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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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Related articles in PubMed

  1. Navβ subunits modulate the inhibition of Nav1.8 by the analgesic gating modifier μO-conotoxin MrVIB. Wilson MJ, et al. J Pharmacol Exp Ther, 2011 Aug. PMID 21586605, Free PMC Article
  2. CAP-1A is a novel linker that binds clathrin and the voltage-gated sodium channel Na(v)1.8. Liu C, et al. Mol Cell Neurosci, 2005 Apr. PMID 15797711
  3. Centriole distal appendages promote membrane docking, leading to cilia initiation. Tanos BE, et al. Genes Dev, 2013 Jan 15. PMID 23348840, Free PMC Article
  4. C2cd3 is critical for centriolar distal appendage assembly and ciliary vesicle docking in mammals. Ye X, et al. Proc Natl Acad Sci U S A, 2014 Feb 11. PMID 24469809, Free PMC Article
  5. Novel asymmetrically localizing components of human centrosomes identified by complementary proteomics methods. Jakobsen L, et al. EMBO J, 2011 Apr 20. PMID 21399614, Free PMC Article

See all (7) citations in PubMed

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

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