Human Gene STBD1 (ENST00000237642.7_4) from GENCODE V47lift37
  Description: starch binding domain 1 (from RefSeq NM_003943.5)
Gencode Transcript: ENST00000237642.7_4
Gencode Gene: ENSG00000118804.9_8
Transcript (Including UTRs)
   Position: hg19 chr4:77,227,886-77,232,283 Size: 4,398 Total Exon Count: 2 Strand: +
Coding Region
   Position: hg19 chr4:77,227,923-77,231,153 Size: 3,231 Coding Exon Count: 2 

Page IndexSequence and LinksUniProtKB CommentsPrimersCTDGene Alleles
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr4:77,227,886-77,232,283)mRNA (may differ from genome)Protein (358 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
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HGNCMGIOMIMPubMedReactomeUniProtKB
BioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: STBD1_HUMAN
DESCRIPTION: RecName: Full=Starch-binding domain-containing protein 1; AltName: Full=Genethonin-1;
FUNCTION: May have the capability to bind to carbohydrates (Potential).
INTERACTION: O95166:GABARAP; NbExp=5; IntAct=EBI-2947137, EBI-712001; Q9H0R8:GABARAPL1; NbExp=7; IntAct=EBI-2947137, EBI-746969; P60520:GABARAPL2; NbExp=3; IntAct=EBI-2947137, EBI-720116; Q9GZQ8:MAP1LC3B; NbExp=2; IntAct=EBI-2947137, EBI-373144;
SUBCELLULAR LOCATION: Membrane; Single-pass type III membrane protein (Probable). Note=Distributed in the transverse tubules and/or near the junctional sarcoplasmic reticulum.
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).
SIMILARITY: Contains 1 CBM20 (carbohydrate binding type-20) domain.

-  Primer design for this transcript
 

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3


-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 11.92 RPKM in Muscle - Skeletal
Total median expression: 136.85 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -9.1037-0.246 Picture PostScript Text
3' UTR -323.101130-0.286 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR013784 - Carb-bd-like_fold
IPR002044 - CBM_fam20
IPR013783 - Ig-like_fold

Pfam Domains:
PF00686 - Starch binding domain

SCOP Domains:
81296 - E set domains
49452 - Starch-binding domain-like

ModBase Predicted Comparative 3D Structure on O95210
FrontTopSide
The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologNo orthologNo orthologNo orthologNo orthologNo ortholog
Gene DetailsGene Details    
Gene SorterGene Sorter    
 RGDEnsembl   
      
      

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0005515 protein binding
GO:0019899 enzyme binding
GO:0030246 carbohydrate binding
GO:0030247 polysaccharide binding
GO:2001069 glycogen binding
GO:2001070 starch binding

Biological Process:
GO:0005975 carbohydrate metabolic process
GO:0005977 glycogen metabolic process
GO:0005980 glycogen catabolic process
GO:0006914 autophagy
GO:0043312 neutrophil degranulation
GO:0046907 intracellular transport
GO:0061723 glycophagy

Cellular Component:
GO:0005622 intracellular
GO:0005783 endoplasmic reticulum
GO:0005789 endoplasmic reticulum membrane
GO:0005829 cytosol
GO:0005886 plasma membrane
GO:0005887 integral component of plasma membrane
GO:0016020 membrane
GO:0016021 integral component of membrane
GO:0030315 T-tubule
GO:0034045 pre-autophagosomal structure membrane
GO:0048471 perinuclear region of cytoplasm
GO:0070821 tertiary granule membrane
GO:0101003 ficolin-1-rich granule membrane


-  Descriptions from all associated GenBank mRNAs
  AK092277 - Homo sapiens cDNA FLJ34958 fis, clone NTONG2003409, highly similar to Genethonin-1.
AK316039 - Homo sapiens cDNA, FLJ78938 complete cds, highly similar to Genethonin-1.
AK296418 - Homo sapiens cDNA FLJ59708 complete cds, highly similar to Genethonin-1.
AK090914 - Homo sapiens cDNA FLJ33595 fis, clone BRAMY2013169, highly similar to Genethonin-1.
AK123795 - Homo sapiens cDNA FLJ41801 fis, clone NHNPC2001931, highly similar to Genethonin-1.
AF062534 - Homo sapiens genethonin 1 mRNA, complete cds.
AK074635 - Homo sapiens cDNA FLJ90154 fis, clone HEMBB1002162.
BC022301 - Homo sapiens starch binding domain 1, mRNA (cDNA clone MGC:22536 IMAGE:4694574), complete cds.
DQ891974 - Synthetic construct clone IMAGE:100004604; FLH181984.01X; RZPDo839B05138D genethonin 1 (GENX-3414) gene, encodes complete protein.
DQ895165 - Synthetic construct Homo sapiens clone IMAGE:100009625; FLH181980.01L; RZPDo839B05137D genethonin 1 (GENX-3414) gene, encodes complete protein.
CU692542 - Synthetic construct Homo sapiens gateway clone IMAGE:100022180 5' read STBD1 mRNA.
KJ892665 - Synthetic construct Homo sapiens clone ccsbBroadEn_02059 STBD1 gene, encodes complete protein.
AK002155 - Homo sapiens cDNA FLJ11293 fis, clone PLACE1009670, highly similar to Genethonin-1.
JD496399 - Sequence 477423 from Patent EP1572962.
JD146515 - Sequence 127539 from Patent EP1572962.
JD205373 - Sequence 186397 from Patent EP1572962.
JD053065 - Sequence 34089 from Patent EP1572962.
JD166489 - Sequence 147513 from Patent EP1572962.
JD020013 - Sequence 1037 from Patent EP1572962.
JD486267 - Sequence 467291 from Patent EP1572962.
JD032798 - Sequence 13822 from Patent EP1572962.
JD345298 - Sequence 326322 from Patent EP1572962.
JD223466 - Sequence 204490 from Patent EP1572962.
JD318033 - Sequence 299057 from Patent EP1572962.
JD122523 - Sequence 103547 from Patent EP1572962.
JD386233 - Sequence 367257 from Patent EP1572962.
JD415469 - Sequence 396493 from Patent EP1572962.
JD101530 - Sequence 82554 from Patent EP1572962.
JD492133 - Sequence 473157 from Patent EP1572962.
JD545423 - Sequence 526447 from Patent EP1572962.

-  Biochemical and Signaling Pathways
  Reactome (by CSHL, EBI, and GO)

Protein O95210 (Reactome details) participates in the following event(s):

R-HSA-6798747 Exocytosis of tertiary granule membrane proteins
R-HSA-6800426 Exocytosis of ficolin-rich granule membrane proteins
R-HSA-6798695 Neutrophil degranulation
R-HSA-168249 Innate Immune System
R-HSA-168256 Immune System

-  Other Names for This Gene
  Alternate Gene Symbols: B3KVZ9, ENST00000237642.1, ENST00000237642.2, ENST00000237642.3, ENST00000237642.4, ENST00000237642.5, ENST00000237642.6, GENX-3414, NM_003943, O95210, STBD1 , STBD1_HUMAN, uc317ecv.1, uc317ecv.2
UCSC ID: ENST00000237642.7_4
RefSeq Accession: NM_003943.5
Protein: O95210 (aka STBD1_HUMAN)

-  Gene Model Information
  Click here for a detailed description of the fields of the table above.

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.