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    TNFAIP8L2-SCNM1 TNFAIP8L2-SCNM1 readthrough [ Homo sapiens (human) ]

    Gene ID: 100534012, updated on 17-Sep-2024

    Summary

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    Gene symbol
    TNFAIP8L2-SCNM1
    Gene description
    TNFAIP8L2-SCNM1 readthrough
    See related
    Ensembl:ENSG00000163156
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    SCNM1
    Summary
    This locus represents naturally occurring read-through transcription between the neighboring TNFAIP8L2 (tumor necrosis factor, alpha-induced protein 8-like 2) and SCNM1 (sodium channel modifier 1) genes on chromosome 1. The protein-coding read-through transcript variant encodes a protein that shares sequence identity with the downstream gene product but its N-terminal region is shorter due to alternate exon use relative to the downstream gene. [provided by RefSeq, Dec 2016]
    Expression
    Ubiquitous expression in spleen (RPKM 7.7), lymph node (RPKM 7.7) and 25 other tissues See more
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    Genomic context

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    See TNFAIP8L2-SCNM1 in Genome Data Viewer
    Location:
    1q21.3
    Exon count:
    7
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (151156649..151170296)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (150280351..150294025)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (151129125..151142772)

    Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124904418 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1707 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:151104130-151104914 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1313 Neighboring gene semaphorin 6C Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1314 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1315 Neighboring gene LysM domain containing 1 Neighboring gene TNF alpha induced protein 8 like 2 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:151137860-151138565 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:151138566-151139272 Neighboring gene sodium channel modifier 1 Neighboring gene tropomodulin 4 Neighboring gene vacuolar protein sorting 72 homolog Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1710 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1711 Neighboring gene uncharacterized LOC124904419 Neighboring gene phosphatidylinositol-4-phosphate 5-kinase type 1 alpha

    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 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. Expression of conjoined genes: another mechanism for gene regulation in eukaryotes. Prakash T, et al. PLoS One, 2010 Oct 12. PMID 20967262, Free PMC Article
    2. An interactome perturbation framework prioritizes damaging missense mutations for developmental disorders. Chen S, et al. Nat Genet, 2018 Jul. PMID 29892012, Free PMC Article

    GeneRIFs: Gene References Into Functions

    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

    • FLJ23467

    General protein information

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    Preferred Names
    TNFAIP8L2-SCNM1 protein
    Names
    Sodium channel modifier 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_001204848.2 → NP_001191777.1  TNFAIP8L2-SCNM1 protein

      See identical proteins and their annotated locations for NP_001191777.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longer transcript and encodes the protein.
      Source sequence(s)
      AL592424, BG531092
      UniProtKB/Swiss-Prot
      Q9BWG6
      Related
      ENSP00000473282.1, ENST00000602841.5
      Conserved Domains (2) summary
      pfam15803
      Location:9 → 35
      zf-SCNM1; Zinc-finger of sodium channel modifier 1
      pfam15805
      Location:148 → 193
      SCNM1_acidic; Acidic C-terminal region of sodium channel modifier 1 SCNM1

    RNA

    1. NR_144937.2 RNA Sequence

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) uses an alternate splice site in an internal exon, resulting in a shorter transcript compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
      Source sequence(s)
      AL592424

    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_000001.11 Reference GRCh38.p14 Primary Assembly

      Range
      151156649..151170296
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060925.1 Alternate T2T-CHM13v2.0

      Range
      150280351..150294025
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version

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