Human Gene MTCL1 (ENST00000306329.16_9) from GENCODE V47lift37
  Description: microtubule crosslinking factor 1, transcript variant 2 (from RefSeq NM_001378206.1)
Gencode Transcript: ENST00000306329.16_9
Gencode Gene: ENSG00000168502.18_15
Transcript (Including UTRs)
   Position: hg19 chr18:8,705,554-8,832,776 Size: 127,223 Total Exon Count: 15 Strand: +
Coding Region
   Position: hg19 chr18:8,705,659-8,828,944 Size: 123,286 Coding Exon Count: 14 

Page IndexSequence and LinksUniProtKB CommentsPrimersGene AllelesRNA-Seq Expression
Microarray ExpressionRNA StructureProtein StructureOther SpeciesGO AnnotationsmRNA Descriptions
Other NamesGeneReviewsModel InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr18:8,705,554-8,832,776)mRNA (may differ from genome)Protein (1905 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
MGIOMIMPubMedUniProtKBWikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: SOGA2_HUMAN
DESCRIPTION: RecName: Full=Protein SOGA2; AltName: Full=Coiled-coil domain-containing protein 165;
PTM: Isoform 4 is phosphorylated upon DNA damage, probably by ATM or ATR.
SIMILARITY: Belongs to the SOGA family.
SEQUENCE CAUTION: Sequence=BAA34522.2; Type=Erroneous initiation; Note=Translation N-terminally shortened;

-  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 -49.50105-0.471 Picture PostScript Text
3' UTR -291.801190-0.245 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
IPR021507 - DUF3166

Pfam Domains:
PF11365 - Protein SOGA
PF14818 - Domain of unknown function (DUF4482)

SCOP Domains:
58026 - Delta-sleep-inducing peptide immunoreactive peptide
57997 - Tropomyosin

ModBase Predicted Comparative 3D Structure on Q9Y4B5
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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 orthologNo orthologNo orthologNo orthologNo ortholog
Gene DetailsGene Details    
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-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0003723 RNA binding
GO:0005515 protein binding
GO:0008017 microtubule binding
GO:0042803 protein homodimerization activity

Biological Process:
GO:0001578 microtubule bundle formation
GO:0010506 regulation of autophagy
GO:0045197 establishment or maintenance of epithelial cell apical/basal polarity
GO:0090314 positive regulation of protein targeting to membrane
GO:2000576 positive regulation of microtubule motor activity

Cellular Component:
GO:0000922 spindle pole
GO:0005615 extracellular space
GO:0005737 cytoplasm
GO:0005856 cytoskeleton
GO:0005886 plasma membrane
GO:0016020 membrane
GO:0016324 apical plasma membrane
GO:0016327 apicolateral plasma membrane
GO:0016328 lateral plasma membrane
GO:0030496 midbody
GO:0097427 microtubule bundle


-  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.
JD458517 - Sequence 439541 from Patent EP1572962.
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, E9PAY7, ENST00000306329.1, ENST00000306329.10, ENST00000306329.11, ENST00000306329.12, ENST00000306329.13, ENST00000306329.14, ENST00000306329.15, ENST00000306329.2, ENST00000306329.3, ENST00000306329.4, ENST00000306329.5, ENST00000306329.6, ENST00000306329.7, ENST00000306329.8, ENST00000306329.9, KIAA0802, MTCL1_HUMAN, NM_001378206, Q6ZMQ9, Q8IWA9, Q9Y4B5, SOGA2, uc317nva.1, uc317nva.2
UCSC ID: ENST00000306329.16_9
RefSeq Accession: NM_001378205.1
Protein: Q9Y4B5 (aka SOGA2_HUMAN)

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

-  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.