Human Gene SH3D21 (uc010oia.1)
  Description: Homo sapiens SH3 domain containing 21 (SH3D21), transcript variant 1, mRNA.
Transcript (Including UTRs)
   Position: hg19 chr1:36,771,994-36,787,379 Size: 15,386 Total Exon Count: 16 Strand: +
Coding Region
   Position: hg19 chr1:36,772,022-36,786,728 Size: 14,707 Coding Exon Count: 16 

Page IndexSequence and LinksPrimersCTDGene AllelesRNA-Seq Expression
Microarray ExpressionRNA StructureProtein StructureOther SpeciesmRNA DescriptionsOther Names
Model InformationMethods
Data last updated at UCSC: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr1:36,771,994-36,787,379)mRNA (may differ from genome)Protein (756 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
H-INVHGNCLynxMGIPubMedUniProtKB
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


-  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.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 29.30 RPKM in Thyroid
Total median expression: 198.50 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 -7.3028-0.261 Picture PostScript Text
3' UTR -331.20651-0.509 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
IPR000108 - p67phox
IPR011511 - SH3_2
IPR001452 - SH3_domain

Pfam Domains:
PF00018 - SH3 domain
PF07653 - Variant SH3 domain
PF14604 - Variant SH3 domain

SCOP Domains:
50044 - SH3-domain

ModBase Predicted Comparative 3D Structure on J3KQM5
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 orthologGenome BrowserNo orthologNo orthologNo ortholog
Gene Details     
Gene Sorter     
  Ensembl   
  Protein Sequence   
  Alignment   

-  Descriptions from all associated GenBank mRNAs
  AK297015 - Homo sapiens cDNA FLJ58582 complete cds.
AK056459 - Homo sapiens cDNA FLJ31897 fis, clone NT2RP7004080, weakly similar to CELL SURFACE GLYCOPROTEIN 1 PRECURSOR.
JD437127 - Sequence 418151 from Patent EP1572962.
JD279111 - Sequence 260135 from Patent EP1572962.
JD278637 - Sequence 259661 from Patent EP1572962.
JD071475 - Sequence 52499 from Patent EP1572962.
JD498122 - Sequence 479146 from Patent EP1572962.
JD206509 - Sequence 187533 from Patent EP1572962.
JD382146 - Sequence 363170 from Patent EP1572962.
JD327746 - Sequence 308770 from Patent EP1572962.
JD354168 - Sequence 335192 from Patent EP1572962.
BC101676 - Homo sapiens chromosome 1 open reading frame 113, mRNA (cDNA clone IMAGE:8069182), partial cds.
BC101678 - Homo sapiens chromosome 1 open reading frame 113, mRNA (cDNA clone IMAGE:8069184), partial cds.
JD125996 - Sequence 107020 from Patent EP1572962.
BC048273 - Homo sapiens chromosome 1 open reading frame 113, mRNA (cDNA clone IMAGE:4450991), partial cds.
AK026591 - Homo sapiens cDNA: FLJ22938 fis, clone KAT08023.
BC036763 - Homo sapiens chromosome 1 open reading frame 113, mRNA (cDNA clone IMAGE:5723875), partial cds.
JD258106 - Sequence 239130 from Patent EP1572962.
JD465870 - Sequence 446894 from Patent EP1572962.
JD339926 - Sequence 320950 from Patent EP1572962.
JD439643 - Sequence 420667 from Patent EP1572962.

-  Other Names for This Gene
  Alternate Gene Symbols: C1orf113, hCG_2031984, J3KQM5, J3KQM5_HUMAN, NM_001162530, NP_078952
UCSC ID: uc010oia.1
RefSeq Accession: NM_001162530
Protein: J3KQM5

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_001162530.1
exon count: 16CDS single in 3' UTR: no RNA size: 2527
ORF size: 2271CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 4499.00frame shift in genome: no % Coverage: 99.68
has start codon: yes stop codon in genome: no # of Alignments: 1
has end codon: yes retained intron: yes # AT/AC introns 0
selenocysteine: no end bleed into intron: 569# 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.