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RTL9 Gene(Protein Coding)

Retrotransposon Gag Like 9

GCID:
GC0XP110359
GIFtS:
26
Genes Participants
UDN Logo

Aliases for RTL9 Gene

Aliases for RTL9 Gene

  • Retrotransposon Gag Like 9 2 3 5
  • Retrotransposon Gag Domain-Containing Protein 1 3 4
  • Retrotransposon Gag Domain Containing 1 2 3
  • Sushi-Ichi Retrotransposon Homolog 10 2 3
  • Mammalian Retrotransposon-Derived 9 2 3
  • Tumor Antigen BJ-HCC-23 3 4
  • RGAG1 3 4
  • Retrotransposon Gag-Like Protein 9 3
  • Tumor Antigen BJHCC23 3
  • KIAA1318 4
  • SIRH10 3
  • MART9 3
  • MAR9 3

External Ids for RTL9 Gene

Previous HGNC Symbols for RTL9 Gene

  • RGAG1

Summaries for RTL9 Gene

GeneCards Summary for RTL9 Gene

RTL9 (Retrotransposon Gag Like 9) is a Protein Coding gene.

Additional gene information for RTL9 Gene

No data available for Entrez Gene Summary , CIViC summary , UniProtKB/Swiss-Prot , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for RTL9 Gene

Genomics for RTL9 Gene

Products:

  1. Regulatory Element

GeneHancer (GH) Regulatory Elements for RTL9 Gene

Promoters and enhancers for RTL9 Gene
GeneHancer (GH) Identifier GH Type GH
Score		 GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites		 Gene Targets
GH0XI110315 Promoter/Enhancer 2 EPDnew Ensembl ENCODE 11.9 -41.4 -41413 3.5 SIN3A FEZF1 GLI4 ZNF2 YY1 POLR2B ZNF766 GLIS2 ZNF213 ATF7 LOC105373312 AMMECR1 RTL9 AMMECR1-IT1
GH0XI110402 Enhancer 1.3 FANTOM5 Ensembl ENCODE 12.2 +44.5 44492 3.6 HDGF RAD21 TCF12 GATA2 ZNF366 SCRT2 RCOR1 FOS CREM CEBPB RTL9 GC0XM110384 GC0XP110441 AMMECR1
GH0XI110176 Enhancer 1.1 Ensembl ENCODE 11.8 -178.5 -178472 6.7 HDGF PKNOX1 SMAD1 ARNT NCOA2 TCF12 ZNF766 GATA2 FOS ATF7 RTL9 LOC101928589 GC0XP110194 TMEM164
GH0XI110020 Enhancer 1.1 FANTOM5 Ensembl ENCODE 11.4 -336.5 -336520 2.8 SCRT1 GFI1B CEBPB EBF1 OSR2 ZNF148 GLIS1 PATZ1 IKZF1 SCRT2 RTL9 TMEM164 GC0XP110056
GH0XI110408 Enhancer 1 Ensembl ENCODE 11.6 +51.3 51311 2.6 ATF1 TCF12 SCRT2 FOS ATF7 CREM ZEB2 ZNF592 MEF2D IKZF1 AMMECR1 RTL9 GC0XM110384 GC0XP110441
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around RTL9 on UCSC Golden Path with GeneCards custom track

Genomic Locations for RTL9 Gene

Genomic Locations for RTL9 Gene
chrX:110,358,776-110,456,334
(GRCh38/hg38)
Size:
97,559 bases
Orientation:
Plus strand
chrX:109,602,044-109,699,562
(GRCh37/hg19)

Genomic View for RTL9 Gene

Genes around RTL9 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
RTL9 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for RTL9 Gene
GeneLoc Logo Genomic Neighborhood • Exon Structure • Gene Density

RefSeq DNA sequence for RTL9 Gene

Proteins for RTL9 Gene

Products:

  1. Antibody
  2. Protein
  3. Assay

  • Protein details for RTL9 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q8NET4-RTL9_HUMAN
    Recommended name:
    Retrotransposon Gag-like protein 9
    Protein Accession:
    Q8NET4
    Secondary Accessions:
    • Q9P2M8

    Protein attributes for RTL9 Gene

    Size:
    1388 amino acids
    Molecular mass:
    144280 Da
    Quaternary structure:
    No Data Available
    Miscellaneous:
    • RTL9 is one of at least 11 genes called Mar or Mart related to long terminal repeat retrotransposons. They do not correspond to functional retrotransposons, but rather to neofunctionalized retrotransposons genes.
    SequenceCaution:
    • Sequence=BAA92556.1; Type=Erroneous initiation; Note=Translation N-terminally shortened.; Evidence={ECO:0000305};

neXtProt entry for RTL9 Gene

Post-translational modifications for RTL9 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for RTL9 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for RTL9 Gene

Domains & Families for RTL9 Gene

Gene Families for RTL9 Gene

HGNC:
Human Protein Atlas (HPA):
  • Predicted intracellular proteins

Protein Domains for RTL9 Gene

ProtoNet:

Suggested Antigen Peptide Sequences for RTL9 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

genes like me logo Genes that share domains with RTL9: view

No data available for UniProtKB/Swiss-Prot for RTL9 Gene

Function for RTL9 Gene

Products:

  1. Animal Model
  2. CRISPR
  3. miRNA
  4. Inhibitory RNA
  5. Clone
  6. Cell Line

Phenotypes for RTL9 Gene

GenomeRNAi human phenotypes for RTL9:
genes like me logo Genes that share phenotypes with RTL9: view

Animal Model Products

Inhibitory RNA Products

No data available for Molecular function , Enzyme Numbers (IUBMB) , Phenotypes From GWAS Catalog , Gene Ontology (GO) - Molecular Function , Human Phenotype Ontology , Animal Models , miRNA , Transcription Factor Targets and HOMER Transcription for RTL9 Gene

Localization for RTL9 Gene

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for RTL9 gene
Compartment Confidence
nucleus 2
cytosol 2
mitochondrion 1

No data available for Subcellular locations from UniProtKB/Swiss-Prot , Subcellular locations from the Human Protein Atlas (HPA) and Gene Ontology (GO) - Cellular Components for RTL9 Gene

Pathways & Interactions for RTL9 Gene

SuperPathways for RTL9 Gene

PathCards logo More details on SuperPathways for RTL9
No Data Available

Interacting Proteins for RTL9 Gene

STRING Interaction Network Preview (showing 1 interactants - click image to see details)
http://version10.5.string-db.org/api/image/networkList?limit=0&targetmode=proteins&caller_identity=gene_cards&network_flavor=evidence&identifiers=9606.ENSP00000419786%0d%0a9606.ENSP00000301522%0d%0a
Selected Interacting proteins: Q8NET4-RTL9_HUMAN ENSP00000419786 for RTL9 Gene via IID STRING

Gene Ontology (GO) - Biological Process for RTL9 Gene

None

No data available for Pathways by source and SIGNOR curated interactions for RTL9 Gene

Drugs & Compounds for RTL9 Gene

Products:

  1. Drug
No Compound Related Data Available

Transcripts for RTL9 Gene

Products:

  1. CRISPR
  2. miRNA
  3. Inhibitory RNA
  4. Clone

mRNA/cDNA for RTL9 Gene

(5) REFSEQ mRNAs :
(10) Selected AceView cDNA sequences:
(3) Ensembl transcripts including schematic representations, and UCSC links where relevant :

Inhibitory RNA Products

Alternative Splicing Database (ASD) splice patterns (SP) for RTL9 Gene

No ASD Table

Relevant External Links for RTL9 Gene

GeneLoc Exon Structure for
RTL9
ECgene alternative splicing isoforms for
RTL9

Expression for RTL9 Gene

Products:

  1. Primer

NURSA nuclear receptor signaling pathways regulating expression of RTL9 Gene:

RTL9
No Expression Related Data Available

Primer Products

No data available for mRNA expression in normal human tissues , mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues , Protein differential expression in normal tissues , Protein expression , Protein tissue co-expression partners , mRNA Expression by UniProt/SwissProt , Evidence on tissue expression from TISSUES and Phenotype-based relationships between genes and organs from Gene ORGANizer for RTL9 Gene

Orthologs for RTL9 Gene

This gene was present in the common ancestor of chordates.

Orthologs for RTL9 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
 Mammalia RGAG1 33 34
  • 99.23 (n)
dog
(Canis familiaris)
 Mammalia RGAG1 33 34
  • 82.61 (n)
cow
(Bos Taurus)
 Mammalia RGAG1 33 34
  • 81.67 (n)
mouse
(Mus musculus)
 Mammalia Rgag1 33 34
  • 79.76 (n)
Rtl9 16
rat
(Rattus norvegicus)
 Mammalia LOC100912526 33
  • 79.35 (n)
lizard
(Anolis carolinensis)
 Reptilia RGAG1 34
  • 31 (a)
 OneToOne
Species where no ortholog for RTL9 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • chicken (Gallus gallus)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • fruit fly (Drosophila melanogaster)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • oppossum (Monodelphis domestica)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • platypus (Ornithorhynchus anatinus)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea squirt (Ciona intestinalis)
  • sea squirt (Ciona savignyi)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • tropical clawed frog (Silurana tropicalis)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)
  • zebrafish (Danio rerio)

Evolution for RTL9 Gene

ENSEMBL:
Gene Tree for RTL9 (if available)
TreeFam:
Gene Tree for RTL9 (if available)

Paralogs for RTL9 Gene

No data available for Paralogs for RTL9 Gene

Variants for RTL9 Gene

Sequence variations from dbSNP and Humsavar for RTL9 Gene

SNP ID Clin Chr 0X pos Variation AA Info Type
rs771130284 uncertain-significance, Spinocerebellar ataxia, X-linked 110,453,979(+) C/T coding_sequence_variant, missense_variant
rs1000053110 -- 110,362,214(+) C/G/T genic_upstream_transcript_variant, intron_variant
rs1000103740 -- 110,361,767(+) A/T genic_upstream_transcript_variant, intron_variant
rs1000103882 -- 110,423,688(+) T/G genic_upstream_transcript_variant, intron_variant
rs1000164254 -- 110,445,362(+) A/G intron_variant

Structural Variations from Database of Genomic Variants (DGV) for RTL9 Gene

Variant ID Type Subtype PubMed ID
esv2758884 CNV loss 17122850

Variation tolerance for RTL9 Gene

Residual Variation Intolerance Score: 90.7% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 3.59; 56.22% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for RTL9 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
RTL9

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for RTL9 Gene

Disorders for RTL9 Gene

Additional Disease Information for RTL9

ATLAS of Genetics and Cytogenetics in Oncology and Haematology
ATLAS of Genetics and Cytogenetics in Oncology and Haematology

No disorders were found for RTL9 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for RTL9 Gene

Publications for RTL9 Gene

  1. A family of neofunctionalized Ty3/gypsy retrotransposon genes in mammalian genomes. (PMID: 16093683) Brandt J … Volff JN (Cytogenetic and genome research 2005) 2 3 4 58
  2. 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. (PMID: 10718198) Nagase T … Ohara O (DNA research : an international journal for rapid publication of reports on genes and genomes 2000) 2 3 4 58
  3. Transposable elements as a source of genetic innovation: expression and evolution of a family of retrotransposon-derived neogenes in mammals. (PMID: 15716091) Brandt J … Volff JN (Gene 2005) 2 3 58
  4. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard DS … MGC Project Team (Genome research 2004) 3 4 58
  5. Architecture of the human interactome defines protein communities and disease networks. (PMID: 28514442) Huttlin EL … Harper JW (Nature 2017) 3 58

Products for RTL9 Gene

Sources for RTL9 Gene

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