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

    Gene ID: 757, updated on 5-Mar-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, Apr 2022]
    Expression
    Ubiquitous expression in thyroid (RPKM 53.6), gall bladder (RPKM 21.3) and 24 other tissues See more
    Orthologs
    mouse all
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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_2023_10 current GRCh38.p14 (GCF_000001405.40) 21 NC_000021.9 (33432486..33479974, complement)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 21 NC_060945.1 (31804757..31861806, complement)
    105.20220307 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
    • 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)

    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

    • FLJ26146, DKFZp686C2482

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables molecular_function ND
    No biological Data available
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in biological_process ND
    No biological Data available
    more info
    		  
    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_2023_10

    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

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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