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

Summary

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

See TNFAIP8L2-SCNM1 in Genome Data Viewer

Location:: 1q21.3

Exon count:: 7

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	1	NC_000001.11 (151156649..151170296)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	1	NC_060925.1 (150280351..150294025)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	1	NC_000001.10 (151129125..151142772)

Chromosome 1 - NC_000001.11 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

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

D11S2921 (e-PCR)
- UniSTS:152074

D8S2279 (e-PCR)
- UniSTS:473907

WIAF-1603 (e-PCR)
- UniSTS:69200

L18426 (e-PCR)
- UniSTS:34648

D1S1423 (e-PCR)
- UniSTS:149619

D11S3114 (e-PCR)
- UniSTS:152207

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)

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

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