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Aliases for RTL1 Gene

Aliases for RTL1 Gene

  • Retrotransposon Gag 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
  • Retrotransposon-Like 1 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 Kagami-Ogata Syndrome and Temple Syndrome. An important paralog of this gene is RTL3.

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.

Additional gene information for RTL1 Gene

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

GeneHancer (GH) Regulatory Elements for RTL1 Gene

Promoters and enhancers for RTL1 Gene
GeneHancer (GH) Identifier GH Type GH
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH14I100883 Enhancer 0.5 ENCODE dbSUPER 550.8 +0.0 14 2.8 ZKSCAN1 GC14P103096 MIR127 MIR136 MIR432 RTL1 MEG3 MIR370 SNORD113-1 SNORD113-2 PPP2R5C
GH14I100819 Promoter/Enhancer 2 FANTOM5 Ensembl ENCODE dbSUPER 10.7 +58.3 58311 13.4 ELF3 PKNOX1 FOXA2 ZSCAN4 NFXL1 ZNF48 RAD21 RFX5 ZNF280A SLC30A9 ENSG00000274884 DLK1 MEG3 MIR493 MIR337 MIR431 RTL1 MIR127 MIR136 MIR433
GH14I100691 Enhancer 1.6 FANTOM5 Ensembl ENCODE dbSUPER 10 +191.4 191430 4.1 FOXA2 MLX ZNF48 ETS1 GLIS2 ZNF143 FOS SP5 REST ZNF623 DLK1 MIR493 MIR337 MIR431 MIR433 MIR127 MIR136 RTL1 LINC00523 LOC105370668
GH14I100486 Enhancer 1.6 FANTOM5 Ensembl ENCODE dbSUPER 8.8 +398.4 398408 0.6 ARID4B SIN3A FEZF1 ZNF2 ZNF48 ZNF143 ATF7 RUNX3 JUNB MXD4 RN7SKP92 MIR337 MIR493 MIR431 RTL1 MIR433 MIR136 MIR127 GC14P103283 GC14M100431
GH14I100657 Enhancer 1.4 Ensembl ENCODE dbSUPER 9.6 +220.3 220336 13.4 ATF1 FOXA2 ARID4B DMAP1 ZNF2 ZNF48 ZNF143 ATF7 FOS RXRA LOC105370667 DLK1 WARS WDR25 BEGAIN MEG9 MIR493 MIR337 MIR127 MIR431
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around RTL1 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the RTL1 gene promoter:

Genomic Locations for RTL1 Gene

Genomic Locations for RTL1 Gene
4,193 bases
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:
    Recommended name:
    Retrotransposon-like protein 1
    Protein Accession:
    Secondary Accessions:
    • E9PKS8

    Protein attributes for RTL1 Gene

    1358 amino acids
    Molecular mass:
    155048 Da
    Quaternary structure:
    No Data Available
    • 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

Human Protein Atlas (HPA):
  • Predicted membrane proteins

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.

Phenotypes From GWAS Catalog for RTL1 Gene

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

Animal Models for RTL1 Gene

MGI Knock Outs for RTL1:

Animal Model 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

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

Subcellular locations from the

Human Protein Atlas (HPA)

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:

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
ECgene alternative splicing isoforms for

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:


SOURCE GeneReport for Unigene cluster for RTL1 Gene:

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

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
(Pan troglodytes)
Mammalia RTL1 33
  • 99.44 (n)
(Canis familiaris)
Mammalia RTL1 33
  • 82.1 (n)
cfa-mir-432 34
  • 75 (a)
(Bos Taurus)
Mammalia RTL1 33
  • 79.52 (n)
bta-mir-433 34
  • 72 (a)
(Mus musculus)
Mammalia Rtl1 16 34 33
  • 74.35 (n)
(Anolis carolinensis)
Reptilia RTL1 34
  • 19 (a)
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

Gene Tree for RTL1 (if available)
Gene Tree for RTL1 (if available)

Paralogs for RTL1 Gene

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

Variants for RTL1 Gene

Sequence variations from dbSNP and Humsavar for RTL1 Gene

SNP ID Clin Chr 14 pos Variation AA Info Type
rs1000212566 -- 100,885,599(-) C/T upstream_transcript_variant
rs1000267233 -- 100,880,894(-) T/A coding_sequence_variant, missense_variant
rs1000317571 -- 100,881,905(-) G/A coding_sequence_variant, missense_variant
rs1002034807 -- 100,883,388(-) A/C/G coding_sequence_variant, missense_variant, synonymous_variant
rs1002381353 -- 100,885,978(-) G/A upstream_transcript_variant

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)

Additional Variant Information for RTL1 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for

SNP Genotyping and Copy Number Assay Products

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

Disorders for RTL1 Gene

MalaCards: The human disease database

(4) MalaCards diseases for RTL1 Gene - From: Orphanet and DISEASES

Disorder Aliases PubMed IDs
kagami-ogata syndrome
  • kos
temple syndrome
  • uniparental disomy, maternal, chromosome 14
chromosome 15q24 deletion syndrome
  • 15q24 microdeletion syndrome
alstrom syndrome
  • alms
- elite association - COSMIC cancer census association via MalaCards
Search RTL1 in MalaCards View complete list of genes associated with diseases

Additional Disease Information for 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 DG (Nature genetics 2010) 3 44 58
  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 (Nature genetics 2008) 3 4 58
  3. RNAi-mediated allelic trans-interaction at the imprinted Rtl1/Peg11 locus. (PMID: 15854907) Davis E … Charlier C (Current biology : CB 2005) 2 3 58
  4. A small family of sushi-class retrotransposon-derived genes in mammals and their relation to genomic imprinting. (PMID: 16155747) Youngson NA … Ferguson-Smith AC (Journal of molecular evolution 2005) 2 3 58
  5. A family of neofunctionalized Ty3/gypsy retrotransposon genes in mammalian genomes. (PMID: 16093683) Brandt J … Volff JN (Cytogenetic and genome research 2005) 3 4 58

Products for RTL1 Gene

Sources for RTL1 Gene

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