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SLITRK4 SLIT and NTRK like family member 4 [ Homo sapiens (human) ]

Gene ID: 139065, updated on 7-Apr-2024

Summary

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Official Symbol
SLITRK4provided by HGNC
Official Full Name
SLIT and NTRK like family member 4provided by HGNC
Primary source
HGNC:HGNC:23502
See related
Ensembl:ENSG00000179542 MIM:300562; AllianceGenome:HGNC:23502
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Summary
This gene encodes a transmembrane protein belonging to the the SLITRK family. These family members include two N-terminal leucine-rich repeat domains similar to those found in the axonal growth-controlling protein SLIT, as well as C-terminal regions similar to neurotrophin receptors. Studies of an homologous protein in mouse suggest that this family member functions to suppress neurite outgrowth. Alternative splicing results in multiple transcript variants. [provided by RefSeq, May 2010]
Expression
Biased expression in adrenal (RPKM 4.6), brain (RPKM 4.3) and 9 other tissues See more
Orthologs
mouse all
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Genomic context

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Location:
Xq27.3
Exon count:
6
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) X NC_000023.11 (143622790..143636101, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) X NC_060947.1 (141932069..141945367, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) X NC_000023.10 (142710595..142723920, complement)

Chromosome X - NC_000023.11Genomic Context describing neighboring genes Neighboring gene SPANX family member N3 Neighboring gene MYCL pseudogene 3 Neighboring gene heterogeneous nuclear ribonucleoprotein H1 pseudogene 2 Neighboring gene SPANX family member N2

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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Related articles in PubMed

  1. A transcriptional profile of the decidua in preeclampsia. Løset M, et al. Am J Obstet Gynecol, 2011 Jan. PMID 20934677, Free PMC Article
  2. Aberrant overexpression of HOTAIR inhibits abdominal adipogenesis through remodelling of genome-wide DNA methylation and transcription. Kuo FC, et al. Mol Metab, 2022 Jun. PMID 35292404, Free PMC Article
  3. Serum estradiol levels associated with specific gene expression patterns in normal breast tissue and in breast carcinomas. Haakensen VD, et al. BMC Cancer, 2011 Aug 3. PMID 21812955, Free PMC Article
  4. Slitrks control excitatory and inhibitory synapse formation with LAR receptor protein tyrosine phosphatases. Yim YS, et al. Proc Natl Acad Sci U S A, 2013 Mar 5. PMID 23345436, Free PMC Article
  5. Human SLITRK family genes: genomic organization and expression profiling in normal brain and brain tumor tissue. Aruga J, et al. Gene, 2003 Oct 2. PMID 14557068

See all (16) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Aberrant overexpression of HOTAIR inhibits abdominal adipogenesis through remodelling of genome-wide DNA methylation and transcription.
    Title: Aberrant overexpression of HOTAIR inhibits abdominal adipogenesis through remodelling of genome-wide DNA methylation and transcription.
Submit: New GeneRIF Correction

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • DKFZp547M2010

Gene Ontology Provided by GOA

Process Evidence Code Pubs
involved_in axonogenesis IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in positive regulation of synapse assembly IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in regulation of presynapse assembly IEA
Inferred from Electronic Annotation
more info
  
involved_in regulation of synapse organization IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in regulation of synapse organization IMP
Inferred from Mutant Phenotype
more info
 PubMed 
Component Evidence Code Pubs
is_active_in glutamatergic synapse IBA
Inferred from Biological aspect of Ancestor
more info
  
is_active_in glutamatergic synapse IDA
Inferred from Direct Assay
more info
 PubMed 
is_active_in glutamatergic synapse IMP
Inferred from Mutant Phenotype
more info
 PubMed 
located_in plasma membrane TAS
Traceable Author Statement
more info
  

General protein information

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Preferred Names
SLIT and NTRK-like protein 4
Names
slit and trk like gene 4

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.

Genomic

  1. NG_021344.2 RefSeqGene

    Range
    5011..18322
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001184749.3 → NP_001171678.1  SLIT and NTRK-like protein 4 precursor

    See identical proteins and their annotated locations for NP_001171678.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longest transcript. Variants 1, 2 and 3 encode the same protein.
    Source sequence(s)
    AC239921
    Consensus CDS
    CCDS14679.1
    UniProtKB/Swiss-Prot
    Q5JXG3, Q8IW52, Q8TCM8, Q96DL3
    UniProtKB/TrEMBL
    B2RCC8
    Related
    ENSP00000349400.1, ENST00000356928.2
    Conserved Domains (4) summary
    TIGR00864
    Location:502 → 563
    PCC; polycystin cation channel protein
    smart00082
    Location:213 → 253
    LRRCT; Leucine rich repeat C-terminal domain
    sd00033
    Location:109 → 132
    LRR_RI; leucine-rich repeat [structural motif]
    pfam13855
    Location:402 → 461
    LRR_8; Leucine rich repeat

  2. NM_001184750.2 → NP_001171679.1  SLIT and NTRK-like protein 4 precursor

    See identical proteins and their annotated locations for NP_001171679.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) differs in the 5' UTR compared to variant 1. Variants 1, 2 and 3 encode the same protein.
    Source sequence(s)
    AC239921
    Consensus CDS
    CCDS14679.1
    UniProtKB/Swiss-Prot
    Q5JXG3, Q8IW52, Q8TCM8, Q96DL3
    UniProtKB/TrEMBL
    B2RCC8
    Related
    ENSP00000469205.1, ENST00000596188.2
    Conserved Domains (4) summary
    TIGR00864
    Location:502 → 563
    PCC; polycystin cation channel protein
    smart00082
    Location:213 → 253
    LRRCT; Leucine rich repeat C-terminal domain
    sd00033
    Location:109 → 132
    LRR_RI; leucine-rich repeat [structural motif]
    pfam13855
    Location:402 → 461
    LRR_8; Leucine rich repeat

  3. NM_173078.5 → NP_775101.1  SLIT and NTRK-like protein 4 precursor

    See identical proteins and their annotated locations for NP_775101.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) differs in the 5' UTR compared to variant 1. Variants 1, 2 and 3 encode the same protein.
    Source sequence(s)
    AC239921
    Consensus CDS
    CCDS14679.1
    UniProtKB/Swiss-Prot
    Q5JXG3, Q8IW52, Q8TCM8, Q96DL3
    UniProtKB/TrEMBL
    B2RCC8
    Related
    ENSP00000336627.4, ENST00000338017.8
    Conserved Domains (4) summary
    TIGR00864
    Location:502 → 563
    PCC; polycystin cation channel protein
    smart00082
    Location:213 → 253
    LRRCT; Leucine rich repeat C-terminal domain
    sd00033
    Location:109 → 132
    LRR_RI; leucine-rich repeat [structural motif]
    pfam13855
    Location:402 → 461
    LRR_8; Leucine rich repeat

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

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

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000023.11 Reference GRCh38.p14 Primary Assembly

    Range
    143622790..143636101 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011531265.3 → XP_011529567.1  SLIT and NTRK-like protein 4 isoform X1

    See identical proteins and their annotated locations for XP_011529567.1

    UniProtKB/Swiss-Prot
    Q5JXG3, Q8IW52, Q8TCM8, Q96DL3
    UniProtKB/TrEMBL
    B2RCC8
    Conserved Domains (4) summary
    TIGR00864
    Location:502 → 563
    PCC; polycystin cation channel protein
    smart00082
    Location:213 → 253
    LRRCT; Leucine rich repeat C-terminal domain
    sd00033
    Location:109 → 132
    LRR_RI; leucine-rich repeat [structural motif]
    pfam13855
    Location:402 → 461
    LRR_8; Leucine rich repeat

  2. XM_005262365.5 → XP_005262422.1  SLIT and NTRK-like protein 4 isoform X1

    See identical proteins and their annotated locations for XP_005262422.1

    UniProtKB/Swiss-Prot
    Q5JXG3, Q8IW52, Q8TCM8, Q96DL3
    UniProtKB/TrEMBL
    B2RCC8
    Conserved Domains (4) summary
    TIGR00864
    Location:502 → 563
    PCC; polycystin cation channel protein
    smart00082
    Location:213 → 253
    LRRCT; Leucine rich repeat C-terminal domain
    sd00033
    Location:109 → 132
    LRR_RI; leucine-rich repeat [structural motif]
    pfam13855
    Location:402 → 461
    LRR_8; Leucine rich repeat

RNA

  1. XR_007068180.1 RNA Sequence

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060947.1 Alternate T2T-CHM13v2.0

    Range
    141932069..141945367 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054326452.1 → XP_054182427.1  SLIT and NTRK-like protein 4 isoform X1

    UniProtKB/Swiss-Prot
    Q5JXG3, Q8IW52, Q8TCM8, Q96DL3

  2. XM_054326453.1 → XP_054182428.1  SLIT and NTRK-like protein 4 isoform X1

    UniProtKB/Swiss-Prot
    Q5JXG3, Q8IW52, Q8TCM8, Q96DL3

RNA

  1. XR_008485450.1 RNA Sequence

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q8IW52.1 GenPept UniProtKB/Swiss-Prot:Q8IW52

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