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SHANK2-AS3 Gene

RNA gene   GIFtS: 26
GCID: GC11P070709

SHANK2 Antisense RNA 3

(Previous names: chromosome 11 open reading frame 76, SHANK2 antisense RNA...)
(Previous symbol: C11orf76)
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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): antisense

Quality score for this RNA gene is 3

Aliases
SHANK2 Antisense RNA 31 2
C11orf761 2 3
Chromosome 11 Open Reading Frame 761
SHANK2 Antisense RNA 3 (Non-Protein Coding)1

External Ids:    HGNC: 250981   Entrez Gene: 2200702   Ensembl: ENSG000001716717   UniProtKB: Q9BTD13   
ORGUL members:         

Export aliases for SHANK2-AS3 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 SHANK2-AS3 Gene:
SHANK2-AS3 (SHANK2 antisense RNA 3) is an RNA gene, and is affiliated with the antisense RNA 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_000011.9  NC_018922.2  NT_167190.2  
Regulatory elements:
   Search for regulatory transcription factor binding sites for SHANK2-AS3
         Other transcription factors

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Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat SHANK2-AS3


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

Entrez Gene cytogenetic band: 11q13.4   Ensembl cytogenetic band:  11q13.4   HGNC cytogenetic band: 11q13.4

SHANK2-AS3 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
SHANK2-AS3 gene location

GeneLoc information about chromosome 11         GeneLoc Exon Structure

GeneLoc location for GC11P070709:  view genomic region     (about GC identifiers)

Start:
70,708,895 bp from pter      End:
70,711,220 bp from pter
Size:
2,326 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., 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/Swiss-Prot: SHAS3_HUMAN, Q9BTD1 (See protein sequence)
Recommended Name: Putative uncharacterized protein SHANK2-AS3  
Size: 123 amino acids; 13317 Da
Caution: Product of a dubious CDS prediction
Sequence caution: Sequence=AAH04224.1; Type=Erroneous initiation; Note=Translation N-terminally extended;

Explore the universe of human proteins at neXtProt for SHANK2-AS3: NX_Q9BTD1


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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: Q9BTD1


(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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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 SHANK2-AS3
Interactions:

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(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 SHANK2-AS3 (SHAS3)



(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 SHANK2-AS3 gene: 
NM_145308.2  

Unigene Cluster for SHANK2-AS3:

SHANK2 antisense RNA 3
Hs.326766  [show with all ESTs]
Unigene Representative Sequence: BC004224
1 Ensembl transcript including schematic representation, and UCSC links where relevant:
ENST00000307548(antisense)
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Additional mRNA sequence: 

BC004224.2 NR_073536.1 

1 DOTS entry:

DT.91806877 

5 AceView cDNA sequences:

BC004224 NM_145308 BX283738 BE264934 BQ338929 

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 SHANK2-AS3:none

SHANK2-AS3 expression in normal human tissues (normalized intensities)
See probesets specificity/sensitivity at GeneAnnot
About this imageBioGPS <intensity>2/3
CGAP TAG: --
SHANK2-AS3 Expression
About this image

SHANK2-AS3 Protein expression data from MOPED1, PaxDb2 and MaxQB3 --

SOURCE GeneReport for Unigene cluster: Hs.326766
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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 SHANK2-AS3 (if available)
TreeFam Gene Tree for SHANK2-AS3 (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 SHANK2-AS3 (see all 119)    About this table                                 

Genomic DataTranscription Related DataAllele Frequencies
SNP IDValidClinical
significance
Chr 11 posSequence#AA
Chg
TypeMore#Allele
freq
PopTotal
sample
More
----------
rs30198371,2
C,A,H--70552114(+) TGTTCG/AAGACC 1 -- us2k113Minor allele frequency- A:0.14NA WA CSA EA 378
rs1909320411,2
--70552313(+) GCACAC/TGGGGA 1 -- us2k10--------
rs759615051,2
F--70552324(+) GCAGCG/ACTGGC 1 -- us2k11Minor allele frequency- A:0.01WA 118
rs1821793431,2
--70552334(+) CCTTTC/TCGGGC 1 -- us2k10--------
rs1465565281,2
C--70552460(+) CCTGAA/GGGTTT 1 -- us2k10--------
rs1389925111,2
--70552511(+) ACTATG/TATGCC 1 -- us2k10--------
rs1151417461,2
C,F--70552550(+) CCACAC/TCTAGT 1 -- us2k11Minor allele frequency- T:0.01WA 118
rs2002335181,2
--70552752(+) CTGAC-/AAAAAA 1 -- us2k10--------
rs1415890781,2
C--70552859(+) GTTAA-/TTTTTT 1 -- us2k10--------
rs29213261,2
C,F,A,H--70552926(-) AACTGA/GCTCGT 1 -- us2k126Minor allele frequency- G:0.31NS EA NA WA CSA 2664

HapMap Linkage Disequilibrium report for SHANK2-AS3 (70708895 - 70711220 bp)

Structural Variations
      Database of Genomic Variants (DGV) variations for SHANK2-AS3: --
Site Specific Mutation Identification with PCR Assays
Search QIAGEN SeqTarget long-range PCR primers for resequencing SHANK2-AS3
DNA2.0 Custom Variant and Variant Library Synthesis for SHANK2-AS3

(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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(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 SHANK2-AS3 gene integrated from 10 sources:
(articles sorted by number of sources associating them with SHANK2-AS3)
    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, 2 Gerhard D.S.... Malek J. (Genome Res. 2004)
  2. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. (PubMed id 12477932)1, 3 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: 220070 HGNC: 25098 AceView: LOC220070 Ensembl:ENSG00000171671 euGenes: HUgn220070
ECgene: SHANK2-AS3 H-InvDB: SHANK2-AS3

(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 SHANK2-AS3 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 SHANK2-AS3 gene:
Search GeneIP for patents involving SHANK2-AS3

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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