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    Tmem53 transmembrane protein 53 [ Mus musculus (house mouse) ]

    Gene ID: 68777, updated on 27-Nov-2024

    Summary

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    Official Symbol
    Tmem53provided by MGI
    Official Full Name
    transmembrane protein 53provided by MGI
    Primary source
    MGI:MGI:1916027
    See related
    Ensembl:ENSMUSG00000048772 AllianceGenome:MGI:1916027
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Mus musculus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
    Also known as
    1110038M16Rik; 1500001P22Rik; 1700012A05Rik
    Summary
    Involved in several processes, including negative regulation of BMP signaling pathway; negative regulation of ossification; and negative regulation of osteoblast differentiation. Located in nuclear outer membrane. Is expressed in chondrocranium; forelimb long bone; long bone epiphyseal plate; long bone epiphyseal plate proliferative zone; and periosteum. Used to study craniotubular dysplasia Ikegawa type. Human ortholog(s) of this gene implicated in craniotubular dysplasia Ikegawa type. Orthologous to human TMEM53 (transmembrane protein 53). [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Biased expression in testis adult (RPKM 307.2), adrenal adult (RPKM 61.0) and 4 other tissues See more
    Orthologs
    human all
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    Genomic context

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    See Tmem53 in Genome Data Viewer
    Location:
    4 D1; 4 53.43 cM
    Exon count:
    6
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCm39 (GCF_000001635.27) 4 NC_000070.7 (117109148..117125785)
    108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 4 NC_000070.6 (117251951..117268588)

    Chromosome 4 - NC_000070.7Genomic Context describing neighboring genes Neighboring gene STARR-positive B cell enhancer ABC_E1651 Neighboring gene predicted gene, 23143 Neighboring gene predicted gene, 23287 Neighboring gene armadillo-like helical domain containing 1 Neighboring gene CapStarr-seq enhancer MGSCv37_chr4:116923419-116923602 Neighboring gene STARR-positive B cell enhancer ABC_E7982 Neighboring gene STARR-seq mESC enhancer starr_11163 Neighboring gene ring finger protein 220 Neighboring gene predicted gene 12843 Neighboring gene predicted gene, 40231

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: Mouse ENCODE transcriptome data
    • Description: RNA profiling data sets generated by the Mouse ENCODE project.
    • BioProject: PRJNA66167
    • Publication: PMID 25409824
    • Analysis date: n/a

    Bibliography

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    Related articles in PubMed

    1. Cell-specific and lamin-dependent targeting of novel transmembrane proteins in the nuclear envelope. Malik P, et al. Cell Mol Life Sci, 2010 Apr. PMID 20091084, Free PMC Article
    2. Deficiency of TMEM53 causes a previously unknown sclerosing bone disorder by dysregulation of BMP-SMAD signaling. Guo L, et al. Nat Commun, 2021 Apr 6. PMID 33824347, Free PMC Article
    3. Tissue expression patterns identify mouse cilia genes. McClintock TS, et al. Physiol Genomics, 2008 Jan 17. PMID 17971504
    4. Irisin Mediates Effects on Bone and Fat via αV Integrin Receptors. Kim H, et al. Cell, 2018 Dec 13. PMID 30550785, Free PMC Article
    5. A conditional knockout resource for the genome-wide study of mouse gene function. Skarnes WC, et al. Nature, 2011 Jun 15. PMID 21677750, Free PMC Article

    See all (14) citations in PubMed

    GeneRIFs: Gene References Into Functions

    Variation

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    Alleles

    Alleles of this type are documented at Mouse Genome Informatics  (MGI)

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Homology

    Gene Ontology Provided by MGI

    Function Evidence Code Pubs
    enables molecular_function ND
    No biological Data available
    more info
    		  
    Process Evidence Code Pubs
    involved_in biological_process ND
    No biological Data available
    more info
    		  
    involved_in negative regulation of BMP signaling pathway IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in negative regulation of BMP signaling pathway ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in negative regulation of BMP signaling pathway ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in negative regulation of ossification IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in negative regulation of ossification ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in negative regulation of ossification ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in negative regulation of osteoblast differentiation IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in regulation of nucleocytoplasmic transport IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in regulation of nucleocytoplasmic transport ISO
    Inferred from Sequence Orthology
    more info
    		  
    Component Evidence Code Pubs
    located_in nuclear membrane ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in nuclear membrane ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    located_in nuclear outer membrane IDA
    Inferred from Direct Assay
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    transmembrane protein 53
    Names
    nuclear envelope transmembrane protein 4

    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_001285812.1 → NP_001272741.1  transmembrane protein 53 isoform a

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) encodes the longest isoform (a).
      Source sequence(s)
      AK004164, AL671866, AL844169, AW049729
      Consensus CDS
      CCDS71453.1
      UniProtKB/TrEMBL
      A0A0A0MQK8
      Related
      ENSMUSP00000102042.2, ENSMUST00000106434.8
      Conserved Domains (1) summary
      pfam05705
      Location:41 → 277
      DUF829; Eukaryotic protein of unknown function (DUF829)

    2. NM_001285814.1 → NP_001272743.1  transmembrane protein 53 isoform c

      Status: VALIDATED

      Description
      Transcript Variant: This variant (4) differs in its 5' UTR and 5' coding region, and initiates translation at an alternate start codon, compared to variant 1. The encoded isoform (c) has a distinct and shorter N-terminus, compared to isoform a. Both variants 3 and 4 encode isoform c.
      Source sequence(s)
      AK004164, AL671866, AL844169, AW049729
      Consensus CDS
      CCDS71454.1
      UniProtKB/TrEMBL
      A0A0A0MQK8
      Related
      ENSMUSP00000121458.2, ENSMUST00000125943.8
      Conserved Domains (1) summary
      pfam05705
      Location:19 → 255
      DUF829; Eukaryotic protein of unknown function (DUF829)

    3. NM_001285815.1 → NP_001272744.1  transmembrane protein 53 isoform d

      Status: VALIDATED

      Description
      Transcript Variant: This variant (5) differs in its 5' UTR and initiates translation at a downstream in-frame start codon, compared to variant 1. The encoded isoform (d) is shorter at the N-terminus, compared to isoform a. Both variants 5 and 6 encode isoform d.
      Source sequence(s)
      AK004164, AL671866, AL844169, AW049729, BE647557
      UniProtKB/Swiss-Prot
      Q9D0Z3
      Conserved Domains (1) summary
      pfam05705
      Location:13 → 199
      DUF829; Eukaryotic protein of unknown function (DUF829)

    4. NM_001285816.1 → NP_001272745.1  transmembrane protein 53 isoform d

      Status: VALIDATED

      Description
      Transcript Variant: This variant (6) lacks a portion of the 5' coding region and initiates translation at a downstream in-frame start codon, compared to variant 1. The encoded isoform (d) is shorter at the N-terminus, compared to isoform a. Both variants 5 and 6 encode isoform d.
      Source sequence(s)
      AK004164, AL671866, AL844169, AW049729
      UniProtKB/Swiss-Prot
      Q9D0Z3
      Conserved Domains (1) summary
      pfam05705
      Location:13 → 199
      DUF829; Eukaryotic protein of unknown function (DUF829)

    5. NM_026837.3 → NP_081113.1  transmembrane protein 53 isoform b

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) uses an alternate in-frame splice site in the 5' coding region, compared to variant 1, resulting in an isoform (b) that is shorter than isoform a.
      Source sequence(s)
      AK004164, AL671866, AL844169, AW049729
      Consensus CDS
      CCDS18533.1
      UniProtKB/Swiss-Prot
      A2AE66, Q8VDW5, Q9D0Z3, Q9DAF0
      UniProtKB/TrEMBL
      A0A0A0MQK8
      Related
      ENSMUSP00000061523.6, ENSMUST00000062824.12
      Conserved Domains (1) summary
      pfam05705
      Location:34 → 270
      DUF829; Eukaryotic protein of unknown function (DUF829)

    6. NM_029589.1 → NP_083865.1  transmembrane protein 53 isoform c

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) includes alternate 5' exon structure and it thus differs in its 5' UTR and 5' coding region, and initiates translation at an alternate start codon, compared to variant 1. The encoded isoform (c) has a distinct and shorter N-terminus, compared to isoform a. Both variants 3 and 4 encode isoform c.
      Source sequence(s)
      AK005104, AK005885, AL844169
      Consensus CDS
      CCDS71454.1
      UniProtKB/TrEMBL
      A0A0A0MQK8
      Related
      ENSMUSP00000102041.2, ENSMUST00000106433.2
      Conserved Domains (1) summary
      pfam05705
      Location:19 → 255
      DUF829; Eukaryotic protein of unknown function (DUF829)

    RefSeqs of Annotated Genomes: GCF_000001635.27-RS_2024_02

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCm39 C57BL/6J

    Genomic

    1. NC_000070.7 Reference GRCm39 C57BL/6J

      Range
      117109148..117125785
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_030253755.2 → XP_030109615.1  transmembrane protein 53 isoform X1

      Conserved Domains (1) summary
      pfam05705
      Location:13 → 199
      DUF829; Eukaryotic protein of unknown function (DUF829)
    Nucleotide Protein Strain
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9D0Z3.1 GenPept UniProtKB/Swiss-Prot:Q9D0Z3

    Gene LinkOut

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

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