U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

Links from Nucleotide

    • Showing Current items.

    Rtl9 retrotransposon Gag like 9 [ Mus musculus (house mouse) ]

    Gene ID: 209540, updated on 5-Mar-2024

    Summary

    Go to the top of the page Help
    Official Symbol
    Rtl9provided by MGI
    Official Full Name
    retrotransposon Gag like 9provided by MGI
    Primary source
    MGI:MGI:2685231
    See related
    Ensembl:ENSMUSG00000085584 AllianceGenome:MGI:2685231
    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
    Mar9; Gm385; Mart9; Rgag1
    Summary
    Is expressed in brain. Orthologous to human RTL9 (retrotransposon Gag like 9). [provided by Alliance of Genome Resources, Apr 2022]
    Expression
    Low expression observed in reference dataset See more
    Orthologs
    human all
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    Go to the top of the page Help
    See Rtl9 in Genome Data Viewer
    Location:
    X F2; X 64.02 cM
    Exon count:
    5
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCm39 (GCF_000001635.27) X NC_000086.8 (141841655..141888326)
    108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) X NC_000086.7 (143058276..143105330)

    Chromosome X - NC_000086.8Genomic Context describing neighboring genes Neighboring gene transmembrane protein 164 Neighboring gene POU domain, class 5, transcription factor 1, related sequence 13 Neighboring gene STARR-seq mESC enhancer starr_48025 Neighboring gene AMMECR nuclear protein 1 Neighboring gene STARR-seq mESC enhancer starr_48026 Neighboring gene STARR-seq mESC enhancer starr_48027 Neighboring gene STARR-seq mESC enhancer starr_48028 Neighboring gene STARR-seq mESC enhancer starr_48029 Neighboring gene actin, beta pseudogene Neighboring gene STARR-seq mESC enhancer starr_48030 Neighboring gene chordin-like 1

    Genomic regions, transcripts, and products

    Go to the top of the page Help

    Go to nucleotide: Graphics FASTA GenBank

    Expression

    Go to the top of the page Help
    • 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

    Go to the top of the pageHelp

    Related articles in PubMed

    1. A small family of sushi-class retrotransposon-derived genes in mammals and their relation to genomic imprinting. Youngson NA, et al. J Mol Evol, 2005 Oct. PMID 16155747
    2. Transposable elements as a source of genetic innovation: expression and evolution of a family of retrotransposon-derived neogenes in mammals. Brandt J, et al. Gene, 2005 Jan 17. PMID 15716091
    3. A family of neofunctionalized Ty3/gypsy retrotransposon genes in mammalian genomes. Brandt J, et al. Cytogenet Genome Res, 2005. PMID 16093683
    4. BraInMap Elucidates the Macromolecular Connectivity Landscape of Mammalian Brain. Pourhaghighi R, et al. Cell Syst, 2020 Apr 22. PMID 32325033, Free PMC Article
    5. A high-resolution anatomical atlas of the transcriptome in the mouse embryo. Diez-Roux G, et al. PLoS Biol, 2011 Jan 18. PMID 21267068, Free PMC Article

    GeneRIFs: Gene References Into Functions

    Variation

    Go to the top of the page Help

    Alleles

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

    Interactions

    Go to the top of the page Help
    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Go to the top of the page Help

    Homology

    Clone Names

    • KIAA1318, mKIAA1318

    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
    		  
    Component Evidence Code Pubs
    is_active_in cellular_component ND
    No biological Data available
    more info
    		  

    General protein information

    Go to the top of the page Help
    Preferred Names
    retrotransposon Gag-like protein 9
    Names
    retrotransposon gag domain containing 1
    retrotransposon gag domain-containing protein 1
    sushi-XF2

    NCBI Reference Sequences (RefSeq)

    Go to the top of the page Help

    NEW Try the new Transcript table

    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_001040434.2 → NP_001035524.2  retrotransposon Gag-like protein 9

      See identical proteins and their annotated locations for NP_001035524.2

      Status: VALIDATED

      Source sequence(s)
      AK220382, AL731548
      Consensus CDS
      CCDS72442.1
      UniProtKB/Swiss-Prot
      Q32KG4, Q5DTY8
      Related
      ENSMUSP00000128287.2, ENSMUST00000165829.4
      Conserved Domains (3) summary
      PHA03247
      Location:787 → 1141
      PHA03247; large tegument protein UL36; Provisional
      pfam05109
      Location:136 → 461
      Herpes_BLLF1; Herpes virus major outer envelope glycoprotein (BLLF1)
      cl29674
      Location:1169 → 1260
      Retrotrans_gag; Retrotransposon gag protein

    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_000086.8 Reference GRCm39 C57BL/6J

      Range
      141841655..141888326
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_011247808.3 → XP_011246110.1  retrotransposon Gag-like protein 9 isoform X1

      See identical proteins and their annotated locations for XP_011246110.1

      UniProtKB/Swiss-Prot
      Q32KG4, Q5DTY8
      Conserved Domains (3) summary
      PHA03247
      Location:787 → 1141
      PHA03247; large tegument protein UL36; Provisional
      pfam05109
      Location:136 → 461
      Herpes_BLLF1; Herpes virus major outer envelope glycoprotein (BLLF1)
      cl29674
      Location:1169 → 1260
      Retrotrans_gag; Retrotransposon gag protein

    2. XM_011247807.3 → XP_011246109.1  retrotransposon Gag-like protein 9 isoform X1

      See identical proteins and their annotated locations for XP_011246109.1

      UniProtKB/Swiss-Prot
      Q32KG4, Q5DTY8
      Conserved Domains (3) summary
      PHA03247
      Location:787 → 1141
      PHA03247; large tegument protein UL36; Provisional
      pfam05109
      Location:136 → 461
      Herpes_BLLF1; Herpes virus major outer envelope glycoprotein (BLLF1)
      cl29674
      Location:1169 → 1260
      Retrotrans_gag; Retrotransposon gag protein
    Nucleotide Protein Strain
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q32KG4.1 GenPept UniProtKB/Swiss-Prot:Q32KG4

    Gene LinkOut

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

    Molecular Biology Databases
    Research Materials
    Tools
    Miscellaneous