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    RTL3 retrotransposon Gag like 3 [ Homo sapiens (human) ]

    Gene ID: 203430, updated on 5-Mar-2024

    Summary

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    Official Symbol
    RTL3provided by HGNC
    Official Full Name
    retrotransposon Gag like 3provided by HGNC
    Primary source
    HGNC:HGNC:22997
    See related
    Ensembl:ENSG00000179300 AllianceGenome:HGNC:22997
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    Mar3; ZHC5; Mart3; SIRH9; ZCCHC5
    Summary
    This gene is a member of a family of gag-related retrotransposon genes. These genes appear to have lost the ability to retrotranspose; however, their open reading frames have remained intact, which may indicate that these genes have acquired new functions in the cell. [provided by RefSeq, Nov 2009]
    Expression
    Low expression observed in reference dataset See more
    Orthologs
    mouse all
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    Genomic context

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    See RTL3 in Genome Data Viewer
    Location:
    Xq21.1
    Exon count:
    2
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) X NC_000023.11 (78656068..78659328, complement)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) X NC_060947.1 (77092886..77096144, complement)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) X NC_000023.10 (77911565..77914825, complement)

    Chromosome X - NC_000023.11Genomic Context describing neighboring genes Neighboring gene high mobility group nucleosome binding domain 1 pseudogene 34 Neighboring gene UBE2V1 pseudogene 7 Neighboring gene uncharacterized LOC107985670 Neighboring gene phosphoribosyl pyrophosphate amidotransferase pseudogene 2 Neighboring gene lysophosphatidic acid receptor 4

    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. 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. The DNA sequence of the human X chromosome. Ross MT, et al. Nature, 2005 Mar 17. PMID 15772651, Free PMC Article
    4. Complete sequencing and characterization of 21,243 full-length human cDNAs. Ota T, et al. Nat Genet, 2004 Jan. PMID 14702039
    5. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. Strausberg RL, et al. Proc Natl Acad Sci U S A, 2002 Dec 24. PMID 12477932, Free PMC Article

    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)

    Genotypes

    General gene information

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    Markers

    Homology

    Clone Names

    • FLJ38865

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables nucleic acid binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables zinc ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    located_in nucleus IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

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    Preferred Names
    retrotransposon Gag-like protein 3
    Names
    Sushi-Ichi retrotransposon homolog 9
    mammalian retrotransposon-derived 3
    zinc finger CCHC domain-containing protein 5
    zinc finger CCHC-type containing 5
    zinc finger, CCHC domain containing 5

    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.

    Genomic

    1. NG_015973.1 RefSeqGene

      Range
      5001..8261
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_152694.3 → NP_689907.1  retrotransposon Gag-like protein 3

      See identical proteins and their annotated locations for NP_689907.1

      Status: REVIEWED

      Source sequence(s)
      AI091777, AK096184, AL662885
      Consensus CDS
      CCDS14440.1
      UniProtKB/Swiss-Prot
      B2RMZ0, Q5JQE9, Q8N8U3
      Related
      ENSP00000316794.1, ENST00000321110.2
      Conserved Domains (3) summary
      PHA03160
      Location:31 → 161
      PHA03160; hypothetical protein; Provisional
      pfam00098
      Location:443 → 459
      zf-CCHC; Zinc knuckle
      pfam16297
      Location:237 → 316
      DUF4939; Domain of unknown function (DUF4939)

    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_000023.11 Reference GRCh38.p14 Primary Assembly

      Range
      78656068..78659328 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060947.1 Alternate T2T-CHM13v2.0

      Range
      77092886..77096144 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q8N8U3.1 GenPept UniProtKB/Swiss-Prot:Q8N8U3

    Gene LinkOut

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

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