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Aliases for RTL5 Gene

Aliases for RTL5 Gene

  • Retrotransposon Gag Like 5 2 3 5
  • Retrotransposon Gag Domain-Containing Protein 4 3 4
  • Retrotransposon Gag Domain Containing 4 2 3
  • Sushi-Ichi Retrotransposon Homolog 8 2 3
  • Mammalian Retrotransposon-Derived 5 2 3
  • RGAG4 3 4
  • Retrotransposon Gag-Like Protein 5 3
  • 6430402L03Rik 3
  • KIAA2001 4
  • MART5 3
  • SIRH8 3
  • MAR5 3

External Ids for RTL5 Gene

Previous HGNC Symbols for RTL5 Gene

  • RGAG4

Summaries for RTL5 Gene

GeneCards Summary for RTL5 Gene

RTL5 (Retrotransposon Gag Like 5) is a Protein Coding gene. An important paralog of this gene is RTL6.

Additional gene information for RTL5 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 RTL5 Gene

Genomics for RTL5 Gene

GeneHancer (GH) Regulatory Elements for RTL5 Gene

Promoters and enhancers for RTL5 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
GH0XI072130 Promoter/Enhancer 1.8 EPDnew Ensembl ENCODE 550.8 +0.1 97 1.8 MXI1 ZBTB6 BMI1 E2F1 ZFHX2 GLIS2 ZNF213 POLR2A ZNF366 PATZ1 RTL5 PIN4 PIR46676 NHSL2
GH0XI072271 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE 39.6 -143.0 -143004 6 HDGF SMAD1 ARNT ARID4B SIN3A FEZF1 DMAP1 ZNF2 YY1 POLR2B RPS4X TAF1 NONO LOC100420758 ERCC6L OGT RTL5 LOC392489 ENSG00000229601 TOMM20P4
GH0XI072107 Enhancer 1.5 FANTOM5 Ensembl ENCODE dbSUPER 41.4 +23.9 23906 1.2 KLF17 RAD21 GLIS2 ATF7 EGR2 CEBPB ZNF398 ZEB2 ZNF781 ZFP69B RTL5 FLJ44635 ZMYM3 NHSL2 HDAC8 OGT PIR32507 PIR46676
GH0XI072713 Promoter/Enhancer 1.9 EPDnew Ensembl ENCODE 25.2 -582.5 -582473 2.7 ATF1 ARNT SIN3A GLI4 ZNF2 GLIS2 ZNF548 SP3 RXRA SP5 PHKA1 RTL5 CHIC1 HDAC8 GC0XM072728 ENSG00000273788
GH0XI071181 Enhancer 1.8 FANTOM5 Ensembl ENCODE dbSUPER 19.4 +949.0 949030 3.5 PKNOX1 FOXA2 ARNT ZFP64 ARID4B SIN3A FEZF1 DMAP1 YY1 POLR2B TAF1 NONO MED12 OGT LOC100420758 ENSG00000229601 P2RY4 ARR3 RPS26P11 RTL5
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around RTL5 on UCSC Golden Path with GeneCards custom track

Genomic Locations for RTL5 Gene

Genomic Locations for RTL5 Gene
chrX:72,127,110-72,131,901
(GRCh38/hg38)
Size:
4,792 bases
Orientation:
Minus strand
chrX:71,346,958-71,351,758
(GRCh37/hg19)

Genomic View for RTL5 Gene

Genes around RTL5 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
RTL5 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for RTL5 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for RTL5 Gene

Proteins for RTL5 Gene

  • Protein details for RTL5 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q5HYW3-RTL5_HUMAN
    Recommended name:
    Retrotransposon Gag-like protein 5
    Protein Accession:
    Q5HYW3
    Secondary Accessions:
    • A7E2W7
    • Q8NCM4
    • Q9NPX1

    Protein attributes for RTL5 Gene

    Size:
    569 amino acids
    Molecular mass:
    64711 Da
    Quaternary structure:
    No Data Available
    Miscellaneous:
    • RTL5 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=BAC02710.1; Type=Erroneous initiation; Note=Translation N-terminally shortened.; Evidence={ECO:0000305};

neXtProt entry for RTL5 Gene

Post-translational modifications for RTL5 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for RTL5 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for RTL5 Gene

Domains & Families for RTL5 Gene

Gene Families for RTL5 Gene

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

Protein Domains for RTL5 Gene

InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for RTL5 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

genes like me logo Genes that share domains with RTL5: view

No data available for UniProtKB/Swiss-Prot for RTL5 Gene

Function for RTL5 Gene

Phenotypes for RTL5 Gene

genes like me logo Genes that share phenotypes with RTL5: 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 RTL5 Gene

Localization for RTL5 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 RTL5 gene
Compartment Confidence
nucleus 3
cytosol 3
plasma membrane 1
extracellular 1
cytoskeleton 1
mitochondrion 1
peroxisome 1
golgi apparatus 1

Subcellular locations from the

Human Protein Atlas (HPA)

No data available for Subcellular locations from UniProtKB/Swiss-Prot and Gene Ontology (GO) - Cellular Components for RTL5 Gene

Pathways & Interactions for RTL5 Gene

No Data Available

Interacting Proteins for RTL5 Gene

Gene Ontology (GO) - Biological Process for RTL5 Gene

None

No data available for Pathways by source and SIGNOR curated interactions for RTL5 Gene

Drugs & Compounds for RTL5 Gene

No Compound Related Data Available

Transcripts for RTL5 Gene

mRNA/cDNA for RTL5 Gene

Inhibitory RNA Products

Alternative Splicing Database (ASD) splice patterns (SP) for RTL5 Gene

No ASD Table

Relevant External Links for RTL5 Gene

GeneLoc Exon Structure for
RTL5
ECgene alternative splicing isoforms for
RTL5

Expression for RTL5 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

NURSA nuclear receptor signaling pathways regulating expression of RTL5 Gene:

RTL5
genes like me logo Genes that share expression patterns with RTL5: view

Primer Products

No data available for mRNA expression in normal human tissues , 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 RTL5 Gene

Orthologs for RTL5 Gene

This gene was present in the common ancestor of mammals.

Orthologs for RTL5 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia RGAG4 34 33
  • 97.93 (n)
OneToOne
mouse
(Mus musculus)
Mammalia Rgag4 34 33
  • 82.57 (n)
OneToOne
Rtl5 16
cow
(Bos Taurus)
Mammalia RGAG4 34 33
  • 82.23 (n)
OneToOne
dog
(Canis familiaris)
Mammalia RGAG4 34 33
  • 82.21 (n)
OneToOne
rat
(Rattus norvegicus)
Mammalia LOC100911832 33
  • 81.3 (n)
Species where no ortholog for RTL5 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)
  • lizard (Anolis carolinensis)
  • 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 RTL5 Gene

ENSEMBL:
Gene Tree for RTL5 (if available)
TreeFam:
Gene Tree for RTL5 (if available)

Paralogs for RTL5 Gene

Paralogs for RTL5 Gene

genes like me logo Genes that share paralogs with RTL5: view

Variants for RTL5 Gene

Sequence variations from dbSNP and Humsavar for RTL5 Gene

SNP ID Clin Chr 0X pos Variation AA Info Type
rs1000974492 -- 72,129,395(-) T/C 3_prime_UTR_variant
rs1000991693 -- 72,132,425(-) T/C upstream_transcript_variant
rs1001868107 -- 72,132,458(-) T/C upstream_transcript_variant
rs1002432998 -- 72,132,993(-) G/C upstream_transcript_variant
rs1004099478 -- 72,132,930(-) C/T upstream_transcript_variant

Variation tolerance for RTL5 Gene

Residual Variation Intolerance Score: 90.2% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 4.64; 65.63% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for RTL5 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
RTL5

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot and Structural Variations from Database of Genomic Variants (DGV) for RTL5 Gene

Disorders for RTL5 Gene

No disorders were found for RTL5 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for RTL5 Gene

Publications for RTL5 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. Characterization of size-fractionated cDNA libraries generated by the in vitro recombination-assisted method. (PMID: 12056414) Ohara O … Koseki H (DNA research : an international journal for rapid publication of reports on genes and genomes 2002) 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 DNA sequence of the human X chromosome. (PMID: 15772651) Ross MT … Bentley DR (Nature 2005) 3 4 58
  5. Genome-scale RNAi screen for host factors required for HIV replication. (PMID: 18976975) Zhou H … Espeseth AS (Cell host & microbe 2008) 3 58

Products for RTL5 Gene

Sources for RTL5 Gene

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