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    Sclt1 sodium channel and clathrin linker 1 [ Rattus norvegicus (Norway rat) ]

    Gene ID: 266809, updated on 2-Nov-2024

    Summary

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    Official Symbol
    Sclt1provided by RGD
    Official Full Name
    sodium channel and clathrin linker 1provided by RGD
    Primary source
    RGD:628721
    See related
    EnsemblRapid:ENSRNOG00000014139 AllianceGenome:RGD:628721
    Gene type
    protein coding
    RefSeq status
    PROVISIONAL
    Organism
    Rattus norvegicus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
    Also known as
    Sap1; CAP-1A
    Summary
    Enables clathrin binding activity and sodium channel regulator activity. Involved in clustering of voltage-gated sodium channels. Part of clathrin complex. Orthologous to human SCLT1 (sodium channel and clathrin linker 1). [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Biased expression in Testes (RPKM 99.1), Brain (RPKM 71.7) and 9 other tissues See more
    Orthologs
    human mouse all
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    Genomic context

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    See Sclt1 in Genome Data Viewer
    Location:
    2q26
    Exon count:
    25
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 2 NC_086020.1 (126533436..126691879, complement)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 2 NC_051337.1 (124605445..124763964, complement)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 2 NC_005101.4 (128523376..128675668, complement)

    Chromosome 2 - NC_086020.1Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC102553773 Neighboring gene ribosome biogenesis protein NSA2 homolog Neighboring gene jade family PHD finger 1 Neighboring gene similar to human chromosome 4 open reading frame 33 Neighboring gene 40S ribosomal protein S21-like

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
    • Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
    • BioProject: PRJNA238328
    • Publication: PMID 24510058
    • Analysis date: Mon Jun 6 17:44:12 2016

    Bibliography

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    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Coexpression of beta-subunits of NaV1.8 strongly influences the affinity of the muO-conotoxin MrVIB conopeptide for the channel.
      Title: Navβ subunits modulate the inhibition of Nav1.8 by the analgesic gating modifier μO-conotoxin MrVIB.
    2. SAP-1 is the first example of an adapter protein that links clathrin and a sodium channel and may regulate Na(v)1.8 channel density at the cell surface.
      Title: CAP-1A is a novel linker that binds clathrin and the voltage-gated sodium channel Na(v)1.8.
    Submit: New GeneRIF Correction

    Pathways from PubChem

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    General gene information

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    Homology

    Gene Ontology Provided by RGD

    Function Evidence Code Pubs
    enables clathrin binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables sodium channel regulator activity IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in cilium assembly IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    acts_upstream_of_or_within cilium assembly ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in cilium assembly ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in cilium assembly ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in clustering of voltage-gated sodium channels IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in clustering of voltage-gated sodium channels IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    Component Evidence Code Pubs
    is_active_in centriole IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in centriole ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in centriole ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    located_in centrosome ISO
    Inferred from Sequence Orthology
    more info
    		  
    part_of ciliary transition fiber ISO
    Inferred from Sequence Orthology
    more info
    		  
    part_of clathrin complex IDA
    Inferred from Direct Assay
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    sodium channel and clathrin linker 1
    Names
    clathrin-associated protein 1A
    sodium channel Nav1.8-binding protein
    sodium channel-associated protein 1

    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)

    1. NM_153740.1 → NP_714962.1  sodium channel and clathrin linker 1

      See identical proteins and their annotated locations for NP_714962.1

      Status: PROVISIONAL

      Source sequence(s)
      AF421190
      UniProtKB/Swiss-Prot
      Q8CJ83, Q8CJ84, Q8CJ98, Q8CJ99
      UniProtKB/TrEMBL
      A0A8I6AEY4
      Related
      ENSRNOP00000019256.4, ENSRNOT00000019256.8
      Conserved Domains (2) summary
      TIGR02168
      Location:189 → 483
      SMC_prok_B; chromosome segregation protein SMC, common bacterial type
      TIGR02169
      Location:325 → 683
      SMC_prok_A; chromosome segregation protein SMC, primarily archaeal type

    RefSeqs of Annotated Genomes: GCF_036323735.1-RS_2024_02

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

    Reference GRCr8

    Genomic

    1. NC_086020.1 Reference GRCr8

      Range
      126533436..126691879 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_039101819.2 → XP_038957747.1  sodium channel and clathrin linker 1 isoform X4

      UniProtKB/TrEMBL
      A6II55
      Conserved Domains (2) summary
      PTZ00121
      Location:62 → 420
      PTZ00121; MAEBL; Provisional
      PRK11448
      Location:461 → 553
      hsdR; type I restriction enzyme EcoKI subunit R; Provisional

    2. XM_039101816.2 → XP_038957744.1  sodium channel and clathrin linker 1 isoform X1

      UniProtKB/TrEMBL
      A0A8I6AEY4
      Conserved Domains (2) summary
      COG1196
      Location:212 → 558
      Smc; Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]
      PRK11448
      Location:610 → 702
      hsdR; type I restriction enzyme EcoKI subunit R; Provisional

    3. XM_039101818.2 → XP_038957746.1  sodium channel and clathrin linker 1 isoform X3

      UniProtKB/TrEMBL
      A6II56
      Conserved Domains (2) summary
      COG1196
      Location:65 → 379
      Smc; Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]
      TIGR02168
      Location:256 → 566
      SMC_prok_B; chromosome segregation protein SMC, common bacterial type

    4. XM_039101820.2 → XP_038957748.1  sodium channel and clathrin linker 1 isoform X5

      UniProtKB/TrEMBL
      A6II56
      Conserved Domains (2) summary
      COG1196
      Location:12 → 326
      Smc; Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]
      TIGR02168
      Location:203 → 513
      SMC_prok_B; chromosome segregation protein SMC, common bacterial type

    5. XM_039101823.2 → XP_038957751.1  sodium channel and clathrin linker 1 isoform X8

      UniProtKB/TrEMBL
      A6II56
      Conserved Domains (2) summary
      PTZ00121
      Location:21 → 332
      PTZ00121; MAEBL; Provisional
      PRK11448
      Location:373 → 465
      hsdR; type I restriction enzyme EcoKI subunit R; Provisional

    6. XM_039101822.2 → XP_038957750.1  sodium channel and clathrin linker 1 isoform X7

      UniProtKB/TrEMBL
      A6II56
      Conserved Domains (1) summary
      TIGR02168
      Location:17 → 290
      SMC_prok_B; chromosome segregation protein SMC, common bacterial type

    7. XM_039101821.2 → XP_038957749.1  sodium channel and clathrin linker 1 isoform X6

      UniProtKB/TrEMBL
      A6II56
      Conserved Domains (2) summary
      PTZ00121
      Location:4 → 376
      PTZ00121; MAEBL; Provisional
      PRK11448
      Location:417 → 509
      hsdR; type I restriction enzyme EcoKI subunit R; Provisional

    8. XM_039101824.2 → XP_038957752.1  sodium channel and clathrin linker 1 isoform X9

      UniProtKB/TrEMBL
      A6II57
      Conserved Domains (1) summary
      TIGR02168
      Location:18 → 333
      SMC_prok_B; chromosome segregation protein SMC, common bacterial type

    9. XM_039101817.2 → XP_038957745.1  sodium channel and clathrin linker 1 isoform X2

      UniProtKB/TrEMBL
      A0A8I5ZLA1
      Conserved Domains (1) summary
      COG1196
      Location:212 → 558
      Smc; Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]

    10. XM_063281378.1 → XP_063137448.1  sodium channel and clathrin linker 1 isoform X10

    RNA

    1. XR_005500249.2 RNA Sequence

    2. XR_005500251.2 RNA Sequence

    Nucleotide Protein Strain
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q8CJ99.1 GenPept UniProtKB/Swiss-Prot:Q8CJ99

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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