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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
  • Retrotransposon Gag-Like Protein 6 3
  • DJ1033E15.2 3
  • Mart6 3
  • SIRH3 3
  • MART6 4
  • Mar6 3
  • MAR6 4

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

GeneHancer (GH) Regulatory Elements for RTL6 Gene

Promoters and enhancers for RTL6 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
GH22J044496 Promoter/Enhancer 1.8 EPDnew Ensembl ENCODE 661.7 +0.4 374 2.6 PKNOX1 BMI1 RAD21 YY1 ZNF335 ELK1 EGR1 RCOR1 FOS ZNF362 RTL6 GC22M044498 GC22M044500 PIR44780 PIR45096
GH22J044454 Enhancer 1.1 FANTOM5 ENCODE dbSUPER 22.9 +42.6 42572 2.6 NCOA3 ESRRA EBF1 BATF ZIC2 CTBP1 GATA3 EED RCOR1 FOS RTL6 SHISAL1 GC22P044453 GC22P044472
GH22J044330 Enhancer 0.9 Ensembl 23.7 +166.7 166676 2.6 ZNF133 GLI4 ZNF2 GLIS2 KLF7 YY2 TSHZ1 GLIS1 ZNF624 WT1 SHISAL1 ENSG00000273243 RTL6 PHF21B ENSG00000236079 RPS10P31 NUP50 ENSG00000273287 FAM118A LOC101927499
GH22J044020 Enhancer 1.4 FANTOM5 Ensembl ENCODE dbSUPER 11.1 +476.6 476587 2.2 ZNF473 ZSCAN4 INSM2 GLI4 ZEB1 ZNF335 ZNF366 FOS YY2 ZNF662 ENSG00000261251 LOC100506679 SAMM50 RPL35AP36 RTL6 SHISAL1 PHF21B TTLL1 PARVB GC22M044040
GH22J044448 Enhancer 1.4 FANTOM5 Ensembl ENCODE dbSUPER 10.6 +49.0 49006 2.4 SIN3A STAT5A BATF IRF4 FOS ETV6 IKZF2 RUNX3 CREM SMARCC1 RTL6 PARVG GC22P044453 LINC01656
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around RTL6 on UCSC Golden Path with GeneCards custom track

Genomic Locations for RTL6 Gene

Genomic Locations for RTL6 Gene
chr22:44,492,570-44,498,298
(GRCh38/hg38)
Size:
5,729 bases
Orientation:
Minus strand
chr22:44,888,450-44,894,178
(GRCh37/hg19)
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

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

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

Clone Products

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

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

Clone Products

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

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 34 33
  • 99.02 (n)
OneToOne
dog
(Canis familiaris)
Mammalia LDOC1L 34 33
  • 87.59 (n)
OneToOne
cow
(Bos Taurus)
Mammalia LDOC1L 34 33
  • 85.08 (n)
OneToOne
mouse
(Mus musculus)
Mammalia Ldoc1l 34 33
  • 81.73 (n)
OneToOne
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)
Aminode:
Evolutionary constrained regions (ECRs) for RTL6: view image

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 Variation AA Info Type
rs1000635163 -- 44,494,481(-) CC/ 3_prime_UTR_variant
rs1000640909 -- 44,498,421(-) C/A/G/T upstream_transcript_variant
rs1000721586 -- 44,492,693(-) C/T 3_prime_UTR_variant
rs1000742902 -- 44,493,106(-) G/A 3_prime_UTR_variant
rs1001013708 -- 44,499,221(-) A/T upstream_transcript_variant

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)

Additional Variant Information 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

Additional Disease Information for 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 58
  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 58
  3. A genome annotation-driven approach to cloning the human ORFeome. (PMID: 15461802) Collins JE … Dunham I (Genome biology 2004) 3 4 58
  4. Architecture of the human interactome defines protein communities and disease networks. (PMID: 28514442) Huttlin EL … Harper JW (Nature 2017) 3 58
  5. The BioPlex Network: A Systematic Exploration of the Human Interactome. (PMID: 26186194) Huttlin EL … Gygi SP (Cell 2015) 3 58

Products for RTL6 Gene

Sources for RTL6 Gene

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