Rtl1 (retrotransposon Gaglike 1) - Rat Genome Database

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Gene: Rtl1 (retrotransposon Gaglike 1) Mus musculus
Analyze
Symbol: Rtl1
Name: retrotransposon Gaglike 1
RGD ID: 1316561
MGI Page MGI
Description: Involved in several processes, including placenta development; skeletal muscle satellite cell proliferation; and skeletal muscle tissue development. Acts upstream of or within angiogenesis and labyrinthine layer development. Is active in Z disc. Is expressed in several structures, including diaphragm; genitourinary system; immune system; musculature; and neocortex layer. Orthologous to human RTL1 (retrotransposon Gag like 1).
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: 6430411K18Rik; M; mammalian retrotransposon derived protein 1; Mar; Mart1; Mo; Mor1; paternally expressed gene 11 protein; Peg11; retrotransposon-derived protein PEG11; retrotransposon-like 1; retrotransposon-like protein 1
RGD Orthologs
Human
Rat
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: GRCm39 - Mouse Genome Assembly GRCm39
Position:
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm3912109,531,141 - 109,570,852 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl12109,555,627 - 109,566,764 (-)EnsemblGRCm39 Ensembl
GRCm3812109,564,900 - 109,604,418 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl12109,589,193 - 109,600,330 (-)EnsemblGRCm38mm10GRCm38
MGSCv3712110,828,379 - 110,833,613 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv3612110,037,976 - 110,043,210 (-)NCBIMGSCv36mm8
Celera12110,784,688 - 110,790,104 (-)NCBICelera
Cytogenetic Map12F1NCBI
cM Map1260.38NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Object Symbol
Species
Term
Qualifier
Evidence
With
Reference
Notes
Source
Original Reference(s)
Rtl1MouseKagami-Ogata syndrome  ISORTL1 (Homo sapiens)8554872ClinVar Annotator: match by term: Paternal uniparental disomy 14ClinVarPMID:18176563

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Object Symbol
Species
Term
Qualifier
Evidence
With
Reference
Notes
Source
Original Reference(s)
Rtl1Mouse(-)-alpha-phellandrene decreases expressionISORTL1 (Homo sapiens)6480464alpha phellandrene results in decreased expression of RTL1 mRNACTDPMID:25075043
Rtl1Mouse3,4-methylenedioxymethamphetamine decreases expressionEXP 6480464N-Methyl-3 and 4-methylenedioxyamphetamine results in decreased expression of RTL1 mRNACTDPMID:20188158
Rtl1Mouse3,7-dihydropurine-6-thione decreases expressionISORtl1 (Rattus norvegicus)6480464Mercaptopurine results in decreased expression of RTL1 mRNACTDPMID:23358152
Rtl1Mousealpha-phellandrene decreases expressionISORTL1 (Homo sapiens)6480464alpha phellandrene results in decreased expression of RTL1 mRNACTDPMID:25075043
Rtl1Mousebenzo[a]pyrene decreases expressionEXP 6480464Benzo(a)pyrene results in decreased expression of RTL1 mRNACTDPMID:27195522
Rtl1Mousebenzo[a]pyrene affects methylationISORTL1 (Homo sapiens)6480464Benzo(a)pyrene affects the methylation of RTL1 promoterCTDPMID:27901495
Rtl1Mousebis(2-ethylhexyl) phthalate affects expressionEXP 6480464Diethylhexyl Phthalate affects the expression of RTL1 mRNA and Diethylhexyl Phthalate affects the expression of RTL1 mRNA alternative formCTDPMID:21636974
Rtl1Mousebisphenol A affects expressionEXP 6480464bisphenol A affects the expression of RTL1 mRNA and bisphenol A affects the expression of RTL1 mRNA alternative formCTDPMID:21636974
Rtl1Mousebisphenol A decreases methylationEXP 6480464bisphenol A results in decreased methylation of RTL1 promoterCTDPMID:27312807
Rtl1Mousebisphenol A decreases expressionISORtl1 (Rattus norvegicus)6480464bisphenol A results in decreased expression of RTL1 mRNACTDPMID:25181051
Rtl1Mousechlorpyrifos increases expressionEXP 6480464Chlorpyrifos results in increased expression of RTL1 mRNACTDPMID:37019170
Rtl1Mouseethylparaben decreases expressionISORTL1 (Homo sapiens)6480464ethyl-p-hydroxybenzoate results in decreased expression of RTL1 mRNACTDPMID:37690743
Rtl1Mousemercaptopurine decreases expressionISORtl1 (Rattus norvegicus)6480464Mercaptopurine results in decreased expression of RTL1 mRNACTDPMID:23358152
Rtl1Mouseparaquat decreases expressionISORtl1 (Rattus norvegicus)6480464Paraquat results in decreased expression of RTL1 mRNACTDPMID:32680482
Rtl1Mousephenobarbital increases expressionEXP 6480464Phenobarbital results in increased expression of RTL1 mRNA and Phenobarbital results in increased expression of RTL1 mRNA alternative formCTDPMID:23091169 and PMID:28541575
Rtl1Mousephenobarbital increases expressionISORTL1 (Homo sapiens)6480464Phenobarbital results in increased expression of RTL1 mRNA alternative formCTDPMID:28541575
Rtl1Mousepurine-6-thiol decreases expressionISORtl1 (Rattus norvegicus)6480464Mercaptopurine results in decreased expression of RTL1 mRNACTDPMID:23358152
Rtl1Mousevalproic acid increases methylationISORTL1 (Homo sapiens)6480464Valproic Acid results in increased methylation of RTL1 geneCTDPMID:29154799

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Biological Process
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Cellular Component

  
Object Symbol
Species
Term
Qualifier
Evidence
With
Reference
Notes
Source
Original Reference(s)
Rtl1Mousemembrane located_inIEAUniProtKB-SubCell:SL-01622290270 UniProtGO_REF:0000044
Rtl1MouseZ disc is_active_inIDA 2290270 PMID:32878913MGIPMID:32878913
Rtl1MouseZ disc located_inIDA 2290270 PMID:32878913MGIPMID:32878913

Molecular Function

  
Object Symbol
Species
Term
Qualifier
Evidence
With
Reference
Notes
Source
Original Reference(s)
Rtl1Mousemolecular_function enablesND 2290270 MGIGO_REF:0000015


#
Reference Title
Reference Citation
1. Functional annotation of a full-length mouse cDNA collection. Kawai J, etal., Nature. 2001 Feb 8;409(6821):685-90.
2. Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs. Okazaki Y, etal., Nature. 2002 Dec 5;420(6915):563-73.
3. Mouse MP Annotation Import Pipeline RGD automated import pipeline
4. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
5. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
PMID:8889548   PMID:12796779   PMID:12937418   PMID:15716091   PMID:16093683   PMID:16309881   PMID:16575173   PMID:16575184   PMID:16602821   PMID:17216273   PMID:17901046   PMID:18176565  
PMID:18854139   PMID:19126398   PMID:19194500   PMID:19264764   PMID:19762426   PMID:20610486   PMID:22326222   PMID:23085235   PMID:23139813   PMID:23195472   PMID:26138477   PMID:26487685  
PMID:27904015   PMID:28111885   PMID:28378742   PMID:28934383   PMID:29931170   PMID:31301299   PMID:31686651   PMID:31882978   PMID:32878913   PMID:33484574   PMID:35513363   PMID:35567414  
PMID:37372444   PMID:38521877   PMID:39382697  



Rtl1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm3912109,531,141 - 109,570,852 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl12109,555,627 - 109,566,764 (-)EnsemblGRCm39 Ensembl
GRCm3812109,564,900 - 109,604,418 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl12109,589,193 - 109,600,330 (-)EnsemblGRCm38mm10GRCm38
MGSCv3712110,828,379 - 110,833,613 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv3612110,037,976 - 110,043,210 (-)NCBIMGSCv36mm8
Celera12110,784,688 - 110,790,104 (-)NCBICelera
Cytogenetic Map12F1NCBI
cM Map1260.38NCBI
RTL1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh3814100,879,753 - 100,903,722 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl14100,879,753 - 100,903,722 (-)EnsemblGRCh38hg38GRCh38
GRCh3714101,346,090 - 101,370,059 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 3614100,416,802 - 100,420,878 (-)NCBINCBI36Build 36hg18NCBI36
Celera1481,400,811 - 81,405,006 (-)NCBICelera
Cytogenetic Map14q32.2-q32.31NCBI
HuRef1481,528,723 - 81,532,918 (-)NCBIHuRef
CHM1_114101,285,181 - 101,289,375 (-)NCBICHM1_1
T2T-CHM13v2.01495,115,189 - 95,139,155 (-)NCBIT2T-CHM13v2.0
Rtl1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr86134,325,231 - 134,335,780 (-)NCBIGRCr8
mRatBN7.26128,543,904 - 128,549,384 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl6128,543,939 - 128,549,182 (-)EnsemblmRatBN7.2 Ensembl
Rnor_6.06133,710,207 - 133,721,191 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl6133,711,154 - 133,716,847 (-)NCBIRnor6.0rn6Rnor6.0
Cytogenetic Map6q32NCBI
Rtl1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_004955538176,998 - 181,184 (-)EnsemblChiLan1.0
ChiLan1.0NW_004955538177,078 - 181,557 (-)NCBIChiLan1.0ChiLan1.0
RTL1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v215102,031,676 - 102,058,137 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan114101,246,821 - 101,262,055 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v01481,498,463 - 81,529,551 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.114100,811,749 - 100,816,359 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl14100,812,227 - 100,816,306 (-)Ensemblpanpan1.1panPan2
RTL1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1869,102,081 - 69,126,209 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl869,102,644 - 69,106,687 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha868,619,982 - 68,646,853 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0869,385,732 - 69,412,597 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl869,386,134 - 69,390,177 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1869,047,435 - 69,074,288 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0869,113,293 - 69,140,165 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0869,511,471 - 69,534,272 (-)NCBIUU_Cfam_GSD_1.0
Rtl1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_0244086405,411,964 - 5,434,210 (+)NCBIHiC_Itri_2
SpeTri2.0NW_0049366044,648,928 - 4,655,418 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
RTL1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl7121,707,122 - 121,711,414 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.17121,706,955 - 121,720,472 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.27132,097,039 - 132,100,222 (-)NCBISscrofa10.2Sscrofa10.2susScr3
RTL1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12478,840,599 - 78,865,282 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl2478,842,440 - 78,846,519 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366605365,999,877 - 66,028,159 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Rtl1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046247343,219,270 - 3,227,154 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

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Variants in Rtl1
197 total Variants

Predicted Target Of
Summary Value
Count of predictions:355
Count of miRNA genes:277
Interacting mature miRNAs:297
Transcripts:ENSMUST00000149046
Prediction methods:Miranda, Rnahybrid
Result types:miRGate_prediction

The detailed report is available here: Full Report CSV TAB Printer

miRNA Target Status data imported from miRGate (http://mirgate.bioinfo.cnio.es/).
For more information about miRGate, see PMID:25858286 or access the full paper here.


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The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD ID
Symbol
Name
LOD
P Value
Trait
Sub Trait
Chr
Start
Stop
Species
39128213Lwq23_mliver weight QTL 10 (mouse)1280956708113383533Mouse
1300883Ath21_matherosclerosis 21 (mouse)Not determined1285961579119961683Mouse
12910532Nrq10a_mnoise-induced hearing loss resistant QTL 10a (mouse)1292750025120092757Mouse
12910533Nrq10_mnoise-induced hearing loss resistant QTL 10 (mouse)1292750025120092757Mouse
1357463Vtbt14_mvertebral trabecular bone trait 14 (mouse)Not determined1292936097120092757Mouse
1301269Sluc12_msusceptibility to lung cancer 12 (mouse)Not determined1296860337120092757Mouse
4142007Chlq17_mcirculating hormone level QTL 17 (mouse)Not determined1288052874120092757Mouse
4142002Tbqt3_mtibia bone quality traits 3 (mouse)Not determined1235285496109936243Mouse
11039526Ccc1_mcolitis susceptibility in the Collaborative Cross 1 (mouse)1293528334111028223Mouse
4141297Plyid_mPolymeric IgA dominance (mouse)Not determined109183385115885122Mouse

1 to 10 of 30 rows






Ensembl Acc Id: ENSMUST00000149046   ⟹   ENSMUSP00000115957
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl12109,555,627 - 109,566,764 (-)Ensembl
GRCm38.p6 Ensembl12109,589,193 - 109,600,330 (-)Ensembl
RefSeq Acc Id: NM_184109   ⟹   NP_908998
RefSeq Status: VALIDATED
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm3912109,555,627 - 109,566,764 (-)NCBI
GRCm3812109,589,193 - 109,600,330 (-)NCBI
MGSCv3712110,828,379 - 110,833,613 (-)RGD
Celera12110,784,688 - 110,790,104 (-)RGD
cM Map12 ENTREZGENE
Sequence:
RefSeq Acc Id: XM_030246797   ⟹   XP_030102657
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm3912109,531,141 - 109,570,852 (-)NCBI
GRCm3812109,564,900 - 109,604,418 (-)NCBI
Sequence:
Protein RefSeqs NP_908998 (Get FASTA)   NCBI Sequence Viewer  
  XP_030102657 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein ACF20046 (Get FASTA)   NCBI Sequence Viewer  
  ACF20051 (Get FASTA)   NCBI Sequence Viewer  
  DAA01153 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSMUSP00000115957
  ENSMUSP00000115957.3
GenBank Protein Q7M732 (Get FASTA)   NCBI Sequence Viewer  
RefSeq Acc Id: NP_908998   ⟸   NM_184109
- UniProtKB: Q7M732 (UniProtKB/Swiss-Prot),   B4YB44 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_030102657   ⟸   XM_030246797
- Peptide Label: isoform X1
- UniProtKB: Q7M732 (UniProtKB/Swiss-Prot),   B4YB44 (UniProtKB/TrEMBL)
Ensembl Acc Id: ENSMUSP00000115957   ⟸   ENSMUST00000149046
Name Modeler Protein Id AA Range Protein Structure
AF-Q7M732-F1-model_v2 AlphaFold Q7M732 1-1744 view protein structure

RGD ID:8679242
Promoter ID:EPDNEW_M17652
Type:single initiation site
Name:Rtl1_1
Description:Mus musculus retrotransposon Gaglike 1 , mRNA.
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm3812109,600,341 - 109,600,401EPDNEW
RGD ID:6823377
Promoter ID:MM_KWN:12722
Type:CpG-Island
SO ACC ID:SO:0000170
Source:MPROMDB
Tissues & Cell Lines:Brain,   MEF_B4,   MEF_B6
Transcripts:NM_184109
Position:
Mouse AssemblyChrPosition (strand)Source
MGSCv3612110,829,071 - 110,834,402 (-)MPROMDB
RGD ID:6823171
Promoter ID:MM_KWN:12723
Type:Non-CpG
SO ACC ID:SO:0000170
Source:MPROMDB
Tissues & Cell Lines:Brain,   MEF_B6
Transcripts:NR_002848,   NR_029952
Position:
Mouse AssemblyChrPosition (strand)Source
MGSCv3612110,830,121 - 110,830,902 (+)MPROMDB


1 to 24 of 24 rows
Database
Acc Id
Source(s)
Ensembl Genes ENSMUSG00000006551
  ENSMUSG00000085925 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENSMUST00000149046 ENTREZGENE
  ENSMUST00000149046.4 UniProtKB/Swiss-Prot
Gene3D-CATH 2.40.70.10 UniProtKB/Swiss-Prot
  3.30.70.270 UniProtKB/Swiss-Prot
InterPro DNA/RNA_pol_sf UniProtKB/Swiss-Prot
  DUF4939 UniProtKB/Swiss-Prot
  LDOC1-rel UniProtKB/Swiss-Prot
  Peptidase_aspartic_dom_sf UniProtKB/Swiss-Prot
  Rev_trsase/Diguanyl_cyclase UniProtKB/Swiss-Prot
  RT_RNaseH_2 UniProtKB/Swiss-Prot
KEGG Report mmu:353326 UniProtKB/Swiss-Prot
MGD MGI:2656842 ENTREZGENE
NCBI Gene 353326 ENTREZGENE
PANTHER PTHR15503 UniProtKB/Swiss-Prot
  RETROTRANSPOSON-LIKE PROTEIN 1 UniProtKB/Swiss-Prot
Pfam DUF4939 UniProtKB/Swiss-Prot
  RT_RNaseH_2 UniProtKB/Swiss-Prot
PhenoGen Rtl1 PhenoGen
Superfamily-SCOP SSF50630 UniProtKB/Swiss-Prot
  SSF56672 UniProtKB/Swiss-Prot
UniProt B4YB44 ENTREZGENE, UniProtKB/TrEMBL
  Q7M732 ENTREZGENE, UniProtKB/Swiss-Prot
1 to 24 of 24 rows


Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2017-08-22 Rtl1  retrotransposon Gaglike 1    retrotransposon-like 1  Symbol and/or name change 5135510 APPROVED