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BPESC1 Gene

RNA gene   GIFtS: 29
GCID: GC03P138823

Blepharophimosis, Epicanthus Inversus And Ptosis, Candidate...

(Previous names: blepharophimosis, epicanthus inversus and ptosis, candidate...)
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(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 3

Aliases
Blepharophimosis, Epicanthus Inversus And Ptosis, Candidate 1
(Non-Protein Coding)1 2
Blepharophimosis, Epicanthus Inversus And Ptosis, Candidate 11
Non-Protein Coding RNA 1871
NCRNA001872
BPES Candidate 13

External Ids:    HGNC: 132281   Entrez Gene: 604672   Ensembl: ENSG000002324167   UniProtKB: Q9GZL83   
ORGUL members:         

Export aliases for BPESC1 gene to outside databases

Previous GC identifers: GC03P135716 GC03P139679 GC03P140104 GC03P140143 GC03P140305 GC03U901049 GC03P136198


(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 BPESC1 Gene:
BPESC1 (blepharophimosis, epicanthus inversus and ptosis, candidate 1 (non-protein coding)) is an RNA gene, and is affiliated with the lncRNA class.


(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 at NCBI GenBank:
NC_000003.11  NC_018914.2  NT_005612.17  
Regulatory elements:
   Search for regulatory transcription factor binding sites for BPESC1
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidBPESC1 promoter sequence
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Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat BPESC1


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

Entrez Gene cytogenetic band: 3q23   Ensembl cytogenetic band:  3q23   HGNC cytogenetic band: 3q23

BPESC1 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
BPESC1 gene location

GeneLoc information about chromosome 3         GeneLoc Exon Structure

GeneLoc location for GC03P138823:  view genomic region     (about GC identifiers)

Start:
138,823,027 bp from pter      End:
138,844,009 bp from pter
Size:
20,983 bases      Orientation:
plus strand

(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, Cloud-Clone Corp., eBioscience, and/or antibodies-online,
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UniProtKB/Swiss-Prot: BPEC1_HUMAN, Q9GZL8 (See protein sequence)
Recommended Name: Putative BPES syndrome breakpoint region protein  
Size: 116 amino acids; 12676 Da
Secondary accessions: Q0VDG2

Explore the universe of human proteins at neXtProt for BPESC1: NX_Q9GZL8


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(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

ProtoNet protein and cluster: Q9GZL8


(According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, 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, Vector BioLabs and/or Addgene, Cell Lines from GenScript, ESI BIO, In Situ Hybridization Assays from Advanced Cell Diagnostics, Flow cytometry from eBioscience, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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     Gene Ontology (GO): 1 molecular function term:    About this table

GO IDQualified GO termEvidencePubMed IDs
GO:0003674molecular_function ND--
     
Find genes that share ontologies with BPESC1           About GenesLikeMe


Phenotypes:
     1 GenomeRNAi human phenotype for BPESC1:
 Increased gamma-H2AX phosphory 

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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Gene Ontology (GO): 1 cellular component term:    About this table

GO IDQualified GO termEvidencePubMed IDs
GO:0005575cellular_component ND--

Find genes that share ontologies with BPESC1           About GenesLikeMe


(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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Interactions:

    Search GeneGlobe Interaction Network for BPESC1

Gene Ontology (GO): 1 biological process term:    About this table

GO IDQualified GO termEvidencePubMed IDs
GO:0008150biological_process ND--

Find genes that share ontologies with BPESC1           About GenesLikeMe



(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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(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, and/or Addgene, Primers from OriGene, and/or QIAGEN, Flow cytometry from eBioscience )
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REFSEQ mRNAs for BPESC1 gene: 
NM_021812.1  

Unigene Cluster for BPESC1:

Blepharophimosis, epicanthus inversus and ptosis, candidate 1 (non-protein coding)
Hs.512673  [show with all ESTs]
Unigene Representative Sequence: NR_026783
1 Ensembl transcript including schematic representation, and UCSC links where relevant:
ENST00000418282(lincRNA)(uc003eta.3)
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Additional mRNA sequence: 

BC119686.1 BC119687.1 NR_026783.1 

1 DOTS entry:

DT.40129417 

3 AceView cDNA sequences:

BX091809 AI032396 NM_021812 

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 BPESC1:none

BPESC1 expression in normal human tissues (normalized intensities)
See probesets specificity/sensitivity at GeneAnnot
About this imageBioGPS <intensity>2/3
CGAP TAG: --
BPESC1 Expression
About this image

BPESC1 Protein expression data from MOPED1, PaxDb2 and MaxQB3 --

SOURCE GeneReport for Unigene cluster: Hs.512673

UniProtKB/Swiss-Prot: BPEC1_HUMAN, Q9GZL8
Tissue specificity: Seems to be expressed only in testis

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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 BPESC1 (if available)
TreeFam Gene Tree for BPESC1 (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 BPESC1 (see all 496)    About this table                                 

Genomic DataTranscription Related DataAllele Frequencies
SNP IDValidClinical
significance
Chr 3 posSequence#AA
Chg
TypeMore#Allele
freq
PopTotal
sample
More
----------
rs38412701,2
C--138821148(-) TGCAG-/GTTCTA 1 -- us2k12Minor allele frequency- G:0.00NA CSA 4
rs2018156041,2
C--138821148(-) TGCAGG/TTTCTA 1 -- us2k10--------
rs22466711,2
C,F,A,H--138821205(+) TAGATG/ATCATC 1 -- us2k133Minor allele frequency- A:0.46NS EA NA WA CSA 2998
rs1498848831,2
--138821332(+) GTGCAA/GGAGGA 1 -- us2k10--------
rs1879373071,2
--138821335(+) CAGGAA/GGATTC 1 -- us2k10--------
rs1448699361,2
--138821376(+) GGCCAC/TAGCTT 1 -- us2k10--------
rs801701691,2
F--138821406(+) TGATTT/GCGGTG 1 -- us2k12Minor allele frequency- G:0.11CSA WA 120
rs1460837201,2
C--138821947(+) TGGCT-/GGGGG 
        
GTAGT
1 -- us2k10--------
rs1895253441,2
--138821957(+) TCCAGG/TTTATC 1 -- us2k10--------
rs1485883421,2
--138822034(+) ACAGAA/GGCCCT 1 -- us2k10--------

HapMap Linkage Disequilibrium report for BPESC1 (138823027 - 138844009 bp)

Structural Variations
     Database of Genomic Variants (DGV) 3 variations for BPESC1:    About this table    
Variant IDTypeSubtypePubMed ID
esv2663804CNV Deletion23128226
esv1587056CNV Insertion17803354
nsv829736CNV Gain17160897

Site Specific Mutation Identification with PCR Assays
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(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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Find genes that share disorders with BPESC1           About GenesLikeMe

Genetic Association Database (GAD): BPESC1

Export disorders for BPESC1 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 BPESC1 gene integrated from 10 sources:
(articles sorted by number of sources associating them with BPESC1)
    Utopia: connect your pdf to the dynamic
world of online information

  1. Identification of BPESC1, a novel gene disrupted by a balanced chromosomal translocation, t(3;4)(q23;p15.2), in a patient with BPES. (PubMed id 10995571)1, 2, 3 De Baere E.... Messiaen L. (Genomics 2000)
  2. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PubMed id 15489334)1, 2 Gerhard D.S.... Malek J. (Genome Res. 2004)
  3. Genome-wide scan for loci of adolescent obesity and their relationship with blood pressure. (PubMed id 22013104)4 Melka M.G....Pausova Z. (J. Clin. Endocrinol. Metab. 2012)
  4. The DNA sequence, annotation and analysis of human chromosome 3. (PubMed id 16641997)2 Muzny D.M....Gibbs R.A. (Nature 2006)
  5. 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. (Proc. Natl. Acad. Sci. U.S.A. 2002)

(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: 60467 HGNC: 13228 AceView: BPESC1 Ensembl:ENSG00000232416 euGenes: HUgn60467
ECgene: BPESC1 H-InvDB: BPESC1

(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 BPESC1 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 BPESC1 gene:
Search GeneIP for patents involving BPESC1

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, eBioscience, antibodies-online, and/or others, Gene Editing from DNA2.0. Clones from OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Addgene, Cell lines from GenScript, and ESI BIO, Flow cytometery from eBioscience, 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 genOway)
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