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

Gene ID: 57529, updated on 17-Sep-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
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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: HPA RNA-seq normal tissues 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. 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 (15) 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)

Genotypes

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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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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