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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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