Rtl6 (retrotransposon Gag like 6) - Rat Genome Database

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Gene: Rtl6 (retrotransposon Gag like 6) Mus musculus
Analyze
Symbol: Rtl6
Name: retrotransposon Gag like 6
RGD ID: 1622987
MGI Page MGI
Description: Is expressed in several structures, including genitourinary system; immune system; lung; nervous system; and sensory organ. Orthologous to human RTL6 (retrotransposon Gag like 6).
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: BC058638; gag-like protein; Ldo; Ldoc1l; leucine zipper, down-regulated in cancer 1-like; Ma; mammalian retrotransposon-derived protein 6; Mar; Mar6; Mart6; MGC73499; retrotransposon Gag-like protein 6
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
GRCm391584,437,599 - 84,442,024 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1584,437,599 - 84,442,024 (-)EnsemblGRCm39 Ensembl
GRCm381584,553,398 - 84,557,823 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1584,553,398 - 84,557,823 (-)EnsemblGRCm38mm10GRCm38
MGSCv371584,383,828 - 84,388,253 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361584,381,165 - 84,385,549 (-)NCBIMGSCv36mm8
Celera1586,686,561 - 86,690,981 (-)NCBICelera
Cytogenetic Map15E2NCBI
cM Map1539.88NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component

Molecular Function

Phenotype Annotations     Click to see Annotation Detail View

Mammalian Phenotype
References

References - curated
# Reference Title Reference Citation
1. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:8889548   PMID:10349636   PMID:11042159   PMID:11076861   PMID:11217851   PMID:12466851   PMID:12477932   PMID:15716091   PMID:16093683   PMID:16141072   PMID:16141073   PMID:16155747  
PMID:21267068   PMID:34321999   PMID:36162816   PMID:37834332  


Genomics

Comparative Map Data
Rtl6
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391584,437,599 - 84,442,024 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1584,437,599 - 84,442,024 (-)EnsemblGRCm39 Ensembl
GRCm381584,553,398 - 84,557,823 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1584,553,398 - 84,557,823 (-)EnsemblGRCm38mm10GRCm38
MGSCv371584,383,828 - 84,388,253 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361584,381,165 - 84,385,549 (-)NCBIMGSCv36mm8
Celera1586,686,561 - 86,690,981 (-)NCBICelera
Cytogenetic Map15E2NCBI
cM Map1539.88NCBI
RTL6
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh382244,492,583 - 44,498,233 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl2244,492,583 - 44,498,233 (-)EnsemblGRCh38hg38GRCh38
GRCh372244,888,463 - 44,894,113 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 362243,267,114 - 43,272,669 (-)NCBINCBI36Build 36hg18NCBI36
Build 342243,208,986 - 43,214,542NCBI
Celera2228,800,351 - 28,805,906 (-)NCBICelera
Cytogenetic Map22q13.31NCBI
HuRef2227,837,944 - 27,843,466 (-)NCBIHuRef
CHM1_12244,847,172 - 44,852,725 (-)NCBICHM1_1
T2T-CHM13v2.02244,976,418 - 44,982,051 (-)NCBIT2T-CHM13v2.0
Rtl6
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr87117,564,780 - 117,569,865 (-)NCBIGRCr8
mRatBN7.27115,684,812 - 115,689,897 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl7115,684,739 - 115,690,052 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx7117,434,119 - 117,439,204 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.07119,659,837 - 119,664,922 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.07119,629,291 - 119,634,376 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.07125,461,410 - 125,466,522 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl7125,465,117 - 125,465,848 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.07125,191,747 - 125,196,864 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.47122,569,018 - 122,570,166 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.17122,540,659 - 122,624,694 (-)NCBI
Celera7111,986,405 - 111,990,859 (-)NCBICelera
Cytogenetic Map7q34NCBI
Rtl6
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495541329,242,588 - 29,243,307 (-)EnsemblChiLan1.0
ChiLan1.0NW_00495541329,238,719 - 29,244,112 (-)NCBIChiLan1.0ChiLan1.0
RTL6
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v22354,330,081 - 54,335,831 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan12257,022,492 - 57,028,248 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v02225,390,101 - 25,395,691 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.12243,575,888 - 43,581,070 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl2243,580,096 - 43,580,815 (-)Ensemblpanpan1.1panPan2
RTL6
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11021,316,145 - 21,317,422 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1021,316,309 - 21,317,028 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha1021,257,571 - 21,262,791 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.01022,064,550 - 22,069,769 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl1022,064,106 - 22,069,760 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.11021,783,717 - 21,788,929 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.01022,105,388 - 22,106,652 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.01022,278,331 - 22,283,547 (+)NCBIUU_Cfam_GSD_1.0
Rtl6
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_0244049455,011,671 - 5,016,538 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049367181,963,636 - 1,968,484 (-)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049367181,963,627 - 1,968,494 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
RTL6
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl54,649,183 - 4,655,205 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.154,649,137 - 4,654,898 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.252,004,254 - 2,009,795 (+)NCBISscrofa10.2Sscrofa10.2susScr3
RTL6
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11926,976,277 - 26,981,092 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl1926,979,791 - 26,980,510 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366604598,417,894 - 98,423,646 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Rtl6
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046247524,815,450 - 4,816,172 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046247524,814,643 - 4,820,080 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Rtl6
136 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:1055
Count of miRNA genes:608
Interacting mature miRNAs:721
Transcripts:ENSMUST00000069476
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.


QTLs in Region (GRCm39)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1300800Ses3_msalmonella enteritidis susceptibility 3 (mouse)Not determined155711700591117153Mouse
1300851Heal4_mwound healing/regeneration 4 (mouse)Not determined1577527592104073951Mouse
1300627Sluc26_msusceptibility to lung cancer 26 (mouse)Not determined1570345653104073951Mouse
1300648Dbsty4_mdiabesity 4 (mouse)Not determined1570349271104073951Mouse
1300726Pitm4_mprion incubation time 4 (mouse)Not determined1570349271104073951Mouse
1301119Drb7_mdopamine receptor binding 7 (mouse)Not determined156533657899341028Mouse
1301171Brm2_mbrachyury modifier 2 (mouse)Not determined156552537699525499Mouse
1301284Cosz3_mcocaine seizure 3 (mouse)Not determined1580313634104073951Mouse
1300974Pgia9_mproteoglycan induced arthritis 9 (mouse)Not determined1580884933104073951Mouse
1301708Cocrb14_mcocaine related behavior 14 (mouse)Not determined155180651585806651Mouse
1301472Pain1_mpain 1 (mouse)Not determined157532084690813185Mouse
1301601Faq9_mfluctuating asymmetry QTL 9 (mouse)Not determined156316390397163995Mouse
1302197Bhr2_mbronchial hyperresponsiveness 2 (mouse)Not determined1564306334103425899Mouse
1302074Bmd4_mbone mineral density 4 (mouse)Not determined1556186708103425899Mouse
1302080Szs13_mseizure susceptibility 13 (mouse)Not determined155168583285694449Mouse
1357407Pfat4_mpredicted fat percentage 4 (mouse)8.6Body fat amountpredicted fat percentage155711700591117153Mouse
1357526Hyplip2_mhyperlipidemia 2 (mouse)Not determined1512402203102896555Mouse
1357894Epfpq3_mepididymal fat percentage QTL 3 (mouse)Not determined1578601103102901704Mouse
1558985Eae32_mexperimental allergic encephalomyelitis susceptibility 32 (mouse)Not determined1532578416103425899Mouse
4141135Cia35_mcollagen induced arthritis 35 (mouse)Not determined156481182698811946Mouse
4141511Gdcr1_mglycerolphosphate dehydrogenase regulator 1 (mouse)Not determined82615474104073951Mouse
4141897Imrfq2_mimmune response to Factor IX QTL 2 (mouse)Not determined79908940104073951Mouse
4141902Cia37_mcollagen induced arthritis 37 (mouse)Not determined1580884933104073951Mouse
4141921Pstc3_mperiosteal circumference 3 (mouse)Not determined1567270698101270847Mouse
4142060W3q6_mweight 3 weeks QTL 6 (mouse)Not determined78601103102901704Mouse
4142198Hbtq_mhabituation QTL (mouse)Not determined155116070885160833Mouse
10402490Dipa5_mdrug induced psychomotor activation 5 (mouse)Not determined1579163411104073951Mouse
10412067Pain2_mpain 2 (mouse)Not determined155164533985645626Mouse
10045637Heal27_mwound healing/regeneration 29 (mouse)Not determined155141836185418511Mouse
11532732Pitm5_mprion incubation time 5 (mouse)158296406187054388Mouse
12880411V125Dq11_mvitamin D active form serum level QTL 11 (mouse)1578897881104073951Mouse
13504731Cath5_mcarotid atherosclerosis 5 (mouse)155478912988789129Mouse
12880420V25Dq8_mvitamin D inactive form serum level QTL 8 (mouse)156158420095584200Mouse
12791003Aath8_maortic arch atherosclerosis 8 (mouse)1573430144104073951Mouse
27226777Tibl8_mtibia length 8, 5 week (mouse)15692948184584201Mouse
27095936Ulnl4_mulna length 4, 5 week (mouse)155676339687684201Mouse
14928306Manh79_mmandible shape 79 (mouse)1578847557104073951Mouse
14747011Mancz13_mmandible centroid size 13 (mouse)1572382669104073951Mouse
38501067Tip3_mtuberculosis immunophenotype 3, IFN-g level (mouse)155356339689584203Mouse
26884397Humsd5_mhumerus midshaft diameter 5, 10 week (mouse)154836339698397881Mouse
26884399Humsd1_mhumerus midshaft diameter 1, 5 week (mouse)1548363396101708435Mouse
26884402Cvht9_mcranial vault height 9, 16 week (mouse)154216339695497881Mouse
26884425Cvht2_mcranial vault height 2, 5 week (mouse)1528800146102008435Mouse
26884442Sklq6_mskull length QTL 6, 5 week (mouse)156129481100797881Mouse
27226729Tibmd2_mtibia midshaft diameter 2, 5 week (mouse)153800024486684201Mouse
27226734Tibmd5_mtibia midshaft diameter 5, 10 week (mouse)15612948186684201Mouse


Expression


Sequence


Reference Sequences
RefSeq Acc Id: ENSMUST00000069476   ⟹   ENSMUSP00000069947
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl1584,437,599 - 84,442,024 (-)Ensembl
GRCm38.p6 Ensembl1584,553,398 - 84,557,823 (-)Ensembl
RefSeq Acc Id: NM_177630   ⟹   NP_808298
RefSeq Status: VALIDATED
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm391584,437,599 - 84,442,024 (-)NCBI
GRCm381584,553,398 - 84,557,823 (-)ENTREZGENE
MGSCv371584,383,828 - 84,388,253 (-)RGD
Celera1586,686,561 - 86,690,981 (-)RGD
cM Map15 ENTREZGENE
Sequence:
Protein Sequences
Protein RefSeqs NP_808298 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAH58638 (Get FASTA)   NCBI Sequence Viewer  
  AAH94559 (Get FASTA)   NCBI Sequence Viewer  
  BAC39047 (Get FASTA)   NCBI Sequence Viewer  
  CAI99158 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSMUSP00000069947
  ENSMUSP00000069947.5
GenBank Protein Q505G4 (Get FASTA)   NCBI Sequence Viewer  
Reference Protein Sequences
RefSeq Acc Id: NP_808298   ⟸   NM_177630
- UniProtKB: Q8BNE4 (UniProtKB/Swiss-Prot),   Q505G4 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSMUSP00000069947   ⟸   ENSMUST00000069476

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q505G4-F1-model_v2 AlphaFold Q505G4 1-243 view protein structure

Promoters
RGD ID:6826140
Promoter ID:MM_KWN:19288
Type:CpG-Island
SO ACC ID:SO:0000170
Source:MPROMDB
Tissues & Cell Lines:ES_Cell,   Lung
Transcripts:NM_177630
Position:
Mouse AssemblyChrPosition (strand)Source
MGSCv361584,386,956 - 84,388,067 (-)MPROMDB
RGD ID:8684606
Promoter ID:EPDNEW_M20334
Type:initiation region
Name:Rtl6_1
Description:Mus musculus retrotransposon Gag like 6 , 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
GRCm381584,557,864 - 84,557,924EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene MGI:2675858 AgrOrtholog
Ensembl Genes ENSMUSG00000055745 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENSMUST00000069476 ENTREZGENE
  ENSMUST00000069476.5 UniProtKB/Swiss-Prot
InterPro DUF4939 UniProtKB/Swiss-Prot
  LDOC1-rel UniProtKB/Swiss-Prot
KEGG Report mmu:223732 UniProtKB/Swiss-Prot
MGD MGI:2675858 ENTREZGENE
NCBI Gene 223732 ENTREZGENE
PANTHER PTHR15503 UniProtKB/Swiss-Prot
  RETROTRANSPOSON GAG-LIKE PROTEIN 6 UniProtKB/Swiss-Prot
Pfam DUF4939 UniProtKB/Swiss-Prot
PhenoGen Rtl6 PhenoGen
UniProt Q505G4 ENTREZGENE
  Q8BNE4 ENTREZGENE
  RTL6_MOUSE UniProtKB/Swiss-Prot
UniProt Secondary Q8BNE4 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2017-08-22 Rtl6  retrotransposon Gag like 6  Ldoc1l  leucine zipper, down-regulated in cancer 1-like  Symbol and/or name change 5135510 APPROVED