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HAR1B Gene

RNA gene   GIFtS: 20
GCID: GC20M061726

Highly Accelerated Region 1B (Non-Protein Coding)

(Previous name: highly accelerated region 1B (non-protein-coding RNA))
  See related disease
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 5

Aliases
Highly Accelerated Region 1B (Non-Protein Coding)1 2     Non-Protein Coding RNA 651
HAR1R2 5     reverse1
Highly Accelerated Region 1B (Non-Protein-Coding RNA)1     LINC000652
Human Accelerated Region 11     NCRNA000652
Long Intergenic Non-Protein Coding RNA 651     

External Ids:    HGNC: 331181   Entrez Gene: 7680972   Ensembl: ENSG000002311337   OMIM: 6105575   
ORGUL members:    fRNAdb10:FR009087 FR178260 FR407603      
H-InvDB12:HIT000393906    
NCBI13:DQ860410 DQ860411 DQ860409    
NONCODE14:n378807 n342953    
RNAdb15:LIT3338 LIT3339    

Export aliases for HAR1B gene to outside databases

Previous GC identifers: GC20U900287 GC20M061197 GC20M058445


(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 HAR1B Gene:
HAR1B (highly accelerated region 1B (non-protein coding)) is an RNA gene, and is affiliated with the lncRNA class. Diseases associated with HAR1B include williams-beuren syndrome.

fRNAdb sequence ontologies for HAR1B - the ORGUL cluster for this gene includes several descriptions:
antisense_RNA - Antisense RNA is RNA that is transcribed from the coding, rather than the template, strand of DNA. It is therefore complementary to mRNA.
ncRNA - An RNA transcript that does not encode for a protein rather the RNA molecule is the gene product.

View fRNAdb secondary structures for HAR1B

(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_000020.11  NC_018931.2  NT_011362.11  
Regulatory elements:
   Regulatory transcription factor binding sites in the HAR1B gene promoter:
         NCX/Ncx   CUTL1   GATA-1   POU2F1   POU2F1b   POU2F1a   POU2F1c   En-1   
         Other transcription factors

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Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat HAR1B


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

Entrez Gene cytogenetic band: 20q13.33   Ensembl cytogenetic band:  20q13.33   HGNC cytogenetic band: 20q13.33

HAR1B Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
HAR1B gene location

GeneLoc information about chromosome 20         GeneLoc Exon Structure

GeneLoc location for GC20M061726:  view genomic region     (about GC identifiers)

Start:
61,726,845 bp from pter      End:
61,733,671 bp from pter
Size:
6,827 bases      Orientation:
minus strand
ORGUL member locations:
Legend (see complete legend)

ORGUL Member Locations for HAR1B

(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, and/or Cloud-Clone Corp.)
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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 HAR1B
Interactions:

    Search GeneGlobe Interaction Network for HAR1B

(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 Tocris compounds for HAR1B



(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,
Conferences by KenesGroup, 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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2 fRNAdb Secondary structures:


Unigene Cluster for HAR1B:

Highly accelerated region 1B (non-protein coding)
Hs.635159  [show with all ESTs]
Unigene Representative Sequence: BM809061
2 Ensembl transcripts including schematic representations, and UCSC links where relevant:
ENST00000608031(lincRNA) ENST00000447910(lincRNA)(uc002yee.1)
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Additional mRNA sequence: 

DQ860410.1 DQ860411.1 NR_003245.1 

2 DOTS entries:

DT.75198099  DT.97766495 

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 HAR1B:RNAdb

HAR1B expression in normal human tissues (normalized intensities)
See probesets specificity/sensitivity at GeneAnnot
About this imageBioGPS <intensity>2/3
CGAP TAG: --
HAR1B Expression
About this image

HAR1B Protein expression data from MOPED1, PaxDb2 and MaxQB3 --

SOURCE GeneReport for Unigene cluster: Hs.635159
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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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  --

ENSEMBL Gene Tree for HAR1B (if available)
TreeFam Gene Tree for HAR1B (if available)

(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 HAR1B (see all 93)    About this table    
Genomic DataTranscription Related DataAllele Frequencies
SNP IDValidClinical
significance
Chr 20 posSequence#AA
Chg
TypeMore#Allele
freq
PopTotal
sample
More
----------
rs1159051701,2
C,F--61726351(+) GCAGCA/G/TTTTGG 1 -- ds50011WA 118
rs350331001,2
C,F--61726373(+) AATATT/CTGGGA 1 -- ds50014Minor allele frequency- C:0.05NA 126
rs759562091,2
C,F--61726376(+) ATTTGG/TGACAG 1 -- ds50011Minor allele frequency- T:0.09WA 118
rs1845699651,2
--61726524(+) AGACTC/GATGGG 1 -- ds50010--------
rs1895013141,2
--61726549(+) CCCCTA/CAACAT 1 -- ds50010--------
rs1434103411,2
--61726626(+) GGTGAC/TCCTGG 1 -- ds50010--------
rs1513295351,2
--61726659(+) AATCTC/TGGGCC 1 -- ds50010--------
rs1807318011,2
--61726680(+) GAGGCA/GGAGGG 1 -- ds50010--------
rs1153511881,2
C,F--61726709(+) CGAGAC/AACCAC 1 -- ds50011Minor allele frequency- A:0.01WA 118
rs1407738491,2
--61726780(+) AGGAAC/GCAGCC 1 -- ds50010--------

HapMap Linkage Disequilibrium report for HAR1B (61726845 - 61733671 bp)

Structural Variations
     Database of Genomic Variants (DGV) Selected variations for HAR1B (see all 16):    About this table    
Variant IDTypeSubtypePubMed ID
nsv3444CNV Insertion18451855
nsv513560CNV Insertion21212237
esv1000562CNV Insertion20482838
nsv509783CNV Insertion20534489
nsv834028CNV Loss17160897
dgv4623n71CNV Loss21882294
nsv913073CNV Loss21882294
nsv913162CNV Loss21882294
dgv4618n71CNV Loss21882294
nsv913163CNV Loss21882294

Site Specific Mutation Identification with PCR Assays
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DNA2.0 Custom Variant and Variant Library Synthesis for HAR1B

(in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Conferences by KenesGroup, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
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OMIM gene information: 610557OMIM information: 610556    
1 disease for HAR1B:    
About MalaCards
williams-beuren syndrome


HAR1B for disorders           About GeneDecksing


Export disorders for HAR1B 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 HAR1B gene integrated from 10 sources:
(articles sorted by number of sources associating them with HAR1B)
    Utopia: connect your pdf to the dynamic
world of online information

  1. An RNA gene expressed during cortical development evolved rapidly in humans. (PubMed id 16915236)1, 3 Pollard K.S....Haussler D. (Nature 2006)
  2. (PubMed id 15608161)10 
  3. (PubMed id 15103394)10 
  4. (PubMed id 18089548)10 

(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: 768097 HGNC: 33118 Ensembl:ENSG00000231133 euGenes: HUgn768097 ECgene: HAR1B
H-InvDB: HAR1B

(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 HAR1B 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 HAR1B gene:
Search GeneIP for patents involving HAR1B

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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