Slitrk6 SLIT and NTRK-like family, member 6 [Mus musculus (house mouse)] - Gene

Summary

Official Symbol: Slitrk6provided by MGI
Official Full Name: SLIT and NTRK-like family, member 6provided by MGI
Primary source: MGI:MGI:2443198
See related: Ensembl:ENSMUSG00000045871 AllianceGenome:MGI:2443198
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Mus musculus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
Also known as: Sltk6; 4832410J21Rik
Summary: Acts upstream of or within several processes, including auditory behavior; linear vestibuloocular reflex; and nervous system development. Located in cell periphery. Is expressed in several structures, including brain; gut; limb bud; lung; and sensory organ. Used to study high myopia-sensorineural deafness syndrome and sensorineural hearing loss. Human ortholog(s) of this gene implicated in high myopia-sensorineural deafness syndrome. Orthologous to human SLITRK6 (SLIT and NTRK like family member 6). [provided by Alliance of Genome Resources, Nov 2024]
Expression: Biased expression in bladder adult (RPKM 3.5), limb E14.5 (RPKM 3.4) and 10 other tissues See more
Orthologs: human all
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Genomic context

Location:: 14 E3; 14 57.2 cM

Exon count:: 2

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCm39 (GCF_000001635.27)	14	NC_000080.7 (110984770..110992640, complement)
108.20200622	previous assembly	GRCm38.p6 (GCF_000001635.26)	14	NC_000080.6 (110747338..110755204, complement)

Chromosome 14 - NC_000080.7 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

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Expression

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See details

Project title: Mouse ENCODE transcriptome data
Description: RNA profiling data sets generated by the Mouse ENCODE project.
BioProject: PRJNA66167
Publication: PMID 25409824
Analysis date: n/a

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

SLITRK6 plays a crucial role in the development of normal hearing as well as vision in humans and in mice and that its disruption leads to a syndrome characterized by severe myopia and deafness.
Title: SLITRK6 mutations cause myopia and deafness in humans and mice.
the altered responses of Slitrk6-KO mice to the novel environment suggest a role of Slitrk6 in some cognitive functions.
Title: Impaired auditory-vestibular functions and behavioral abnormalities of Slitrk6-deficient mice.
Slitrk6 promotes innervation and survival of inner ear sensory neurons by regulating the expression of trophic and/or tropic factors including neurotrophins from sensory epithelia
Title: Disorganized innervation and neuronal loss in the inner ear of Slitrk6-deficient mice.
Slitrk6 gene expression profile in the mouse embryo.
Title: Slitrk6 expression profile in the mouse embryo and its relationship to that of Nlrr3.

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Variation

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Alleles

Alleles of this type are documented at Mouse Genome Informatics (MGI)

Endonuclease-mediated (3)
Targeted (1) 1 citation

General gene information

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Gene Ontology Provided by MGI

Function	Evidence Code	Pubs
enables molecular_function	ND No biological Data available more info

Process	Evidence Code	Pubs
acts_upstream_of_or_within adult locomotory behavior	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within auditory behavior	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within auditory receptor cell morphogenesis	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in axonogenesis	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within axonogenesis	IDA Inferred from Direct Assay more info	PubMed
acts_upstream_of_or_within camera-type eye development	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within cochlea development	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within inner ear morphogenesis	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within innervation	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within lens development in camera-type eye	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within linear vestibuloocular reflex	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within multicellular organism growth	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within neuron projection morphogenesis	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of synapse assembly	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within positive regulation of synapse assembly	IDA Inferred from Direct Assay more info	PubMed
involved_in sensory perception of sound	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within startle response	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within synapse assembly	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within synapse assembly	ISO Inferred from Sequence Orthology more info	PubMed
acts_upstream_of_or_within vestibular reflex	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within vestibulocochlear nerve development	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within visual perception	IMP Inferred from Mutant Phenotype more info	PubMed

Component	Evidence Code	Pubs
located_in cell periphery	IDA Inferred from Direct Assay more info	PubMed
located_in cell surface	ISO Inferred from Sequence Orthology more info	PubMed
located_in membrane	ISS Inferred from Sequence or Structural Similarity more info	PubMed
is_active_in plasma membrane	IBA Inferred from Biological aspect of Ancestor more info
located_in plasma membrane	ISO Inferred from Sequence Orthology more info
located_in plasma membrane	ISS Inferred from Sequence or Structural Similarity more info

General protein information

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Preferred Names: SLIT and NTRK-like protein 6

Names: neuronal transmembrane protein Slitrk6; slit and trk like gene 6

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

NM_175499.4 → NP_780708.1 SLIT and NTRK-like protein 6 precursor

See identical proteins and their annotated locations for NP_780708.1

Status: VALIDATED

Source sequence(s)

AK029275, AK044796, BB374017, BC138664

Consensus CDS

CCDS27326.1

UniProtKB/Swiss-Prot

Q8BLL0, Q8C110

UniProtKB/TrEMBL

A6H6M2

Related

ENSMUSP00000077492.3, ENSMUST00000078386.4

Conserved Domains (6) summary

smart00082
Location:516 → 566

LRRCT; Leucine rich repeat C-terminal domain

sd00031
Location:210 → 222

LRR_1; leucine-rich repeat [structural motif]

sd00033
Location:94 → 113

LRR_RI; leucine-rich repeat [structural motif]

pfam12799
Location:388 → 426

LRR_4; Leucine Rich repeats (2 copies)

pfam13855
Location:387 → 444

LRR_8; Leucine rich repeat

cl15307
Location:218 → 268

TPKR_C2; Tyrosine-protein kinase receptor C2 Ig-like domain

RefSeqs of Annotated Genomes: GCF_000001635.27-RS_2024_02

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCm39 C57BL/6J

Genomic

NC_000080.7 Reference GRCm39 C57BL/6J

Range

110984770..110992640 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_006519009.5 → XP_006519072.1 SLIT and NTRK-like protein 6 isoform X1

Conserved Domains (5) summary

smart00082
Location:493 → 543

LRRCT; Leucine rich repeat C-terminal domain

sd00031
Location:187 → 199

LRR_1; leucine-rich repeat [structural motif]

sd00033
Location:71 → 90

LRR_RI; leucine-rich repeat [structural motif]

pfam13855
Location:364 → 421

LRR_8; Leucine rich repeat

cl15307
Location:195 → 245

TPKR_C2; Tyrosine-protein kinase receptor C2 Ig-like domain