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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
lncRNA
Number of RNA Genes sources:
3 / 17
Aliases for HCG9 Gene
External Ids for HCG9 Gene
- HGNC: 21243
- Entrez Gene: 10255
- Ensembl: ENSG00000204625
- OMIM: 615797
Additional 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
-
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.
Additional gene information for HCG9 Gene
- HGNC(21243)
- Entrez Gene(10255)
- Ensembl(ENSG00000204625)
- OMIM(615797)
- Open Targets Platform(ENSG00000204625)
- Monarch Initiative
- Search for HCG9 at DataMed
- Search for HCG9 at HumanCyc
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 Score |
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
- chr6:29,975,112-29,978,410
- (GRCh38/hg38)
- Size:
- 3,299 bases
- Orientation:
- Plus strand
- chr6:29,942,889-29,946,183
- (GRCh37/hg19)
- Size:
- 3,295 bases
- Orientation:
- 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:
-
- 6p22.1 by HGNC
- 6p22.1 by Entrez Gene
- 6p22.1 by Ensembl
HCG9 Gene in genomic location: bands according to
Ensembl, locations according to GeneLoc
(and/or Entrez Gene and/or Ensembl if different)
Genomic Neighborhood
• Exon Structure
• Gene Density
RefSeq DNA sequence for HCG9 Gene
Proteins for HCG9 Gene
Post-translational modifications for HCG9 Gene
No Post-translational modifications
Antibody Products
- Novus Biologicals Antibodies for HCG9
- Invitrogen Antibodies for HCG9 (AFLGC-HCGIX)
- antibodies-online: Search results for available HCG9 related products ranked by validation data
Protein Products
- Search Origene for Purified Proteins, MassSpec and Protein Over-expression Lysates for HCG9
- Origene Custom Protein Services for HCG9
- antibodies-online: Search results for available HCG9 related products ranked by validation data
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)
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
- GenomeRNAi human phenotypes for HCG9:
Animal Model Products
- Taconic Biosciences: Generate A Custom CRISPR Mouse Model For Your Study
CRISPR Products
- Applied Biological Materials (abm): CRISPR Clones for HCG9 - Select products 50% OFF >
- * HCG9 CRISPR as ready-to-use vector or virus: ORF | Lenti- | Adeno- | AAV- | Protein Vector - Browse All
- * Gene synthesis, site-directed mutagenesis, subcloning, and more services - Browse All
- Browse CRISPR knockouts for HCG9
- Search GeneCopoeia for CRISPR/Cas9 clones, lentivirus and AAV products for HCG9
miRNA Products
Inhibitory RNA Products
- Origene shrna, sirna, and RNAi products in human, mouse, rat for HCG9
- Browse OriGene Inhibitory RNA Products For HCG9
- Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for HCG9
Clone Products
- Applied Biological Materials (abm): Clones for HCG9 - Select products 50% OFF >
- * HCG9 as ready-to-use vector or virus: ORF | Lenti- | Retro- | Adeno- | AAV- | Protein Vector - Browse All
- * Gene synthesis, site-directed mutagenesis, subcloning, and more services - Browse All
- Search GeneCopoeia for ORF cDNA, lentivirus, AAV viral particles and/or promoter 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
| 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
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, NONCODE: NONHSAT116910.2, |
| URS00008C3CAF_9606 | lncRNA | 659 | 3 |
Ensembl: ENST00000445934 (view in UCSC) , LncBook: HSALNT0103679, NONCODE: NONHSAT116556.2, |
| URS00008C2B05_9606 | lncRNA | 662 | 2 |
Ensembl: ENST00000416207 (view in UCSC) , NONCODE: NONHSAT117598.2, |
| URS00008C3CC6_9606 | lncRNA | 662 | 2 |
Ensembl: ENST00000383616 (view in UCSC) , NONCODE: NONHSAT117919.2, |
| URS00008C0E2B_9606 | lncRNA | 654 | 2 |
Ensembl: ENST00000413215 (view in UCSC) , NONCODE: NONHSAT117261.2, |
HCG9 in the GeneCards ncRNA compendium hub on the UCSC Golden Path
Additional transcripts not in RNAcentral for HCG9 Gene
- 1 REFSEQ mRNAs :
- 4 NCBI additional mRNA sequence :
CRISPR Products
- Applied Biological Materials (abm): CRISPR Clones for HCG9 - Select products 50% OFF >
- * HCG9 CRISPR as ready-to-use vector or virus: ORF | Lenti- | Adeno- | AAV- | Protein Vector - Browse All
- * Gene synthesis, site-directed mutagenesis, subcloning, and more services - Browse All
- Browse CRISPR knockouts for HCG9
- Search GeneCopoeia for CRISPR/Cas9 clones, lentivirus and AAV products for HCG9
miRNA Products
Inhibitory RNA Products
- Origene shrna, sirna, and RNAi products in human, mouse, rat for HCG9
- Browse OriGene Inhibitory RNA Products For HCG9
- Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for HCG9
Clone Products
- Applied Biological Materials (abm): Clones for HCG9 - Select products 50% OFF >
- * HCG9 as ready-to-use vector or virus: ORF | Lenti- | Retro- | Adeno- | AAV- | Protein Vector - Browse All
- * Gene synthesis, site-directed mutagenesis, subcloning, and more services - Browse All
- Search GeneCopoeia for ORF cDNA, lentivirus, AAV viral particles and/or promoter clone products for HCG9
Relevant External Links for HCG9 Gene
- GeneLoc Exon Structure for
- HCG9
Expression for HCG9 Gene
Transcriptomic regulation report from SPP (The Signaling Pathways Project) for HCG9
SOURCE GeneReport for Unigene cluster for HCG9 Gene:
Hs.656251Primer Products
-
OriGene qPCR primer pairs for HCG9
Gene Expression Assay 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
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
No data available for Paralogs for HCG9 Gene
Variants 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
- HCG9
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
- (GAD)
- Human Genome Epidemiology Navigator
- (HuGE)
- 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
- 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
- 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
- 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
- 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
- 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
ExternalLinks
Products for HCG9 Gene
- Browse OriGene Antibodies
- Custom Antibody Services
- Browse OriGene ELISA Kits
- Custom Assay Services
- Search Origene for Purified Proteins, MassSpec and Protein Over-expression Lysates for HCG9
- Origene Custom Protein Services for HCG9
- Origene shrna, sirna, and RNAi products in human, mouse, rat for HCG9
- Browse OriGene Inhibitory RNA Products For HCG9
- OriGene qPCR primer pairs for HCG9
- Browse CRISPR knockouts for HCG9
- Custom cloning services - gene synthesis, subcloning, mutagenesis, variant library, vector shuttling
- Browse OriGene miRNA Products For HCG9
- Browse Sino Biological cDNA Clones
- Browse Sino Biological Recombinant Proteins
- Browse Sino Biological Cell Lysates
- Browse Sino Biological Antibodies
- Browse Sino Biological Assays
- Browse ELISA Kits
- Browse CRO Services
- High-throughput Antibody Production Service
- Protein Production Service
- Epitope Tag Antibodies & Reporter Protein Antibodies
- Lentiviral ORF Clones
- Novus Biologicals Antibodies for HCG9
- Browse Antibodies
- Browse Peptides and Proteins
- Browse Lysates
- Browse ELISA Kits
- Invitrogen Antibodies for HCG9 (AFLGC-HCGIX)
- VectorBuilder Custom and pre-made DNA vectors for HCG9 (ie. gene expression, shRNA knockdown, CRISPR)
- VectorBuilder Viral vectors for HCG9 (ie. lentivirus, AAV, adenovirus)
- VectorBuilder CRISPR vectors for HCG9 (ie. knockout, knockin, CRISPRa, CRISPRi)
- VectorBuilder Virus packaging for HCG9 CRISPR vectors (ie. lentivirus, AAV, adenovirus)
- VectorBuilder Stable cell line generation for HCG9
- antibodies-online: Search results for available HCG9 related products ranked by validation data
- antibodies-online: Search results for available HCG9 related products ranked by validation data
- antibodies-online: Search results for available HCG9 related products ranked by validation data
- Browse GeneCopoeia Cell Lines
- Search GeneCopoeia for CRISPR/Cas9 clones, lentivirus and AAV products for HCG9
- Search GeneCopoeia for ORF cDNA, lentivirus, AAV viral particles and/or promoter clone products for HCG9
- Search GeneCopoeia for miRNA 3'UTR Target clone products for HCG9
- Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for HCG9
Sources for HCG9 Gene
- (1) GeneCards
- (2) HGNC
- (3) NCBI Entrez Gene
- (4) UniProtKB/Swiss-Prot
- (5) Ensembl
- (6) OMIM
- (7) GeneLoc
- (8) Gene Wiki
- (9) UCSC
- (10) PhosphoSitePlus
- (11) Cell Signaling Technology
- (12) GO
- (13) UniProtKB/TrEMBL
- (14) InterPro
- (15) ProtoNet
- (16) Blocks
- (17) MGI
- (18) IUBMB
- (19) KEGG
- (20) MINT
- (21) STRING
- (22) IntAct
- (23) Novoseek
- (24) PharmGKB
- (25) DrugBank
- (26) HMDB
- (27) ASD
- (28) SAGE
- (29) SOURCE
- (30) HomoloGene
- (31) PanEnsembl
- (32) euGenes
- (33) SGD
- (34) FlyBase
- (35) WormBase
- (36) Pseudogene
- (37) DGV
- (38) dbSNP
- (39) GenAtlas
- (40) HGMD
- (41) GAD
- (42) BGMUT
- (43) HuGE
- (44) Atlas
- (45) GenBank
- (46) HORDE
- (47) HUGE
- (48) IMGT
- (49) Leiden
- (50) miRBase
- (51) DME
- (52) OriGene
- (53) PubMed
- (54) R&D Systems
- (55) TGDB
- (56) Tocris
- (57) Abcam
- (58) Novus Biologicals
- (59) ProSpec
- (60) Sino Biological
- (61) GenScript
- (62) Qiagen
- (63) OCA
- (64) Proteopedia
- (65) MOPED
- (66) neXtProt
- (67) Reactome
- (68) GeneGo (Thomson Reuters)
- (69) DISEASES
- (70) SIMAP
- (71) GenomeRNAi
- (72) LifeMap
- (73) miRTarBase
- (74) MalaCards
- (75) Invitrogen
- (76) BitterDB
- (77) ESI-BIO
- (78) RefSeq
- (79) BioSystems
- (80) MaxQB
- (81) IUPHAR
- (82) BioGPS
- (83) Illumina
- (84) COMPARTMENTS
- (85) HOMER
- (86) PaxDb
- (87) ApexBio
- (88) Addgene
- (89) antibodies-online
- (90) CYP
- (91) NONCODE
- (92) TreeFam
- (93) PathCards
- (94) GeneReviews
- (95) GeneTex
- (96) Taconic Biosciences
- (97) GTEx
- (98) ProteomicsDB
- (99) SCBT
- (100) DGIdb
- (101) ClinicalTrials
- (102) RVIS
- (103) SIGNOR
- (104) diseasecard
- (105) NIH Rare Diseases
- (106) Orphanet
- (107) UMLS
- (108) GTR
- (109) Disease Ontology
- (110) Genetics Home Reference
- (111) MeSH
- (112) MedlinePlus
- (113) CDC
- (114) NINDS
- (115) NCBI Bookshelf
- (116) ClinVar
- (117) Gene Damage Index
- (118) HPO
- (119) UDN
- (120) VISTA
- (121) FANTOM5
- (122) ENCODE
- (123) ProSci
- (124) Horizon
- (125) The Signaling Pathways Project (SPP)
- (126) IID
- (127) VectorBuilder
- (128) SNPedia
- (129) BRCA Exchange
- (130) CIViC
- (131) ProteoGenix
- (132) dbSUPER
- (133) TISSUES
- (134) Gene ORGANizer
- (135) abm
- (136) Human Protein Atlas
- (137) GWAS Catalog
- (138) Monarch Initiative
- (139) DataMed
- (140) HumanCyc
- (141) UCNEbase
- (142) EPDnew
- (143) Applied Biosystems
- (144) GlyConnect
- (145) Aminode
- (146) GeneCopoeia
- (147) GPS-Prot
- (148) RNACentral
- (149) LncRNADisease
- (150) LOVD
- (151) miR2Disease
- (152) DiseaseEnhancer
- (153) Boster Bio
- (154) Biorbyt
- (155) Biocompare
- (156) Mastermind
- (157) CTD^2 Dashboard
- (158) CraniofacialAtlas
- (159) GeneImprint
- (160) Synthego
- (161) ENA
- (162) GtRNAdb
- (163) LncBase
- (164) LncBook
- (165) LNCipedia
- (166) Modomics
- (167) PDBe
- (168) Rfam
- (169) SILVA
- (170) snOPY
- (171) SRPDB
- (172) GENCODE
- (173) TarBase
- (174) Signalway Antibody
- (175) Open Targets Platform
- (176) 5SRRNADB
- (177) snoDB
- (178) MirGeneDB