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TLCD4-RWDD3 TLCD4-RWDD3 readthrough [ Homo sapiens (human) ]

Gene ID: 100527978, updated on 2-Nov-2024

Summary

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Official Symbol
TLCD4-RWDD3provided by HGNC
Official Full Name
TLCD4-RWDD3 readthroughprovided by HGNC
Primary source
HGNC:HGNC:49388
See related
Ensembl:ENSG00000271092 AllianceGenome:HGNC:49388
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
TMEM56-RWDD3
Summary
This locus represents naturally occurring read-through transcription between the neighboring TMEM56 (transmembrane protein 56) and RWDD3 (RWD domain containing 3) genes on chromosome 1. The read-through transcript encodes a protein that shares sequence identity with the upstream gene product, but it contains a distinct C-terminus due to frameshifts versus the downstream gene coding sequence. [provided by RefSeq, Dec 2010]
Expression
Ubiquitous expression in liver (RPKM 11.5), heart (RPKM 6.5) and 25 other tissues See more
Orthologs
all
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Genomic context

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See TLCD4-RWDD3 in Genome Data Viewer
Location:
1p21.3
Exon count:
8
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (95117923..95244955)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (94966360..95093048)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (95583479..95710511)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene ALG14 UDP-N-acetylglucosaminyltransferase subunit Neighboring gene uncharacterized LOC105378863 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr1:95508724-95509332 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:95509333-95509941 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1352 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1353 Neighboring gene ALG14 antisense RNA 1 Neighboring gene CRISPRi-validated cis-regulatory element chr1.7351 Neighboring gene CRISPRi-validated cis-regulatory element chr1.7352 Neighboring gene CRISPRi-validated cis-regulatory element chr1.7353 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1354 Neighboring gene CRISPRi-validated cis-regulatory element chr1.7357 Neighboring gene CRISPRi-validated cis-regulatory element chr1.7358 Neighboring gene CRISPRi-validated cis-regulatory element chr1.7359 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1104 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:95582918-95583064 Neighboring gene TLC domain containing 4 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:95600812-95601312 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:95601313-95601813 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:95602368-95602560 Neighboring gene RWDD3 divergent transcript Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:95682171-95682671 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1105 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1106 Neighboring gene RWD domain containing 3 Neighboring gene MPRA-validated peak328 silencer Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:95762972-95763562 Neighboring gene Sharpr-MPRA regulatory region 5488 Neighboring gene uncharacterized LOC105378864 Neighboring gene uncharacterized LOC105379825 Neighboring gene long intergenic non-protein coding RNA 1760

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. SUMOylation-triggered ALIX activation modulates extracellular vesicles circTLCD4-RWDD3 to promote lymphatic metastasis of non-small cell lung cancer. Diao X, et al. Signal Transduct Target Ther, 2023 Nov 4. PMID 37925421, Free PMC Article
  2. Genome-wide association study identifies variants associated with histologic features of nonalcoholic Fatty liver disease. Chalasani N, et al. Gastroenterology, 2010 Nov. PMID 20708005, Free PMC Article
  3. Genome-wide association study identifies novel loci associated with concentrations of four plasma phospholipid fatty acids in the de novo lipogenesis pathway: results from the Cohorts for Heart and Aging Research in Genomic Epidemiology (CHARGE) consortium. Wu JH, et al. Circ Cardiovasc Genet, 2013 Apr. PMID 23362303, Free PMC Article
  4. 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
  5. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. Strausberg RL, et al. Proc Natl Acad Sci U S A, 2002 Dec 24. PMID 12477932, Free PMC Article

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. SUMOylation-triggered ALIX activation modulates extracellular vesicles circTLCD4-RWDD3 to promote lymphatic metastasis of non-small cell lung cancer.
    Title: SUMOylation-triggered ALIX activation modulates extracellular vesicles circTLCD4-RWDD3 to promote lymphatic metastasis of non-small cell lung cancer.
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

EBI GWAS Catalog

Description
Genome-wide association study identifies novel loci associated with concentrations of four plasma phospholipid fatty acids in the de novo lipogenesis pathway: results from the Cohorts for Heart and Aging Research in Genomic Epidemiology (CHARGE) consortiu
EBI GWAS Catalog
Genome-wide association study identifies variants associated with histologic features of nonalcoholic Fatty liver disease.
EBI GWAS Catalog

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

General gene information

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Markers

Homology

Clone Names

  • FLJ99167

General protein information

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Preferred Names
TMEM56-RWDD3 protein
Names
TMEM56-RWDD3 readthrough

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_001199691.1 → NP_001186620.1  TMEM56-RWDD3 protein

    Status: VALIDATED

    Source sequence(s)
    AC092802, BC063464
    UniProtKB/TrEMBL
    S4R434
    Related
    ENSP00000475025.1, ENST00000604534.5
    Conserved Domains (1) summary
    cl02759
    Location:44 → 158
    TRAM_LAG1_CLN8; TLC domain

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
    95117923..95244955
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060925.1 Alternate T2T-CHM13v2.0

    Range
    94966360..95093048
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

Gene LinkOut

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