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LINC00277 Gene

RNA gene   GIFtS: 23
GCID: GC15P069367

Long Intergenic Non-Protein Coding RNA 277

(Previous names: transmembrane protein 84, non-protein coding RNA 277)
(Previous symbols: TMEM84, NCRNA00277)
  Search for LINC00277
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 3

Aliases
Long Intergenic Non-Protein Coding RNA 2771 2
NCRNA002771 2
TMEM841 2
Non-Protein Coding RNA 2771
Transmembrane Protein 841

External Ids:    HGNC: 265961   Entrez Gene: 2836732   Ensembl: ENSG000002127667   
ORGUL members:         

Export aliases for LINC00277 gene to outside databases


(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 LINC00277 Gene:
LINC00277 (long intergenic non-protein coding RNA 277) 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:
NC_000015.10  NC_018926.2  NT_010194.18  
Regulatory elements:
   Search for regulatory transcription factor binding sites for LINC00277
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidLINC00277 promoter sequence
   Search Chromatin IP Primers for LINC00277

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat LINC00277


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

Entrez Gene cytogenetic band: 15q23   Ensembl cytogenetic band:  15q23   HGNC cytogenetic band: 15q23

LINC00277 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
LINC00277 gene location

GeneLoc information about chromosome 15         GeneLoc Exon Structure

GeneLoc location for GC15P069367:  view genomic region     (about GC identifiers)

Start:
69,365,266 bp from pter      End:
69,388,164 bp from pter
Size:
22,899 bases      Orientation:
plus strand
ORGUL member locations:
Legend (see complete legend)

ORGUL Member Locations for LINC00277

(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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Phenotypes:
     1 GenomeRNAi human phenotype for LINC00277:
 Decreased Wnt reporter activit 

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 LINC00277
Interactions:

    Search GeneGlobe Interaction Network for LINC00277

(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 LINC00277



(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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REFSEQ mRNAs for LINC00277 gene: 
NM_173610.1  

Unigene Cluster for LINC00277:

Long intergenic non-protein coding RNA 277
Hs.177927  [show with all ESTs]
Unigene Representative Sequence: NR_026949
8 Ensembl transcripts including schematic representations, and UCSC links where relevant:
ENST00000415504(lincRNA)(uc002art.3) ENST00000559914(lincRNA) ENST00000558369(lincRNA) ENST00000558922(lincRNA)
ENST00000559964(lincRNA) ENST00000558147(lincRNA) ENST00000440444(lincRNA)(uc002arv.3 uc010big.3)
ENST00000435479(lincRNA)
miRNA
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Additional mRNA sequence: 

AK097560.1 AK292174.1 BC101594.1 BC101596.1 NR_026949.1 

2 DOTS entries:

DT.407032  DT.91787344 

22 AceView cDNA sequences:

AW189829 BQ944191 AA412498 BE728369 AA843716 NM_173610 BU182543 AK091087 
BF026680 AI192044 AK097560 AX746773 BQ953607 BQ949306 AA412585 BX493526 
BG476431 BU853671 AA393719 AW149320 AA397930 BE067040 

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 LINC00277:none

LINC00277 expression in normal human tissues (normalized intensities)
See probesets specificity/sensitivity at GeneAnnot
About this imageBioGPS <intensity>2/3
CGAP TAG: --
LINC00277 Expression
About this image

LINC00277 Protein expression data from MOPED1, PaxDb2 and MaxQB3 --

SOURCE GeneReport for Unigene cluster: Hs.177927
    Custom PCR Arrays for LINC00277
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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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  --

ENSEMBL Gene Tree for LINC00277 (if available)
TreeFam Gene Tree for LINC00277 (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 LINC00277 (see all 409)    About this table    
Genomic DataTranscription Related DataAllele Frequencies
SNP IDValidClinical
significance
Chr 15 posSequence#AA
Chg
TypeMore#Allele
freq
PopTotal
sample
More
----------
rs711475881,2
C--69371281(-) CTACCA/-AAAAA 1 -- us2k11Minor allele frequency- -:0.00NA 2
rs1893160491,2
--69371423(+) CCATAA/TTTTTT 1 -- us2k10--------
rs359993381,2
C,F--69371426(+) TAATTG/TTTTTT 1 -- us2k11Minor allele frequency- T:0.50NA 2
rs1809459901,2
--69371460(+) TCACTA/GTGTTG 1 -- us2k10--------
rs58135261,2
C--69371517(+) GACCT-/ACCAAA 1 -- us2k12Minor allele frequency- A:0.25NA CSA 4
rs1115196191,2
C--69371517(+) GACCTA/CCCAAA 1 -- us2k10--------
rs3118871,2
C--69371523(+) ccaaaG/Atgctg 1 -- us2k111Minor allele frequency- A:0.00NA WA CSA 19
rs1163241201,2
F--69371552(+) ACTGCG/ACCTGG 1 -- us2k11Minor allele frequency- A:0.02WA 118
rs1157679051,2
F--69371612(+) CGAAGG/TATATA 1 -- us2k11Minor allele frequency- T:0.03WA 118
rs169527821,2
C,F,H--69371622(+) ACAGAA/GTAAGC 1 -- us2k112Minor allele frequency- G:0.12NA NS EA CSA 773

HapMap Linkage Disequilibrium report for LINC00277 (69365266 - 69388164 bp)

Structural Variations
      Database of Genomic Variants (DGV) variations for LINC00277: --
Site Specific Mutation Identification with PCR Assays
Search QIAGEN SeqTarget long-range PCR primers for resequencing LINC00277
DNA2.0 Custom Variant and Variant Library Synthesis for LINC00277

(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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  --

(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 LINC00277 gene integrated from 10 sources:
(articles sorted by number of sources associating them with LINC00277)
    Utopia: connect your pdf to the dynamic
world of online information

  1. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PubMed id 15489334)1 Gerhard D.S.... Malek J. (Genome Res. 2004)
  2. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)1 Ota T.... Sugano S. (Nat. Genet. 2004)
  3. 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: 283673 HGNC: 26596 AceView: FLJ33768 Ensembl:ENSG00000212766 euGenes: HUgn283673
ECgene: LINC00277 H-InvDB: LINC00277

(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 LINC00277 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 LINC00277 gene:
Search GeneIP for patents involving LINC00277

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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