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TMEM50B transmembrane protein 50B [ Homo sapiens (human) ]

Gene ID: 757, updated on 14-Nov-2024

Summary

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Official Symbol
TMEM50Bprovided by HGNC
Official Full Name
transmembrane protein 50Bprovided by HGNC
Primary source
HGNC:HGNC:1280
See related
Ensembl:ENSG00000142188 MIM:617894; AllianceGenome:HGNC:1280
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
C21orf4; HCVP7TP3
Summary
Predicted to be involved in late endosome to vacuole transport via multivesicular body sorting pathway. Located in endoplasmic reticulum. [provided by Alliance of Genome Resources, Nov 2024]
Expression
Ubiquitous expression in thyroid (RPKM 53.6), gall bladder (RPKM 21.3) and 24 other tissues See more
Orthologs
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Genomic context

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See TMEM50B in Genome Data Viewer
Location:
21q22.11
Exon count:
11
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 21 NC_000021.9 (33432486..33479974, complement)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 21 NC_060945.1 (31804757..31861806, complement)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 21 NC_000021.8 (34804793..34852281, complement)

Chromosome 21 - NC_000021.9Genomic Context describing neighboring genes Neighboring gene IFNAR2-IL10RB readthrough Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13254 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18373 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18374 Neighboring gene interleukin 10 receptor subunit beta Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18375 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:34676441-34676940 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13255 Neighboring gene IFNAR1 promoter region Neighboring gene interferon alpha and beta receptor subunit 1 Neighboring gene upstream transcription factor 1 pseudogene 1 Neighboring gene Sharpr-MPRA regulatory region 14728 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr21:34738709-34739908 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr21:34752348-34753547 Neighboring gene Sharpr-MPRA regulatory region 6397 Neighboring gene ReSE screen-validated silencer GRCh37_chr21:34758349-34758554 Neighboring gene IFNGR2 promoter region Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13257 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13258 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13259 Neighboring gene CRISPRi-FlowFISH-validated IFNGR2 regulatory element GRCh37_chr21:34776289-34777452 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:34784507-34785261 Neighboring gene ReSE screen-validated silencer GRCh37_chr21:34785395-34785563 Neighboring gene interferon gamma receptor 2 Neighboring gene RPS5 pseudogene 3 Neighboring gene DnaJ heat shock protein family (Hsp40) member C28

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. Comparative genomic analysis of the interferon/interleukin-10 receptor gene cluster. Reboul J, et al. Genome Res, 1999 Mar. PMID 10077530, Free PMC Article
  2. Transmembrane protein 50b (C21orf4), a candidate for Down syndrome neurophenotypes, encodes an intracellular membrane protein expressed in the rodent brain. Moldrich RX, et al. Neuroscience, 2008 Jul 17. PMID 18541381
  3. Prominent use of distal 5' transcription start sites and discovery of a large number of additional exons in ENCODE regions. Denoeud F, et al. Genome Res, 2007 Jun. PMID 17567994, Free PMC Article
  4. Common genetic variants associated with cognitive performance identified using the proxy-phenotype method. Rietveld CA, et al. Proc Natl Acad Sci U S A, 2014 Sep 23. PMID 25201988, Free PMC Article
  5. Cell array-based intracellular localization screening reveals novel functional features of human chromosome 21 proteins. Hu YH, et al. BMC Genomics, 2006 Jun 16. PMID 16780588, Free PMC Article

See all (18) citations in PubMed

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

EBI GWAS Catalog

Description
Common genetic variants associated with cognitive performance identified using the proxy-phenotype method.
EBI GWAS Catalog
Host-microbe interactions have shaped the genetic architecture of inflammatory bowel 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)

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • FLJ26146, DKFZp686C2482

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
Process Evidence Code Pubs
involved_in late endosome to vacuole transport via multivesicular body sorting pathway IBA
Inferred from Biological aspect of Ancestor
more info
  
Component Evidence Code Pubs
located_in Golgi membrane IEA
Inferred from Electronic Annotation
more info
  
located_in endoplasmic reticulum IDA
Inferred from Direct Assay
more info
  
located_in endoplasmic reticulum membrane IEA
Inferred from Electronic Annotation
more info
  
located_in plasma membrane HDA PubMed 

General protein information

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Preferred Names
transmembrane protein 50B
Names
HCV p7-trans-regulated protein 3
HCV p7-transregulated protein 3

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_006134.7 → NP_006125.2  transmembrane protein 50B

    See identical proteins and their annotated locations for NP_006125.2

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) represents the shorter transcript and encodes the functional protein.
    Source sequence(s)
    AL355685, BC000569, BF696480, DA286739
    Consensus CDS
    CCDS13625.1
    UniProtKB/Swiss-Prot
    B2R4L4, D3DSF1, O60537, P56557, Q5PY47
    Related
    ENSP00000439768.2, ENST00000542230.7
    Conserved Domains (1) summary
    pfam05255
    Location:9 → 157
    UPF0220; Uncharacterized protein family (UPF0220)

RNA

  1. NR_040016.2 RNA Sequence

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) includes several additional 3' exons, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most supported translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AP000300, BX537378, DA286739

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_000021.9 Reference GRCh38.p14 Primary Assembly

    Range
    33432486..33479974 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011529746.3 → XP_011528048.1  transmembrane protein 50B isoform X1

    See identical proteins and their annotated locations for XP_011528048.1

    UniProtKB/Swiss-Prot
    B2R4L4, D3DSF1, O60537, P56557, Q5PY47
    Related
    ENSP00000397773.1, ENST00000420455.5
    Conserved Domains (1) summary
    pfam05255
    Location:9 → 157
    UPF0220; Uncharacterized protein family (UPF0220)

  2. XM_047440989.1 → XP_047296945.1  transmembrane protein 50B isoform X3

    UniProtKB/TrEMBL
    Q2V8N0

  3. XM_047440988.1 → XP_047296944.1  transmembrane protein 50B isoform X2

    UniProtKB/TrEMBL
    F8WDH1
    Related
    ENSP00000409942.1, ENST00000442441.5

Reference GRCh38.p14 ALT_REF_LOCI_1

Genomic

  1. NW_003315970.2 Reference GRCh38.p14 ALT_REF_LOCI_1

    Range
    27058..84103 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054329611.1 → XP_054185586.1  transmembrane protein 50B isoform X1

    UniProtKB/Swiss-Prot
    B2R4L4, D3DSF1, O60537, P56557, Q5PY47

RNA

  1. XR_008485655.1 RNA Sequence

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060945.1 Alternate T2T-CHM13v2.0

    Range
    31804757..31861806 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054324851.1 → XP_054180826.1  transmembrane protein 50B isoform X1

    UniProtKB/Swiss-Prot
    B2R4L4, D3DSF1, O60537, P56557, Q5PY47

RNA

  1. XR_008485344.1 RNA Sequence

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

  1. NR_038211.1: Suppressed sequence

    Description
    NR_038211.1: This RefSeq was temporarily suppressed because it is 5'' partial compared to available transcript evidence.
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
P56557.2 GenPept UniProtKB/Swiss-Prot:P56557

Gene LinkOut

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