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Aliases for SLITRK6 Gene

Aliases for SLITRK6 Gene

  • SLIT And NTRK Like Family Member 6 2 3 5
  • SLIT And NTRK-Like Family, Member 6 2
  • SLIT And NTRK-Like Protein 6 3
  • Slit And Trk Like Gene 6 3
  • 4832410J21Rik 3
  • DFNMYP 3

External Ids for SLITRK6 Gene

Previous GeneCards Identifiers for SLITRK6 Gene

  • GC13M084165
  • GC13M084164
  • GC13M085264
  • GC13M086366
  • GC13M067078

Summaries for SLITRK6 Gene

Entrez Gene Summary for SLITRK6 Gene

  • 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]

GeneCards Summary for SLITRK6 Gene

SLITRK6 (SLIT And NTRK Like Family Member 6) is a Protein Coding gene. Diseases associated with SLITRK6 include Deafness And Myopia and Autosomal Recessive Non-Syndromic Sensorineural Deafness Type Dfnb. An important paralog of this gene is SLITRK5.

UniProtKB/Swiss-Prot for SLITRK6 Gene

  • Regulator of neurite outgrowth required for normal hearing and vision.

Gene Wiki entry for SLITRK6 Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for SLITRK6 Gene

Genomics for SLITRK6 Gene

Regulatory Elements for SLITRK6 Gene

Enhancers for SLITRK6 Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH13G085588 0.2 ENCODE 4.4 +209.9 209888 1.7 SLITRK6 GC13M085585 RNU6-72P
GH13G085799 0.9 Ensembl ENCODE 0.7 0.0 -31 1.0 CTCF PKNOX1 ZNF384 DPF2 CHD7 RAD21 EP300 FOXA1 CTBP1 GATA3 SLITRK6 ENSG00000278580
GH13G085824 0.4 ENCODE 0.3 -26.1 -26083 1.2 PKNOX1 JUND ENSG00000278580 SLITRK6
GH13G085728 0.4 ENCODE 0.2 +70.2 70187 1.1 FOS RNU6-72P SLITRK6 GC13M085585
GH13G085651 0.6 ENCODE 0.1 +147.9 147888 0.2 JUND MTA2 BHLHE40 IKZF1 DPF2 TBX21 RNU6-72P GC13M085585 SLITRK6
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around SLITRK6 on UCSC Golden Path with GeneCards custom track

Genomic Location for SLITRK6 Gene

Chromosome:
13
Start:
85,792,787 bp from pter
End:
85,799,488 bp from pter
Size:
6,702 bases
Orientation:
Minus strand

Genomic View for SLITRK6 Gene

Genes around SLITRK6 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
SLITRK6 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for SLITRK6 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for SLITRK6 Gene

Proteins for SLITRK6 Gene

  • Protein details for SLITRK6 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9H5Y7-SLIK6_HUMAN
    Recommended name:
    SLIT and NTRK-like protein 6
    Protein Accession:
    Q9H5Y7
    Secondary Accessions:
    • A8K9S8
    • Q495Q0
    • Q6AW93
    • Q9HAA8
    • Q9NT60

    Protein attributes for SLITRK6 Gene

    Size:
    841 amino acids
    Molecular mass:
    95110 Da
    Quaternary structure:
    No Data Available
    SequenceCaution:
    • Sequence=BAB13941.1; Type=Erroneous initiation; Note=Translation N-terminally extended.; Evidence={ECO:0000305}; Sequence=BAB13941.1; Type=Miscellaneous discrepancy; Note=Aberrant splicing.; Evidence={ECO:0000305}; Sequence=BAB15480.1; Type=Erroneous initiation; Note=Translation N-terminally extended.; Evidence={ECO:0000305}; Sequence=BAB15480.1; Type=Frameshift; Positions=468, 489, 501, 519; Evidence={ECO:0000305};

neXtProt entry for SLITRK6 Gene

Post-translational modifications for SLITRK6 Gene

  • Glycosylation at isoforms=322
  • Modification sites at PhosphoSitePlus

Other Protein References for SLITRK6 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for SLITRK6 Gene

Domains & Families for SLITRK6 Gene

Suggested Antigen Peptide Sequences for SLITRK6 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

Q9H5Y7

UniProtKB/Swiss-Prot:

SLIK6_HUMAN :
  • Belongs to the SLITRK family.
Family:
  • Belongs to the SLITRK family.
genes like me logo Genes that share domains with SLITRK6: view

No data available for Gene Families for SLITRK6 Gene

Function for SLITRK6 Gene

Molecular function for SLITRK6 Gene

UniProtKB/Swiss-Prot Function:
Regulator of neurite outgrowth required for normal hearing and vision.
genes like me logo Genes that share phenotypes with SLITRK6: view

Human Phenotype Ontology for SLITRK6 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for SLITRK6 Gene

MGI Knock Outs for SLITRK6:

Animal Model Products

CRISPR Products

miRNA for SLITRK6 Gene

miRTarBase miRNAs that target SLITRK6

Inhibitory RNA Products

Clone Products

No data available for Enzyme Numbers (IUBMB) , Gene Ontology (GO) - Molecular Function , Transcription Factor Targets and HOMER Transcription for SLITRK6 Gene

Localization for SLITRK6 Gene

Subcellular locations from UniProtKB/Swiss-Prot for SLITRK6 Gene

Cell membrane; Single-pass type I membrane protein.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for SLITRK6 gene
Compartment Confidence
plasma membrane 5

Gene Ontology (GO) - Cellular Components for SLITRK6 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005886 plasma membrane IDA,TAS --
GO:0005887 integral component of plasma membrane IDA 23543054
GO:0009986 cell surface IDA 23543054
GO:0016020 membrane IEA --
GO:0016021 integral component of membrane IEA --
genes like me logo Genes that share ontologies with SLITRK6: view

Pathways & Interactions for SLITRK6 Gene

SuperPathways for SLITRK6 Gene

No Data Available

Interacting Proteins for SLITRK6 Gene

STRING Interaction Network Preview (showing 5 interactants - click image to see 25)
http://version10.5.string-db.org/api/image/networkList?limit=0&targetmode=proteins&caller_identity=gene_cards&network_flavor=evidence&identifiers=9606.ENSP00000383143%0d%0a9606.ENSP00000349932%0d%0a9606.ENSP00000348812%0d%0a9606.ENSP00000353030%0d%0a9606.ENSP00000377047%0d%0a9606.ENSP00000254667%0d%0a
Selected Interacting proteins: ENSP00000383143 Q9H5Y7-SLIK6_HUMAN for SLITRK6 Gene via STRING IID

Gene Ontology (GO) - Biological Process for SLITRK6 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001964 startle response IEA --
GO:0002088 lens development in camera-type eye IEA --
GO:0002093 auditory receptor cell morphogenesis IEA --
GO:0007409 axonogenesis IEA,IBA --
GO:0007416 synapse assembly IMP 23543054
genes like me logo Genes that share ontologies with SLITRK6: view

No data available for Pathways by source and SIGNOR curated interactions for SLITRK6 Gene

Drugs & Compounds for SLITRK6 Gene

No Compound Related Data Available

Transcripts for SLITRK6 Gene

mRNA/cDNA for SLITRK6 Gene

(1) REFSEQ mRNAs :
(9) Additional mRNA sequences :
(37) Selected AceView cDNA sequences:
(1) Ensembl transcripts including schematic representations, and UCSC links where relevant :

Unigene Clusters for SLITRK6 Gene

SLIT and NTRK-like family, member 6:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for SLITRK6 Gene

No ASD Table

Relevant External Links for SLITRK6 Gene

GeneLoc Exon Structure for
SLITRK6
ECgene alternative splicing isoforms for
SLITRK6

Expression for SLITRK6 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for SLITRK6 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for SLITRK6 Gene

This gene is overexpressed in Bladder (x13.3) and Minor Salivary Gland (x12.4).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, and MOPED for SLITRK6 Gene



Protein tissue co-expression partners for SLITRK6 Gene

NURSA nuclear receptor signaling pathways regulating expression of SLITRK6 Gene:

SLITRK6

SOURCE GeneReport for Unigene cluster for SLITRK6 Gene:

Hs.525105

mRNA Expression by UniProt/SwissProt for SLITRK6 Gene:

Q9H5Y7-SLIK6_HUMAN
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.

Evidence on tissue expression from TISSUES for SLITRK6 Gene

  • Nervous system(4.2)
  • Intestine(4.1)

Phenotype-based relationships between genes and organs from Gene ORGANizer for SLITRK6 Gene

Germ Layers:
  • ectoderm
  • endoderm
  • mesoderm
Systems:
  • cardiovascular
  • immune
  • integumentary
  • nervous
  • skeletal muscle
  • skeleton
  • urinary
Organs:
Head and neck:
  • brain
  • cerebellum
  • cranial nerve
  • ear
  • eye
  • head
  • inner ear
  • middle ear
  • outer ear
  • skull
Abdomen:
  • kidney
General:
  • blood
  • blood vessel
  • coagulation system
  • peripheral nerve
  • peripheral nervous system
  • red blood cell
  • skin
genes like me logo Genes that share expression patterns with SLITRK6: view

Primer Products

No data available for Protein differential expression in normal tissues for SLITRK6 Gene

Orthologs for SLITRK6 Gene

This gene was present in the common ancestor of chordates.

Orthologs for SLITRK6 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia SLITRK6 34 35
  • 99.01 (n)
cow
(Bos Taurus)
Mammalia SLITRK6 34 35
  • 89.68 (n)
dog
(Canis familiaris)
Mammalia SLITRK6 34 35
  • 89.4 (n)
oppossum
(Monodelphis domestica)
Mammalia SLITRK6 35
  • 86 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Slitrk6 34 16 35
  • 84.25 (n)
rat
(Rattus norvegicus)
Mammalia Slitrk6 34
  • 83.61 (n)
chicken
(Gallus gallus)
Aves SLITRK6 34 35
  • 74.96 (n)
lizard
(Anolis carolinensis)
Reptilia SLITRK6 35
  • 77 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia slitrk6 34
  • 65.57 (n)
zebrafish
(Danio rerio)
Actinopterygii slitrk6 34
  • 59.2 (n)
SLITRK6 35
  • 54 (a)
OneToOne
Species where no ortholog for SLITRK6 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • fruit fly (Drosophila melanogaster)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • platypus (Ornithorhynchus anatinus)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea squirt (Ciona intestinalis)
  • sea squirt (Ciona savignyi)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)

Evolution for SLITRK6 Gene

ENSEMBL:
Gene Tree for SLITRK6 (if available)
TreeFam:
Gene Tree for SLITRK6 (if available)

Paralogs for SLITRK6 Gene

Paralogs for SLITRK6 Gene

(7) SIMAP similar genes for SLITRK6 Gene using alignment to 1 proteins:

genes like me logo Genes that share paralogs with SLITRK6: view

Variants for SLITRK6 Gene

Sequence variations from dbSNP and Humsavar for SLITRK6 Gene

SNP ID Clin Chr 13 pos Sequence Context AA Info Type
rs587777069 Pathogenic 85,795,269(+) TTTTT(A/G)TAATC reference, stop-gained
rs587777070 Pathogenic 85,795,619(+) TAGTT(G/T)ACATG reference, stop-gained
rs587777071 Pathogenic 85,795,968(+) AAATC(A/G)GAAGA reference, stop-gained
rs869312872 Uncertain significance 85,794,593(-) AAGAT(-/T)ACAAA reference, frameshift-variant
rs1001470482 -- 85,796,661(+) GGGTA(C/G)CTTGC intron-variant

Variation tolerance for SLITRK6 Gene

Residual Variation Intolerance Score: 8.29% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 2.42; 42.70% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for SLITRK6 Gene

Human Gene Mutation Database (HGMD)
SLITRK6
SNPedia medical, phenotypic, and genealogical associations of SNPs for
SLITRK6

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot and Structural Variations from Database of Genomic Variants (DGV) for SLITRK6 Gene

Disorders for SLITRK6 Gene

MalaCards: The human disease database

(5) MalaCards diseases for SLITRK6 Gene - From: OMIM, ClinVar, GeneTests, Orphanet, DISEASES, and GeneCards

Disorder Aliases PubMed IDs
deafness and myopia
  • deafness and myopia syndrome
autosomal recessive non-syndromic sensorineural deafness type dfnb
  • autosomal recessive isolated neurosensory deafness type dfnb
myopia
  • near vision
supratentorial primitive neuroectodermal tumor
  • supratentorial pnet
auditory neuropathy
  • auditory dys-synchrony
- elite association - COSMIC cancer census association via MalaCards

UniProtKB/Swiss-Prot

SLIK6_HUMAN
  • Deafness and myopia (DFNMYP) [MIM:221200]: An autosomal recessive disorder characterized by prelingual sensorineural hearing loss associated with high myopia. {ECO:0000269 PubMed:23543054, ECO:0000269 PubMed:23946138}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Relevant External Links for SLITRK6

Atlas of Genetics and Cytogenetics in Oncology and Haematology:
SLITRK6
genes like me logo Genes that share disorders with SLITRK6: view

No data available for Genatlas for SLITRK6 Gene

Publications for SLITRK6 Gene

  1. Human SLITRK family genes: genomic organization and expression profiling in normal brain and brain tumor tissue. (PMID: 14557068) Aruga J. … Mikoshiba K. (Gene 2003) 2 3 4 22 64
  2. SLITRK6 mutations cause myopia and deafness in humans and mice. (PMID: 23543054) Tekin M. … Crosby A.H. (J. Clin. Invest. 2013) 3 4 64
  3. A homozygous SLITRK6 nonsense mutation is associated with progressive auditory neuropathy in humans. (PMID: 23946138) Morlet T. … Strauss K.A. (Laryngoscope 2013) 3 4 64
  4. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T. … Sugano S. (Nat. Genet. 2004) 3 4 64
  5. The DNA sequence and analysis of human chromosome 13. (PMID: 15057823) Dunham A. … Ross M.T. (Nature 2004) 3 4 64

Products for SLITRK6 Gene

Sources for SLITRK6 Gene

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