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Category   Symbol Source: HGNC EntrezGene Ensembl GeneCards RNA genes CroW21
GIFtS

RTL1 Gene

protein-coding   GIFtS: 39
GCID: GC14M101347

Retrotransposon-Like 1

  See related diseases
at  

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, 10fRNAdb, 12H-InvDB, 13NCBI, 14NONCODE, and/or 15RNAdb)
About This Section

Aliases
Retrotransposon-Like 11 2     MART12 3
PEG112 3 5     Mar12
Mammalian Retrotransposon Derived Protein 12 3     Retrotransposon-Like Protein 12
Paternally Expressed Gene 11 Protein2 3     MAR13
Retrotransposon-Derived Protein PEG112 3     

External Ids:    HGNC: 146651   Entrez Gene: 3880152   Ensembl: ENSG000002546567   OMIM: 6118965   UniProtKB: A6NKG53   

Export aliases for RTL1 gene to outside databases

Previous GC identifers: GC14M100417 GC14M081528


(According to Entrez Gene, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
About This Section

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-like 1) is a protein-coding gene. Diseases associated with RTL1 include maternal uniparental disomy, chromosome 14, and abdominal wall defect.

UniProtKB/Swiss-Prot: RTL1_HUMAN, A6NKG5
Function: Plays an essential role in capillaries endothelial cells for the maintenance of feto-maternal interface
and for development of the placenta (By similarity)




(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 37),
and/or miRBase,
Genomic Views according to UCSC (hg19) and Ensembl (release 73), Regulatory elements and Epigenetics data according to QIAGEN, SABiosciences, and/or SwitchGear Genomics)
About This Section
RefSeq DNA sequence:
NC_000014.8  NT_026437.12  NC_018925.2  
Regulatory elements:
   SABiosciences Regulatory transcription factor binding sites in the RTL1 gene promoter:
         AML1a   Pax-5   Olf-1   MyoD   E4BP4   C/EBPalpha   FOXJ2 (long isoform)   FOXJ2   
         Other transcription factors

Browse SwitchGear Promoter luciferase reporter plasmids
   Search SABiosciences Chromatin IP Primers for RTL1

Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat RTL1


Genomic Location:
Genomic View: UCSC Golden Path with GeneCards custom track

Entrez Gene cytogenetic band: 14q32.2   Ensembl cytogenetic band:  14q32.2   HGNC cytogenetic band: 14q32.2

RTL1 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
RTL1 gene location

GeneLoc information about chromosome 14         GeneLoc Exon Structure

GeneLoc location for GC14M101347:  view genomic region     (about GC identifiers)

Start:
101,346,992 bp from pter      End:
101,351,184 bp from pter
Size:
4,193 bases      Orientation:
minus strand

(According to UniProtKB, HORDE, neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MAXQB RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from EMD Millipore, R&D Systems, GenScript, Enzo Life Sciences, OriGene, Novus Biologicals, Sino Biological, ProSpec, and/or Cloud-Clone Corp.,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Cloud-Clone Corp., Ontologies according to Gene Ontology Consortium 01 Oct 2013 and Entrez Gene, Antibodies by EMD Millipore, R&D Systems, GenScript, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, and/or Cloud-Clone Corp.)
About This Section

UniProtKB/Swiss-Prot: RTL1_HUMAN, A6NKG5 (See protein sequence)
Recommended Name: Retrotransposon-like protein 1  
Size: 1358 amino acids; 155048 Da
Subcellular location: Membrane; Multi-pass membrane protein (Potential)
Miscellaneous: 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
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
Secondary accessions: E9PKS8

Explore the universe of human proteins at neXtProt for RTL1: NX_A6NKG5

Post-translational modifications:

  • View modification sites using PhosphoSitePlus
  • View neXtProt modification sites for NX_A6NKG5

  • RTL1 Protein expression data from MOPED1, PaxDb2 and MAXQB3 : --
    REFSEQ proteins: NP_001128360.1  
    ENSEMBL proteins: 
     ENSP00000435342  

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    Gene Ontology (GO): 1 cellular component term (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0016021integral to membrane IEA--

    RTL1 for ontologies           About GeneDecksing



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    (According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
    About This Section
    2 InterPro protein domains:
     IPR021109 Peptidase_aspartic
     IPR005162 Retrotrans_gag

    Graphical View of Domain Structure for InterPro Entry A6NKG5

    ProtoNet protein and cluster: A6NKG5


    RTL1 for domains           About GeneDecksing


    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, inGenious Targeting Laboratory, genOway,
    bound targets from SABiosciences, miRNA Gene Targets from miRTarBase, shRNA from OriGene, RNAi from EMD Millipore, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, Gene Editing from DNA2.0, Sirion Biotech, Clones from EMD Millipore, OriGene, SwitchGear Genomics, GenScript, Sino Biological, DNA2.0, Vector BioLabs, and Sirion Biotech, Cell Lines from GenScript, LifeMap BioReagents, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Oct 2013 via Entrez Gene.)
    About This Section

    Molecular Function:

         UniProtKB/Swiss-Prot Summary: RTL1_HUMAN, A6NKG5
    Function: Plays an essential role in capillaries endothelial cells for the maintenance of feto-maternal interface
    and for development of the placenta (By similarity)

    Phenotypes:
         4 MGI mutant phenotypes (inferred from 1 allele(MGI details for Rtl1):

     embryogenesis  growth/size  mortality/aging  other 

    RTL1 for phenotypes           About GeneDecksing

    Animal Models:
         MGI mouse knock-out Rtl1tm1Fuis for RTL1

       inGenious Targeting Laboratory - Custom generated mouse model solutions for RTL1 
       inGenious Targeting Laboratory - Custom generated inducible mouse model solutions for RTL1

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    (Pathways according to EMD Millipore, R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Sino Biological, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to SABiosciences, and/or STRING, Interactions according to 1UniProtKB, 2MINT, 3I2D, and/or 4STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Oct 2013 via Entrez Gene).
    About This Section



    Interactions:

        Search SABiosciences Gene Network CentralTM Interacting Genes and Proteins Networks for RTL1

    5 Interacting proteins for RTL1 (A6NKG53) via UniProtKB, MINT, STRING, and/or I2D
    InteractantInteraction Details
    GeneCardExternal ID(s)
    FNBP1LQ5T0N53I2D: score=2 
    CCT4P509913I2D: score=1 
    GSK3BP498413I2D: score=1 
    HSP90AA1P079003I2D: score=1 
    SRPK2P783623I2D: score=1 
    About this table

    Gene Ontology (GO): 1 biological process term (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0007275multicellular organismal development IEA--

    RTL1 for ontologies           About GeneDecksing



    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB, with drugs/clinical trials/news search links to CenterWatch)
    About This Section
    Browse Small Molecules at EMD Millipore
    Browse drugs & compounds from Enzo Life Sciences

    Browse Tocris compounds for RTL1

    Search CenterWatch for drugs/clinical trials and news about RTL1

    (Secondary structures according to fRNAdb,
    GenBank/EMBL/DDBJ Accessions according to
    Unigene (Build 236 Homo sapiens; Apr 25 2013) or GenBank,
    RefSeq according to Entrez Gene,
    DOTS (version 10), and/or AceView, transcript ids from Ensembl with links to UCSC,
    Conferences by KenesGroup, exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
    RNAi Products from EMD Millipore,
    siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN,
    Tagged/untagged cDNA clones from OriGene, SwitchGear Genomics, GenScript, DNA2.0, Vector BioLabs, Sirion Biotech, Primers from OriGene, SABiosciences, and/or QIAGEN )
    About This Section

    REFSEQ mRNAs for RTL1 gene: 
    NM_001134888.2  

    Unigene Cluster for RTL1:

    Retrotransposon-like 1
    Hs.298602  [show with all ESTs]
    Unigene Representative Sequence: NM_001134888
    1 Ensembl transcript including schematic representation, and UCSC links where relevant:
    ENST00000534062(uc010txj.1)
    miRNA
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    Inhib. RNA
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    Clone
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                         Customized lentivirus expression plasmids for stable overexpression of RTL1 
    Primer
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      QIAGEN QuantiTect SYBR Green Assays in human, mouse, rat RTL1
      QIAGEN QuantiFast Probe-based Assays in human, mouse, rat RTL1

    Additional mRNA sequence: BC150617.1 

    2 DOTS entries:

    DT.120754501  DT.97811948 

    2 AceView cDNA sequences:

    AI338830 BF514033 

    GeneLoc Exon Structure


    (RNA expression data according to H-InvDB, NONCODE, miRBase, and RNAdb, Expression images according to data from BioGPS, Illumina Human BodyMap, and CGAP SAGE, Sets of similar genes according to GeneDecks, in vivo and in vitro expression data from LifeMap Discovery™, plus additional links to Genevestigator, and/or SOURCE, and/or BioGPS, and/or UniProtKB,
    PCR Arrays from SABiosciences, Primers from OriGene, SABiosciences, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
    About This Section

    RTL1 expression in normal human tissues (normalized intensities)      RTL1 embryonic expression: see
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: ACGGCCTGCA
    RTL1 Expression
    About this image


    RTL1 expression in embryonic tissues and stem cells    About this table
    Data from LifeMap, the Embryonic Development and Stem Cells Database 
     5/1 selected tissues (see all 1) fully expand
     
     Pancreas (Endocrine System)
             Pancreatic endoderm/endocrine precursor-like cells ( A scalable, suspension protocol...

    SOURCE GeneReport for Unigene cluster: Hs.298602
        SABiosciences Custom PCR Arrays for RTL1
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    QIAGEN QuantiFast Probe-based Assays in human, mouse, rat RTL1
    In Situ
    Assay Products:
     

     
    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for RTL1

    (Orthologs according to 1,2HomoloGene (2older version, for species not in 1newer version), 3euGenes, 4SGD , 5MGI Mar 06 2013, with possible further links to Flybase and/or WormBase, and/or 6Ensembl pan taxonomic compara , Gene Trees according to Ensembl and TreeFam)
    About This Section

    This gene was present in the common ancestor of human and mouse.

    Orthologs for RTL1 gene from 1/5 species (see all 5)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Rtl11 , 5 retrotransposon-like 11, 5 73.33(n)1
    65.56(a)1
      12 (60.38 cM)5
    3533261  NM_184109.11  NP_908998.11 
     1095901695 


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

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
    About This Section
    Paralogs for RTL1 gene
    3 SIMAP similar genes for RTL1 using alignment to 2 protein entries:     RTL1_HUMAN (see all proteins):
    FAM127B    FAM127C    FAM127A

    RTL1 for paralogs           About GeneDecksing



    (SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, 4UniProtKB, and DNA2.0, Linkage Disequilibrium by HapMap, Structural Variations(CNVs/InDels/Inversions) from the Database of Genomic Variants, Mutations from the Human Gene Mutation Database (HGMD) and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers from QIAGEN, Cancer Mutation PCR Arrays and Assays and Copy Number PCR Arrays from SABiosciences)
    About This Section

    10/34 SNPs in RTL1 are shown (see all 34)    About this table     
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 14 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    VAR_0439374
    ----see VAR_0439372 E Q mis40--------
    rs1490839141,2
    --101351689(+) CTTGGC/TTGTGG 1 -- us2k10--------
    rs1421408461,2
    --101351697(+) TGGAGC/TGGGAA 1 -- us2k10--------
    rs19506251,2
    --101351848(+) GGTGTG/TTACAG 1 -- us2k10--------
    rs58110141,2
    C--101351861(+) CTGGG-/TTTTTT 1 -- us2k10--------
    rs588082451,2
    C--101351861(+) CTGGGTT/-TTTTT 1 -- us2k11Minor allele frequency- -:0.50NA 2
    rs1512273241,2
    C--101351893(+) ATAACA/GTACCT 1 -- us2k10--------
    rs1403635211,2
    --101352324(+) CTGACA/GGTCCC 1 -- us2k10--------
    rs1153450931,2
    C,F--101352487(+) TACTGC/ATCTTT 1 -- us2k11Minor allele frequency- A:0.02WA 118
    rs1503055211,2
    --101352584(+) CCTTAC/TGTGAA 1 -- us2k10--------

    HapMap Linkage Disequilibrium report for RTL1 (101346992 - 101351184 bp)

    Structural Variations
         Database of Genomic Variants (DGV) 3 variations for RTL1:    About this table     
    Variant IDTypeSubtypePubMed ID
    nsv509549CNV Insertion20534489
    nsv902241CNV Loss21882294
    nsv902240CNV Loss21882294

    SABiosciences Cancer Mutation PCR Assays
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    (in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Conferences by KenesGroup, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
    About This Section
    OMIM gene information: 611896    OMIM disorders: --

    4 diseases for RTL1:    About MalaCards
    maternal uniparental disomy, chromosome 14    abdominal wall defect    type 1 diabetes    endotheliitis


    RTL1 for disorders           About GeneDecksing

    Genetic Association Database (GAD): RTL1

    Export disorders for RTL1 gene to outside databases

    (in PubMed. Associations of this gene to articles via 1Entrez Gene, 2UniProtKB/Swiss-Prot, 3HGNC, 4GAD, 5PharmGKB, 6HMDB, 7DrugBank, 8UniProtKB/TrEMBL, 9 Novoseek, and/or 10fRNAdb)
    About This Section

    PubMed articles for RTL1 gene integrated from 9 sources:
    (articles sorted by number of sources associating them with RTL1)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. The imprinted DLK1-MEG3 gene region on chromosome 14q 32.2 alters susceptibility to type 1 diabetes. (PubMed id 19966805)1, 4 Wallace C....Clayton D.G. (2010)
    2. Deletions and epimutations affecting the human 14q32.2 imprinted region in individuals with paternal and maternal upd(14)-like phenotypes. (PubMed id 18176563)1, 2 Kagami M.... Ogata T. (2008)
    3. A family of neofunctionalized Ty3/gypsy retrotransposon genes in mammalian genomes. (PubMed id 16093683)1, 2 Brandt J....Volff J.N. (2005)
    4. A small family of sushi-class retrotransposon-derived genes in mammals and their relation to genomic imprinting. (PubMed id 16155747)1, 3 Youngson N.A....Ferguson-Smith A.C. (2005)
    5. RNAi-mediated allelic trans-interaction at the imprinted Rtl1/Peg11 locus. (PubMed id 15854907)1, 3 Davis E....Charlier C. (2005)
    6. The DNA sequence and analysis of human chromosome 14. (PubMed id 12508121)1, 2 Heilig R.... Weissenbach J. (2003)
    7. Imprinted microRNA genes transcribed antisense to a reciprocally imprinted retrotransposon-like gene. (PubMed id 12796779)1, 3 Seitz H....Cavaille J. (2003)
    8. Identification of rtl1, a retrotransposon-derived impr inted gene, as a novel driver of hepatocarcinogenesis. (PubMed id 23593033)1 Riordan J.D....Dupuy A.J. (2013)
    9. A genome-wide association study of type 2 diabetes in Finns detects multiple susceptibility variants. (PubMed id 17463248)4 Scott L.J....Boehnke M. (2007)
    10. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. (PubMed id 12477932)1 Strausberg R.L....Marra M.A. (2002)

    (in PubMed, OMIM, and NCBI Bookshelf)
    About This Section
     ANDOR
    Aliases
    Free Text  

      Query String
    PubMed
    OMIM
    NCBI Bookshelf
      (Note: In FireFox, select the above section and copy using Ctrl-C)

    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
    About This Section
    Entrez Gene: 388015 HGNC: 14665 AceView: LOC388015 Ensembl:ENSG00000254656 euGenes: HUgn388015
    ECgene: RTL1 H-InvDB: RTL1

    (According to HUGE)
    About This Section
      --

    (According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL,
    Wikipedia and/or GeneReviews via UniProtKB/Swiss-Prot)
    About This Section
    NameDescription
    PharmGKB entry for RTL1 Pharmacogenomics, SNPs, Pathways

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
    About This Section
    Patent Information for RTL1 gene:
    Search GeneIP for patents involving RTL1

    GeneCards and IP:
    Japan Patent Office Licenses GeneCards     European Patent Office Licenses GeneCards     Improving the IP Search



    (Antibodies, recombinant proteins, and assays from EMD Millipore, R&D Systems, OriGene, QIAGEN, GenScript, Cell Signaling Technology, SABiosciences, Novus Biologicals, Sino Biological, Enzo Life Sciences, Abcam, ProSpec, Cloud-Clone Corp., Thermo Fisher Scientific, LSBio, Gene Editing from DNA2.0 and Sirion Biotech, Clones from EMD Millipore, OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Sirion Biotech, Cell lines from GenScript, and LifeMap BioReagents, PCR Arrays from SABiosciences, Drugs and/or compounds from EMD Millipore, Tocris Bioscience, and/or Enzo Life Sciences, In Situ Hybridization Assays from
    Advanced Cell Diagnostics, Animal models from inGenious Targeting Laboratory, genOway)
    About This Section

     
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    GeneCards Homepage - Last full update: 23 Oct 2013 - Incrementals: 3 Nov 2013 , 7 Nov 2013 , 23 Jan 2014

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    Category
    (GIFtS: 73)
    transforming growth factor, beta 1
    GIFtS Group
    The GeneCards human gene database gene index: 1 3 5 6 A B C D E F G H I J K L M N O P Q R S T U V W X Y Z 


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