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    RTL9 retrotransposon Gag like 9 [ Homo sapiens (human) ]

    Gene ID: 57529, updated on 10-Dec-2024

    Summary

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    Official Symbol
    RTL9provided by HGNC
    Official Full Name
    retrotransposon Gag like 9provided by HGNC
    Primary source
    HGNC:HGNC:29245
    See related
    Ensembl:ENSG00000243978 MIM:300965; AllianceGenome:HGNC:29245
    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
    MAR9; MART9; RGAG1; SIRH10
    Expression
    Restricted expression toward testis (RPKM 5.0) See more
    Orthologs
    mouse all
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    Genomic context

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    See RTL9 in Genome Data Viewer
    Location:
    Xq23
    Exon count:
    6
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) X NC_000023.11 (110358848..110456334)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) X NC_060947.1 (108806758..108904244)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) X NC_000023.10 (109602076..109699562)

    Chromosome X - NC_000023.11Genomic Context describing neighboring genes Neighboring gene AMMECR nuclear protein 1 Neighboring gene ReSE screen-validated silencer GRCh37_chrX:109561279-109561613 Neighboring gene uncharacterized LOC105373312 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29853 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29854 Neighboring gene G protein subunit gamma 5B Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29855 Neighboring gene H3K4me1 hESC enhancer GRCh37_chrX:109661556-109662056 Neighboring gene NANOG hESC enhancer GRCh37_chrX:109670142-109670791 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chrX:109763200-109764196 Neighboring gene cripto, EGF-CFC family member 3 Neighboring gene H3K4me1 hESC enhancer GRCh37_chrX:109844205-109844705 Neighboring gene M6PR pseudogene 1

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: Tissue-specific circular RNA induction during human fetal development
    • Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
    • BioProject: PRJNA270632
    • Publication: PMID 26076956
    • Analysis date: Mon Apr 2 22:54:59 2018

    Bibliography

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    Related articles in PubMed

    1. 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
    2. A family of neofunctionalized Ty3/gypsy retrotransposon genes in mammalian genomes. Brandt J, et al. Cytogenet Genome Res, 2005. PMID 16093683
    3. Interaction proteomics analysis of polycomb proteins defines distinct PRC1 complexes in mammalian cells. Vandamme J, et al. Mol Cell Proteomics, 2011 Apr. PMID 21282530, Free PMC Article
    4. Prediction of the coding sequences of unidentified human genes. XVI. The complete sequences of 150 new cDNA clones from brain which code for large proteins in vitro. Nagase T, et al. DNA Res, 2000 Feb 28. PMID 10718198
    5. BioID-based Identification of Skp Cullin F-box (SCF)β-TrCP1/2 E3 Ligase Substrates. Coyaud E, et al. Mol Cell Proteomics, 2015 Jul. PMID 25900982, Free PMC Article

    See all (16) 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

    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

    • KIAA1318, MGC142230

    General protein information

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    Preferred Names
    retrotransposon Gag-like protein 9
    Names
    Sushi-Ichi retrotransposon homolog 10
    mammalian retrotransposon-derived 9
    retrotransposon gag domain containing 1
    retrotransposon gag domain-containing protein 1
    tumor antigen BJ-HCC-23
    tumor antigen BJHCC23

    NCBI Reference Sequences (RefSeq)

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    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.

    Genomic

    1. NG_016402.3 RefSeqGene

      Range
      5002..102488
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001385449.1 → NP_001372378.1  retrotransposon Gag-like protein 9

      Status: VALIDATED

      Source sequence(s)
      AC000113, AL031319
      Consensus CDS
      CCDS14552.1
      UniProtKB/Swiss-Prot
      Q8NET4, Q9P2M8
      Related
      ENSP00000430395.2, ENST00000520821.6
      Conserved Domains (4) summary
      PRK07003
      Location:793 → 1072
      PRK07003; DNA polymerase III subunit gamma/tau
      PRK10263
      Location:139 → 349
      PRK10263; DNA translocase FtsK; Provisional
      pfam05109
      Location:281 → 641
      Herpes_BLLF1; Herpes virus major outer envelope glycoprotein (BLLF1)
      cl29674
      Location:1189 → 1280
      Retrotrans_gag; Retrotransposon gag protein

    2. NM_020769.2 → NP_065820.1  retrotransposon Gag-like protein 9

      See identical proteins and their annotated locations for NP_065820.1

      Status: VALIDATED

      Source sequence(s)
      AB037739, AC000113
      Consensus CDS
      CCDS14552.1
      UniProtKB/Swiss-Prot
      Q8NET4, Q9P2M8
      Related
      ENSP00000419786.2, ENST00000465301.2
      Conserved Domains (4) summary
      PRK07003
      Location:793 → 1072
      PRK07003; DNA polymerase III subunit gamma/tau
      PRK10263
      Location:139 → 349
      PRK10263; DNA translocase FtsK; Provisional
      pfam05109
      Location:281 → 641
      Herpes_BLLF1; Herpes virus major outer envelope glycoprotein (BLLF1)
      cl29674
      Location:1189 → 1280
      Retrotrans_gag; Retrotransposon gag protein

    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_000023.11 Reference GRCh38.p14 Primary Assembly

      Range
      110358848..110456334
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047442284.1 → XP_047298240.1  retrotransposon Gag-like protein 9 isoform X1

      UniProtKB/Swiss-Prot
      Q8NET4, Q9P2M8

    2. XM_047442283.1 → XP_047298239.1  retrotransposon Gag-like protein 9 isoform X1

      UniProtKB/Swiss-Prot
      Q8NET4, Q9P2M8

    3. XM_017029695.2 → XP_016885184.1  retrotransposon Gag-like protein 9 isoform X1

      UniProtKB/Swiss-Prot
      Q8NET4, Q9P2M8
      Conserved Domains (4) summary
      PRK07003
      Location:793 → 1072
      PRK07003; DNA polymerase III subunit gamma/tau
      PRK10263
      Location:139 → 349
      PRK10263; DNA translocase FtsK; Provisional
      pfam05109
      Location:281 → 641
      Herpes_BLLF1; Herpes virus major outer envelope glycoprotein (BLLF1)
      cl29674
      Location:1189 → 1280
      Retrotrans_gag; Retrotransposon gag protein

    4. XM_047442285.1 → XP_047298241.1  retrotransposon Gag-like protein 9 isoform X1

      UniProtKB/Swiss-Prot
      Q8NET4, Q9P2M8

    5. XM_047442288.1 → XP_047298244.1  retrotransposon Gag-like protein 9 isoform X1

      UniProtKB/Swiss-Prot
      Q8NET4, Q9P2M8

    6. XM_011530999.3 → XP_011529301.1  retrotransposon Gag-like protein 9 isoform X1

      See identical proteins and their annotated locations for XP_011529301.1

      UniProtKB/Swiss-Prot
      Q8NET4, Q9P2M8
      Conserved Domains (4) summary
      PRK07003
      Location:793 → 1072
      PRK07003; DNA polymerase III subunit gamma/tau
      PRK10263
      Location:139 → 349
      PRK10263; DNA translocase FtsK; Provisional
      pfam05109
      Location:281 → 641
      Herpes_BLLF1; Herpes virus major outer envelope glycoprotein (BLLF1)
      cl29674
      Location:1189 → 1280
      Retrotrans_gag; Retrotransposon gag protein

    7. XM_047442286.1 → XP_047298242.1  retrotransposon Gag-like protein 9 isoform X1

      UniProtKB/Swiss-Prot
      Q8NET4, Q9P2M8

    8. XM_047442287.1 → XP_047298243.1  retrotransposon Gag-like protein 9 isoform X1

      UniProtKB/Swiss-Prot
      Q8NET4, Q9P2M8

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060947.1 Alternate T2T-CHM13v2.0

      Range
      108806758..108904244
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054327457.1 → XP_054183432.1  retrotransposon Gag-like protein 9 isoform X1

      UniProtKB/Swiss-Prot
      Q8NET4, Q9P2M8

    2. XM_054327456.1 → XP_054183431.1  retrotransposon Gag-like protein 9 isoform X1

      UniProtKB/Swiss-Prot
      Q8NET4, Q9P2M8

    3. XM_054327461.1 → XP_054183436.1  retrotransposon Gag-like protein 9 isoform X1

      UniProtKB/Swiss-Prot
      Q8NET4, Q9P2M8

    4. XM_054327458.1 → XP_054183433.1  retrotransposon Gag-like protein 9 isoform X1

      UniProtKB/Swiss-Prot
      Q8NET4, Q9P2M8

    5. XM_054327460.1 → XP_054183435.1  retrotransposon Gag-like protein 9 isoform X1

      UniProtKB/Swiss-Prot
      Q8NET4, Q9P2M8

    6. XM_054327455.1 → XP_054183430.1  retrotransposon Gag-like protein 9 isoform X1

      UniProtKB/Swiss-Prot
      Q8NET4, Q9P2M8

    7. XM_054327459.1 → XP_054183434.1  retrotransposon Gag-like protein 9 isoform X1

      UniProtKB/Swiss-Prot
      Q8NET4, Q9P2M8

    8. XM_054327462.1 → XP_054183437.1  retrotransposon Gag-like protein 9 isoform X1

      UniProtKB/Swiss-Prot
      Q8NET4, Q9P2M8
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q8NET4.1 GenPept UniProtKB/Swiss-Prot:Q8NET4

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