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HLA complex group 4 (non-protein coding)(Previous names: HLA complex group 4, HLA complex group 4 pseudogene 10...)
(Previous symbol: HCG4P10)
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Aliases
for HCG4 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): non-coding RNA
Quality score for this RNA gene is 3
| Aliases |
|---|
| HLA Complex Group 4 (Non-Protein Coding)1 2 | | HCG4P101 2 | | HCGIV-101 2 | | HCGIV.91 2 | | HLA Complex Group 41 | | HLA Complex Group 4 Pseudogene 101 |
Export aliases for HCG4 gene to outside databasesPrevious GC identifers: GC06M029529 GC06M029867 GC06M029869 GC06M029870 GC06M029871 GC06M029873 GC06M029876 GC06M029881 GC06M029761 GC06M029774 GC06M029778 GC06M029792 GC06M029794 |
Summaries
for HCG4 gene(According to Entrez Gene,
Tocris Bioscience,
Wikipedia's
Gene Wiki,
PharmGKB,
UniProtKB/Swiss-Prot,
and/or
UniProtKB/TrEMBL)
About This Section
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-- |
Genomic Views
for HCG4 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_167244.1 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 HCG4 gene promoter:
Max1 AP-1 ATF-2 XBP-1 NF-E2 p45 AP-2gamma CREB deltaCREB c-Jun NF-E2
Other transcription factors
Search SABiosciences Chromatin IP Primers for HCG4
Epigenetics:
| | QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat HCG4 |
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: 6p22.1HCG4 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 GC06M029806: view genomic region
(about GC identifiers)
Start:
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29,758,808 bp from pter |
End:
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29,760,850 bp from pter |
Size:
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2,043 bases |
Orientation:
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minus strand |
6/7 alternative locations (see all 7):
| Chr6-,ALT_REF_LOCI_5 29,670,690-29,672,732 | Chr6-,ALT_REF_LOCI_3 29,756,212-29,769,284 | Chr6-,ALT_REF_LOCI_2 29,753,438-29,793,923 | | Chr6-,ALT_REF_LOCI_1 29,759,783-29,769,380 | Chr6-,ALT_REF_LOCI_4 29,678,886-29,680,928 | Chr6-,ALT_REF_LOCI_6 29,756,937-29,793,815 | |
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Proteins
for HCG4 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
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UniProtKB/TrEMBL: O95141 (See
protein sequence)Recommended Name: Putative uncharacterized protein Size: 331 amino acids; 35809 Da |
Protein
Domains /
Families
for HCG4 gene(According to InterPro, ProtoNet,
UniProtKB, and/or BLOCKS,
Sets of similar genes according to GeneDecks)
About This Section
| ProtoNet protein and cluster: O95141 |
Function
for HCG4 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
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Pathways & Interactions
for HCG4 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 HCG4
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Drugs & Compounds
for HCG4 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
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 Browse Tocris compounds for HCG4
Search CenterWatch for drugs/clinical trials and news about HCG4 
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Transcripts
for HCG4 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
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Unigene Cluster for HCG4: HLA complex group 4 (non-protein coding) Hs.660431 [show with all ESTs]Unigene Representative Sequence: NR_0021392 Ensembl transcripts including schematic representations, and UCSC links where relevant: ENST00000418983(uc003nns.3) ENST00000320533
Additional cDNA sequence: AF036977.1 BC011879.1 BC021249.2 NR_002139.2 6 DOTS entries: DT.40114307 DT.402222 DT.121345649 DT.40128730 DT.75177312 DT.91806393 19 AceView cDNA sequences: BC021249 BC011879 AF036976 AF036977 NR_002139 BV188852 BV190142 CA424707 BE276167 AA018771 BV188853 AI991381 BV183502 BX437311 BE277632 BX282951 AI400452 AA018247 BE391655
GeneLoc Exon Structure
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Expression
for HCG4 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 HCG4:none
HCG4 expression in normal human tissues (normalized intensities)
See probesets specificity/sensitivity at GeneAnnot
About this imageBioGPS
CGAP TAG: --
About this image
Genevestigator expression for HCG4
SOURCE GeneReport for Unigene cluster: Hs.660431
SABiosciences Custom PCR Arrays for HCG4
Primer
Products: |  | OriGene genome-wide validated SYBR primer pairs in human, mouse, rat for HCG4
Browse OriGene validated miRNA SYBR primer pairs
| | | SABiosciences RT2 qPCR Primer Assay in human, mouse / rat HCG4 | | | Search QIAGEN QuantiTect SYBR Green Assays in human, mouse, rat HCG4 | | | QIAGEN QuantiFast Probe-based Assays in human, mouse, rat HCG4 |
Orthologs
for HCG4 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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This gene was present in the common ancestor of human and mouse.
Orthologs for HCG4 gene from 1 species (see representative species ) About this table
| Organism |
Taxonomic
classification |
Gene |
Description |
Human
Similarity |
Orthology
Type |
Details |
mouse
(Mus musculus) |
Mammalia |
5430410E06Rik5 |
RIKEN cDNA 5430410E06 gene |
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17 - |
ENSEMBL Gene Tree for HCG4 (if available)
TreeFam Gene Tree for HCG4 (if available) |
Paralogs
for HCG4 gene(Paralogs according to
1HomoloGene,
2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
About This Section
| -- |
Genomic Variants
for HCG4 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
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| 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 HCG4 (29758808 - 29760850 bp)
Structural Variations (Copy Number Variations, Insertions/Deletions, Inversions)
Database of Genomic Variants (DGV): 3 variations for HCG4
3 CNVs: 64462 31268 64460 | SABiosciences Cancer Mutation PCR Assays |
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Disorders
/ Diseases
for HCG4 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
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HCG4 for disorders About GeneDecksing
2  diseases for HCG4: About MalaCardsmultiple sclerosis colorectal cancer
Human Genome Epidemiology (HuGE) Navigator: HCG4 (1 document)
Export disorders for HCG4 gene to outside databases
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Publications
for HCG4 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
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PubMed articles for HCG4 gene integrated from 9 sources:
(articles sorted by number of sources associating them with HCG4) | |  | Utopia: connect your pdf to the dynamic
world of online information |
- SNP mapping and candidate gene sequencing in the class I region of the HLA complex: searching for multiple sclerosis susceptibility genes in Tasmanians. (PubMed id 17971048)1, 9 Burfoot R.K....Rubio J.P. (2008)
- Down-regulation of HLA Class I and NKG2D ligands thro ugh a concerted action of MAPK and DNA methyltransferases in colorectal cancer cells. (PubMed id 19569244)1 Sers C....SchAofer R. (2009)
- Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. (PubMed id 12477932)1 Strausberg R.L....Marra M.A. (2002)
- 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. (1999)
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External Searches for HCG4 gene
(in PubMed,
OMIM, and NCBI Bookshelf)
About This Section
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Genome Databases showing HCG4 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 HCG4 gene
(According to HUGE)
About This Section
| -- |
Specialized Databases showing HCG4 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 HCG4 | Pharmacogenomics, SNPs, Pathways |
|
| | |
About This Section
| Patent Information for HCG4 gene:
Search GeneIP for patents involving HCG4
GeneCards and IP:
Japan Patent Office Licenses GeneCards European Patent Office Licenses GeneCards Improving the IP Search
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Products
for HCG4 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 HCG4 | | | Search QIAGEN SeqTarget long-range PCR primers in human, mouse, rat for resequencing HCG4 | | | QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat HCG4 | | | QIAGEN FlexiTube/FlexiPlate siRNA for gene silencing in human, mouse, rat HCG4 | | | QIAGEN QuantiFast Probe-based Assays in human, mouse, rat HCG4 | | | Search QIAGEN QuantiTect SYBR Green Assays in human, mouse, rat HCG4 |
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| | | | Search Tocris compounds for HCG4 |
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 | | | | |  |  |  | | | | Search ThermoFisher Antibodies for HCG4 |
| | | Search Vector BioLabs for ready-to-use adenovirus/AAV for human, mouse, rat HCG4 |
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