Rtl6 (retrotransposon Gag like 6) - Rat Genome Database

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Gene: Rtl6 (retrotransposon Gag like 6) Rattus norvegicus
Analyze
Symbol: Rtl6
Name: retrotransposon Gag like 6
RGD ID: 1306472
Description: Orthologous to human RTL6 (retrotransposon Gag like 6); INTERACTS WITH 17alpha-ethynylestradiol; 2,3,7,8-tetrachlorodibenzodioxine; amphetamine.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: breast cancer, up-regulated 1; Ldoc1l; leucine zipper, down-regulated in cancer 1-like; LOC300114; retrotransposon Gag-like protein 6; RGD1306472; similar to leucine zipper, down-regulated in cancer 1
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Black Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: GRCr8 - GRCr8 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr87117,564,780 - 117,569,865 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl7117,563,239 - 117,570,129 (-)EnsemblGRCr8
mRatBN7.27115,684,812 - 115,689,897 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl7115,684,739 - 115,690,052 (-)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx7117,434,119 - 117,439,204 (-)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.07119,659,837 - 119,664,922 (-)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.07119,629,291 - 119,634,376 (-)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.07125,461,410 - 125,466,522 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl7125,465,117 - 125,465,848 (-)Ensemblrn6Rnor6.0
Rnor_5.07125,191,747 - 125,196,864 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.47122,569,018 - 122,570,166 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera7111,986,405 - 111,990,859 (-)NCBICelera
RGSC_v3.17122,540,659 - 122,624,694 (-)NCBI
Cytogenetic Map7q34NCBI
JBrowse:




Disease Annotations     Click to see Annotation Detail View

References

References - curated
# Reference Title Reference Citation
1. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions

Genomics

Comparative Map Data
Rtl6
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr87117,564,780 - 117,569,865 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl7117,563,239 - 117,570,129 (-)EnsemblGRCr8
mRatBN7.27115,684,812 - 115,689,897 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl7115,684,739 - 115,690,052 (-)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx7117,434,119 - 117,439,204 (-)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.07119,659,837 - 119,664,922 (-)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.07119,629,291 - 119,634,376 (-)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.07125,461,410 - 125,466,522 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl7125,465,117 - 125,465,848 (-)Ensemblrn6Rnor6.0
Rnor_5.07125,191,747 - 125,196,864 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.47122,569,018 - 122,570,166 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera7111,986,405 - 111,990,859 (-)NCBICelera
RGSC_v3.17122,540,659 - 122,624,694 (-)NCBI
Cytogenetic Map7q34NCBI
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 (-)Ensemblhg38GRCh38
GRCh372244,888,463 - 44,894,113 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 362243,267,114 - 43,272,669 (-)NCBIBuild 36Build 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
(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 EnsemblGRCm39
GRCm381584,553,398 - 84,557,823 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1584,553,398 - 84,557,823 (-)Ensemblmm10GRCm38
MGSCv371584,383,828 - 84,388,253 (-)NCBIMGSCv37MGSCv37mm9NCBIm37
MGSCv361584,381,165 - 84,385,549 (-)NCBIMGSCv36mm8
Celera1586,686,561 - 86,690,981 (-)NCBICelera
Cytogenetic Map15E2NCBI
cM Map1539.88NCBI
Rtl6
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495541329,242,588 - 29,243,307 (-)Ensembl
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 (-)EnsemblpanPan2panpan1.1
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 (+)EnsemblcanFam3CanFam3.1
Dog10K_Boxer_Tasha1021,257,571 - 21,262,791 (+)NCBIDog10K_Boxer_TashaDog10K_Boxer_Tasha
ROS_Cfam_1.01022,064,550 - 22,069,769 (+)NCBIROS_Cfam_1.0ROS_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_1.0UU_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 (-)EnsemblSpeTri2.0 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 (+)EnsemblsusScr11Sscrofa11.1
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 (-)EnsemblChlSab1.1 EnsemblchlSab2Vervet-AGM
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_1.0 EnsemblhetGla2HetGla_female_1.0 Ensembl
HetGla 1.0NW_0046247524,814,643 - 4,820,080 (+)NCBIHetGla 1.0HetGla 1.0hetGla2
Rtl6
(Rattus rattus - black rat)
Black Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rrattus_CSIRO_v11253,945,473 - 253,950,568 (-)NCBIRrattus_CSIRO_v1

Variants

.
Variants in Rtl6
12 total Variants
miRNA Target Status (No longer updated)

Predicted Target Of
Summary Value
Count of predictions:116
Count of miRNA genes:101
Interacting mature miRNAs:107
Transcripts:ENSRNOT00000039588
Prediction methods:Microtar, 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 (GRCr8)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1300179Kidm5Kidney mass QTL 53.51kidney mass (VT:0002707)left kidney wet weight (CMO:0000083)792388565119280177Rat
1331728Bp214Blood pressure QTL 2142.825arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)782111245123048330Rat
1331731Bp216Blood pressure QTL 2162.851arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)7104186212135371468Rat
70159Bp61Blood pressure QTL 610.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)773618702118618702Rat
631687Hcas1Hepatocarcinoma susceptibility QTL 13.90.001liver integrity trait (VT:0010547)liver tumorous lesion volume to total liver volume ratio (CMO:0001082)793302009131686183Rat
61397Bw17Body weight QTL 176.3body mass (VT:0001259)body weight (CMO:0000012)795485047137014596Rat
1358914Bp266Blood pressure QTL 266arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)7115313999136544683Rat
631504Cm27Cardiac mass QTL 273.45heart left ventricle mass (VT:0007031)heart left ventricle wet weight (CMO:0000071)746307490127866166Rat
634322Bw12Body weight QTL 120body mass (VT:0001259)body weight (CMO:0000012)785043242130043242Rat
70173Niddm19Non-insulin dependent diabetes mellitus QTL 194.330.00005blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)785497398130497398Rat
1549899Stresp8Stress response QTL 84.370.0008stress-related behavior trait (VT:0010451)defensive burying duration (CMO:0001961)792362341137014596Rat
2317052Aia17Adjuvant induced arthritis QTL 172.13joint integrity trait (VT:0010548)left rear ankle joint diameter (CMO:0002149)783626689128626689Rat
631529Tls2T-lymphoma susceptibility QTL 200.001thymus integrity trait (VT:0010555)percentage of study population developing T-cell lymphomas during a period of time (CMO:0001911)782111382132099989Rat
731176Glom5Glomerulus QTL 52.50.0035kidney glomerulus morphology trait (VT:0005325)count of superficial glomeruli not directly contacting the kidney surface (CMO:0001002)798549867137014596Rat
7411607Foco15Food consumption QTL 150.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)777807807122807807Rat
631201Panci1Pancreas inflammation QTL 100.001pancreas integrity trait (VT:0010560)percentage of study population displaying chronic pancreatitis at a point in time (CMO:0001214)773557047118557047Rat
1331768Kidm10Kidney mass QTL 104.62096kidney mass (VT:0002707)left kidney wet weight (CMO:0000083)782111245123048330Rat
2313102Bmd79Bone mineral density QTL 792.30.0001tibia mineral mass (VT:1000283)total volumetric bone mineral density (CMO:0001728)796700404118618702Rat
61357Bp38Blood pressure QTL 381.60.052arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)740540077123682549Rat
1331748Bp215Blood pressure QTL 2154.043arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)7110725024135371468Rat
10450862Kidm55Kidney mass QTL 554.9kidney mass (VT:0002707)kidney weight (CMO:0000081)772725037117725037Rat
61428Scl3Serum cholesterol level QTL 33.2blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)7100548246137014596Rat
1331746Kidm9Kidney mass QTL 93.934kidney mass (VT:0002707)right kidney wet weight (CMO:0000082)782111245134948181Rat
7411654Foco25Food consumption QTL 259.30.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)777807807122807807Rat
10450856Livw4Liver weight QTL 43.8liver mass (VT:0003402)liver weight (CMO:0000092)772725037117725037Rat
2299163Iddm34Insulin dependent diabetes mellitus QTL 342.71blood glucose amount (VT:0000188)age at onset/diagnosis of type 1 diabetes mellitus (CMO:0001140)7116269196132020414Rat
10402855Bp379Blood pressure QTL 3790.21arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)778682549123682549Rat
631540Bw9Body weight QTL 94.5body mass (VT:0001259)body weight (CMO:0000012)771621154119349044Rat
1358891Bp265Blood pressure QTL 2652.21arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)771827901136544683Rat


Expression

RNA-SEQ Expression

alimentary part of gastrointestinal system
appendage
circulatory system
ectoderm
endocrine system
endoderm
exocrine system
hemolymphoid system
hepatobiliary system
integumental system
mesenchyme
mesoderm
musculoskeletal system
nervous system
renal system
reproductive system
respiratory system
sensory system
visual system
16 12 67 163 91 90 59 89 59 6 352 189 11 142 80 92 31 17 17

Sequence


Ensembl Acc Id: ENSRNOT00000039588   ⟹   ENSRNOP00000032987
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl7125,465,117 - 125,465,848 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000097662   ⟹   ENSRNOP00000081919
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl7117,563,239 - 117,569,900 (-)Ensembl
mRatBN7.2 Ensembl7115,684,739 - 115,690,052 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000149197   ⟹   ENSRNOP00000106178
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl7117,564,780 - 117,570,129 (-)Ensembl
RefSeq Acc Id: NM_001399726   ⟹   NP_001386655
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr87117,564,780 - 117,569,865 (-)NCBI
mRatBN7.27115,684,812 - 115,689,897 (-)NCBI
Protein Sequences
Protein RefSeqs NP_001386655 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000081919
  ENSRNOP00000081919.1
  ENSRNOP00000106178.1
Ensembl Acc Id: ENSRNOP00000032987   ⟸   ENSRNOT00000039588
Ensembl Acc Id: ENSRNOP00000081919   ⟸   ENSRNOT00000097662
RefSeq Acc Id: NP_001386655   ⟸   NM_001399726
- UniProtKB: A0A8I6G8M7 (UniProtKB/TrEMBL)
Ensembl Acc Id: ENSRNOP00000106178   ⟸   ENSRNOT00000149197
Protein Domains
DUF4939

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D3ZI44-F1-model_v2 AlphaFold D3ZI44 1-243 view protein structure

Transcriptome

eQTL   View at Phenogen
WGCNA   View at Phenogen
Tissue/Strain Expression   View at Phenogen


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1306472 AgrOrtholog
BioCyc Gene G2FUF-32575 BioCyc
Ensembl Genes ENSRNOG00000021671 Ensembl
  ENSRNOG00000064516 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000097662 ENTREZGENE
  ENSRNOT00000097662.2 UniProtKB/TrEMBL
  ENSRNOT00000149197.1 UniProtKB/TrEMBL
InterPro DUF4939 UniProtKB/TrEMBL
NCBI Gene 300114 ENTREZGENE
Pfam DUF4939 UniProtKB/TrEMBL
PhenoGen Rtl6 PhenoGen
RatGTEx ENSRNOG00000021671 RatGTEx
  ENSRNOG00000064516 RatGTEx
UniProt A0A8I6G8M7 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2022-06-02 Rtl6  retrotransposon Gag like 6  Rtl6  retrotransposon Gag like 6  Data merged from RGD:149736438 737654 PROVISIONAL
2021-08-09 Rtl6  retrotransposon Gag like 6      Symbol and Name status set to provisional 45752 PROVISIONAL
2017-04-05 Rtl6  retrotransposon Gag like 6  Ldoc1l  leucine zipper, down-regulated in cancer 1-like  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-03-07 Ldoc1l  leucine zipper, down-regulated in cancer 1-like  RGD1306472_predicted  similar to leucine zipper, down-regulated in cancer 1; breast cancer, up-regulated 1 (predicted)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2005-01-20 RGD1306472_predicted  similar to leucine zipper, down-regulated in cancer 1; breast cancer, up-regulated 1 (predicted)  LOC300114_predicted    Symbol and Name status set to approved 1331353 APPROVED
2005-01-12 LOC300114_predicted  similar to leucine zipper, down-regulated in cancer 1; breast cancer, up-regulated 1 (predicted)      Symbol and Name status set to provisional 70820 PROVISIONAL