Rtl6 (retrotransposon Gag like 6) - Rat Genome Database

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Gene: Rtl6 (retrotransposon Gag like 6) Ictidomys tridecemlineatus
Analyze
Symbol: Rtl6
Name: retrotransposon Gag like 6
RGD ID: 12718626
Description: ASSOCIATED WITH intellectual disability (ortholog); Phelan-McDermid syndrome (ortholog); substance-related disorder (ortholog)
Type: protein-coding
RefSeq Status: MODEL
Previously known as: LDOC1 like; Ldoc1l; leucine zipper down-regulated in cancer 1 like; retrotransposon Gag-like protein 6
RGD Orthologs
Human
Mouse
Rat
Chinchilla
Bonobo
Dog
Pig
Green Monkey
Naked Mole-Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: SpeTri2.0 - Squirrel SpeTri2.0 Assembly
Position:
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
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

References

Genomics

Comparative Map Data
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
(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
(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
(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
(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


Expression


Sequence

Nucleotide Sequences
RefSeq Transcripts XM_021735472 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide JAESOR010000004 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSSTOT00000005212   ⟹   ENSSTOP00000018477
Type: CODING
Position:
Squirrel AssemblyChrPosition (strand)Source
SpeTri2.0 EnsemblNW_0049367181,963,636 - 1,968,484 (-)Ensembl
RefSeq Acc Id: XM_021735472   ⟹   XP_021591147
Type: CODING
Position:
Squirrel AssemblyChrPosition (strand)Source
HiC_Itri_2NW_0244049455,011,671 - 5,016,538 (+)NCBI
SpeTri2.0NW_0049367181,963,627 - 1,968,494 (-)NCBI
Sequence:
Protein Sequences
Protein RefSeqs XP_021591147 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSSTOP00000018477.1
GenBank Protein KAG3290766 (Get FASTA)   NCBI Sequence Viewer  
Reference Protein Sequences
RefSeq Acc Id: XP_021591147   ⟸   XM_021735472
- UniProtKB: I3N281 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSSTOP00000018477   ⟸   ENSSTOT00000005212
Protein Domains
DUF4939


Additional Information

Database Acc Id Source(s)
Ensembl Genes ENSSTOG00000005224 Ensembl, UniProtKB/TrEMBL
Ensembl Transcript ENSSTOT00000005212.3 UniProtKB/TrEMBL
InterPro DUF4939 UniProtKB/TrEMBL
  LDOC1-rel UniProtKB/TrEMBL
NCBI Gene Ldoc1l ENTREZGENE
PANTHER PTHR15503 UniProtKB/TrEMBL
  RETROTRANSPOSON GAG-LIKE PROTEIN 6 UniProtKB/TrEMBL
Pfam DUF4939 UniProtKB/TrEMBL
UniProt I3N281 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2017-03-28 Rtl6  retrotransposon Gag like 6  Ldoc1l  LDOC1 like  Symbol and/or name change 5135510 APPROVED
2017-02-07 Ldoc1l  LDOC1 like    leucine zipper down-regulated in cancer 1 like  Symbol and/or name change 5135510 APPROVED