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TINCR Gene

RNA gene   GIFtS: 24
GCID: GC19M005558

Tissue Differentiation-Inducing Non-Protein Coding RNA

(Previous names: placenta-specific 2, placenta-specific 2 (non-protein coding))
(Previous symbol: PLAC2)
  Search for TINCR
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
Tissue Differentiation-Inducing Non-Protein Coding RNA1 2     Placenta-Specific 2 (Non-Protein Coding)1
PLAC21 2     Terminal Differentiation-Induced NcRNA1
Long Intergenic Non-Protein Coding RNA 361     LINC000362
Non-Protein Coding RNA 361     NCRNA000362
Placenta-Specific 21     

External Ids:    HGNC: 146071   Entrez Gene: 2570002   Ensembl: ENSG000002235737   OMIM: 6152415   

Export aliases for TINCR 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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Entrez Gene summary for TINCR Gene:
This locus is inferred to be non-protein-coding based on the observations that a) there is no homology support for
predicted open reading frames; and b) the location of the longer predicted open reading frame renders the
transcript a candidate for nonsense-mediated decay (NMD) as the stop codon is >50 nucleotides upstream of the
terminal splice site. (provided by RefSeq, Feb 2009)

GeneCards Summary for TINCR Gene:
TINCR (tissue differentiation-inducing non-protein coding RNA) 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_000019.10  NC_018930.2  NT_011295.12  
Regulatory elements:
   Search for regulatory transcription factor binding sites for TINCR
         Other transcription factors

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


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

Entrez Gene cytogenetic band: 19p13.3   Ensembl cytogenetic band:  19p13.3   HGNC cytogenetic band: 19p13.3

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

GeneLoc information about chromosome 19         GeneLoc Exon Structure

GeneLoc location for GC19M005558:  view genomic region     (about GC identifiers)

Start:
5,558,178 bp from pter      End:
5,568,045 bp from pter
Size:
9,868 bases      Orientation:
minus strand
ORGUL member locations:
Legend (see complete legend)

ORGUL Member Locations for TINCR

(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., and/or eBioscience,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, Cloud-Clone Corp., and/or eBioscience, Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, Cloud-Clone Corp, and/or others.)
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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, 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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Phenotypes:
     1 GenomeRNAi human phenotype for TINCR:
 Decreased viability with pacli 

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 TINCR
Interactions:

    Search GeneGlobe Interaction Network for TINCR

(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 TINCR



(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 TINCR gene: 
NM_153375.1  

Unigene Cluster for TINCR:

Tissue differentiation-inducing non-protein coding RNA
Hs.515575  [show with all ESTs]
Unigene Representative Sequence: BC036545
3 Ensembl transcripts including schematic representations, and UCSC links where relevant:
ENST00000448587(lincRNA)(uc002mcc.4) ENST00000590789(lincRNA) ENST00000587632(lincRNA)
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Additional mRNA sequence: 

AF370401.1 AK075215.1 BC036545.1 BC047562.1 BC120980.1 BC120981.1 NR_027064.1 

7 DOTS entries:

DT.436765  DT.449739  DT.422145  DT.91725625  DT.121455623  DT.100746827  DT.121202518 

Selected AceView cDNA sequences (see all 100):

BM987765 AI088233 BU859960 AA716708 AI207389 AI436037 AI468031 AI188436 
AI168247 CR591932 BF055371 BQ023603 BG354568 AI864672 AI207365 AW662172 
BF109397 AI218695 R31195 BU680747 AI027842 AI148749 BC047562 AI497885 

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 TINCR:none

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

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

SOURCE GeneReport for Unigene cluster: Hs.515575
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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 TINCR (if available)
TreeFam Gene Tree for TINCR (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 TINCR (see all 200)    About this table                                 

Genomic DataTranscription Related DataAllele Frequencies
SNP IDValidClinical
significance
Chr 19 posSequence#AA
Chg
TypeMore#Allele
freq
PopTotal
sample
More
----------
rs1841021461,2
--5557744(+) GAACCA/GCCTGG 1 -- ds50010--------
rs1484922761,2
C--5557844(+) ACGCCA/GCGGGC 1 -- ds50010--------
rs748968161,2
C,F--5557899(+) AGCCCA/GGACTT 1 -- ds50011Minor allele frequency- G:0.04WA 118
rs1452989121,2
--5557934(+) AGAGGC/TCCTGG 1 -- ds50010--------
rs110851421,2
C,F,H--5557949(+) GAGCGG/AGCAGG 1 -- ds500119Minor allele frequency- A:0.01NS EA NA WA CSA 1252
rs1176554471,2
C,F--5558009(+) AACTGG/AAGTAA 1 -- ds50011Minor allele frequency- A:0.02NA 120
rs1476339821,2
--5558037(+) ACAGCA/GTCACC 1 -- ds50010--------
rs1883949631,2
--5558113(+) AAAACC/TATAGA 1 -- ds50010--------
rs1421863121,2
C--5558261(+) CTGCGA/GCCCCA 1 -- nc-transcript-variant0--------
rs744118371,2
F--5558274(+) GGTAGC/TGATGA 1 -- nc-transcript-variant0--------

HapMap Linkage Disequilibrium report for TINCR (5558178 - 5568045 bp)

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

(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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OMIM gene information: 615241    OMIM disorders: --


Find genes that share disorders with TINCR           About GenesLikeMe


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

  1. TINCR, staufen1, and cellular differentiation. (PubMed id 24019000)1, 3 Kretz M. (RNA Biol 2013)
  2. Control of somatic tissue differentiation by the long non-coding RNA TINCR. (PubMed id 23201690)1, 3 Kretz M....Khavari P.A. (Nature 2013)
  3. Signal sequence and keyword trap in silico for selection of full- length human cDNAs encoding secretion or membrane proteins from oligo- capped cDNA libraries. (PubMed id 16303743)1 Otsuki T....Isogai T. (DNA Res. 2005)
  4. 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)
  5. Large-scale cDNA transfection screening for genes related to cancer development and progression. (PubMed id 15498874)1 Wan D....Gu J. (Proc. Natl. Acad. Sci. U.S.A. 2004)
  6. 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: 257000 HGNC: 14607 AceView: PLAC2 Ensembl:ENSG00000223573 euGenes: HUgn257000
ECgene: TINCR H-InvDB: TINCR

(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 TINCR 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 TINCR gene:
Search GeneIP for patents involving TINCR

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, eBioscience, 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 inGenious Targeting Laboratory, genOway)
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