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Category   Symbol Source: HGNC EntrezGene Ensembl GeneCards RNA genes CroW21
GIFtS

FAM47E-STBD1 Gene

protein-coding   GIFtS: 25
GCID: GC04P077174

FAM47E-STBD1 Readthrough

  Search for FAM47E-STBD1
at  

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, 10fRNAdb, 12H-InvDB, 13NCBI, 14NONCODE, and/or 15RNAdb)
About This Section

Aliases
FAM47E-STBD1 Readthrough1 2
Uncharacterized Protein LOC1006313832
Genethonin-13

External Ids:    HGNC: 446671   Entrez Gene: 1006313832   Ensembl: ENSG000001188047   UniProtKB: O952103   

Export aliases for FAM47E-STBD1 gene to outside databases

Previous GC identifer: GC04U901512


(According to Entrez Gene, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
About This Section

Entrez Gene summary for FAM47E-STBD1 Gene:
This locus represents naturally occurring read-through transcription between the neighboring FAM47E (family with
sequence similarity 47, member E) and STBD1 (starch binding domain 1) genes on chromosome 4. The read-through
transcript encodes a protein that shares sequence identity with the upstream gene product but its C-terminal
region is distinct due to frameshifts relative to the downstream gene. (provided by RefSeq, Jul 2011)

GeneCards Summary for FAM47E-STBD1 Gene: 
FAM47E-STBD1 (FAM47E-STBD1 readthrough) is a protein-coding gene.

UniProtKB/Swiss-Prot: STBD1_HUMAN, O95210
Function: May have the capability to bind to carbohydrates (Potential)




(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 73), Regulatory elements and Epigenetics data according to QIAGEN, SABiosciences, and/or SwitchGear Genomics)
About This Section
Regulatory elements:
   Search SABiosciences Regulatory transcription factor binding sites for FAM47E-STBD1
         Other transcription factors

Browse SwitchGear Promoter luciferase reporter plasmids
   Search SABiosciences Chromatin IP Primers for FAM47E-STBD1

Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat FAM47E-STBD1


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

Entrez Gene cytogenetic band: 4q   Ensembl cytogenetic band:  4q21.1   HGNC cytogenetic band: 4q21.1

FAM47E-STBD1 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
FAM47E-STBD1 gene location

GeneLoc information about chromosome 4         GeneLoc Exon Structure

GeneLoc location for GC04P077174:  view genomic region     (about GC identifiers)

Start:
77,172,886 bp from pter      End:
77,232,752 bp from pter
Size:
59,867 bases      Orientation:
plus strand

(According to UniProtKB, HORDE, neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MAXQB 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., Ontologies according to Gene Ontology Consortium 01 Oct 2013 and Entrez Gene, Antibodies by EMD Millipore, R&D Systems, GenScript, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, and/or Cloud-Clone Corp.)
About This Section

UniProtKB/Swiss-Prot: STBD1_HUMAN, O95210 (See protein sequence)
Recommended Name: Starch-binding domain-containing protein 1  
Size: 358 amino acids; 39007 Da
Subcellular location: Membrane; Single-pass type III membrane protein (Probable). Note=Distributed in the
transverse tubules and/or near the junctional sarcoplasmic reticulum
Secondary accessions: B3KVZ9

Explore the universe of human proteins at neXtProt for FAM47E-STBD1: NX_O95210

Explore proteomics data for FAM47E-STBD1 at MOPED 

Post-translational modifications:

  • View modification sites using PhosphoSitePlus
  • View neXtProt modification sites for NX_O95210

  • FAM47E-STBD1 Protein expression data from MOPED1, PaxDb2 and MAXQB3 :    About this image 

    FAM47E-STBD1 Protein Expression
    REFSEQ proteins: NP_001229868.1  
    ENSEMBL proteins: 
     ENSP00000237642   ENSP00000442265  

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    Gene Ontology (GO): 2 cellular component terms (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005887integral to plasma membrane ----
    GO:0016020membrane ----

    FAM47E-STBD1 for ontologies           About GeneDecksing



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    (According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
    About This Section
    3 InterPro protein domains:
     IPR013784 Carb-bd-like_fold
     IPR002044 CBM_fam20
     IPR013783 Ig-like_fold

    Graphical View of Domain Structure for InterPro Entry O95210

    ProtoNet protein and cluster: O95210

    UniProtKB/Swiss-Prot: STBD1_HUMAN, O95210
    Similarity: Contains 1 CBM20 (carbohydrate binding type-20) domain


    FAM47E-STBD1 for domains           About GeneDecksing


    (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,
    bound targets from SABiosciences, miRNA Gene Targets from miRTarBase, shRNA from OriGene, RNAi from EMD Millipore, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, Gene Editing from DNA2.0, Sirion Biotech, Clones from EMD Millipore, OriGene, SwitchGear Genomics, GenScript, Sino Biological, DNA2.0, Vector BioLabs, and Sirion Biotech, Cell Lines from GenScript, LifeMap BioReagents, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Oct 2013 via Entrez Gene.)
    About This Section

    Molecular Function:

         UniProtKB/Swiss-Prot Summary: STBD1_HUMAN, O95210
    Function: May have the capability to bind to carbohydrates (Potential)

         Gene Ontology (GO): 3 molecular function terms (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005515protein binding ----
    GO:0030246carbohydrate binding ----
    GO:2001070starch binding ----
         
    FAM47E-STBD1 for ontologies           About GeneDecksing


    Phenotypes:
         1 GenomeRNAi human phenotype for FAM47E-STBD1:
     Decreased TP53 protein express 

    Animal Models:
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    (Pathways according to EMD Millipore, 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 SABiosciences, 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 Oct 2013 via Entrez Gene).
    About This Section



    Interactions:

        Search SABiosciences Gene Network CentralTM Interacting Genes and Proteins Networks for FAM47E-STBD1

    STRING Interaction Network Preview (showing 2 interactants - click image to see more details)

    5/9 Interacting proteins for FAM47E-STBD1 (O952101, 2, 3 ENSP000002376424) via UniProtKB, MINT, STRING, and/or I2D (see all 9)
    InteractantInteraction Details
    GeneCardExternal ID(s)
    GABARAPL1Q9H0R81, 3, ENSP000002664584EBI-2947137,EBI-746969 I2D: score=3 STRING: ENSP00000266458
    ATF7IPQ6VMQ62, 3MINT-61889 I2D: score=3 
    GABARAPL2P605201, 3EBI-2947137,EBI-720116 I2D: score=3 
    MAP1LC3BQ9GZQ81, 3EBI-2947137,EBI-373144 I2D: score=1 
    GABARAPO951661, 3, ENSP000003068664EBI-2947137,EBI-712001 I2D: score=3 STRING: ENSP00000306866
    About this table

    Gene Ontology (GO): 1 biological process term (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0006936muscle contraction ----

    FAM47E-STBD1 for ontologies           About GeneDecksing



    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB, with drugs/clinical trials/news search links to CenterWatch)
    About This Section
    Browse Small Molecules at EMD Millipore
    Browse drugs & compounds from Enzo Life Sciences

    Browse Tocris compounds for FAM47E-STBD1 (STBD1)

    Search CenterWatch for drugs/clinical trials and news about FAM47E-STBD1 / STBD1

    (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,
    RNAi Products from EMD Millipore,
    siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN,
    Tagged/untagged cDNA clones from OriGene, SwitchGear Genomics, GenScript, DNA2.0, Vector BioLabs, Sirion Biotech, Primers from OriGene, SABiosciences, and/or QIAGEN )
    About This Section

    REFSEQ mRNAs for FAM47E-STBD1 gene: 
    NM_001242939.1  

    2 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000237642(uc003hka.3) ENST00000539752
    miRNA
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    Inhib. RNA
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    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™, plus additional links to Genevestigator, and/or SOURCE, and/or BioGPS, and/or UniProtKB,
    PCR Arrays from SABiosciences, Primers from OriGene, SABiosciences, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
    About This Section

    FAM47E-STBD1 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: --
    FAM47E-STBD1 Expression
    About this image


    See FAM47E-STBD1 Protein Expression from SPIRE MOPED and PaxDB

    UniProtKB/Swiss-Prot: STBD1_HUMAN, O95210
    Tissue specificity: Expressed at high level in skeletal and cardiac muscles. Moderately expressed in liver and
    placenta. No expression is found in pancreas, kidney or lung. Present in skeletal muscle, heart and placenta (at
    protein level)

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    In Situ
    Assay Products:
     

     
    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for FAM47E-STBD1

    (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)
    About This Section

    This gene was present in the common ancestor of chordates.

    Orthologs for FAM47E-STBD1 gene from 3/8 species (see all 8)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    chicken
    (Gallus gallus)
    Aves FAM47E-STBD16
    FAM47E-STBD1 readthrough
    39(a)
    1 ↔ 1
    4(49315135-49316800)
    lizard
    (Anolis carolinensis)
    Reptilia FAM47E-STBD16
    FAM47E-STBD1 readthrough
    29(a)
    1 ↔ 1
    5(146818502-146829152)
    zebrafish
    (Danio rerio)
    Actinopterygii --
    --
    16(a)
    1 ↔ 1
    17(49792966-49810137)
            Species with no ortholog for FAM47E-STBD1

    ENSEMBL Gene Tree for FAM47E-STBD1 (if available)
    TreeFam Gene Tree for FAM47E-STBD1 (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
    About This Section
    Paralogs for FAM47E-STBD1 gene

    FAM47E-STBD1 for paralogs           About GeneDecksing


    1 Pseudogenes.org Pseudogene for FAM47E-STBD1
    PGOHUM00000258674


    (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) and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers from QIAGEN, Cancer Mutation PCR Arrays and Assays and Copy Number PCR Arrays from SABiosciences)
    About This Section

    10/341 SNPs in FAM47E-STBD1 are shown (see all 341)    About this table     
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 4 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs1388761841,2
    C--77205451(+) ATTACC/TCAGCC 1 -- int10--------
    rs1891946231,2
    --77205471(+) CCTTTG/TTAGCA 1 -- int10--------
    rs65323231,2
    C--77205629(+) ATACTG/CTCTGG 1 -- int19Minor allele frequency- C:0.01NA WA CSA 134
    rs28698811,2
    C,F,A--77205745(+) CCCTTC/TTGCCT 1 -- int17Minor allele frequency- T:0.20WA NA CSA EA 366
    rs28698821,2
    C,A--77205746(+) CCTTTA/TGCCTA 1 -- int17Minor allele frequency- T:0.19WA NA CSA EA 366
    rs1930595391,2
    --77205923(+) ACATAC/TAGGGA 1 -- int10--------
    rs1854848341,2
    --77206115(+) TCTAGA/GTTTTA 1 -- int10--------
    rs1889132111,2
    --77206172(+) GCCCTA/CCACCC 1 -- int10--------
    rs1919248021,2
    --77206727(+) TGCATC/TTCTCT 1 -- int10--------
    rs1470551031,2
    C--77206895(+) TAGGCC/TTTTGT 1 -- int10--------

    HapMap Linkage Disequilibrium report for FAM47E-STBD1 (77172886 - 77232752 bp)

    Structural Variations
         Database of Genomic Variants (DGV) 5 variations for FAM47E-STBD1:    About this table     
    Variant IDTypeSubtypePubMed ID
    esv2661271CNV Deletion23128226
    esv2421530CNV Deletion20811451
    nsv516357CNV Loss19592680
    nsv461559CNV Loss19166990
    nsv7363OTHER Inversion18451855

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    (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.)
    About This Section
      --

    (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)
    About This Section

    PubMed articles for FAM47E-STBD1 gene integrated from 9 sources:
    (articles sorted by number of sources associating them with FAM47E-STBD1)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)1, 2 Ota T.... Sugano S. (2004)
    2. Web-based genome-wide association study identifies tw o novel loci and a substantial genetic component for Parkinson's disease. (PubMed id 21738487)1 Do C.B....Eriksson N. (2011)
    3. Expression of conjoined genes: another mechanism for gene regulation in eukaryotes. (PubMed id 20967262)1 Prakash T....Taylor T.D. (2010)
    4. Genome-wide association study reveals genetic risk un derlying Parkinson's disease. (PubMed id 19915575)1 SimA^n-SA!nchez J....Gasser T. (2009)
    5. A quantitative atlas of mitotic phosphorylation. (PubMed id 18669648)2 Dephoure N.... Gygi S.P. (2008)
    6. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PubMed id 15489334)2 Gerhard D.S....Malek J. (2004)
    7. A motif of a microbial starch-binding domain found in human genethonin. (PubMed id 12424126)2 Janecek S. (2002)
    8. The sequence of the human genome. (PubMed id 11181995)1 Venter J.C.... Zhu X. (2001)
    9. Toward a complete human genome sequence. (PubMed id 9847074)1 Wilson R. (1998)
    10. Molecular cloning and functional expression of a novel human gene encoding two 41-43 kDa skeletal muscle internal membrane proteins. (PubMed id 9794794)2 Bouju S.... Dechesne C.A. (1998)

    (in PubMed, OMIM, and NCBI Bookshelf)
    About This Section
     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)
    About This Section
    Entrez Gene: 100631383 HGNC: 44667 Ensembl:ENSG00000118804 euGenes: HUgn100631383 ECgene: FAM47E-STBD1
    H-InvDB: FAM47E-STBD1

    (According to HUGE)
    About This Section
      --

    (According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL,
    Wikipedia and/or GeneReviews via UniProtKB/Swiss-Prot)
    About This Section
      --

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
    About This Section
    Patent Information for FAM47E-STBD1 gene:
    Search GeneIP for patents involving FAM47E-STBD1

    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, SABiosciences, Novus Biologicals, Sino Biological, Enzo Life Sciences, Abcam, ProSpec, Cloud-Clone Corp., Thermo Fisher Scientific, LSBio, Gene Editing from DNA2.0 and Sirion Biotech, Clones from EMD Millipore, OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Sirion Biotech, Cell lines from GenScript, and LifeMap BioReagents, PCR Arrays from SABiosciences, Drugs and/or compounds from EMD Millipore, Tocris Bioscience, and/or Enzo Life Sciences, In Situ Hybridization Assays from
    Advanced Cell Diagnostics, Animal models from inGenious Targeting Laboratory, genOway)
    About This Section

     
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    GeneCards Homepage - Last full update: 23 Oct 2013 - Incrementals: 4 Nov 2013 , 7 Nov 2013 , 23 Jan 2014

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    (GIFtS: 73)
    transforming growth factor, beta 1
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