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

    Gene ID: 139065, updated on 10-Dec-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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    See SLITRK4 in Genome Data Viewer
    Location:
    Xq27.3
    Exon count:
    6
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) X NC_000023.11 (143622790..143636101, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) X NC_060947.1 (141932069..141945367, complement)
    RS_2024_09 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. 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
    5. 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

    See all (19) 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)

    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

    Function Evidence Code Pubs
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    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 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_2024_08

    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
      UniProtKB/TrEMBL
      B2RCC8

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

      UniProtKB/Swiss-Prot
      Q5JXG3, Q8IW52, Q8TCM8, Q96DL3
      UniProtKB/TrEMBL
      B2RCC8

    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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