Human Gene ENTR1 (ENST00000298537.11_11) from GENCODE V47lift37
  Description: endosome associated trafficking regulator 1, transcript variant 2 (from RefSeq NM_006643.4)
Gencode Transcript: ENST00000298537.11_11
Gencode Gene: ENSG00000165689.17_18
Transcript (Including UTRs)
   Position: hg19 chr9:139,296,377-139,305,061 Size: 8,685 Total Exon Count: 9 Strand: -
Coding Region
   Position: hg19 chr9:139,297,240-139,304,849 Size: 7,610 Coding Exon Count: 9 

Page IndexSequence and LinksUniProtKB CommentsPrimersGene AllelesRNA-Seq Expression
Microarray ExpressionRNA StructureProtein StructureOther SpeciesGO AnnotationsmRNA Descriptions
Other NamesModel InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr9:139,296,377-139,305,061)mRNA (may differ from genome)Protein (412 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneTable SchemaAlphaFold
BioGPSEnsemblEntrez GeneExonPrimerGeneCardsMGI
OMIMPubMedUniProtKBBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: SDCG3_HUMAN
DESCRIPTION: RecName: Full=Serologically defined colon cancer antigen 3; AltName: Full=Antigen NY-CO-3;
FUNCTION: May be involved in modulation of TNF response. May be involved in presentation of TNFRSF1A on the cell surface (By similarity).
SUBCELLULAR LOCATION: Cytoplasm (By similarity).
SIMILARITY: Belongs to the SDCCAG3 family.
SEQUENCE CAUTION: Sequence=BAA91607.1; Type=Erroneous initiation; Note=Translation N-terminally extended; Sequence=CAI13936.1; Type=Erroneous gene model prediction; Sequence=CAI13942.2; Type=Erroneous gene model prediction; Sequence=CAI13943.2; Type=Erroneous gene model prediction;

-  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


+  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: 29.03 RPKM in Testis
Total median expression: 577.06 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 -122.50212-0.578 Picture PostScript Text
3' UTR -280.40863-0.325 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
IPR026757 - SDCCAG3

SCOP Domains:
52540 - P-loop containing nucleoside triphosphate hydrolases
90257 - Myosin rod fragments
57997 - Tropomyosin
161270 - PspA lactotransferrin-binding region

ModBase Predicted Comparative 3D Structure on Q96C92
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    
 RGD    
      
      

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0005515 protein binding

Biological Process:
GO:0007049 cell cycle
GO:0015031 protein transport
GO:0032465 regulation of cytokinesis
GO:0051301 cell division
GO:1990126 retrograde transport, endosome to plasma membrane

Cellular Component:
GO:0005737 cytoplasm
GO:0005768 endosome
GO:0005769 early endosome
GO:0030496 midbody
GO:0055037 recycling endosome
GO:0030904 retromer complex


-  Descriptions from all associated GenBank mRNAs
  AK001296 - Homo sapiens cDNA FLJ10434 fis, clone NT2RP1000481.
AF039688 - Homo sapiens antigen NY-CO-3 (NY-CO-3) mRNA, partial cds.
BC014515 - Homo sapiens serologically defined colon cancer antigen 3, mRNA (cDNA clone MGC:966 IMAGE:3547130), complete cds.
AY129014 - Homo sapiens clone FP17859 unknown mRNA.
JD353840 - Sequence 334864 from Patent EP1572962.
JD453429 - Sequence 434453 from Patent EP1572962.
JD378757 - Sequence 359781 from Patent EP1572962.
JD519540 - Sequence 500564 from Patent EP1572962.
JD128241 - Sequence 109265 from Patent EP1572962.
JD530363 - Sequence 511387 from Patent EP1572962.
JD488722 - Sequence 469746 from Patent EP1572962.
DQ893083 - Synthetic construct clone IMAGE:100005713; FLH193526.01X; RZPDo839H0278D serologically defined colon cancer antigen 3 (SDCCAG3) gene, encodes complete protein.
DQ896349 - Synthetic construct Homo sapiens clone IMAGE:100010809; FLH193522.01L; RZPDo839H0268D serologically defined colon cancer antigen 3 (SDCCAG3) gene, encodes complete protein.
AY349357 - Homo sapiens serologically defined colon cancer antigen 3 (SDCCAG3) mRNA, complete cds; alternatively spliced.
KJ902160 - Synthetic construct Homo sapiens clone ccsbBroadEn_11554 SDCCAG3 gene, encodes complete protein.
DQ580248 - Homo sapiens piRNA piR-48360, complete sequence.
JD226587 - Sequence 207611 from Patent EP1572962.
JD119592 - Sequence 100616 from Patent EP1572962.

-  Other Names for This Gene
  Alternate Gene Symbols: A6NCP1, ENST00000298537.1, ENST00000298537.10, ENST00000298537.2, ENST00000298537.3, ENST00000298537.4, ENST00000298537.5, ENST00000298537.6, ENST00000298537.7, ENST00000298537.8, ENST00000298537.9, ENTR1 , ENTR1_HUMAN, NM_006643, O60525, Q5SXN1, Q5SXN2, Q5SXN3, Q5SXN4, Q5SXN8, Q6V704, Q96C92, Q9NVY5, SDCCAG3, uc317mex.1, uc317mex.2
UCSC ID: ENST00000298537.11_11
RefSeq Accession: NM_006643.4
Protein: Q96C92 (aka SDCG3_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.