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Aliases for RTL6 Gene

Aliases for RTL6 Gene

  • Retrotransposon Gag Like 6 2 3 5
  • Leucine Zipper Protein Down-Regulated In Cancer Cells-Like 3 4
  • Leucine Zipper Down-Regulated In Cancer 1 Like 2 3
  • Mammalian Retrotransposon-Derived Protein 6 3 4
  • Sushi-Ichi Retrotransposon Homolog 3 2 3
  • Mammalian Retrotransposon-Derived 6 2 3
  • Protein LDOC1L 3 4
  • LDOC1 Like 2 3
  • LDOC1L 3 4
  • Mart6 3 4
  • Mar6 3 4
  • Retrotransposon Gag-Like Protein 6 3
  • DJ1033E15.2 3
  • SIRH3 3

External Ids for RTL6 Gene

Previous HGNC Symbols for RTL6 Gene

  • LDOC1L

Summaries for RTL6 Gene

GeneCards Summary for RTL6 Gene

RTL6 (Retrotransposon Gag Like 6) is a Protein Coding gene. An important paralog of this gene is RTL5.

Additional gene information for RTL6 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 RTL6 Gene

Genomics for RTL6 Gene

Regulatory Elements for RTL6 Gene

Enhancers for RTL6 Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH22H044454 1.2 FANTOM5 ENCODE dbSUPER 22.9 +42.6 42573 2 ESRRA BATF ZIC2 CTBP1 GATA3 EED RCOR1 FOS RUNX3 CREM RTL6 KIAA1644 GC22P044453 GC22P044472
GH22H044330 1 Ensembl 23.7 +166.7 166676 2 ZNF133 GLI4 ZNF2 GLIS2 KLF7 YY2 TSHZ1 ZNF292 GLIS1 ZNF624 ENSG00000273243 RTL6 PHF21B ENSG00000236079 RPS10P31 NUP50 KIAA1644 ENSG00000273287 FAM118A LOC101927499
GH22H044020 1.7 FANTOM5 Ensembl ENCODE dbSUPER 11.1 +476.6 476588 2 ZNF473 ZSCAN4 INSM2 GLI4 ZEB1 ZNF366 FOS ZNF391 YY2 TSHZ1 ENSG00000261251 LOC100506679 SAMM50 RPL35AP36 RTL6 KIAA1644 PHF21B TTLL1 PARVB GC22M044040
GH22H044448 1.6 FANTOM5 Ensembl ENCODE dbSUPER 10.6 +49.0 49006 2 BATF RAD21 FOS ETV6 RUNX3 IKZF2 CREM SMARCC1 CBFB JUNB RTL6 PARVG GC22P044453 LINC01656
GH22H045289 1.5 Ensembl ENCODE dbSUPER 11.2 -792.6 -792553 1 HDGF PKNOX1 ZNF133 GLI4 ZNF2 GLIS2 ZNF302 ZNF416 ATF7 ZNF548 CDPF1 LINC00899 ENSG00000273243 FAM118A LOC642648 PHF21B RPS10P31 ENSG00000236079 FBLN1 SMC1B
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around RTL6 on UCSC Golden Path with GeneCards custom track

Promoters for RTL6 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000147061 -2 1400 TBP PKNOX1 BMI1 RAD21 EGR1 ELK1 RCOR1 FOS SP3 ZNF362

Genomic Location for RTL6 Gene

Chromosome:
22
Start:
44,492,570 bp from pter
End:
44,498,298 bp from pter
Size:
5,729 bases
Orientation:
Minus strand

Genomic View for RTL6 Gene

Genes around RTL6 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
RTL6 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for RTL6 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for RTL6 Gene

Proteins for RTL6 Gene

  • Protein details for RTL6 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q6ICC9-RTL6_HUMAN
    Recommended name:
    Retrotransposon Gag-like protein 6
    Protein Accession:
    Q6ICC9
    Secondary Accessions:
    • Q6ZTR1

    Protein attributes for RTL6 Gene

    Size:
    239 amino acids
    Molecular mass:
    26154 Da
    Quaternary structure:
    No Data Available
    Miscellaneous:
    • RTL6 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 RTL6 Gene

Post-translational modifications for RTL6 Gene

No Post-translational modifications

Other Protein References for RTL6 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for RTL6 Gene

Domains & Families for RTL6 Gene

Gene Families for RTL6 Gene

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

Protein Domains for RTL6 Gene

InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for RTL6 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

Q6ICC9

UniProtKB/Swiss-Prot:

RTL6_HUMAN :
  • Belongs to the LDOC1 family.
Family:
  • Belongs to the LDOC1 family.
genes like me logo Genes that share domains with RTL6: view

Function for RTL6 Gene

Phenotypes From GWAS Catalog for RTL6 Gene

genes like me logo Genes that share phenotypes with RTL6: view

Animal Model Products

CRISPR Products

Inhibitory RNA Products

Clone Products

  • Applied Biological Materials Clones for RTL6
  • Vectors and viruses for ORF, Lenti, Retro, Adenovirus, AAV, and more

No data available for Molecular function , Enzyme Numbers (IUBMB) , Gene Ontology (GO) - Molecular Function , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for RTL6 Gene

Localization for RTL6 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 RTL6 gene
Compartment Confidence
nucleus 3
cytosol 3

Subcellular locations from the

Human Protein Atlas (HPA)
  • Cytosol (2)
  • Nuclear speckles (2)
See all subcellular structures

No data available for Subcellular locations from UniProtKB/Swiss-Prot and Gene Ontology (GO) - Cellular Components for RTL6 Gene

Pathways & Interactions for RTL6 Gene

No Data Available

Interacting Proteins for RTL6 Gene

Gene Ontology (GO) - Biological Process for RTL6 Gene

None

No data available for Pathways by source and SIGNOR curated interactions for RTL6 Gene

Drugs & Compounds for RTL6 Gene

No Compound Related Data Available

Transcripts for RTL6 Gene

mRNA/cDNA for RTL6 Gene

CRISPR Products

Inhibitory RNA Products

Clone Products

  • Applied Biological Materials Clones for RTL6
  • Vectors and viruses for ORF, Lenti, Retro, Adenovirus, AAV, and more

Alternative Splicing Database (ASD) splice patterns (SP) for RTL6 Gene

No ASD Table

Relevant External Links for RTL6 Gene

GeneLoc Exon Structure for
RTL6
ECgene alternative splicing isoforms for
RTL6

Expression for RTL6 Gene

NURSA nuclear receptor signaling pathways regulating expression of RTL6 Gene:

RTL6

Evidence on tissue expression from TISSUES for RTL6 Gene

  • Nervous system(4.2)
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 and Phenotype-based relationships between genes and organs from Gene ORGANizer for RTL6 Gene

Orthologs for RTL6 Gene

This gene was present in the common ancestor of mammals.

Orthologs for RTL6 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia LDOC1L 33 34
  • 99.02 (n)
dog
(Canis familiaris)
Mammalia LDOC1L 33 34
  • 87.59 (n)
cow
(Bos Taurus)
Mammalia LDOC1L 33 34
  • 85.08 (n)
mouse
(Mus musculus)
Mammalia Ldoc1l 33 34
  • 81.73 (n)
Rtl6 16
rat
(Rattus norvegicus)
Mammalia Ldoc1l 33
  • 81.03 (n)
Species where no ortholog for RTL6 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 RTL6 Gene

ENSEMBL:
Gene Tree for RTL6 (if available)
TreeFam:
Gene Tree for RTL6 (if available)

Paralogs for RTL6 Gene

Paralogs for RTL6 Gene

genes like me logo Genes that share paralogs with RTL6: view

Variants for RTL6 Gene

Sequence variations from dbSNP and Humsavar for RTL6 Gene

SNP ID Clin Chr 22 pos Sequence Context AA Info Type
rs1000635163 -- 44,494,481(+) CTGCT(-/CC)GTGTT utr-variant-3-prime
rs1000640909 -- 44,498,421(+) TGATG(A/C)ACAAA upstream-variant-2KB
rs1000721586 -- 44,492,693(+) ACAAT(C/T)GCTCC utr-variant-3-prime
rs1000742902 -- 44,493,106(+) ATTTA(A/G)TAATC utr-variant-3-prime
rs1001013708 -- 44,499,221(+) CCGCA(A/T)AGTAT upstream-variant-2KB

Structural Variations from Database of Genomic Variants (DGV) for RTL6 Gene

Variant ID Type Subtype PubMed ID
nsv1072217 CNV deletion 25765185
nsv1144977 CNV deletion 24896259

Variation tolerance for RTL6 Gene

Residual Variation Intolerance Score: 25.3% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 0.26; 5.77% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for RTL6 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
RTL6

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for RTL6 Gene

Disorders for RTL6 Gene

Relevant External Links for RTL6

Atlas of Genetics and Cytogenetics in Oncology and Haematology:
RTL6
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
RTL6

No disorders were found for RTL6 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for RTL6 Gene

Publications for RTL6 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 60
  2. 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 60
  3. A genome annotation-driven approach to cloning the human ORFeome. (PMID: 15461802) Collins JE … Dunham I (Genome biology 2004) 3 4 60
  4. Architecture of the human interactome defines protein communities and disease networks. (PMID: 28514442) Huttlin EL … Harper JW (Nature 2017) 3 60
  5. The BioPlex Network: A Systematic Exploration of the Human Interactome. (PMID: 26186194) Huttlin EL … Gygi SP (Cell 2015) 3 60

Products for RTL6 Gene

Sources for RTL6 Gene

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