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] See more...

Aliases for HCG9 Gene

Subcategory (RNA class) for HCG9 Gene


Number of RNA Genes sources:

3 / 17

Aliases for HCG9 Gene

  • HLA Complex Group 9 2 3 5
  • HCG9 2 5 165
  • HLA Complex Group 9 (Non-Protein Coding) 2 3
  • HCGIX4 2 3
  • HCGIX 2 3
  • NONHSAG046043.2 91
  • NONHSAG045665.2 91
  • NONHSAG045858.2 91
  • NONHSAG043387.2 91
  • NONHSAG046560.2 91
  • NONHSAG046202.2 91
  • NONHSAG046376.2 91
  • HSALNG0049107 164
  • HCGIX-4 2
  • PERB11 2

External Ids for HCG9 Gene

Previous GeneCards Identifiers for HCG9 Gene

  • GC06P029713
  • GC06P030048
  • GC06P030050
  • GC06P029943
  • GC06P030094
  • GC06P030182
  • GC06P030172
  • GC06P030224
  • GC06P032249
  • GC06P032424
  • GC06P032558
  • GC06P033198
  • GC06P030347
  • GC06P030496
  • GC06P030698
  • GC06P030859
  • GC06P031019
  • GC06P031175
  • GC06P031354
  • GC06P031618

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) is an RNA Gene, and is affiliated with the lncRNA class.

No data available for CIViC Summary , UniProtKB/Swiss-Prot Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for HCG9 Gene

Genomics for HCG9 Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for HCG9 Gene
GeneHancer (GH) Identifier GH Type GH
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH06J029976 Promoter/Enhancer 2.2 EPDnew Ensembl ENCODE CraniofacialAtlas dbSUPER 600.7 +1.4 1388 3 RNF2 CREB1 GATAD2A PRDM10 ZNF629 TFE3 ZNF512 IKZF1 CTCF ZNF143 MICD HCG9 POLR1H HLA-K HLA-H HLA-J ENSG00000230521 ENSG00000237669 HLA-A ZFP57
GH06J030857 Enhancer 1 Ensembl ENCODE dbSUPER 6.3 +882.4 882376 1.4 SP1 ZIC2 ARNT ZBTB44 RUNX3 ESR1 TGIF2 BCLAF1 OSR2 BCL11A VARS2 RNU6-1133P MUCL3 HCG21 HCG9 ENSG00000272501 HLA-J RF00017-5407 piR-36588-363 DDR1
GH06J030942 Enhancer 0.7 CraniofacialAtlas 6.4 +967.2 967212 0.6 PRDM1 REST POLR2A ZNF600 ZNF341 ZBTB20 SP1 CTCF ZXDB CTBP1 VARS2 HCG9 MUCL3 SFTA2 RF00017-5401
GH06J030500 Enhancer 0.8 Ensembl ENCODE dbSUPER 5.3 +525.4 525389 3.4 PRDM1 ZBTB33 ZNF652 MCM2 ZNF548 piR-45471-516 piR-55654-435 piR-43583-467 ABCF1 DHX16 MDC1 GNL1 PRR3 HLA-F-AS1 MIR877
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around HCG9 on the GeneHancer Hub at the UCSC Golden Path

Top Transcription factor binding sites by QIAGEN in the HCG9 gene promoter:
  • AML1a
  • AREB6
  • ARP-1
  • ATF
  • HTF
  • p300
  • SREBP-1a
  • SREBP-1b
  • SREBP-1c

Genomic Locations for HCG9 Gene

Genomic Locations for HCG9 Gene
3,299 bases
Plus strand
3,295 bases
Plus strand

Genomic View for HCG9 Gene

Genes around HCG9 on UCSC Golden Path with GeneCards custom track
HCG9 in the GeneCards ncRNA compendium hub on the UCSC Golden Path

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

Gene Families for HCG9 Gene

Suggested Antigen Peptide Sequences for HCG9 Gene

GenScript: Design optimal peptide antigens:
  • HcgIX protein (Q93065_HUMAN)
  • cDNA FLJ76523, highly similar to Homo sapiens HLA complex group 9 (HCG9), mRNA (Q96QB4_HUMAN)
genes like me logo Genes that share domains with HCG9: view

No data available for Protein Domains , Graphical View of Domain Structure and UniProtKB/Swiss-Prot for HCG9 Gene

Function for HCG9 Gene

Phenotypes From GWAS Catalog for HCG9 Gene

Phenotypes for HCG9 Gene

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

Animal Model Products

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for HCG9

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

Subcellular locations from

Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for HCG9 gene
Compartment Confidence
plasma membrane 1
extracellular 1
nucleus 1

No data available for Subcellular locations from UniProtKB/Swiss-Prot , Subcellular locations from the Human Protein Atlas (HPA) and Gene Ontology (GO) - Cellular Components for HCG9 Gene

Pathways & Interactions for HCG9 Gene

PathCards logo

SuperPathways for HCG9 Gene

No Data Available

Gene Ontology (GO) - Biological Process for HCG9 Gene


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

Drugs & Compounds for HCG9 Gene

No Compound Related Data Available

Transcripts for HCG9 Gene

Non-coding RNA (ncRNA) Transcripts from RNAcentral for HCG9 Gene

RNAcentral Transcript ID Subcategory Length (nts) # of Sources Source Identifiers and Annotations
URS000076D015_9606 lncRNA 663 4

Ensembl: ENST00000376800 (view in UCSC) , ENST00000422999 (view in UCSC) ,

LncBook: HSALNT0103672, HSALNT0103673, HSALNT0103674, HSALNT0103675, HSALNT0103677,

LNCipedia: HCG9:2,


URS00008C3CAF_9606 lncRNA 659 3

Ensembl: ENST00000445934 (view in UCSC) ,

LncBook: HSALNT0103679,


URS00008C2B05_9606 lncRNA 662 2

Ensembl: ENST00000416207 (view in UCSC) ,


URS00008C3CC6_9606 lncRNA 662 2

Ensembl: ENST00000383616 (view in UCSC) ,


URS00008C0E2B_9606 lncRNA 654 2

Ensembl: ENST00000413215 (view in UCSC) ,


HCG9 in the GeneCards ncRNA compendium hub on the UCSC Golden Path

Additional transcripts not in RNAcentral for HCG9 Gene

4 NCBI additional mRNA sequence :

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for HCG9

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

No ASD Table

Relevant External Links for HCG9 Gene

GeneLoc Exon Structure for

Expression for HCG9 Gene

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

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for HCG9

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 , mRNA Expression by UniProt/SwissProt , Evidence on tissue expression from TISSUES and Phenotype-based relationships between genes and organs from Gene ORGANizer 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:

  • Q93065_HUMAN
genes like me logo Genes that share paralogs with HCG9: view

No data available for Paralogs for HCG9 Gene

Variants for HCG9 Gene

Additional dbSNP identifiers (rs#s) for HCG9 Gene

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

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

Additional Variant Information for HCG9 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot , Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP and Variation tolerance for HCG9 Gene

Disorders for HCG9 Gene

Additional Disease Information for HCG9

Genetic Association Database
Human Genome Epidemiology Navigator
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
Open Targets Platform

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 XQ … Liu JJ (Nature genetics 2011) 3 41
  2. Variant of TYR and autoimmunity susceptibility loci in generalized vitiligo. (PMID: 20410501) Jin Y … Spritz RA (The New England journal of medicine 2010) 3 41
  3. A major histocompatibility Class I locus contributes to multiple sclerosis susceptibility independently from HLA-DRB1*15:01. (PMID: 20593013) Cree BA … IMSGC (PloS one 2010) 3 41
  4. High-density SNP screening of the major histocompatibility complex in systemic lupus erythematosus demonstrates strong evidence for independent susceptibility regions. (PMID: 19851445) Barcellos LF … Criswell LA (PLoS genetics 2009) 3 41
  5. A 356-Kb sequence of the subtelomeric part of the MHC Class I region. (PMID: 10727083) Hampe A … Galibert F (DNA sequence : the journal of DNA sequencing and mapping 1999) 2 3

Products for HCG9 Gene

Sources for HCG9 Gene