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HCG26 Gene

RNA gene   GIFtS: 21
GCID: GC06P031439

HLA Complex Group 26 (Non-Protein Coding)

(Previous name: HLA complex group 26)
  See related diseases
at  

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, 10fRNAdb, 12H-InvDB, 13NCBI, 14NONCODE, and/or 15RNAdb)
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Subcategory (RNA class): lncRNA

Quality score for this RNA gene is 2

Aliases
HLA Complex Group 26 (Non-Protein Coding)1 2     NCRNA001912
HLA Complex Group 261     bCX205D4.42
Non-Protein Coding RNA 1911     bPG181B23.42
3.8-12     

External Ids:    HGNC: 296711   Entrez Gene: 3529612   
ORGUL members:         

Export aliases for HCG26 gene to outside databases

Previous GC identifers: GC00U915702 GC06U900756 GC06P031547 GC06P031548 GC06P031226


(According to Entrez Gene, GeneCards, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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GeneCards Summary for HCG26 Gene:
HCG26 (HLA complex group 26 (non-protein coding)) is an RNA gene, and is affiliated with the lncRNA class. Diseases associated with HCG26 include hodgkin's lymphoma, and systemic lupus erythematosus.


(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 75), Regulatory elements and Epigenetics data according to QIAGEN, and/or SwitchGear Genomics)
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RefSeq DNA sequence:
NC_000006.12  NC_018917.2  NT_007592.16  NT_113891.3  NT_167245.2  NT_167247.2  NT_167248.2  NT_167249.2  
Regulatory elements:
   Regulatory transcription factor binding sites in the HCG26 gene promoter:
         AhR   Egr-1   Pax-2   Pax-2a   Arnt   Egr-4   AREB6   c-Rel   Ik-1   
         Other transcription factors

Browse SwitchGear Promoter luciferase reporter plasmids
   Search Chromatin IP Primers for HCG26

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat HCG26


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

Entrez Gene cytogenetic band: 6p21.3   HGNC cytogenetic band: 6p21.3

HCG26 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
HCG26 gene location

GeneLoc information about chromosome 6         GeneLoc Exon Structure

GeneLoc location for GC06P031439:  view genomic region     (about GC identifiers)

Start:
31,439,006 bp from pter      End:
31,440,185 bp from pter
Size:
1,180 bases      Orientation:
plus strand

5 alternative locations:
Chr6+,NT_113891.2 2,948,660-2,949,839      Chr6+,NT_167245 2,724,340-2,725,519      Chr6+,NT_167249 2,769,772-2,770,951     
Chr6+,NT_167248 2,732,712-2,733,891      Chr6+,NT_167247 2,818,786-2,819,965     

(According to 1UniProtKB, HORDE, 2neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, 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 Cloud-Clone Corp.,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Cloud-Clone Corp., Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, Cloud-Clone Corp, and/or others.)
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UniProtKB: --


(According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
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HGNC Gene Families:
LNCRNA: Long non-coding RNAs

  --

(According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, inGenious Targeting Laboratory, genOway,
transcription factor targeting from QIAGEN and/or HOMER, miRNA Gene Targets from miRTarBase, shRNA from OriGene, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, SwitchGear Genomics, Gene Editing from DNA2.0, Clones from OriGene, GenScript, Sino Biological, DNA2.0, and Vector BioLabs, Cell Lines from GenScript, ESI BIO, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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Animal Models:
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(According to UniProtKB, COMPARTMENTS Subcellular localization database, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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  --

(SuperPaths according to PathCards, Pathways according to R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Sino Biological, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to QIAGEN, 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 Apr 2014 via Entrez Gene).
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    Custom Pathway & Disease-focused RT2 Profiler PCR Arrays for HCG26
Interactions:

    Search GeneGlobe Interaction Network for HCG26

(Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience, ApexBio, HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB)
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Browse Small Molecules at EMD Millipore
   Browse drugs & compounds from Enzo Life Sciences
  Browse compounds at ApexBio 

Browse Tocris compounds for HCG26



(Secondary structures according to fRNAdb,
GenBank/EMBL/DDBJ Accessions according to
Unigene (Build 236 Homo sapiens; Apr 25 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,
siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN, SwitchGear Genomics,
Tagged/untagged cDNA clones from OriGene, GenScript, DNA2.0, Vector BioLabs, Primers from OriGene, and/or QIAGEN )
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Unigene Cluster for HCG26:

HLA complex group 26 (non-protein coding)
Hs.132807  [show with all ESTs]
Unigene Representative Sequence: L29376
miRNA
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Additional mRNA sequence: 

L29376.1 NR_002812.3 

2 DOTS entries:

DT.75100512  DT.102844665 

GeneLoc Exon Structure


(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™, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MaxQB, plus additional links to SOURCE, and/or BioGPS, and/or UniProtKB,
PCR Arrays from QIAGEN, Primers from OriGene, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
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Expression evidence for HCG26:none

HCG26 expression in normal human tissues (normalized intensities)
See probesets specificity/sensitivity at GeneAnnot
About this imageBioGPS <intensity>2/3
CGAP TAG: AAGCAATGTT
HCG26 Expression
About this image

HCG26 Protein expression data from MOPED1, PaxDb2 and MaxQB3 --

SOURCE GeneReport for Unigene cluster: Hs.132807
    Custom PCR Arrays for HCG26
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In Situ
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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)
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  --

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

(SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, 4UniProtKB, 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), the Human Cytochrome P450 Allele Nomenclature Database, and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers, Cancer Mutation PCR Arrays and Assays, and Copy Number PCR Arrays from QIAGEN)
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Selected SNPs for HCG26 (see all 106)    About this table    
Genomic DataTranscription Related DataAllele Frequencies
SNP IDValidClinical
significance
Chr 6 posSequence#AA
Chg
TypeMore#Allele
freq
PopTotal
sample
More
----------
rs25964521,2
C,F,A--31437158(-) TCACCC/ATTACT 1 -- us2k112Minor allele frequency- A:0.18NA WA CSA EA 373
rs25964511,2
C,F,A--31437195(-) TTGTCC/TCTCCT 1 -- us2k112Minor allele frequency- T:0.18NA WA CSA EA 373
rs25236721,2
C,F,A--31437220(-) GAGAAG/CAGGAG 1 -- us2k112Minor allele frequency- C:0.18NA WA CSA EA 373
rs47134671,2
C,F--31437275(+) GCAAAC/TGTAGC 1 -- us2k11Minor allele frequency- T:0.23EA 120
rs23950311,2
C,F,A,H--31437305(+) CAGCTG/AGAGCA 1 -- us2k127Minor allele frequency- A:0.08NS EA NA WA 3238
rs25236711,2
C,F,A,H--31437318(-) GCACAA/GCTGAT 1 -- us2k115Minor allele frequency- G:0.19NS EA NA WA CSA 766
rs25236701,2
C,H--31437492(-) CAGAGC/GCAGTC 1 -- us2k115Minor allele frequency- G:0.05EA NS NA WA CSA 649
rs28942201,2
C,F,A,H--31437506(+) GGGAGC/TGGGAA 1 -- us2k19Minor allele frequency- T:0.08NS EA WA NA CSA 633
rs94049891,2
C,F,H--31437566(+) cagctG/Tcaaat 1 -- us2k16Minor allele frequency- T:0.10NS EA NA 646
rs92671351,2
C,F,H--31437617(+) ttcagT/Ctttct 1 -- us2k119Minor allele frequency- C:0.09NS EA WA NA CSA 2425

HapMap Linkage Disequilibrium report for HCG26 (31439006 - 31440185 bp)

Structural Variations
     Database of Genomic Variants (DGV) Selected variations for HCG26 (see all 39):    About this table    
Variant IDTypeSubtypePubMed ID
esv2432528CNV Deletion19546169
esv2731822CNV Deletion23290073
dgv1098e199CNV Deletion23128226
nsv435829CNV Deletion17901297
dgv1042e201CNV Deletion23290073
esv3160CNV Duplication18987735
esv1671758CNV Insertion17803354
nsv513736CNV Insertion21212237
esv269295CNV Insertion20981092
esv274516CNV Insertion20981092

Site Specific Mutation Identification with PCR Assays
Search QIAGEN SeqTarget long-range PCR primers for resequencing HCG26
DNA2.0 Custom Variant and Variant Library Synthesis for HCG26

(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.)
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5 diseases for HCG26:    
About MalaCards
hodgkin's lymphoma    systemic lupus erythematosus    multiple sclerosis    lupus erythematosus
neuroblastoma


HCG26 for disorders           About GeneDecksing

Genetic Association Database (GAD): HCG26

Export disorders for HCG26 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)
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PubMed articles for HCG26 gene, integrated from 10 sources (see all 11):
(articles sorted by number of sources associating them with HCG26)
    Utopia: connect your pdf to the dynamic
world of online information

  1. Genome-wide screen for metabolic syndrome susceptibility Loci reveals strong lipid gene contribution but no evidence for common genetic basis for clustering of metabolic syndrome traits. (PubMed id 22399527)1, 4 Kristiansson K....Salomaa V. (Circ Cardiovasc Genet 2012)
  2. Meta-analysis identifies multiple loci associated with kidney function-related traits in east Asian populations. (PubMed id 22797727)1 Okada Y....Tanaka T. (Nat. Genet. 2012)
  3. Genome-wide association study of classical Hodgkin lymphoma and Epstein-Barr virus status-defined subgroups. (PubMed id 22286212)4 Urayama K.Y....McKay J.D. (J. Natl. Cancer Inst. 2012)
  4. Identification of candidate loci at 6p21 and 21q22 in a genome-wide association study of cardiac manifestations of neonatal lupus. (PubMed id 20662065)4 Clancy R.M....Buyon J.P. (Arthritis Rheum. 2010)
  5. Genome-wide association study identifies variants in the MHC class I, IL10, and IL23R-IL12RB2 regions associated with BehAset's disease. (PubMed id 20622878)4 Remmers E.F....GA1l A. (Nat. Genet. 2010)
  6. Chromosome 6p22 locus associated with clinically aggressive neuroblastoma. (PubMed id 18463370)4 Maris J.M....Hakonarson H. (N. Engl. J. Med. 2008)
  7. Association of systemic lupus erythematosus with C8orf13-BLK and ITGAM-ITGAX. (PubMed id 18204098)4 Hom G....Behrens T.W. (N. Engl. J. Med. 2008)
  8. Risk alleles for multiple sclerosis identified by a genomewide study. (PubMed id 17660530)4  ....Hauser S.L. (N. Engl. J. Med. 2007)
  9. 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. (Genetics 2006)
  10. Molecular dynamics of MHC genesis unraveled by sequence analysis of the 1,796,938-bp HLA class I region. (PubMed id 10557312)1 Shiina T....Inoko H. (Proc. Natl. Acad. Sci. U.S.A. 1999)

(in PubMed, OMIM, and NCBI Bookshelf)
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 ANDOR
Aliases
Free Text  

  Query String
PubMed
OMIM
NCBI Bookshelf
  (Note: In FireFox, select the above section and copy using Ctrl-C)

(According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
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Entrez Gene: 352961 HGNC: 29671 euGenes: HUgn352961 ECgene: HCG26 H-InvDB: HCG26

(According to HUGE)
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(According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL, and/or others, e.g. Wikipedia and GeneReviews, via UniProtKB/Swiss-Prot)
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NameDescription
PharmGKB entry for HCG26 Pharmacogenomics, SNPs, Pathways

(Patent information from GeneIP,
Licensable technologies from WIS Yeda, Salk, Tufts,
IP news from LifeMap Sciences, Inc.)
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Patent Information for HCG26 gene:
Search GeneIP for patents involving HCG26

GeneCards and IP:
Japan Patent Office Licenses GeneCards     European Patent Office Licenses GeneCards     Improving the IP Search



(Antibodies, recombinant proteins, and assays from EMD Millipore, R&D Systems, OriGene, QIAGEN, GenScript, Cell Signaling Technology, Novus Biologicals, Sino Biological, Enzo Life Sciences, Abcam, ProSpec, Cloud-Clone Corp., Thermo Fisher Scientific, LSBio, Gene Editing from DNA2.0. Clones from OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Cell lines from GenScript, and ESI BIO, PCR Arrays from QIAGEN, Drugs and/or compounds from EMD Millipore, Tocris Bioscience, Enzo Life Sciences, and/or ApexBio, In Situ Hybridization Assays from
Advanced Cell Diagnostics, Animal models from inGenious Targeting Laboratory, genOway)
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