Human Gene STAG3 (ENST00000615138.5_4) from GENCODE V47lift37
  Description: stromal antigen 3, transcript variant 5 (from RefSeq NM_001375438.1)
Gencode Transcript: ENST00000615138.5_4
Gencode Gene: ENSG00000066923.19_14
Transcript (Including UTRs)
   Position: hg19 chr7:99,775,541-99,812,004 Size: 36,464 Total Exon Count: 34 Strand: +
Coding Region
   Position: hg19 chr7:99,778,180-99,811,638 Size: 33,459 Coding Exon Count: 33 

Page IndexSequence and LinksPrimersMalaCardsCTDGene Alleles
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 (chr7:99,775,541-99,812,004)mRNA (may differ from genome)Protein (1226 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
HGNCMalacardsMGIOMIMPubMedUniProtKB
WikipediaBioGrid CRISPR DB

-  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


-  MalaCards Disease Associations
  MalaCards Gene Search: STAG3
Diseases sorted by gene-association score: premature ovarian failure 8* (919), premature ovarian failure 1 (1)
* = Manually curated disease association

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene

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

+  Microarray Expression Data
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-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -55.20152-0.363 Picture PostScript Text
3' UTR -113.80366-0.311 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
IPR011989 - ARM-like
IPR016024 - ARM-type_fold
IPR020839 - SCD
IPR013721 - STAG

Pfam Domains:
PF08514 - STAG domain

SCOP Domains:
48371 - ARM repeat
48498 - Tetracyclin repressor-like, C-terminal domain

ModBase Predicted Comparative 3D Structure on D6W5U7
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    
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-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Biological Process:
GO:0007129 synapsis
GO:0034502 protein localization to chromosome

Cellular Component:
GO:0000794 condensed nuclear chromosome
GO:0000795 synaptonemal complex
GO:0000800 lateral element
GO:0000802 transverse filament
GO:0001673 male germ cell nucleus
GO:0030893 meiotic cohesin complex
GO:0034991 nuclear meiotic cohesin complex


-  Descriptions from all associated GenBank mRNAs
  AJ007798 - Homo sapiens mRNA for stromal antigen 3 (STAG3 gene).
AK292394 - Homo sapiens cDNA FLJ76939 complete cds, highly similar to Homo sapiens stromal antigen 3 (STAG3), mRNA.
BC146806 - Homo sapiens stromal antigen 3, mRNA (cDNA clone MGC:167012 IMAGE:8860345), complete cds.
AK302693 - Homo sapiens cDNA FLJ60376 complete cds, highly similar to Cohesin subunit SA-3.
BC047490 - Homo sapiens cDNA clone IMAGE:5295486, containing frame-shift errors.
BC028684 - Homo sapiens cDNA clone IMAGE:4829833, containing frame-shift errors.
AL833816 - Homo sapiens mRNA; cDNA DKFZp434L233 (from clone DKFZp434L233).
BC140932 - Homo sapiens stromal antigen 3, mRNA (cDNA clone MGC:176609 IMAGE:9056744), complete cds.
JD159447 - Sequence 140471 from Patent EP1572962.
JD541485 - Sequence 522509 from Patent EP1572962.
JD150510 - Sequence 131534 from Patent EP1572962.
KJ898276 - Synthetic construct Homo sapiens clone ccsbBroadEn_07670 STAG3 gene, encodes complete protein.
AK302587 - Homo sapiens cDNA FLJ55913 complete cds, highly similar to Cohesin subunit SA-3.
JD334354 - Sequence 315378 from Patent EP1572962.
JD307418 - Sequence 288442 from Patent EP1572962.
DQ587573 - Homo sapiens piRNA piR-54685, complete sequence.
AL834328 - Homo sapiens mRNA; cDNA DKFZp434P091 (from clone DKFZp434P091).
JD191450 - Sequence 172474 from Patent EP1572962.
JD127016 - Sequence 108040 from Patent EP1572962.
JD124577 - Sequence 105601 from Patent EP1572962.
JD342586 - Sequence 323610 from Patent EP1572962.
JD258043 - Sequence 239067 from Patent EP1572962.
JD062720 - Sequence 43744 from Patent EP1572962.
JD298275 - Sequence 279299 from Patent EP1572962.
JD183622 - Sequence 164646 from Patent EP1572962.

-  Other Names for This Gene
  Alternate Gene Symbols: D6W5U7, D6W5U7_HUMAN, ENST00000615138.1, ENST00000615138.2, ENST00000615138.3, ENST00000615138.4, hCG_2024106 , NM_001375438, STAG3 , uc327prt.1, uc327prt.2
UCSC ID: ENST00000615138.5_4
RefSeq Accession: NM_001282717.2
Protein: D6W5U7

-  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.