Human Gene STAG3L3 (uc022afp.1)
  Description: Homo sapiens stromal antigen 3-like 3 (STAG3L3), non-coding RNA.
Transcript (Including UTRs)
   Position: hg19 chr7:72,467,989-72,476,448 Size: 8,460 Total Exon Count: 9 Strand: -


Page IndexSequence and LinksPrimersCTDRNA-Seq ExpressionMicroarray Expression
Other SpeciesmRNA DescriptionsOther NamesModel InformationMethods
Data last updated at UCSC: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr7:72,467,989-72,476,448)mRNA (may differ from genome)No protein
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaBioGPS
EnsemblExonPrimerH-INVHGNCLynxPubMed

-  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

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 4.48 RPKM in Testis
Total median expression: 61.10 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.

-  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
      
      
      
      
      

-  Descriptions from all associated GenBank mRNAs
  AK303592 - Homo sapiens cDNA FLJ52235 complete cds, moderately similar to Cohesin subunit SA-3.
AL137492 - Homo sapiens mRNA; cDNA DKFZp434A0131 (from clone DKFZp434A0131).
BC108680 - Homo sapiens stromal antigen 3-like 1, mRNA (cDNA clone IMAGE:5416073), complete cds.
BC010433 - Homo sapiens stromal antigen 3-like 1, mRNA (cDNA clone IMAGE:3531376), **** WARNING: chimeric clone ****.
BC030509 - Homo sapiens stromal antigen 3-like 1, mRNA (cDNA clone IMAGE:4400104), complete cds.
JD397731 - Sequence 378755 from Patent EP1572962.
JD070104 - Sequence 51128 from Patent EP1572962.
JD070105 - Sequence 51129 from Patent EP1572962.
BC119761 - Homo sapiens stromal antigen 3-like 2, mRNA (cDNA clone MGC:149883 IMAGE:40119328), complete cds.
BC119762 - Homo sapiens stromal antigen 3-like 1, mRNA (cDNA clone IMAGE:40119330), complete cds.
DQ587573 - Homo sapiens piRNA piR-54685, complete sequence.
JD204945 - Sequence 185969 from Patent EP1572962.
KJ902644 - Synthetic construct Homo sapiens clone ccsbBroadEn_12038 STAG3L1 gene, encodes complete protein.
BC066937 - Homo sapiens stromal antigen 3-like 3, mRNA (cDNA clone MGC:87278 IMAGE:4826886), complete cds.
AY313779 - Homo sapiens ARM-repeat protein mRNA, complete cds; alternatively spliced.
JD307418 - Sequence 288442 from Patent EP1572962.
AK289466 - Homo sapiens cDNA FLJ78546 complete cds.
AK291820 - Homo sapiens cDNA FLJ76564 complete cds.
JD504038 - Sequence 485062 from Patent EP1572962.
CU688206 - Synthetic construct Homo sapiens gateway clone IMAGE:100021053 5' read LOC442578 mRNA.
HQ448531 - Synthetic construct Homo sapiens clone IMAGE:100071966; CCSB011002_01 similar to Cohesin subunit SA-3 (Stromal antigen 3) (Stromalin 3) (SCC3 homolog 3) (STAG3L3) gene, encodes complete protein.
KJ900777 - Synthetic construct Homo sapiens clone ccsbBroadEn_10171 STAG3L3 gene, encodes complete protein.
JD506478 - Sequence 487502 from Patent EP1572962.
JD497104 - Sequence 478128 from Patent EP1572962.
JD334354 - Sequence 315378 from Patent EP1572962.
JD564669 - Sequence 545693 from Patent EP1572962.

-  Other Names for This Gene
  Alternate Gene Symbols: NR_040582, uc022afq.1
UCSC ID: uc022afp.1
RefSeq Accession: NR_040582

-  Gene Model Information
 
category: noncoding nonsense-mediated-decay: no RNA accession: NR_040582.1
exon count: 9CDS single in 3' UTR: no RNA size: 1993
ORF size: 0CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: -20.00frame shift in genome: no % Coverage: 99.25
has start codon: no stop codon in genome: no # of Alignments: 1
has end codon: no retained intron: no # AT/AC introns 0
selenocysteine: no end bleed into intron: 709# strange splices: 0
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.