Genomics, GenScript, Sino Biological, DNA2.0, and Vector BioLabs, Cell Lines from GenScript, LifeMap BioReagents, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Mar 2013 via Entrez Gene.)
About This Section

Function Summary:

UniProtKB/Swiss-Prot: HIG1A_HUMAN, Q9Y241

Function: Proposed subunit of cytochrome c oxidase (COX, complex IV), which is the terminal component of the

mitochondrial respiratory chain that catalyzes the reduction of oxygen to water. May play a role in the assembly of

respiratory supercomplexes

Induction: By hypoxia

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		8/38 QIAGEN miScript miRNA Assays for microRNAs that regulate HIGD1A (see all 38):
		hsa-miR-596 hsa-miR-15a hsa-miR-4272 hsa-miR-3653 hsa-miR-138-2* hsa-miR-192 hsa-miR-4275 hsa-miR-424

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In Situ Assay
Products:

Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for HIGD1A

1 GenomeRNAi human phenotype for HIGD1A:

Increased cell number in G2M,

(Pathways according to EMD Millipore, R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to SABiosciences, 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 Mar 2013 via Entrez Gene).
About This Section

Interactions:

Search SABiosciences Gene Network Central^TM Interacting Genes and Proteins Networks for HIGD1A

STRING Interaction Network Preview (showing 5 interactants - click image to see 8)

5/9 Interacting proteins for HIGD1A (Q9Y241^{1, 3} ENSP00000398064⁴) via UniProtKB, MINT, STRING, and/or I2D (see all 9)

Interactant		Interaction Details
GeneCard	External ID(s)	Interaction Details
CASP4	P49662¹^,³, ENSP00000388566⁴	EBI-1051940,EBI-1057327 I2D: score=1 STRING: ENSP00000388566
SNRPB	P14678¹^,³	EBI-1051940,EBI-372458 I2D: score=1
PAK7	Q9P286¹^,³, ENSP00000322957⁴	EBI-1051940,EBI-1051061 I2D: score=1 STRING: ENSP00000322957
MYC	P01106³, ENSP00000367207⁴	I2D: score=3 STRING: ENSP00000367207
USP32	Q8NFA0³, ENSP00000300896⁴	I2D: score=1 STRING: ENSP00000300896

About this table

Gene Ontology (GO): 5 biological process terms (GO ID links to tree view): About this table

GO ID	Qualified GO term	Evidence	PubMed IDs
GO:0006950	response to stress	IEA	--
GO:0022900	electron transport chain	IEA	--
GO:0042149	cellular response to glucose starvation	--	--
GO:0043066	negative regulation of apoptotic process	IDA	--
GO:0071456	cellular response to hypoxia	--	--

HIGD1A for ontologies About GeneDecksing

(Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience HMDB, BitterDB, and/or Novoseek, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB, with drugs/clinical trials/news search links to CenterWatch)
About This Section

Browse Small Molecules at EMD Millipore

Browse drugs & compounds from Enzo Life Sciences

Browse Tocris compounds for HIGD1A
Search CenterWatch for drugs/clinical trials and news about HIGD1A / HIG1A

(Secondary structures according to fRNAdb,
GenBank/EMBL/DDBJ Accessions according to
Unigene (Build 235 Homo sapiens; Mar 10 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,
RNAi Products from EMD Millipore,
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Tagged/untagged cDNA clones from OriGene, SwitchGear Genomics, GenScript, DNA2.0, Vector BioLabs, Primers from OriGene, SABiosciences, and/or QIAGEN )
About This Section

REFSEQ mRNAs for HIGD1A gene (3 alternative transcripts):

NM_001099668.1 NM_001099669.1 NM_014056.3

Unigene Clusters for HIGD1A:

HIG1 hypoxia inducible domain family, member 1A

Hs.593134 [show with all ESTs], Hs.728813 [show with all ESTs]

Unigene Representative Sequences: BF790812, AL833541

6 Ensembl transcripts including schematic representations, and UCSC links where relevant:

ENST00000431549 ENST00000321331(uc010hid.3 uc003cma.4 uc003cmb.4)

ENST00000418900 ENST00000470543 ENST00000430190 ENST00000452906

miRNA Products:		OriGene 3'-UTR Clone (see all 3): HIGD1A Browse OriGene MicroRNA Expression Plasmids
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Additional cDNA sequence:

AF077034.1 AF145385.1 AK225571.1 AK311815.1 AL110233.1 AL833541.1 BC000601.1 BC009583.1

BC009594.1 BC070277.1 CR457385.1

24/42 DOTS entries (see all 42):

DT.91680071 DT.100883119 DT.456275 DT.100883118 DT.91780356 DT.120860165 DT.100883126 DT.100883114

DT.410480 DT.100883128 DT.91780416 DT.100883123 DT.91780341 DT.120860055 DT.91780396 DT.120860210

DT.121118912 DT.100045267 DT.100883122 DT.100045266 DT.309429 DT.91780332 DT.100810305 DT.100883127

24/1403 AceView cDNA sequences (see all 1403):

BM709436 BG260730 T36025 C01072 AA356358 N75908 BQ631521 BM768439

BM830327 BG778921 BU508766 AW328744 BM838217 BM856245 CD239280 BM467994

AW674873 BM045358 AL543088 BE559897 AW368698 BI762728 CR604953 CF528427

GeneLoc Exon Structure

5/6 Alternative Splicing Database (ASD) splice patterns (SP) for HIGD1A (see all 6) About this scheme

ExUns:	1a	·	1b	·	1c	·	1d	·	1e	^	2	^	3a	·	3b	^	4a	·	4b	^	5a	·	5b	^	6a	·	6b
SP1:									-		-		-				-		-
SP2:									-				-
SP3:									-		-		-
SP4:									-		-		-		-		-		-
SP5:									-		-						-		-

ECgene alternative splicing isoforms for HIGD1A

(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™, plus additional links to Genevestigator, and/or SOURCE, and/or BioGPS, and/or UniProtKB,
PCR Arrays from SABiosciences, Primers from OriGene, SABiosciences, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
About This Section

HIGD1A expression in normal human tissues (normalized intensities)
See probesets specificity/sensitivity at GeneAnnot
About this imageBioGPS
CGAP TAG: TATCGGGAAT

About this image

HIGD1A expression in embryonic tissues and stem cells

Expression by the Database of Embryonic development, Stem cell research, and Regenerative medicine About this table

1 LifeMap In Vivo Development Anatomical Compartment/Cell

Tissue

Anatomical Compartment

Cell

Category (developmental path)

Head Mesenchyme

Branchial Arch 1

Cranial Neural Crest Cells

Neural Crest

Expression:

Positive

Negative

Selective marker

Experimental details:

Curated

Microarrays

In-situ hybridization

Stem Cell Differentiation: 1 LifeMap Cell

Name

Category

Definitive endoderm-like cells (A scalable, suspensi...)

See HIGD1A Protein Expression from SPIRE MOPED and PaxDB
Genevestigator expression for HIGD1A

SOURCE GeneReport for Unigene clusters: Hs.593134 Hs.728813

SABiosciences Custom PCR Arrays for HIGD1A

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In Situ
Assay Products:

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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)
About This Section

This gene was present in the common ancestor of animals.

Orthologs for HIGD1A gene from 5/16 species (see all 16) About this table

Organism	Taxonomic classification	Gene	Description	Human Similarity	Orthology Type	Details
chicken (Gallus gallus)	Aves	HIGD1A¹	HIG1 hypoxia inducible domain family, member 1A	69.88(n) 73.49(a)		768335 NM_001030957.1 NP_001026128.1
lizard (Anolis carolinensis)	Reptilia	HIGD1A⁶	--	74(a)	1 ↔ 1	GL343332.1(1387724-1392695)
African clawed frog (Xenopus laevis)	Amphibia	AB095361.1²	--	76.47(n)		AB095361.1
zebrafish (Danio rerio)	Actinopterygii	AB094785.1²	--	72.2(n)		373084 AB094785.1
fruit fly (Drosophila melanogaster)	Insecta	CG11825⁶	--	29(a)	1 → many	2R(6307919-6309196)

ENSEMBL Gene Tree for HIGD1A (if available)
TreeFam Gene Tree for HIGD1A (if available)

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

Paralogs for HIGD1A gene

HIGD1B² HIGD1C²

4 SIMAP similar genes for HIGD1A using alignment to 3 protein entries: HIG1A_HUMAN (see all proteins):

HIGD1C HIGD1B HIGD2A HIGD2B

HIGD1A for paralogs About GeneDecksing

5/17 Pseudogenes.org Pseudogenes for HIGD1A (see all 17)
PGOHUM00000242327 PGOHUM00000242605 PGOHUM00000239672 PGOHUM00000239771 PGOHUM00000239792

(SNPs/Variants according to the ¹NCBI SNP Database, ²Ensembl, ³PupaSUITE, UniProtKB, 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) and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers from QIAGEN, Cancer Mutation PCR Arrays and Assays and Copy Number PCR Arrays from SABiosciences)
About This Section

SNP ID	Valid	Clinical significance	Chr 3 pos	Sequence	#	AA Chg	Type	More	#	Allele freq	Pop	Total sample	More
Genomic Data					Transcription Related Data				Allele Frequencies
				--	--	--		--	--
rs188744809^1,2		--	42823912(+)	`GTAAGA/CCCTTT`	3	--	ds500¹		0	--	--	--	--
rs57759767^1,2	C,	--	42823967(+)	`ACTGTC/-CCCAT`	3	--	ds500¹		1		CSA	2
rs78403799^1,2	C	--	42823970(+)	`GTCCCA/CATTTT`	3	--	ds500¹		0	--	--	--	--
rs74635250^1,2	C	--	42823971(+)	`TCCCCA/TTTTTA`	3	--	ds500¹		0	--	--	--	--
rs114815899^1,2	F,	--	42824017(+)	`CAGAAC/TCATGA`	3	--	ds500¹		1		WA	118
rs192813292^1,2		--	42824088(+)	`TTACCA/GTTCTT`	3	--	ds500¹		0	--	--	--	--
rs184125644^1,2		--	42824371(+)	`ACTTAC/TGTAAG`	3	--	ds500¹		0	--	--	--	--
rs147099211^1,2	C,	--	42824392(+)	`ATGAC-/TTTTAG`	3	--	ds500¹		0	--	--	--	--
rs147062284^1,2		--	42824598(+)	`GGGAAC/TGTTTT`	3	--	ut3¹		0	--	--	--	--
rs189888521^1,2		--	42824748(+)	`CAATAA/GTAGTT`	3	--	ut3¹		0	--	--	--	--

HapMap Linkage Disequilibrium report for HIGD1A (42798669 - 42846027 bp)
Structural Variations (Copy Number Variations, Insertions/Deletions, Inversions)
Database of Genomic Variants (DGV): 6 variations for HIGD1A
6 CNVs: 6174 62051 39331 43467 23013 23685

SABiosciences Cancer Mutation PCR Assays

QIAGEN SeqTarget long-range PCR primers in human, mouse, rat for resequencing HIGD1A

DNA2.0 Custom Variant and Variant Library Synthesis for HIGD1A

(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.)
About This Section

HIGD1A for disorders About GeneDecksing

5 diseases for HIGD1A: About MalaCards

hypoxia prostatic hypertrophy cervical cancer cervicitis

prostatitis

Human Genome Epidemiology (HuGE) Navigator: HIGD1A (1 document)

Export disorders for HIGD1A 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)
About This Section

PubMed articles for HIGD1A gene, integrated from 9 sources (see all 23):
(articles sorted by number of sources associating them with HIGD1A)

Utopia: connect your pdf to the dynamic
world of online information

Towards a catalog of human genes and proteins: sequencing and analysis of 500 novel complete protein coding human cDNAs. (PubMed id 11230166)^{1, 2, 3} Wiemann S.... Poustka A. (2001)
Cloning and functional analysis of cDNAs with open reading frames for 300 previously undefined genes expressed in CD34+ hematopoietic stem/progenitor cells. (PubMed id 11042152)^{1, 2, 3} Zhang Q.-H.... Chen Z. (2000)
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. (2004)
Epigenetic regulation of gene expression in cervical cancer cells by the tumor microenvironment. (PubMed id 10690527)^{1, 2} Denko N.C....Giaccia A.J. (2000)
Rcf1 mediates cytochrome oxidase assembly and respirasome formation, revealing heterogeneity of the enzyme complex. (PubMed id 22342701)² Vukotic M.... Deckers M. (2012)
A census of human soluble protein complexes. (PubMed id 22939629)¹ Havugimana P.C....Emili A. (2012)
HIG1, a novel regulator of mitochondrial g-secretase, maintains normal mitochondrial function. (PubMed id 22355194)¹ Hayashi H....Kaneda Y. (2012)
Facile backbone structure determination of human membrane proteins by NMR spectroscopy. (PubMed id 22609626)² Klammt C.... Choe S. (2012)
Initial characterization of the human central proteome. (PubMed id 21269460)² Burkard T.R.... Colinge J. (2011)
A proteome-wide, quantitative survey of in vivo ubiqui tylation sites reveals widespread regulatory roles. (PubMed id 21890473)¹ Wagner S.A....Choudhary C. (2011)

(in PubMed, OMIM, and NCBI Bookshelf)
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		AND	OR
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(According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
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Entrez Gene: 25994	HGNC: 29527	AceView: HIG1	Ensembl:ENSG00000181061	euGenes: HUgn25994
ECgene: HIGD1A	H-InvDB: HIGD1A

(According to HUGE)
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(According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL,
Wikipedia and/or GeneReviews via UniProtKB/Swiss-Prot)
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Name	Description
PharmGKB entry for HIGD1A	Pharmacogenomics, SNPs, Pathways

Intellectual Property for HIGD1A 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 HIGD1A gene:
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GeneCards and IP:
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HIGD1A Gene

HIG1 hypoxia inducible domain family, member 1A

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HIGD1A Gene

HIG1 hypoxia inducible domain family, member 1A

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