Human Gene SLITRK6 (ENST00000647374.2) from GENCODE V44
  Description: Homo sapiens SLIT and NTRK like family member 6 (SLITRK6), mRNA. (from RefSeq NM_032229)
RefSeq Summary (NM_032229): This gene encodes a member of the SLITRK protein family. Members of this family are integral membrane proteins that are characterized by two N-terminal leucine-rich repeat (LRR) domains and a C-terminal region that shares homology with trk neurotrophin receptors. This protein functions as a regulator of neurite outgrowth required for normal hearing and vision. Mutations in this gene are a cause of myopia and deafness. [provided by RefSeq, Dec 2014].
Gencode Transcript: ENST00000647374.2
Gencode Gene: ENSG00000184564.11
Transcript (Including UTRs)
   Position: hg38 chr13:85,792,790-85,799,419 Size: 6,630 Total Exon Count: 2 Strand: -
Coding Region
   Position: hg38 chr13:85,793,983-85,796,508 Size: 2,526 Coding Exon Count: 1 

Page IndexSequence and LinksUniProtKB CommentsPrimersMalaCardsCTD
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsPathwaysOther NamesGeneReviewsMethods
Data last updated at UCSC: 2023-08-18 00:09:47

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr13:85,792,790-85,799,419)mRNA (may differ from genome)Protein (841 aa)
Gene SorterGenome BrowserOther Species FASTATable SchemaAlphaFoldBioGPS
EnsemblEntrez GeneExonPrimerGencodeGeneCardsHGNC
HPRDLynxMalacardsMGIneXtProtOMIM
PubMedReactomeUniProtKBWikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: SLIK6_HUMAN
DESCRIPTION: RecName: Full=SLIT and NTRK-like protein 6; Flags: Precursor;
FUNCTION: Suppresses neurite outgrowth (By similarity).
SUBCELLULAR LOCATION: Membrane; Single-pass type I membrane protein (Potential).
TISSUE SPECIFICITY: In adult brain, highly expressed in putamen with no expression in cerebral cortex. Expressed in adult and fetal lung and fetal liver. Also expressed at high levels in some brain tumors including medulloblastomas and primitive neuroectodermal tumors.
SIMILARITY: Belongs to the SLITRK family.
SIMILARITY: Contains 11 LRR (leucine-rich) repeats.
SIMILARITY: Contains 2 LRRCT domains.
SIMILARITY: Contains 2 LRRNT domains.
SEQUENCE CAUTION: Sequence=BAB13941.1; Type=Erroneous initiation; Note=Translation N-terminally extended; Sequence=BAB13941.1; Type=Miscellaneous discrepancy; Note=Aberrant splicing; Sequence=BAB15480.1; Type=Erroneous initiation; Note=Translation N-terminally extended; Sequence=BAB15480.1; Type=Frameshift; Positions=468, 489, 501, 519;

-  Primer design for this transcript
 

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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


-  MalaCards Disease Associations
  MalaCards Gene Search: SLITRK6
Diseases sorted by gene-association score: deafness and myopia* (1368), autosomal recessive non-syndromic sensorineural deafness type dfnb* (67), myopia (13), auditory neuropathy (5)
* = Manually curated disease association

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 14.42 RPKM in Minor Salivary Gland
Total median expression: 48.67 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 -114.10530-0.215 Picture PostScript Text
3' UTR -249.701193-0.209 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
IPR000483 - Cys-rich_flank_reg_C
IPR001611 - Leu-rich_rpt
IPR003591 - Leu-rich_rpt_typical-subtyp

ModBase Predicted Comparative 3D Structure on Q9H5Y7
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
Genome BrowserGenome BrowserNo orthologNo orthologNo orthologNo ortholog
Gene Details     
Gene Sorter     
MGIRGD    
Protein SequenceProtein Sequence    
AlignmentAlignment    

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Biological Process:
GO:0001964 startle response
GO:0002088 lens development in camera-type eye
GO:0002093 auditory receptor cell morphogenesis
GO:0007409 axonogenesis
GO:0007416 synapse assembly
GO:0007601 visual perception
GO:0007605 sensory perception of sound
GO:0008344 adult locomotory behavior
GO:0021562 vestibulocochlear nerve development
GO:0031223 auditory behavior
GO:0035264 multicellular organism growth
GO:0042472 inner ear morphogenesis
GO:0043010 camera-type eye development
GO:0048812 neuron projection morphogenesis
GO:0050896 response to stimulus
GO:0051965 positive regulation of synapse assembly
GO:0060005 vestibular reflex
GO:0060007 linear vestibuloocular reflex
GO:0060384 innervation
GO:0090102 cochlea development

Cellular Component:
GO:0005886 plasma membrane
GO:0005887 integral component of plasma membrane
GO:0009986 cell surface
GO:0016020 membrane
GO:0016021 integral component of membrane
GO:0071944 cell periphery


-  Descriptions from all associated GenBank mRNAs
  LF210198 - JP 2014500723-A/17701: Polycomb-Associated Non-Coding RNAs.
MA445775 - JP 2018138019-A/17701: Polycomb-Associated Non-Coding RNAs.
BX648640 - Homo sapiens mRNA; cDNA DKFZp686P23120 (from clone DKFZp686P23120).
BC101070 - Homo sapiens SLIT and NTRK-like family, member 6, mRNA (cDNA clone MGC:119594 IMAGE:40008739), complete cds.
BC101071 - Homo sapiens SLIT and NTRK-like family, member 6, mRNA (cDNA clone MGC:119595 IMAGE:40008742), complete cds.
BC101072 - Homo sapiens SLIT and NTRK-like family, member 6, mRNA (cDNA clone MGC:119596 IMAGE:40008743), complete cds.
BC101073 - Homo sapiens SLIT and NTRK-like family, member 6, mRNA (cDNA clone MGC:119597 IMAGE:40008745), complete cds.
AK021931 - Homo sapiens cDNA FLJ11869 fis, clone HEMBA1007002.
JD410061 - Sequence 391085 from Patent EP1572962.
AK292793 - Homo sapiens cDNA FLJ76093 complete cds, highly similar to Homo sapiens SLIT and NTRK-like family, member 6 (SLITRK6), mRNA.
LF335628 - JP 2014500723-A/143131: Polycomb-Associated Non-Coding RNAs.
MA571205 - JP 2018138019-A/143131: Polycomb-Associated Non-Coding RNAs.
AL137517 - Homo sapiens mRNA; cDNA DKFZp564O1278 (from clone DKFZp564O1278).
JD451036 - Sequence 432060 from Patent EP1572962.
AK026427 - Homo sapiens cDNA: FLJ22774 fis, clone KAIA1575.
JD273220 - Sequence 254244 from Patent EP1572962.
KJ894947 - Synthetic construct Homo sapiens clone ccsbBroadEn_04341 SLITRK6 gene, encodes complete protein.
AB463260 - Synthetic construct DNA, clone: pF1KB8628, Homo sapiens SLITRK6 gene for SLIT and NTRK-like family, member 6, without stop codon, in Flexi system.
AM393568 - Synthetic construct Homo sapiens clone IMAGE:100002529 for hypothetical protein (SLITRK6 gene).
JD040624 - Sequence 21648 from Patent EP1572962.
JD041972 - Sequence 22996 from Patent EP1572962.
JD184635 - Sequence 165659 from Patent EP1572962.
JD064221 - Sequence 45245 from Patent EP1572962.
JD539284 - Sequence 520308 from Patent EP1572962.
JD353607 - Sequence 334631 from Patent EP1572962.
JD454820 - Sequence 435844 from Patent EP1572962.
JD360894 - Sequence 341918 from Patent EP1572962.
JD376413 - Sequence 357437 from Patent EP1572962.
JD097791 - Sequence 78815 from Patent EP1572962.
JD455829 - Sequence 436853 from Patent EP1572962.
JD305186 - Sequence 286210 from Patent EP1572962.
JD549907 - Sequence 530931 from Patent EP1572962.
JD548515 - Sequence 529539 from Patent EP1572962.
JD366963 - Sequence 347987 from Patent EP1572962.
JD513291 - Sequence 494315 from Patent EP1572962.
LF335629 - JP 2014500723-A/143132: Polycomb-Associated Non-Coding RNAs.
MA571206 - JP 2018138019-A/143132: Polycomb-Associated Non-Coding RNAs.
JD240228 - Sequence 221252 from Patent EP1572962.
JD151605 - Sequence 132629 from Patent EP1572962.
JD526086 - Sequence 507110 from Patent EP1572962.
JD483527 - Sequence 464551 from Patent EP1572962.
LF335630 - JP 2014500723-A/143133: Polycomb-Associated Non-Coding RNAs.
MA571207 - JP 2018138019-A/143133: Polycomb-Associated Non-Coding RNAs.
LF335631 - JP 2014500723-A/143134: Polycomb-Associated Non-Coding RNAs.
MA571208 - JP 2018138019-A/143134: Polycomb-Associated Non-Coding RNAs.
LF335632 - JP 2014500723-A/143135: Polycomb-Associated Non-Coding RNAs.
MA571209 - JP 2018138019-A/143135: Polycomb-Associated Non-Coding RNAs.
JD296286 - Sequence 277310 from Patent EP1572962.
JD324891 - Sequence 305915 from Patent EP1572962.
JD504888 - Sequence 485912 from Patent EP1572962.

-  Biochemical and Signaling Pathways
  Reactome (by CSHL, EBI, and GO)

Protein Q9H5Y7 (Reactome details) participates in the following event(s):

R-HSA-6797803 PTPRD binds SLITRK1-6
R-HSA-388844 Receptor-type tyrosine-protein phosphatases
R-HSA-6794362 Protein-protein interactions at synapses
R-HSA-112316 Neuronal System

-  Other Names for This Gene
  Alternate Gene Symbols: A8K9S8, ENST00000647374.1, NM_032229, Q495Q0, Q6AW93, Q9H5Y7, Q9HAA8, Q9NT60, SLIK6_HUMAN, uc001vll.1, uc001vll.2, uc001vll.3, uc001vll.4
UCSC ID: ENST00000647374.2
RefSeq Accession: NM_032229
Protein: Q9H5Y7 (aka SLIK6_HUMAN or SLK6_HUMAN)
CCDS: CCDS41903.1

-  GeneReviews for This Gene
  GeneReviews article(s) related to gene SLITRK6:
dfn-myop (Deafness and Myopia Syndrome)

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.