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HLA complex group 27 (non-protein coding)(Previous name: HLA complex group 27 )
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Aliases
for HCG27 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 27 (Non-Protein Coding)1 2 | | BCX101P6.91 | | BPG299F13.91 | | BQB115I13.21 | | FLJ401231 | | HLA Complex Group 271 |
Export aliases for HCG27 gene to outside databasesPrevious GC identifers: GC06P031272 GC06P031273 |
Summaries
for HCG27 gene(According to Entrez Gene,
Tocris Bioscience,
Wikipedia's
Gene Wiki,
PharmGKB,
UniProtKB/Swiss-Prot,
and/or
UniProtKB/TrEMBL)
About This Section
|
-- |
Genomic Views
for HCG27 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_167247.1 NT_167248.1 NT_167249.1
Regulatory elements:
 SABiosciences Regulatory transcription factor binding sites in the HCG27 gene promoter:
TBP STAT3 MyoD Nkx2-5
Other transcription factors
Search SABiosciences Chromatin IP Primers for HCG27
Epigenetics:
| | QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat HCG27 |
Genomic Location:
Genomic View: UCSC Golden Path with GeneCards custom track
Entrez Gene cytogenetic band: 6p21.33 Ensembl cytogenetic band: 6p21.33 HGNC cytogenetic band: 6p21.3HCG27 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 GC06P031166: view genomic region
(about GC identifiers)
Start:
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31,165,537 bp from pter |
End:
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31,171,745 bp from pter |
Size:
|
6,209 bases |
Orientation:
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plus strand |
5 alternative locations:
| Chr6+,ALT_REF_LOCI_3 31,159,280-31,176,523 | Chr6+,ALT_REF_LOCI_5 31,158,926-31,165,182 | Chr6+,ALT_REF_LOCI_6 31,157,983-31,199,776 | | Chr6+,ALT_REF_LOCI_2 31,158,106-31,203,499 | Chr6+,ALT_REF_LOCI_7 31,089,947-31,096,152 |
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Proteins
for HCG27 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: H0YLW2 (See
protein sequence)Recommended Name: Protein HCG27 Size: 189 amino acids; 20927 Da
Caution: The sequence shown here is derived from an Ensembl automatic analysis pipeline and should be considered aspreliminary dataUniProtKB/TrEMBL: H0YMJ2 (See
protein sequence) Recommended Name: Protein HCG27 Size: 163 amino acids; 18059 Da
Caution: The sequence shown here is derived from an Ensembl automatic analysis pipeline and should be considered aspreliminary dataHCG27 Protein expression data from MOPED and PaxDb: --
ENSEMBL proteins: ENSP00000453364 ENSP00000453627
Human Recombinant Protein Products:
HCG27 Antibody Products:
Assay Products for HCG27: |
Protein
Domains /
Families
for HCG27 gene(According to InterPro, ProtoNet,
UniProtKB, and/or BLOCKS,
Sets of similar genes according to GeneDecks)
About This Section
| ProtoNet protein and cluster: H0YLW2 |
Function
for HCG27 gene
(According to 1UniProtKB,
Genatlas,
LifeMap Discovery™,
IUBMB, and/or
2DME,
Human phenotypes from GenomeRNAi,
Animal models from MGI Mar 06 2013,
bound targets from SABiosciences,
miRNA Gene Targets from miRTarBase
shRNA from
OriGene,
RNAi from
EMD Millipore,
siRNAs from
OriGene,
QIAGEN,
microRNA from QIAGEN,
Gene Editing from DNA2.0,
Clones from EMD Millipore,
OriGene,
SwitchGear Genomics,
GenScript,
Sino Biological,
DNA2.0,
and Vector BioLabs,
Cell Lines from GenScript,
LifeMap BioReagents,
In Situ Hybridization Assays from Advanced Cell Diagnostics,
Ontologies according to Gene Ontology Consortium 01 Mar 2013 via
Entrez Gene.)
About This Section
|
In Situ Assay
Products: |
 | Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for HCG27 |
1 GenomeRNAi human phenotype for HCG27:
|
Pathways & Interactions
for HCG27 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 HCG27
|
Drugs & Compounds
for HCG27 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 HCG27
Search CenterWatch for drugs/clinical trials and news about HCG27 
|
Transcripts
for HCG27 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,
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
|
Unigene Cluster for HCG27: HLA complex group 27 (non-protein coding) Hs.659818 [show with all ESTs]Unigene Representative Sequence: AK0950293 Ensembl transcripts including schematic representations, and UCSC links where relevant: ENST00000383331(uc011dni.2) ENST00000424675 ENST00000415276
Additional cDNA sequence: AK095029.1 AK097442.1 BC041465.2 BC104432.1 BC104433.1 NR_026791.1 3 DOTS entries: DT.99930924 DT.100027817 DT.121354515 15 AceView cDNA sequences: BE465078 BQ437085 BC041465 AK097442 AA975338 BI906654 NM_181717 BE218584 BE147199 BG149553 AW136928 N76377 AI685655 N68963 BF351367
GeneLoc Exon Structure
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Expression
for HCG27 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 HCG27:none
HCG27 expression in normal human tissues (normalized intensities)
See probesets specificity/sensitivity at GeneAnnot
About this imageBioGPS
CGAP TAG: --
About this image
Genevestigator expression for HCG27
SOURCE GeneReport for Unigene cluster: Hs.659818
SABiosciences Custom PCR Arrays for HCG27
Primer
Products: |  | Browse OriGene genome-wide validated SYBR primer pairs
Browse OriGene validated miRNA SYBR primer pairs
| | | SABiosciences RT2 qPCR Primer Assay in human, mouse / rat HCG27 | | | QIAGEN QuantiTect SYBR Green Assays in human, mouse, rat HCG27 | | | QIAGEN QuantiFast Probe-based Assays in human, mouse, rat HCG27 | In Situ
Assay Products: |
| Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for HCG27 |
Orthologs
for HCG27 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 HCG27 (if available)
TreeFam Gene Tree for HCG27 (if available) |
Paralogs
for HCG27 gene(Paralogs according to
1HomoloGene,
2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
About This Section
| Paralogs for HCG27 gene
HCG27 for paralogs About GeneDecksing
5/14 Pseudogenes.org Pseudogenes for HCG27 (see all 14)
PGOHUM00000262009 PGOHUM00000261986 PGOHUM00000261978 PGOHUM00000261981 PGOHUM00000261982
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Genomic Variants
for HCG27 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 HCG27 (31165537 - 31171745 bp)
Structural Variations (Copy Number Variations, Insertions/Deletions, Inversions)
Database of Genomic Variants (DGV): 2 variations for HCG27
2 CNVs: 7561 3601 | SABiosciences Cancer Mutation PCR Assays |
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Disorders
/ Diseases
for HCG27 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
|
HCG27 for disorders About GeneDecksing
2  diseases for HCG27: About MalaCardssystemic lupus erythematosus lupus erythematosus
Human Genome Epidemiology (HuGE) Navigator: HCG27 (2 documents)
Export disorders for HCG27 gene to outside databases
|
Publications
for HCG27 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 HCG27 gene integrated from 9 sources:
(articles sorted by number of sources associating them with HCG27) | |  | Utopia: connect your pdf to the dynamic
world of online information |
- Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. (PubMed id 12477932)1, 3 Strausberg R.L....Marra M.A. (2002)
- A genome-wide association study for coronary artery di sease identifies a novel susceptibility locus in the major histocompatibility co mplex. (PubMed id 22319020)1 Davies R.W....McPherson R. (2012)
- Web-based, participant-driven studies yield novel gen etic associations for common traits. (PubMed id 20585627)1 Eriksson N....Mountain J. (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)
- 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)
- Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)1 Ota T.... Sugano S. (2004)
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External Searches for HCG27 gene
(in PubMed,
OMIM, and NCBI Bookshelf)
About This Section
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Genome Databases showing HCG27 gene
(According to
Entrez Gene,
HGNC,
AceView,
euGenes,
Ensembl,
miRBase,
ECgene,
Kegg,
and/or
H-InvDB)
About This Section
|
|
Other Databases showing HCG27 gene
(According to HUGE)
About This Section
| -- |
Specialized Databases showing HCG27 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 HCG27 | Pharmacogenomics, SNPs, Pathways |
|
| | |
About This Section
| Patent Information for HCG27 gene:
Search GeneIP for patents involving HCG27
GeneCards and IP:
Japan Patent Office Licenses GeneCards European Patent Office Licenses GeneCards Improving the IP Search
|
Products
for HCG27 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, Clones from EMD Millipore, OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Cell lines from GenScript and LifeMap BioReagents, 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
About This Section
|
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|  | QIAGEN Custom miScript Target Protector blocks miRNA-binding site of in human, mouse, rat HCG27 | | | Search QIAGEN SeqTarget long-range PCR primers in human, mouse, rat for resequencing HCG27 | | | QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat HCG27 | | | QIAGEN FlexiTube/FlexiPlate siRNA for gene silencing in human, mouse, rat HCG27 | | | QIAGEN QuantiFast Probe-based Assays in human, mouse, rat HCG27 | | | QIAGEN QuantiTect SYBR Green Assays in human, mouse, rat HCG27 |
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| | | | Search Tocris compounds for HCG27 |
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 | | | | | | Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for HCG27 |
|  |  |  | | | | Search ThermoFisher Antibodies for HCG27 |
| | | Search Vector BioLabs for ready-to-use adenovirus/AAV for human, mouse, rat HCG27 |
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