RTL9 Gene (Protein Coding)

Retrotransposon Gag Like 9

GC0XP110359
GIFtS:
23
See more...

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
  • Retrotransposon Gag-Like Protein 9 3 4
  • Tumor Antigen BJ-HCC-23 3 4
  • KIAA1318 2 4
  • SIRH10 2 3
  • RGAG1 3 4
  • Tumor Antigen BJHCC23 3
  • MART9 3
  • Mart9 2
  • MAR9 3
  • RTL9 5
  • Mar9 2

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. Diseases associated with RTL9 include Amme Complex and Embryonal Testis Carcinoma. An important paralog of this gene is MUC4.

Additional gene information for RTL9 Gene

No data available for Entrez Gene Summary , CIViC Summary , UniProtKB/Swiss-Prot Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for RTL9 Gene

Genomics for RTL9 Gene

GeneHancer (GH) Regulatory Elements Pubs

Download GeneHancer 2017 data
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
GH0XJ110346 Promoter 0.6 EPDnew 250.4 -11.2 -11240 0.1 REST CTCF ZBTB33 GNG5P2 HSALNG0139521 RTL9 RF00017-8617 AMMECR1 TMEM164
GH0XJ110358 Promoter 0.3 EPDnew 250.7 +0.7 729 0.1 HSALNG0139522 RTL9 AMMECR1
GH0XJ110315 Promoter/Enhancer 1.9 EPDnew Ensembl ENCODE CraniofacialAtlas 11.9 -40.9 -40890 4.8 TBP ZBTB10 FEZF1 MNT IKZF1 SMAD5 HES1 MBD2 POLR2A BHLHE40 LOC105373312 lnc-CHRDL1-2 lnc-RTL9-6 AMMECR1 RTL9 AMMECR1-IT1 TMEM164
GH0XJ110401 Enhancer 1.2 FANTOM5 Ensembl ENCODE 12.2 +45.4 45400 4.6 CEBPA IKZF1 ZNF217 CEBPB REST NFATC3 MAX CTCF ZNF341 TAL1 RTL9 AMMECR1 HSALNG0139522
GH0XJ110176 Enhancer 1.1 Ensembl ENCODE 11.8 -177.9 -177870 6.9 MBD2 BHLHE40 NONO ZNF513 ARNT ZNF395 VEZF1 NBN TAL1 EBF1 RTL9 lnc-RTL9-2 lnc-TMEM164-2 TMEM164
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around RTL9 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for RTL9

Genomic Locations for RTL9 Gene

Latest Assembly
chrX:110,358,101-110,456,334
(GRCh38/hg38)
Size:
98,234 bases
Orientation:
Plus strand

Previous Assembly
chrX:109,602,076-109,699,562
(GRCh37/hg19 by Entrez Gene)
Size:
97,487 bases
Orientation:
Plus strand

chrX:109,602,044-109,699,562
(GRCh37/hg19 by Ensembl)
Size:
97,519 bases
Orientation:
Plus strand

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. Antibodies for research
  2. Protein products for research
  3. Assay products for research

  • 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
    SequenceCaution:
    • Sequence=BAA92556.1; Type=Erroneous initiation; Note=Extended N-terminus.; Evidence={ECO:0000305};
    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.

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

InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for RTL9 Gene

GenScript: Design optimal peptide antigens:
  • cDNA FLJ60962, highly similar to Homo sapiens retrotransposon gag domain containing 1 (RGAG1), mRNA (B4DYG8_HUMAN)
  • Tumor antigen BJ-HCC-23 (RGAG1_HUMAN)
genes like me logo Genes that share domains with RTL9: view

No data available for Graphical View of Domain Structure and UniProtKB/Swiss-Prot for RTL9 Gene

Function for RTL9 Gene

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  1. Animal Models for research
  2. CRISPR products for research
  3. miRNA products for research
  4. Inhibitory RNAs for research
  5. Clone products for research
  6. Cell Lines for research

Phenotypes From GWAS Catalog for RTL9 Gene

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

No data available for Molecular function , Enzyme Numbers (IUBMB) , 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 1
mitochondrion 0

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

PathCards logo

SuperPathways for RTL9 Gene

No Data Available

Interacting Proteins for RTL9 Gene

STRING Interaction Network Preview (showing top 3 STRING interactants - click image to see details)
STRING Interaction Network
Selected Interacting proteins: ENSP00000419786 Q8NET4-RTL9_HUMAN for RTL9 Gene via STRING IID

GPS-Prot Interaction Network for RTL9

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 products for research
No Compound Related Data Available

Transcripts for RTL9 Gene

Products:

  1. CRISPR products for research
  2. miRNA products for research
  3. Inhibitory RNAs for research
  4. Clone products for research

mRNA/cDNA for RTL9 Gene

2 REFSEQ mRNAs :
5 NCBI additional mRNA sequence :
3 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

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

No ASD Table

Relevant External Links for RTL9 Gene

GeneLoc Exon Structure for
RTL9

Expression for RTL9 Gene

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  1. Primer products for research

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for RTL9

No Expression Related Data Available

Primer products for research

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 30 31
  • 99.23 (n)
 OneToOne
Dog
(Canis familiaris)
 Mammalia RGAG1 30 31
  • 82.61 (n)
 OneToOne
Cow
(Bos Taurus)
 Mammalia RGAG1 30 31
  • 81.67 (n)
 OneToOne
Mouse
(Mus musculus)
 Mammalia Rgag1 30 31
  • 79.76 (n)
 OneToOne
Rtl9 17
Rat
(Rattus norvegicus)
 Mammalia LOC100912526 30
  • 79.35 (n)
Lizard
(Anolis carolinensis)
 Reptilia RGAG1 31
  • 31 (a)
 OneToOne
Species where no ortholog for RTL9 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium 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 Vase (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)
Aminode:
Evolutionary constrained regions (ECRs) for RTL9: view image

Paralogs for RTL9 Gene

Paralogs for RTL9 Gene

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

Variants for RTL9 Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for RTL9 Gene

SNP ID Clinical significance and condition Chr 0X pos Variation AA Info Type
rs760284501 Uncertain Significance: not provided 110,452,751(+) G/A
NM_020769.2(RTL9):c.2134G>A (p.Ala712Thr) 		MISSENSE
rs771130284 Uncertain Significance: Spinocerebellar ataxia, X-linked 110,453,979(+) C/T
NM_020769.2(RTL9):c.3362C>T (p.Ser1121Leu) 		MISSENSE
rs35495390 - p.Pro777Ser

dbSNP identifiers (rs#s) for variants without ClinVar clinical significance for RTL9 Gene

All consequence types are included: molecular consequences (e.g. missense, synonymous), and location-based (e.g. intron, upstream).

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

MalaCards: The human disease database

(3) MalaCards diseases for RTL9 Gene - From: COP

Disorder Aliases PubMed IDs
amme complex
  • alport syndrome, mental retardation, midface hypoplasia, and elliptocytosis
embryonal testis carcinoma
  • embryonal carcinoma of testis
non-syndromic x-linked intellectual disability
  • non-specific x-linked mental retardation
- elite association - COSMIC cancer census association via MalaCards
Search RTL9 in MalaCards View complete list of genes associated with diseases

Additional Disease Information for RTL9

Atlas
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
Open Targets Platform
Open Targets Platform
genes like me logo Genes that share disorders with RTL9: view

No data available for 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
  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
  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
  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
  5. Systematic bromodomain protein screens identify homologous recombination and R-loop suppression pathways involved in genome integrity. (PMID: 31753913) Kim JJ … Miller KM (Genes & development 2019) 3

ExternalLinks

View latest publications for RTL9 gene in Mastermind

Products for RTL9 Gene

Sources for RTL9 Gene