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TVP23C-CDRT4 TVP23C-CDRT4 readthrough [ Homo sapiens (human) ]

Gene ID: 100533496, updated on 2-Nov-2024

Summary

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Official Symbol
TVP23C-CDRT4provided by HGNC
Official Full Name
TVP23C-CDRT4 readthroughprovided by HGNC
Primary source
HGNC:HGNC:42961
See related
Ensembl:ENSG00000259024 AllianceGenome:HGNC:42961
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
TVP23C; FAM18B2; FAM18B2-CDRT4
Summary
This locus represents naturally occurring readthrough transcription between the neighboring TVP23C (trans-golgi network vesicle protein 23 homolog) and CDRT4 (CMT1A duplicated region transcript 4) genes on chromosome 17. Alternative splicing results in multiple transcript variants, one of which encodes a protein that shares sequence identity with the upstream gene product, but its C-terminus is distinct due to frameshifts relative to the downstream gene. [provided by RefSeq, Apr 2014]
Expression
Ubiquitous expression in thyroid (RPKM 9.0), testis (RPKM 8.5) and 25 other tissues See more
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Genomic context

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See TVP23C-CDRT4 in Genome Data Viewer
Location:
17p12
Exon count:
7
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 17 NC_000017.11 (15436015..15563483, complement)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 17 NC_060941.1 (15342066..15469716, complement)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 17 NC_000017.10 (15339332..15466797, complement)

Chromosome 17 - NC_000017.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124903932 Neighboring gene RNA, U6 small nuclear 799, pseudogene Neighboring gene tektin 3 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:15313079-15313579 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:15320989-15321490 Neighboring gene RNA, 7SL, cytoplasmic 792, pseudogene Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:15351635-15352136 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:15352137-15352636 Neighboring gene CMT1A duplicated region transcript 4 Neighboring gene ribosomal protein L9 pseudogene 2 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr17:15393660-15394859 Neighboring gene CMT1A duplicated region transcript 3 Neighboring gene Sharpr-MPRA regulatory region 6604 Neighboring gene peptidylprolyl isomerase A pseudogene 53 Neighboring gene trans-golgi network vesicle protein 23 homolog C Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:15439327-15439826 Neighboring gene NANOG hESC enhancer GRCh37_chr17:15443919-15444544 Neighboring gene proximal CMT1A-REP Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr17:15495673-15496196 Neighboring gene F-box and WD repeat domain containing 10B Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:15545644-15546230 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:15546231-15546817 Neighboring gene H3K27ac hESC enhancer GRCh37_chr17:15547662-15548477 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11743 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:15554223-15555172 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:15562775-15563277 Neighboring gene tripartite motif containing 16 Neighboring gene zinc finger protein 29, pseudogene

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. VIRMA mediates preferential m(6)A mRNA methylation in 3'UTR and near stop codon and associates with alternative polyadenylation. Yue Y, et al. Cell Discov, 2018. PMID 29507755, Free PMC Article
  3. Diversification of transcriptional modulation: large-scale identification and characterization of putative alternative promoters of human genes. Kimura K, et al. Genome Res, 2006 Jan. PMID 16344560, Free PMC Article
  4. Normalization and subtraction: two approaches to facilitate gene discovery. Bonaldo MF, et al. Genome Res, 1996 Sep. PMID 8889548

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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Homology

Clone Names

  • FLJ53614

General protein information

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Preferred Names
uncharacterized protein LOC100533496
Names
FAM18B2-CDRT4 readthrough
Golgi apparatus membrane protein TVP23 homolog C

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_001204478.2 → NP_001191407.1  uncharacterized protein LOC100533496

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) represents the longer transcript and is protein-coding.
    Source sequence(s)
    AB074181, AC005838, CB850543
    UniProtKB/TrEMBL
    A0A0A6YYB9
    Related
    ENSP00000429865.1, ENST00000522212.6
    Conserved Domains (1) summary
    pfam05832
    Location:32 → 154
    DUF846; Eukaryotic protein of unknown function (DUF846)

RNA

  1. NR_037924.2 RNA Sequence

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) lacks an alternate exon in the 5' region, compared to variant 1. This variant is represented as non-coding because the use of the supported translational start codon, as used in variant 1, would render the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AC005517, AC005838, CB850543, DA796743

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_000017.11 Reference GRCh38.p14 Primary Assembly

    Range
    15436015..15563483 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060941.1 Alternate T2T-CHM13v2.0

    Range
    15342066..15469716 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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