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Aliases for HCG9 Gene

Subcategory (RNA class) for HCG9 Gene

non-coding RNA

Quality Score for this RNA gene is


Aliases for HCG9 Gene

  • HLA Complex Group 9 (Non-Protein Coding) 2 3 5
  • HLA Complex Group 9 2
  • HCGIX4 3
  • HCGIX 3

External Ids for HCG9 Gene

Previous GeneCards Identifiers for HCG9 Gene

  • GC06P029713
  • GC06P030048
  • GC06P030050
  • GC06P029943
  • GC06P030094
  • GC06P030182
  • GC06P030172
  • GC06P030224
  • GC06P030347
  • GC06P030496

Summaries for HCG9 Gene

Entrez Gene Summary for HCG9 Gene

  • This gene lies within the MHC class I region on chromosome 6p21.3. This gene is believed to be non-coding, but its function has not been determined. [provided by RefSeq, Jul 2009]

GeneCards Summary for HCG9 Gene

HCG9 (HLA Complex Group 9 (Non-Protein Coding)) is an RNA Gene, and is affiliated with the non-coding RNA class.

No data available for UniProtKB/Swiss-Prot , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for HCG9 Gene

Genomics for HCG9 Gene

Regulatory Elements for HCG9 Gene

Enhancers for HCG9 Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH06F030942 1.2 Ensembl ENCODE 6.4 +967.7 967689 0.8 HDAC1 PKNOX1 INSM2 KLF17 ARID4B ZNF2 RAD21 ZNF366 SCRT2 ZNF143 HCG9 DPCR1 SFTA2
GH06F030531 1 Ensembl ENCODE 5.3 +557.5 557489 1.6 BCOR CTCF TEAD4 ZNF384 RAD21 ZNF366 ADNP SMC3 ZNF652 SMARCE1 GNL1 PRR3 HCG18 C6orf136 ABCF1 ZFP57 HCG9 GC06M030528
GH06F030857 0.7 ENCODE 6.3 +882.6 882576 1.0 PKNOX1 SAP130 FEZF1 ZIC2 RARA NFYB ZNF652 CREM MTA2 GTF2A2 VARS2 RNU6-1133P DPCR1 HCG21 HCG9 ENSG00000272501 HLA-J GC06P030986 LOC105375014
GH06F030500 0.8 Ensembl ENCODE 5.3 +525.7 525689 1.6 ELF3 RNF2 ZNF652 PRDM1 TEAD3 ABCF1 PRR3 GNL1 MIR877 HCG9 RPP21 HLA-E ENSG00000235781
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around HCG9 on UCSC Golden Path with GeneCards custom track

Promoters for HCG9 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000662276 1688 2000 PKNOX1 CREB3L1 ARID4B DMAP1 ZNF2 YY1 SLC30A9 SP3 SP5 REST

Genomic Location for HCG9 Gene

29,975,112 bp from pter
29,978,410 bp from pter
3,299 bases
Plus strand

Genomic View for HCG9 Gene

Genes around HCG9 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
HCG9 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for HCG9 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

Proteins for HCG9 Gene

Post-translational modifications for HCG9 Gene

No Post-translational modifications

No data available for DME Specific Peptides for HCG9 Gene

Domains & Families for HCG9 Gene

Suggested Antigen Peptide Sequences for HCG9 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

No data available for Gene Families , Protein Domains and UniProtKB/Swiss-Prot for HCG9 Gene

Function for HCG9 Gene

Phenotypes for HCG9 Gene

GenomeRNAi human phenotypes for HCG9:
genes like me logo Genes that share phenotypes with HCG9: view

Animal Model Products

No data available for Molecular function , Enzyme Numbers (IUBMB) , Gene Ontology (GO) - Molecular Function , Human Phenotype Ontology , Animal Models , miRNA , Transcription Factor Targets and HOMER Transcription for HCG9 Gene

Localization for HCG9 Gene

No data available for Subcellular locations from UniProtKB/Swiss-Prot , Subcellular locations from COMPARTMENTS and Gene Ontology (GO) - Cellular Components for HCG9 Gene

Pathways & Interactions for HCG9 Gene

No Data Available

Interacting Proteins for HCG9 Gene

Gene Ontology (GO) - Biological Process for HCG9 Gene


No data available for Pathways by source and SIGNOR curated interactions for HCG9 Gene

Transcripts for HCG9 Gene

mRNA/cDNA for HCG9 Gene

(1) REFSEQ mRNAs :
(4) Additional mRNA sequences :
(2) Selected AceView cDNA sequences:
(2) Ensembl transcripts including schematic representations, and UCSC links where relevant :

Unigene Clusters for HCG9 Gene

HLA complex group 9 (non-protein coding):
Representative Sequences:

Alternative Splicing Database (ASD) splice patterns (SP) for HCG9 Gene

No ASD Table

Relevant External Links for HCG9 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for HCG9 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for HCG9 Gene

NURSA nuclear receptor signaling pathways regulating expression of HCG9 Gene:


SOURCE GeneReport for Unigene cluster for HCG9 Gene:

genes like me logo Genes that share expression patterns with HCG9: view

Primer Products

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues , Protein differential expression in normal tissues , Protein expression , Protein tissue co-expression partners and mRNA Expression by UniProt/SwissProt for HCG9 Gene

Orthologs for HCG9 Gene

Evolution for HCG9 Gene

Gene Tree for HCG9 (if available)
Gene Tree for HCG9 (if available)

No data available for Orthologs for HCG9 Gene

Paralogs for HCG9 Gene

(1) SIMAP similar genes for HCG9 Gene using alignment to 1 proteins:

genes like me logo Genes that share paralogs with HCG9: view

No data available for Paralogs for HCG9 Gene

Variants for HCG9 Gene

Sequence variations from dbSNP and Humsavar for HCG9 Gene

SNP ID Clin Chr 06 pos Sequence Context AA Info Type
rs111155355 -- 29,978,407(-) AGTTT(A/C/G)TTATT downstream-variant-500B
rs111281199 -- 29,976,561(+) CAACT(A/G)CGTTT intron-variant
rs111323003 -- 29,976,554(+) GAGCC(A/T)TCAAC intron-variant
rs111782274 -- 29,976,999(+) CGCGG(C/T)GGATT intron-variant
rs111785961 -- 29,976,889(+) CCAGC(-/TG)CGCGG intron-variant

Structural Variations from Database of Genomic Variants (DGV) for HCG9 Gene

Variant ID Type Subtype PubMed ID
nsv601264 CNV loss 21841781
nsv511863 CNV loss 21212237
nsv508398 CNV deletion 20534489
nsv1144137 CNV deletion 24896259
nsv1122126 CNV deletion 24896259
nsv10810 CNV gain+loss 18304495
nsv1074389 CNV deletion 25765185
esv3369212 CNV duplication 20981092
esv3360519 CNV insertion 20981092
esv3350882 CNV duplication 20981092
esv3342659 CNV insertion 20981092
esv3332677 CNV duplication 20981092
esv3310214 CNV mobile element insertion 20981092
esv3303415 CNV mobile element insertion 20981092
esv32544 CNV gain+loss 17666407
esv2759412 CNV gain+loss 17122850
esv2731778 CNV deletion 23290073
esv2731777 CNV deletion 23290073
esv2731775 CNV deletion 23290073
esv2670487 CNV deletion 23128226
esv2641340 CNV deletion 19546169
dgv993e201 CNV deletion 23290073
dgv992e201 CNV deletion 23290073
dgv1088e199 CNV deletion 23128226

Relevant External Links for HCG9 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot and Variation tolerance for HCG9 Gene

Disorders for HCG9 Gene

Relevant External Links for HCG9

Genetic Association Database (GAD)
Human Genome Epidemiology (HuGE) Navigator
Atlas of Genetics and Cytogenetics in Oncology and Haematology:

No disorders were found for HCG9 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for HCG9 Gene

Publications for HCG9 Gene

  1. A genome-wide association study in Han Chinese identifies multiple susceptibility loci for IgA nephropathy. (PMID: 22197929) Yu X.Q. … Liu J.J. (Nat. Genet. 2012) 3 46 64
  2. Variant of TYR and autoimmunity susceptibility loci in generalized vitiligo. (PMID: 20410501) Jin Y. … Spritz R.A. (N. Engl. J. Med. 2010) 3 46 64
  3. A major histocompatibility Class I locus contributes to multiple sclerosis susceptibility independently from HLA-DRB1*15:01. (PMID: 20593013) Cree B.A. … . (PLoS ONE 2010) 3 46 64
  4. High-density SNP screening of the major histocompatibility complex in systemic lupus erythematosus demonstrates strong evidence for independent susceptibility regions. (PMID: 19851445) Barcellos L.F. … Criswell L.A. (PLoS Genet. 2009) 3 46 64
  5. Molecular dynamics of MHC genesis unraveled by sequence analysis of the 1,796,938-bp HLA class I region. (PMID: 10557312) Shiina T. … Inoko H. (Proc. Natl. Acad. Sci. U.S.A. 1999) 2 3 64

Products for HCG9 Gene

Sources for HCG9 Gene

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