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

STBD1 Gene

protein-coding   GIFtS: 47
GCID: GC04P077173

starch binding domain 1
 Explore 1 disease affiliated with
STBD1 via
MalaCards
our new
 Human Malady Compendium 
Biological research products
for STBD1    

Aliases
for STBD1 gene

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, and/or 10fRNAdb)
About This Section
Aliases
Starch Binding Domain 11 2     Genethonin 12
GENEX34142 5     Starch-Binding Domain-Containing Protein 12
FLJ418011     Genethonin-13
GENX-34141     

External Ids:    HGNC: 248541   Entrez Gene: 89872   Ensembl: ENSG000001188047   OMIM: 6074065   UniProtKB: O952103   

Export aliases for STBD1 gene to outside databases

Previous GC identifers: GC04P077446 GC04P077227 GC04P072979


Summaries
for STBD1 gene

(According to Entrez Gene, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
About This Section
UniProtKB/Swiss-Prot: STBD1_HUMAN, O95210
Function: May have the capability to bind to carbohydrates (Potential)




Genomic Views
for STBD1 gene

(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 69), Regulatory elements and Epigenetics data according to QIAGEN, SABiosciences, and/or SwitchGear Genomics)
About This Section
RefSeq DNA sequence:
NC_000004.11  NC_018915.1  NT_016354.19  
Regulatory elements:
   SABiosciences Regulatory transcription factor binding sites in the STBD1 gene promoter:
         Max1   AP-1   Pax-5   Nkx2-2   RelA   NF-kappaB   YY1   Pax-4a   NF-kappaB1   c-Myc   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmid: STBD1 promoter sequence
   Search SABiosciences Chromatin IP Primers for STBD1

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


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

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

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

GeneLoc information about chromosome 4         GeneLoc Exon Structure

GeneLoc location for GC04P077173:  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

Proteins
for STBD1 gene

(According to 1UniProtKB, HORDE, neXtProt, Ensembl, and/or Reactome, Modification sites according to 2PhosphoSitePlus, Specific Peptides from DME, Protein expression images according to data from SPIRE MOPED and PaxDb, 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 Uscn,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Uscn, Ontologies according to Gene Ontology Consortium 01 Mar 2013 and Entrez Gene, Antibodies by EMD Millipore, R&D Systems, GenScript, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, Abcam, and/or Uscn)
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 STBD1: NX_O95210

Post-translational modifications:

  • View modification sites using PhosphoSitePlus2
  • View neXtProt modification sites for NX_O95210

    • STBD1 Protein expression data from MOPED and PaxDb:    About this image 
    Estimated protein expression log10 (pmol).

    REFSEQ proteins: NP_003934.1  
    ENSEMBL proteins: 
     ENSP00000237642   ENSP00000442265  

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    Browse Proteins at Uscn

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

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005624membrane fraction ----
    GO:0005887integral to plasma membrane TAS9794794
    GO:0016020membrane TAS9794794


    STBD1 for ontologies           About GeneDecksing



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    Protein Domains /
    Families
    for STBD1 gene

    (According to InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
    About This Section
    STBD1 for domains           About GeneDecksing

    3 InterPro domains/families:
     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


    Function
    for STBD1 gene

    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013,
    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, Clones from EMD Millipore, OriGene, SwitchGear Genomics, GenScript, Sino Biological, DNA2.0, and Vector BioLabs, Cell Lines from GenScript, LifeMap BioReagents, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Mar 2013 via Entrez Gene.)
    About This Section
    Function Summary:

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

    miRNA
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    Inhib. RNA
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    Clone
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    In Situ Assay
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    Gene Ontology (GO): 2 molecular function terms (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005515protein binding IPI--
    GO:2001070starch binding IEA--


    STBD1 for ontologies           About GeneDecksing


    1 GenomeRNAi human phenotype for STBD1:
     Increased gamma-H2AX phosphory 


    Pathways & Interactions
    for STBD1 gene

    (Pathways according to EMD Millipore, R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, 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 Mar 2013 via Entrez Gene).
    About This Section

    Unified GeneCards pathways  About this table 
    See pathways by source

    Super-pathwaycontained gene-specific pathways
    1Diurnally regulated genes with circadian orthologs
    		Diurnally regulated genes with circadian orthologs1.00


    1 BioSystems Pathway for STBD1 
        Diurnally regulated genes with circadian orthologs


    Interactions:

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

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

    5/9 Interacting proteins for 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-3240381 I2D: score=3 STRING: ENSP00000266458
    ATF7IPQ6VMQ62, 3MINT-61889 I2D: score=3 
    GABARAPL2P605201, 3EBI-2947137,EBI-2973440 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 TAS9794794


    STBD1 for ontologies           About GeneDecksing



    Drugs & Compounds
    for STBD1 gene

    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience HMDB, BitterDB, and/or Novoseek, 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 STBD1
    Search CenterWatch for drugs/clinical trials and news about STBD1 

    Transcripts
    for STBD1 gene

    (Secondary structures according to fRNAdb,
    GenBank/EMBL/DDBJ Accessions according to
    Unigene (Build 235 Homo sapiens; Mar 10 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,
    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, Primers from OriGene, SABiosciences, and/or QIAGEN )
    About This Section
    REFSEQ mRNAs for STBD1 gene: 
    NM_003943.4  

    Unigene Cluster for STBD1:

    Starch binding domain 1
    Hs.109590  [show with all ESTs]
    Unigene Representative Sequence: NM_003943
    2 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000237642(uc003hka.3) ENST00000539752

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    hsa-miR-100* hsa-miR-548p hsa-miR-3688-3p hsa-miR-4302
    SwitchGear 3'UTR luciferase reporter plasmid: STBD1 3' UTR sequence
    Inhib. RNA
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    Clone
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    Primer
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    Additional cDNA sequence: 

    AF062534.1 AK123795.1 BC022301.1 

    6 DOTS entries:

    DT.75101169  DT.116065  DT.100755522  DT.40130086  DT.121235140  DT.121235194 

    24/158 AceView cDNA sequences (see all 158):

    BC022301 BC020802 AK002155 AI340932 AA909924 BM353726 CD370260 AW418551 
    BP382394 CF993883 BU628895 CR594152 AK092277 AL521396 AA131348 BM982744 
    AI376382 W67636 AI817878 BU735981 AA775888 BU739573 AK123795 BM713546 

    GeneLoc Exon Structure


    Expression
    for STBD1 gene

    (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

    STBD1 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS
    CGAP TAG: GGAGCATCTG

    Microarray
    RNAseq (Illumina Body Map)
    (100×FPKM)½
    SAGE (Serial Analysis of Gene Expression)
    About this image

    STBD1 expression in embryonic tissues and stem cells
    Expression by the Database of Embryonic development, Stem cell research, and Regenerative medicine    About this table
    1 LifeMap In Vivo Development Anatomical Compartment/Cell 
    Tissue Anatomical Compartment CellCategory (developmental path)
    LimbLimb BudLimb
    Expression: Positive    Negative     Selective marker
    Experimental details: Curated     Microarrays     In-situ hybridization

    See STBD1 Protein Expression from SPIRE MOPED and PaxDB
    Genevestigator expression for STBD1

    SOURCE GeneReport for Unigene cluster: Hs.109590

    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)

        SABiosciences Expression via Pathway-Focused PCR Array including STBD1: 
              Molecular Toxicology PathwayFinder 384HT in human mouse rat

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    In Situ
    Assay Products:     
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    Orthologs
    for STBD1 gene

    (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 STBD1 gene from 4/10 species (see all 10)    About this table
    Organism Taxonomic
    classification    		 Gene Description Human
    Similarity    		 Orthology
    Type    		 Details
    mouse
    (Mus musculus)    		 Mammalia Stbd11 , 5 starch binding domain 11, 5 78.21(n)1
    67.76(a)1    		   5 (47.21 cM)5
    523311  NM_175096.31  NP_780305.11 
     926030515 
    chicken
    (Gallus gallus)    		 Aves STBD11 starch binding domain 1 51.64(n)
    40.63(a)    		   422637  XM_429975.3  XP_429975.3 
    African clawed frog
    (Xenopus laevis)    		 Amphibia Xl.17652 Xenopus laevis transcribed sequence with weak similarity more 79.13(n)    CA972418.1 
    zebrafish
    (Danio rerio)    		 Actinopterygii BX927369.36
    		 --
    		 19(a)
    		 1 ↔ 1
    		 17(49792966-49810137)


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

    Paralogs
    for STBD1 gene

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

    STBD1 for paralogs           About GeneDecksing


    1 Pseudogenes.org Pseudogene for STBD1
    PGOHUM00000258674


    Genomic Variants
    for STBD1 gene

    (SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, UniProtKB, 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
    SABiosciences Cancer Mutation PCR Assays
    QIAGEN SeqTarget long-range PCR primers in human, mouse, rat for resequencing STBD1
    DNA2.0 Custom Variant and Variant Library Synthesis for STBD1

    Disorders / Diseases
    for STBD1 gene

    (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.)
    About This Section
    STBD1 for disorders           About GeneDecksing

    OMIM gene information: 607406    OMIM disorders: --

    1 disease for STBD1:    About MalaCards
    parkinson's disease


    Export disorders for STBD1 gene to outside databases

    Publications
    for STBD1 gene

    (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 STBD1 gene, integrated from 9 sources (see all 12):
    (articles sorted by number of sources associating them with STBD1)    		    Utopia: connect your pdf to the dynamic
    world of online information

    1. Molecular cloning and functional expression of a novel human gene encoding two 41-43 kDa skeletal muscle internal membrane proteins. (PubMed id 9794794)1, 2, 3, 9 Bouju S.... Dechesne C.A. (1998)
    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. (2004)
    3. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)1, 2 Ota T.... Sugano S. (2004)
    4. Novel gene transcripts preferentially expressed in hu man muscles revealed by quantitative hybridization of a high density cDNA array . (PubMed id 8828038)1, 3 PiActu G....Auffray C. (1996)
    5. Starch-binding domain-containing protein 1 (Stbd1) an d glycogen metabolism: Identification of the Atg8 family interacting motif (AIM ) in Stbd1 required for interaction with GABARAPL1. (PubMed id 21893048)1 Jiang S....Roach P.J. (2011)
    6. Network organization of the human autophagy system. (PubMed id 20562859)1 Behrends C....Harper J.W. (2010)
    7. Genome-wide association study reveals genetic risk un derlying Parkinson's disease. (PubMed id 19915575)1 SimA^n-SA!nchez J....Gasser T. (2009)
    8. A quantitative atlas of mitotic phosphorylation. (PubMed id 18669648)2 Dephoure N.... Gygi S.P. (2008)
    9. 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. (2005)
    10. Functional proteomics mapping of a human signaling pathway. (PubMed id 15231748)1 Colland F....Gauthier J.M. (2004)

    External Searches for STBD1 gene

    (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)

    Genome Databases showing STBD1 gene

    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
    About This Section
    Entrez Gene: 8987 HGNC: 24854 AceView: GENX-3414 Ensembl:ENSG00000118804 euGenes: HUgn8987
    ECgene: STBD1 H-InvDB: STBD1

    Other Databases showing STBD1 gene

    (According to HUGE)
    About This Section
    		   --

    Specialized Databases showing STBD1 gene

    (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
    NameDescription
    PharmGKB entry for STBD1 Pharmacogenomics, SNPs, Pathways

    Intellectual Property
    for STBD1 gene

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

    GeneCards and IP:
    Japan Patent Office Licenses GeneCards     European Patent Office Licenses GeneCards     Improving the IP Search



    Products
    for STBD1 gene

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    In Situ Hybridization Assays from
    Advanced Cell Diagnostics
    About This Section

     
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