Human Gene SHISA6 (uc002gnc.2)
  Description: Homo sapiens shisa homolog 6 (Xenopus laevis) (SHISA6), transcript variant 1, mRNA.
Transcript (Including UTRs)
   Position: hg19 chr17:11,144,740-11,467,380 Size: 322,641 Total Exon Count: 6 Strand: +
Coding Region
   Position: hg19 chr17:11,144,740-11,461,621 Size: 316,882 Coding Exon Count: 6 

Page IndexSequence and LinksPrimersGenetic AssociationsMalaCardsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
mRNA DescriptionsOther NamesModel InformationMethods
Data last updated at UCSC: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr17:11,144,740-11,467,380)mRNA (may differ from genome)Protein (551 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaAlphaFold
BioGPSEnsemblEntrez GeneExonPrimerGeneCardsGeneNetwork
H-INVHGNCHPRDLynxMalacardsMGI
OMIMPubMedUniProtKBBioGrid 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


-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): SHISA6
CDC HuGE Published Literature: SHISA6
Positive Disease Associations: Body Height , Body Mass Index , Hemoglobin A, Glycosylated , Iron
Related Studies:
  1. Body Height
    , , . [PubMed 0]
  2. Body Mass Index
    Caroline S Fox et al. BMC medical genetics 2007, Genome-wide association to body mass index and waist circumference: the Framingham Heart Study 100K project., BMC medical genetics. [PubMed 17903300]
    Adiposity traits are associated with SNPs on the Affymetrix 100K SNP GeneChip. Replication of these initial findings is necessary. These data will serve as a resource for replication as more genes become identified with BMI and WC.
  3. Hemoglobin A, Glycosylated
    Andrew D Paterson et al. Diabetes 2010, A genome-wide association study identifies a novel major locus for glycemic control in type 1 diabetes, as measured by both A1C and glucose., Diabetes. [PubMed 19875614]
    A major locus for A1C and glucose in individuals with diabetes is near SORCS1. This may influence the design and analysis of genetic studies attempting to identify risk factors for long-term diabetic complications.
           more ... click here to view the complete list

-  MalaCards Disease Associations
  MalaCards Gene Search: SHISA6
Diseases sorted by gene-association score: refractive error (3)

-  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: 9.08 RPKM in Brain - Cerebellum
Total median expression: 69.48 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
3' UTR -2131.125759-0.370 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
  Pfam Domains:
PF13908 - Wnt and FGF inhibitory regulator

ModBase Predicted Comparative 3D Structure on Q6ZSJ9-3
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
  AK127379 - Homo sapiens cDNA FLJ45455 fis, clone BRSTN2009247.
BC148579 - Synthetic construct Homo sapiens clone IMAGE:100015467, MGC:183048 FLJ45455 protein (FLJ45455) mRNA, encodes complete protein.
BC156586 - Synthetic construct Homo sapiens clone IMAGE:100062020, MGC:190143 FLJ45455 protein (FLJ45455) mRNA, encodes complete protein.
AB464429 - Synthetic construct DNA, clone: pF1KB7443, Homo sapiens FLJ45455 gene, without stop codon, in Flexi system.
DQ070854 - Homo sapiens FLJ45455-like protein mRNA, complete cds, alternatively spliced.
AK128003 - Homo sapiens cDNA FLJ46122 fis, clone TESTI2039732.
AK095052 - Homo sapiens cDNA FLJ37733 fis, clone BRHIP2020827.
AK094349 - Homo sapiens cDNA FLJ37030 fis, clone BRACE2011183.
JD188866 - Sequence 169890 from Patent EP1572962.
JD554845 - Sequence 535869 from Patent EP1572962.
JD390728 - Sequence 371752 from Patent EP1572962.
JD425125 - Sequence 406149 from Patent EP1572962.
BC105704 - Homo sapiens cDNA clone IMAGE:40024216.
BC105705 - Homo sapiens cDNA clone IMAGE:40024217.
BC105707 - Homo sapiens cDNA clone IMAGE:40024220.
BC105706 - Homo sapiens cDNA clone IMAGE:40024219.
JD337982 - Sequence 319006 from Patent EP1572962.
JD268183 - Sequence 249207 from Patent EP1572962.
JD325129 - Sequence 306153 from Patent EP1572962.
JD403001 - Sequence 384025 from Patent EP1572962.
JD076884 - Sequence 57908 from Patent EP1572962.
JD283644 - Sequence 264668 from Patent EP1572962.
JD555882 - Sequence 536906 from Patent EP1572962.
JD359558 - Sequence 340582 from Patent EP1572962.
JD296111 - Sequence 277135 from Patent EP1572962.
JD375788 - Sequence 356812 from Patent EP1572962.
JD382986 - Sequence 364010 from Patent EP1572962.
JD532707 - Sequence 513731 from Patent EP1572962.
JD098350 - Sequence 79374 from Patent EP1572962.
JD116094 - Sequence 97118 from Patent EP1572962.
JD498503 - Sequence 479527 from Patent EP1572962.
JD046667 - Sequence 27691 from Patent EP1572962.
JD539342 - Sequence 520366 from Patent EP1572962.
JD056515 - Sequence 37539 from Patent EP1572962.
JD080835 - Sequence 61859 from Patent EP1572962.
JD206586 - Sequence 187610 from Patent EP1572962.
JD093724 - Sequence 74748 from Patent EP1572962.
JD444573 - Sequence 425597 from Patent EP1572962.
JD530685 - Sequence 511709 from Patent EP1572962.
JD276714 - Sequence 257738 from Patent EP1572962.
JD296786 - Sequence 277810 from Patent EP1572962.
JD435209 - Sequence 416233 from Patent EP1572962.
JD087749 - Sequence 68773 from Patent EP1572962.
JD043082 - Sequence 24106 from Patent EP1572962.
JD341616 - Sequence 322640 from Patent EP1572962.
JD251545 - Sequence 232569 from Patent EP1572962.
JD239963 - Sequence 220987 from Patent EP1572962.
JD436627 - Sequence 417651 from Patent EP1572962.
JD090977 - Sequence 72001 from Patent EP1572962.
JD171879 - Sequence 152903 from Patent EP1572962.

-  Other Names for This Gene
  Alternate Gene Symbols: NM_207386, NP_997269, Q6ZSJ9-3
UCSC ID: uc002gnc.2
RefSeq Accession: NM_207386
Protein: Q6ZSJ9-3, splice isoform of Q6ZSJ9 CCDS: CCDS45615.1, CCDS54089.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_207386.3
exon count: 6CDS single in 3' UTR: no RNA size: 7415
ORF size: 1656CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 3404.00frame shift in genome: no % Coverage: 100.00
has start codon: yes stop codon in genome: no # of Alignments: 1
has end codon: yes retained intron: no # AT/AC introns 0
selenocysteine: no end bleed into intron: 0# 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.