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HLA complex group 9 (non-protein coding)(Previous name: HLA complex group 9 )
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Aliases
for HCG9 gene
(According to
1HGNC,
2Entrez Gene,
3UniProtKB/Swiss-Prot,
4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc,
7Ensembl,
8DME,
9miRBase,
and/or 10fRNAdb)
About This Section
|
Subcategory (RNA class): processed_transcript
Quality score for this RNA gene is 3
| Aliases |
|---|
| HLA Complex Group 9 (Non-Protein Coding)1 2 | | PERB111 | | HCGIX1 2 4 | | HCG IX4 | | HCGIX41 2 | | HcgIX1 | | HLA Complex Group 91 4 | | HcgIX Protein4 | | HCGIX-41 | | |
Export aliases for HCG9 gene to outside databasesPrevious GC identifers: GC06P029713 GC06P030048 GC06P030050 |
Summaries
for HCG9 gene(According to Entrez Gene,
Tocris Bioscience,
Wikipedia's
Gene Wiki,
PharmGKB,
UniProtKB/Swiss-Prot,
and/or
UniProtKB/TrEMBL)
About This Section
|
Entrez Gene summary for HCG9:
This gene lies within the MHC class I region on chromosome 6p21.3. This gene is believed to be non-coding, but itsfunction has not been determined. (provided by RefSeq, Jul 2009)
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Genomic Views
for HCG9 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 69),
Regulatory elements and Epigenetics data according to
QIAGEN,
SABiosciences, and/or
SwitchGear Genomics)
About This Section
| RefSeq DNA sequence:- NC_000006.11 NC_018917.1 NT_007592.15 NT_113891.2 NT_167245.1 NT_167246.1 NT_167247.1 NT_167248.1
- NT_167249.1
Regulatory elements:
 SABiosciences Regulatory transcription factor binding sites in the HCG9 gene promoter:
AML1a p300 SREBP-1c HTF SREBP-1b AREB6 SREBP-1a ARP-1 ATF
Other transcription factors
Search SABiosciences Chromatin IP Primers for HCG9
Epigenetics:
| | QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat HCG9 |
Genomic Location:
Genomic View: UCSC Golden Path with GeneCards custom track
Entrez Gene cytogenetic band: 6p21.3 Ensembl cytogenetic band: 6p22.1 HGNC cytogenetic band: 6p21.3HCG9 Gene in genomic location: bands according to Ensembl, locations according to
 (and/or Entrez Gene and/or Ensembl if different)
GeneLoc information about chromosome 6 GeneLoc Exon Structure GeneLoc location for GC06P029943: view genomic region
(about GC identifiers)
Start:
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29,942,889 bp from pter |
End:
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29,946,183 bp from pter |
Size:
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3,295 bases |
Orientation:
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plus strand |
6 alternative locations:
| Chr6+,ALT_REF_LOCI_3 29,932,826-29,947,156 | Chr6+,ALT_REF_LOCI_6 29,932,284-29,971,159 | Chr6+,ALT_REF_LOCI_4 29,861,132-29,864,418 | | Chr6+,ALT_REF_LOCI_5 29,936,176-29,939,465 | Chr6+,ALT_REF_LOCI_2 29,932,391-29,974,868 | Chr6+,ALT_REF_LOCI_7 29,861,681-29,864,967 | |
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Proteins
for HCG9 gene
(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/TrEMBL: Q93065 (See
protein sequence)Recommended Name: HCG IX Size: 77 amino acids; 8694 Da |
Protein
Domains /
Families
for HCG9 gene(According to InterPro, ProtoNet,
UniProtKB, and/or BLOCKS,
Sets of similar genes according to GeneDecks)
About This Section
| ProtoNet protein and cluster: Q93065 |
Function
for HCG9 gene
(According to 1UniProtKB,
Genatlas,
LifeMap Discovery™,
IUBMB, and/or
2DME,
Human phenotypes from GenomeRNAi,
Animal models from MGI Mar 06 2013,
inGenious Targeting Laboratory,
bound targets from SABiosciences,
miRNA Gene Targets from miRTarBase,
shRNA from
OriGene,
Sirion Biotech,
RNAi from
EMD Millipore,
siRNAs from
OriGene,
QIAGEN,
microRNA from QIAGEN,
Gene Editing from DNA2.0,
Sirion Biotech,
Clones from EMD Millipore,
OriGene,
SwitchGear Genomics,
GenScript,
Sino Biological,
DNA2.0,
and Vector BioLabs,
Cell Lines from GenScript,
LifeMap BioReagents,
Sirion Biotech,
In Situ Hybridization Assays from Advanced Cell Diagnostics,
Ontologies according to Gene Ontology Consortium 01 Mar 2013 via
Entrez Gene.)
About This Section
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Phenotypes:
1 GenomeRNAi human phenotype for HCG9:
Animal Models:
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Pathways & Interactions
for HCG9 gene
(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
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Interactions:
Search SABiosciences Gene Network CentralTM Interacting Genes and Proteins Networks for HCG9
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Drugs & Compounds
for HCG9 gene(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 Tocris compounds for HCG9
Search CenterWatch for drugs/clinical trials and news about HCG9 
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Transcripts
for HCG9 gene(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,
siRNAs from
OriGene,
QIAGEN,
shRNA from
OriGene,
Sirion Biotech,
microRNA from QIAGEN,
Tagged/untagged cDNA clones from
OriGene,
SwitchGear Genomics,
GenScript,
DNA2.0,
Vector BioLabs,
Primers from
OriGene,
SABiosciences, and/or
QIAGEN
)
About This Section
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REFSEQ mRNAs for HCG9 gene: NM_005844.2 Unigene Cluster for HCG9: HLA complex group 9 (non-protein coding) Hs.656251 [show with all ESTs]Unigene Representative Sequence: BX0979612 Ensembl transcripts including schematic representations, and UCSC links where relevant: ENST00000376800(lincRNA)(uc003rth.3) ENST00000463275(lincRNA)
Additional cDNA sequence: AK289926.1 BC119792.1 NR_028032.1 X95289.1 2 DOTS entries: DT.307579 DT.91802280 2 AceView cDNA sequences: NM_005844 X95289
GeneLoc Exon Structure
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Expression
for HCG9 gene
(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
| Expression evidence for HCG9:none
HCG9 expression in normal human tissues (normalized intensities)
See probesets specificity/sensitivity at GeneAnnot
About this imageBioGPS
CGAP TAG: AGCTTCTACC
About this image
Genevestigator expression for HCG9
SOURCE GeneReport for Unigene cluster: Hs.656251
SABiosciences Custom PCR Arrays for HCG9
Primer
Products: |  | OriGene genome-wide validated SYBR primer pairs in human, mouse, rat for HCG9
Browse OriGene validated miRNA SYBR primer pairs
| | | Search SABiosciences RT2 qPCR
Primer Assays in human, mouse, rat HCG9 | | | QIAGEN QuantiTect SYBR Green Assays in human, mouse, rat HCG9 | | | QIAGEN QuantiFast Probe-based Assays in human, mouse, rat HCG9 |
Orthologs
for HCG9 gene
(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
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ENSEMBL Gene Tree for HCG9 (if available)
TreeFam Gene Tree for HCG9 (if available) |
Paralogs
for HCG9 gene(Paralogs according to
1HomoloGene,
2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
About This Section
| -- |
Genomic Variants
for HCG9 gene(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
|
| Genomic Data | Transcription Related Data | Allele Frequencies | | SNP ID | Valid | Clinical
significance | Chr 6 pos | Sequence | # | AA
Chg | Type | More | # | Allele
freq | Pop | Total
sample | More |
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HapMap Linkage Disequilibrium report for HCG9 (29942889 - 29946183 bp)
Structural Variations (Copy Number Variations, Insertions/Deletions, Inversions)
Database of Genomic Variants (DGV): 6 variations for HCG9
6 CNVs: 99484 7558 4669 31269 3599 2622 | SABiosciences Cancer Mutation PCR Assays |
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Disorders
/ Diseases
for HCG9 gene
(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
|
HCG9 for disorders About GeneDecksing
5  diseases for HCG9: About MalaCardssystemic lupus erythematosus lupus erythematosus multiple sclerosis hodgkin's lymphoma
vitiligo
Human Genome Epidemiology (HuGE) Navigator: HCG9 (4 documents)
Export disorders for HCG9 gene to outside databases
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Publications
for HCG9 gene (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 HCG9 gene, integrated from 9 sources (see all 12):
(articles sorted by number of sources associating them with HCG9) | |  | Utopia: connect your pdf to the dynamic
world of online information |
- Molecular dynamics of MHC genesis unraveled by sequence analysis of the 1,796,938-bp HLA class I region. (PubMed id 10557312)1, 3 Shiina T....Inoko H. (1999)
- A 356-Kb sequence of the subtelomeric part of the MHC class I region. (PubMed id 10727083)1, 3 Hampe A.... Galibert F. (1999)
- A genome-wide association study in Han Chinese identif ies multiple susceptibility loci for IgA nephropathy. (PubMed id 22197929)1 Yu X.Q....Liu J.J. (2012)
- A multi-tissue analysis identifies HLA complex group 9 gene methylation differences in bipolar disorder. (PubMed id 21647149)1 Kaminsky Z....Petronis A. (2012)
- Variant of TYR and autoimmunity susceptibility loci i n generalized vitiligo. (PubMed id 20410501)1 Jin Y....Spritz R.A. (2010)
- A major histocompatibility Class I locus contributes to multiple sclerosis susceptibility independently from HLA-DRB1*15:01. (PubMed id 20593013)1 Cree B.A.... . (2010)
- High-density SNP screening of the major histocompatib ility complex in systemic lupus erythematosus demonstrates strong evidence for independent susceptibility regions. (PubMed id 19851445)1 Barcellos L.F....Criswell L.A. (2009)
- Rapid evolution of major histocompatibility complex class I genes in primates generates new disease alleles in humans via hitchhiking diversity. (PubMed id 16702430)1 Shiina T.... Bahram S. (2006)
- Diversification of transcriptional modulation: large-scale identification and characterization of putative alternative promoters of human genes. (PubMed id 16344560)1 Kimura K.... Sugano S. (2006)
- Physical map of the HLA-A/HLA-F subregion and identification of two new coding sequences. (PubMed id 8575815)1 Pichon L....David V. (1996)
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External Searches for HCG9 gene
(in PubMed,
OMIM, and NCBI Bookshelf)
About This Section
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Genome Databases showing HCG9 gene
(According to
Entrez Gene,
HGNC,
AceView,
euGenes,
Ensembl,
miRBase,
ECgene,
Kegg,
and/or
H-InvDB)
About This Section
|
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Other Databases showing HCG9 gene
(According to HUGE)
About This Section
| -- |
Specialized Databases showing HCG9 gene(According to PharmGKB,
ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL,
Wikipedia and/or GeneReviews via UniProtKB/Swiss-Prot)
About This Section
|
| Name | Description |
| PharmGKB entry for HCG9 | Pharmacogenomics, SNPs, Pathways |
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| | |
About This Section
| Patent Information for HCG9 gene:
Search GeneIP for patents involving HCG9
GeneCards and IP:
Japan Patent Office Licenses GeneCards European Patent Office Licenses GeneCards Improving the IP Search
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Products
for HCG9 gene(Antibodies, recombinant proteins, and assays from EMD Millipore, R&D Systems, OriGene, QIAGEN, GenScript, Cell Signaling Technology, SABiosciences, Novus Biologicals, Sino Biological, Enzo Life Sciences, Abcam, ProSpec, Uscn, Thermo Fisher Scientific, Gene Editing from DNA2.0 and Sirion Biotech, Clones from EMD Millipore, OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Cell lines from GenScript, LifeMap BioReagents, and Sirion Biotech, PCR Arrays from SABiosciences, Drugs and/or compounds from EMD Millipore, Tocris Bioscience, and/or
Enzo Life Sciences, In Situ Hybridization Assays from
Advanced Cell Diagnostics, Animal models from inGenious Targeting Laboratory)
About This Section
|
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|  | QIAGEN Custom miScript Target Protector blocks miRNA-binding site of in human, mouse, rat HCG9 | | | Search QIAGEN SeqTarget long-range PCR primers in human, mouse, rat for resequencing HCG9 | | | QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat HCG9 | | | QIAGEN FlexiTube/FlexiPlate siRNA for gene silencing in human, mouse, rat HCG9 | | | QIAGEN QuantiFast Probe-based Assays in human, mouse, rat HCG9 | | | QIAGEN QuantiTect SYBR Green Assays in human, mouse, rat HCG9 |
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| | | | Search Tocris compounds for HCG9 |
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 | | | | |  |  |  |  | | | | Search ThermoFisher Antibodies for HCG9 |
| | | Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat HCG9 |
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