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    Tm6sf1 transmembrane 6 superfamily member 1 [ Mus musculus (house mouse) ]

    Gene ID: 107769, updated on 9-Dec-2024

    Summary

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    Official Symbol
    Tm6sf1provided by MGI
    Official Full Name
    transmembrane 6 superfamily member 1provided by MGI
    Primary source
    MGI:MGI:1933209
    See related
    Ensembl:ENSMUSG00000038623 AllianceGenome:MGI:1933209
    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
    C630016D09Rik
    Summary
    Located in lysosomal membrane. Is expressed in dentate gyrus subgranular zone. Orthologous to human TM6SF1 (transmembrane 6 superfamily member 1). [provided by Alliance of Genome Resources, Dec 2024]
    Expression
    Ubiquitous expression in thymus adult (RPKM 19.2), spleen adult (RPKM 16.3) and 27 other tissues See more
    Orthologs
    human all
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    Genomic context

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    See Tm6sf1 in Genome Data Viewer
    Location:
    7 D3; 7 45.71 cM
    Exon count:
    13
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCm39 (GCF_000001635.27) 7 NC_000073.7 (81507810..81533827)
    108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 7 NC_000073.6 (81858718..81884079)

    Chromosome 7 - NC_000073.7Genomic Context describing neighboring genes Neighboring gene BTB domain containing 1 Neighboring gene STARR-seq mESC enhancer starr_19371 Neighboring gene predicted gene, 32695 Neighboring gene predicted gene, 51491 Neighboring gene STARR-seq mESC enhancer starr_19372 Neighboring gene CapStarr-seq enhancer MGSCv37_chr7:89025770-89025983 Neighboring gene STARR-seq mESC enhancer starr_19373 Neighboring gene HDGF like 3 Neighboring gene STARR-seq mESC enhancer starr_19374 Neighboring gene STARR-seq mESC enhancer starr_19375 Neighboring gene basonuclin zinc finger protein 1 Neighboring gene STARR-seq mESC enhancer starr_19377 Neighboring gene predicted gene, 46013

    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. Transmembrane 6 superfamily 1 (Tm6sf1) is a novel lysosomal transmembrane protein. Tam WY, et al. Protoplasma, 2015 Jul. PMID 25422095
    2. Cloning of the novel gene TM6SF1 reveals conservation of clusters of paralogous genes between human chromosomes 15q24-->q26 and 19p13.3-->p12. Carim-Todd L, et al. Cytogenet Cell Genet, 2000. PMID 11124529
    3. DLK1 is a novel regulator of bone mass that mediates estrogen deficiency-induced bone loss in mice. Abdallah BM, et al. J Bone Miner Res, 2011 Jul. PMID 21308776
    4. Conserved molecular signatures of neurogenesis in the hippocampal subgranular zone of rodents and primates. Miller JA, et al. Development, 2013 Nov. PMID 24154525, Free PMC Article
    5. Transcriptome analysis of mouse stem cells and early embryos. Sharov AA, et al. PLoS Biol, 2003 Dec. PMID 14691545, Free PMC Article

    See all (17) 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)
    • Endonuclease-mediated (1) 

    General gene information

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    Markers

    Homology

    Clone Names

    • MGC25583

    Gene Ontology Provided by MGI

    Component Evidence Code Pubs
    is_active_in lysosomal membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in lysosomal membrane IDA
    Inferred from Direct Assay
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    transmembrane 6 superfamily member 1

    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_001291282.1 → NP_001278211.1  transmembrane 6 superfamily member 1 isoform 2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) differs in the 5' UTR and coding sequence compared to variant 1. The resulting isoform (2) is shorter at the N-terminus compared to isoform 1.
      Source sequence(s)
      AK083132, AK136581, AK162572
      Consensus CDS
      CCDS80744.1
      UniProtKB/TrEMBL
      D3YX52
      Related
      ENSMUSP00000112400.2, ENSMUST00000119543.2
      Conserved Domains (1) summary
      pfam10914
      Location:126 → 262
      DUF2781; Protein of unknown function (DUF2781)

    2. NM_145375.4 → NP_663350.2  transmembrane 6 superfamily member 1 isoform 1

      See identical proteins and their annotated locations for NP_663350.2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and encodes the longer isoform (1).
      Source sequence(s)
      AK083132, AK162572, BB653227
      Consensus CDS
      CCDS21408.1
      UniProtKB/Swiss-Prot
      P58749, Q8BUN7
      UniProtKB/TrEMBL
      Q3TA39
      Related
      ENSMUSP00000038017.2, ENSMUST00000041890.8
      Conserved Domains (1) summary
      cd21106
      Location:6 → 361
      TM6SF1-like; transmembrane 6 superfamily member 1, member 2, and similar proteins

    RNA

    1. NR_111910.1 RNA Sequence

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) lacks two alternate exons compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
      Source sequence(s)
      AK083132, AK162572, BB653227

    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_000073.7 Reference GRCm39 C57BL/6J

      Range
      81507810..81533827
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_036152557.1 → XP_036008450.1  transmembrane 6 superfamily member 1 isoform X1

      UniProtKB/Swiss-Prot
      P58749, Q8BUN7
      UniProtKB/TrEMBL
      Q3TA39
      Conserved Domains (1) summary
      cd21106
      Location:6 → 361
      TM6SF1-like; transmembrane 6 superfamily member 1, member 2, and similar proteins

    2. XM_030241971.2 → XP_030097831.1  transmembrane 6 superfamily member 1 isoform X4

    3. XM_036152558.1 → XP_036008451.1  transmembrane 6 superfamily member 1 isoform X2

      Conserved Domains (1) summary
      cd21106
      Location:1 → 252
      TM6SF1-like; transmembrane 6 superfamily member 1, member 2, and similar proteins

    4. XM_030241970.1 → XP_030097830.1  transmembrane 6 superfamily member 1 isoform X3

      Conserved Domains (1) summary
      pfam10914
      Location:70 → 205
      DUF2781; Protein of unknown function (DUF2781)
    Nucleotide Protein Strain
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    P58749.2 GenPept UniProtKB/Swiss-Prot:P58749

    Gene LinkOut

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

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