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Aliases for RTL1 Gene

Aliases for RTL1 Gene

  • Retrotransposon Gag Like 1 2 3
  • Retrotransposon-Like 1 2 3 5
  • Mammalian Retrotransposon Derived Protein 1 3 4
  • Retrotransposon-Derived Protein PEG11 3 4
  • Sushi-Ichi Retrotransposon Homolog 2 2 3
  • Paternally Expressed Gene 11 Protein 3 4
  • Mammalian Retrotransposon-Derived 1 2 3
  • Paternally Expressed 11 2 3
  • MART1 3 4
  • PEG11 3 4
  • Mar1 3 4
  • Retrotransposon-Like Protein 1 3
  • SIRH2 3
  • HUR1 3

External Ids for RTL1 Gene

Previous GeneCards Identifiers for RTL1 Gene

  • GC14M100417
  • GC14M101347
  • GC14M081528

Summaries for RTL1 Gene

Entrez Gene Summary for RTL1 Gene

  • This gene is a retrotransposon-derived, paternally expressed imprinted gene that is highly expressed at the late fetal stage in both the fetus and placenta. It has an overlapping maternally expressed antisense transcript, which contains several microRNAs targeting the transcripts of this gene through an RNA interference (RNAi) mechanism. This gene is essential for maintenance of the fetal capillaries. [provided by RefSeq, Jul 2009]

GeneCards Summary for RTL1 Gene

RTL1 (Retrotransposon Gag Like 1) is a Protein Coding gene. Diseases associated with RTL1 include Chromosome 15Q24 Deletion Syndrome and Paternal 14Q32.2 Hypomethylation Syndrome.

UniProtKB/Swiss-Prot for RTL1 Gene

  • Plays an essential role in capillaries endothelial cells for the maintenance of feto-maternal interface and for development of the placenta.

No data available for CIViC summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for RTL1 Gene

Genomics for RTL1 Gene

Regulatory Elements for RTL1 Gene

Enhancers for RTL1 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
GH14G100819 1.8 FANTOM5 Ensembl ENCODE dbSUPER 10.7 +58.3 58312 13.4 PKNOX1 FOXA2 ATF1 MLX ZFP64 ARID4B DMAP1 ZNF48 YY1 SLC30A9 DLK1 MEG3 MIR493 MIR337 MIR431 MIR127 RTL1 MIR433 MIR136 SNORD112
GH14G100691 1.8 FANTOM5 Ensembl ENCODE dbSUPER 10 +191.4 191431 4.1 FOXA2 MLX ZNF48 GLIS2 FOS SP5 PPARG ZNF623 KAT8 SSRP1 DLK1 MIR493 MIR337 MIR127 MIR431 MIR433 MIR136 RTL1 LINC00523 LOC105370668
GH14G101096 1.1 FANTOM5 ENCODE 14.5 -213.5 -213501 3.2 CTCF SUZ12 JUN ZIC2 RAD21 ZNF335 GLIS2 ZNF366 GATA2 POLR2A RTL1 LOC105370670 MEG9 MIR656 MIR541 MIR412 MIR410 MIR409 MIR369 MIR496
GH14G100486 1.8 FANTOM5 Ensembl ENCODE dbSUPER 8.8 +398.4 398409 0.6 ARID4B SIN3A FEZF1 ZNF2 ZNF48 ZNF143 ZNF263 MXD4 JUNB TSHZ1 ENSG00000247970 ENSG00000259031 MIR337 MIR127 MIR136 MIR433 RTL1 MIR493 MIR431 RN7SKP92
GH14G100416 1.7 FANTOM5 Ensembl ENCODE dbSUPER 8.9 +467.4 467420 2.2 TBP HDGF PKNOX1 SIN3A RAD21 RFX5 ZNF143 RCOR1 FOS CREM WARS WDR25 BEGAIN MIR493 MIR431 MIR433 MIR337 MIR127 RTL1 MIR136
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around RTL1 on UCSC Golden Path with GeneCards custom track

Genomic Location for RTL1 Gene

Chromosome:
14
Start:
100,880,655 bp from pter
End:
100,884,847 bp from pter
Size:
4,193 bases
Orientation:
Minus strand

Genomic View for RTL1 Gene

Genes around RTL1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
RTL1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for RTL1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for RTL1 Gene

Proteins for RTL1 Gene

  • Protein details for RTL1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    A6NKG5-RTL1_HUMAN
    Recommended name:
    Retrotransposon-like protein 1
    Protein Accession:
    A6NKG5
    Secondary Accessions:
    • E9PKS8

    Protein attributes for RTL1 Gene

    Size:
    1358 amino acids
    Molecular mass:
    155048 Da
    Quaternary structure:
    No Data Available
    Miscellaneous:
    • RTL1 is an imprinted gene located in a cluster of imprinted genes on chromosome 14. It is expressed from the paternal chromosome and has an antisense transcript with full complementarity to RTL1, RTL1as, expressed from the maternal chromosome, which acts as a repressor for RTL1. Excessive RTL1 expression and decreased RTL1 expression are relevant to upd(14)pat-like and upd(14)mat-like phenotypes, respectively. Paternal and maternal uniparental disomy for chromosome 14 (upd(14)pat and upd(14)mat) cause distinct phenotypes; Upd(14)pat results in a unique phenotype characterized by facial abnormality, a small, bell-shaped thorax and abdominal wall defects, and upd(14)mat leads to pre- and postnatal growth failure and early onset of puberty.
    • Rtl1 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 RTL1 Gene

Post-translational modifications for RTL1 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for RTL1 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for RTL1 Gene

Domains & Families for RTL1 Gene

Gene Families for RTL1 Gene

Protein Domains for RTL1 Gene

Suggested Antigen Peptide Sequences for RTL1 Gene

Graphical View of Domain Structure for InterPro Entry

genes like me logo Genes that share domains with RTL1: view

No data available for UniProtKB/Swiss-Prot for RTL1 Gene

Function for RTL1 Gene

Molecular function for RTL1 Gene

UniProtKB/Swiss-Prot Function:
Plays an essential role in capillaries endothelial cells for the maintenance of feto-maternal interface and for development of the placenta.
genes like me logo Genes that share phenotypes with RTL1: view

Animal Models for RTL1 Gene

MGI Knock Outs for RTL1:

Animal Model Products

CRISPR Products

Inhibitory RNA Products

Clone Products

No data available for Enzyme Numbers (IUBMB) , Gene Ontology (GO) - Molecular Function , Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for RTL1 Gene

Localization for RTL1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for RTL1 Gene

Membrane; Multi-pass membrane protein.

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 RTL1 gene
Compartment Confidence
nucleus 1

Gene Ontology (GO) - Cellular Components for RTL1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0016020 membrane IEA --
GO:0016021 integral component of membrane IEA --
genes like me logo Genes that share ontologies with RTL1: view

Pathways & Interactions for RTL1 Gene

No Data Available

Interacting Proteins for RTL1 Gene

Gene Ontology (GO) - Biological Process for RTL1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0007275 multicellular organism development IEA --
genes like me logo Genes that share ontologies with RTL1: view

No data available for Pathways by source and SIGNOR curated interactions for RTL1 Gene

Drugs & Compounds for RTL1 Gene

No Compound Related Data Available

Transcripts for RTL1 Gene

mRNA/cDNA for RTL1 Gene

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

Unigene Clusters for RTL1 Gene

Retrotransposon-like 1:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for RTL1 Gene

No ASD Table

Relevant External Links for RTL1 Gene

GeneLoc Exon Structure for
RTL1
ECgene alternative splicing isoforms for
RTL1

Expression for RTL1 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for RTL1 Gene

mRNA differential expression in normal tissues according to GTEx for RTL1 Gene

This gene is overexpressed in Brain - Hypothalamus (x22.6) and Ovary (x4.2).

Protein differential expression in normal tissues from HIPED for RTL1 Gene

This gene is overexpressed in Testis (59.8).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, and MOPED for RTL1 Gene



Protein tissue co-expression partners for RTL1 Gene

NURSA nuclear receptor signaling pathways regulating expression of RTL1 Gene:

RTL1

SOURCE GeneReport for Unigene cluster for RTL1 Gene:

Hs.298602
genes like me logo Genes that share expression patterns with RTL1: view

Primer Products

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA Expression by UniProt/SwissProt , Evidence on tissue expression from TISSUES and Phenotype-based relationships between genes and organs from Gene ORGANizer for RTL1 Gene

Orthologs for RTL1 Gene

This gene was present in the common ancestor of chordates.

Orthologs for RTL1 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia RTL1 34
  • 99.44 (n)
dog
(Canis familiaris)
Mammalia RTL1 34
  • 82.1 (n)
cfa-mir-432 35
  • 75 (a)
OneToOne
cow
(Bos Taurus)
Mammalia RTL1 34
  • 79.52 (n)
bta-mir-433 35
  • 72 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Rtl1 34 16 35
  • 74.35 (n)
lizard
(Anolis carolinensis)
Reptilia RTL1 35
  • 19 (a)
OneToOne
Species where no ortholog for RTL1 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)
  • rat (Rattus norvegicus)
  • 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 RTL1 Gene

ENSEMBL:
Gene Tree for RTL1 (if available)
TreeFam:
Gene Tree for RTL1 (if available)

Paralogs for RTL1 Gene

(3) SIMAP similar genes for RTL1 Gene using alignment to 2 proteins:

genes like me logo Genes that share paralogs with RTL1: view

No data available for Paralogs for RTL1 Gene

Variants for RTL1 Gene

Sequence variations from dbSNP and Humsavar for RTL1 Gene

SNP ID Clin Chr 14 pos Sequence Context AA Info Type
rs1000212566 -- 100,885,599(+) TGATT(C/T)TAACT upstream-variant-2KB
rs1000267233 -- 100,880,894(+) GTGGA(A/T)GTGGA upstream-variant-2KB, reference, missense
rs1000317571 -- 100,881,905(+) GGTGA(A/G)CCTGT nc-transcript-variant, upstream-variant-2KB, reference, missense
rs1002034807 -- 100,883,388(+) TTGCC(A/G)ATCAG downstream-variant-500B, upstream-variant-2KB, reference, synonymous-codon
rs1002381353 -- 100,885,978(+) CTTTG(A/G)AATCT upstream-variant-2KB

Structural Variations from Database of Genomic Variants (DGV) for RTL1 Gene

Variant ID Type Subtype PubMed ID
esv3635518 CNV gain 21293372
nsv509549 CNV insertion 20534489

Variation tolerance for RTL1 Gene

Gene Damage Index Score: 10.99; 92.03% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for RTL1 Gene

Human Gene Mutation Database (HGMD)
RTL1
SNPedia medical, phenotypic, and genealogical associations of SNPs for
RTL1

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for RTL1 Gene

Disorders for RTL1 Gene

MalaCards: The human disease database

(10) MalaCards diseases for RTL1 Gene - From: Orphanet, DISEASES, and GeneCards

- elite association - COSMIC cancer census association via MalaCards
Search RTL1 in MalaCards View complete list of genes associated with diseases

Relevant External Links for RTL1

Genetic Association Database (GAD)
RTL1
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
RTL1
genes like me logo Genes that share disorders with RTL1: view

No data available for UniProtKB/Swiss-Prot and Genatlas for RTL1 Gene

Publications for RTL1 Gene

  1. The imprinted DLK1-MEG3 gene region on chromosome 14q32.2 alters susceptibility to type 1 diabetes. (PMID: 19966805) Wallace C. … Clayton D.G. (Nat. Genet. 2010) 3 46 64
  2. Deletions and epimutations affecting the human 14q32.2 imprinted region in individuals with paternal and maternal upd(14)-like phenotypes. (PMID: 18176563) Kagami M. … Ogata T. (Nat. Genet. 2008) 3 4 64
  3. RNAi-mediated allelic trans-interaction at the imprinted Rtl1/Peg11 locus. (PMID: 15854907) Davis E. … Charlier C. (Curr. Biol. 2005) 2 3 64
  4. A small family of sushi-class retrotransposon-derived genes in mammals and their relation to genomic imprinting. (PMID: 16155747) Youngson N.A. … Ferguson-Smith A.C. (J. Mol. Evol. 2005) 2 3 64
  5. A family of neofunctionalized Ty3/gypsy retrotransposon genes in mammalian genomes. (PMID: 16093683) Brandt J. … Volff J.-N. (Cytogenet. Genome Res. 2005) 3 4 64

Products for RTL1 Gene

Sources for RTL1 Gene

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