Human Gene MTCL1 (uc002knr.2)
  Description: Homo sapiens SOGA family member 2 (MTCL1), mRNA.
Transcript (Including UTRs)
   Position: hg19 chr18:8,717,369-8,832,775 Size: 115,407 Total Exon Count: 17 Strand: +
Coding Region
   Position: hg19 chr18:8,718,449-8,828,944 Size: 110,496 Coding Exon Count: 14 

Page IndexSequence and LinksPrimersGene AllelesRNA-Seq ExpressionMicroarray Expression
RNA StructureProtein StructureOther SpeciesmRNA DescriptionsOther NamesGeneReviews
Model InformationMethods
Data last updated at UCSC: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr18:8,717,369-8,832,775)mRNA (may differ from genome)Protein (1586 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
GeneNetworkH-INVHPRDLynxMGIOMIM
PubMedTreefamUniProtKBWikipediaBioGrid 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


+  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: 76.92 RPKM in Brain - Cerebellum
Total median expression: 241.10 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.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -39.80142-0.280 Picture PostScript Text
3' UTR -312.071189-0.262 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:
PF11365 - Protein SOGA
PF14818 - Domain of unknown function (DUF4482)

ModBase Predicted Comparative 3D Structure on Q9Y4B5-3
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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
  AB018345 - Homo sapiens mRNA for KIAA0802 protein, partial cds.
AK131528 - Homo sapiens cDNA FLJ16757 fis, clone BRACE3026993.
AB384528 - Synthetic construct DNA, clone: pF1KA0802, Homo sapiens KIAA0802 gene for KIAA0802 protein, complete cds, without stop codon, in Flexi system.
AK090691 - Homo sapiens cDNA FLJ33372 fis, clone BRACE2005981.
AX746577 - Sequence 102 from Patent EP1308459.
JD211375 - Sequence 192399 from Patent EP1572962.
JD211809 - Sequence 192833 from Patent EP1572962.
JD310964 - Sequence 291988 from Patent EP1572962.
JD476533 - Sequence 457557 from Patent EP1572962.
JD470820 - Sequence 451844 from Patent EP1572962.
JD125553 - Sequence 106577 from Patent EP1572962.
JD396012 - Sequence 377036 from Patent EP1572962.
JD424270 - Sequence 405294 from Patent EP1572962.
JD062590 - Sequence 43614 from Patent EP1572962.
AK307830 - Homo sapiens cDNA, FLJ97778.
BC040542 - Homo sapiens KIAA0802, mRNA (cDNA clone MGC:39663 IMAGE:5268201), complete cds.
BX648911 - Homo sapiens mRNA; cDNA DKFZp686I07268 (from clone DKFZp686I07268).
BX648455 - Homo sapiens mRNA; cDNA DKFZp686P18269 (from clone DKFZp686P18269).
JD518472 - Sequence 499496 from Patent EP1572962.
JD143317 - Sequence 124341 from Patent EP1572962.
JD409884 - Sequence 390908 from Patent EP1572962.
JD234708 - Sequence 215732 from Patent EP1572962.
JD113426 - Sequence 94450 from Patent EP1572962.
JD497463 - Sequence 478487 from Patent EP1572962.
JD178202 - Sequence 159226 from Patent EP1572962.
JD037383 - Sequence 18407 from Patent EP1572962.
JD317910 - Sequence 298934 from Patent EP1572962.
JD404290 - Sequence 385314 from Patent EP1572962.
JD322415 - Sequence 303439 from Patent EP1572962.
JD234794 - Sequence 215818 from Patent EP1572962.

-  Other Names for This Gene
  Alternate Gene Symbols: CCDC165, KIAA0802, NM_015210, NP_056025, Q9Y4B5-3, SOGA2
UCSC ID: uc002knr.2
RefSeq Accession: NM_015210
Protein: Q9Y4B5-3, splice isoform of Q9Y4B5 CCDS: CCDS11841.1

-  GeneReviews for This Gene
  GeneReviews article(s) related to gene MTCL1:
ataxias (Hereditary Ataxia Overview)

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_015210.3
exon count: 17CDS single in 3' UTR: no RNA size: 6092
ORF size: 4761CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 9601.50frame 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.