RTL6 (retrotransposon Gag like 6) - Rat Genome Database

Send us a Message
Submit Data |  Help |  Video Tutorials |  News |  Publications |  Download |  REST API |  Citing RGD |  Contact   
Search RGD Grant Resources Citing RGD About Us Contact Us
Genes Variants Community Projects QTLs Strains Markers Genome Information Ontologies Cell Lines References Download Submit Data
OntoMate (Literature Search) JBrowse (Genome Browser) Synteny Browser (VCMap) Variant Visualizer Multi-Ontology Enrichment (MOET) Gene-Ortholog Location Finder (GOLF) InterViewer (Protein-Protein Interactions) PhenoMiner (Quatitative Phenotypes) Gene Annotator OLGA (Gene List Generator) AllianceMine GViewer (Genome Viewer)
Aging & Age-Related Disease Cancer & Neoplastic Disease Cardiovascular Disease Coronavirus Disease Developmental Disease Diabetes Hematologic Disease Immune & Inflammatory Disease Infectious Disease Liver Disease Neurological Disease Obesity & Metabolic Syndrome Renal Disease Respiratory Disease Sensory Organ Disease
Find Models Genetic Models Autism Models Rat PhenoMiner (Quantitative Phenotypes) Chinchilla PhenoMiner Expected Ranges (Quantitative Phenotype) PhenoMiner Term Comparison Hybrid Rat Diversity Panel Phenotypes Phenotypes in Other Animal Models Animal Husbandry Strain Medical Records Phylogenetics Strain Availability Calendar Rats 101 Submissions Photo Archive
Pathways
Rat Community Forum Directory of Rat Laboratories Video Tutorials News RGD Publications RGD Presentations Archive Nomenclature Guidelines Resource Links Laboratory Resources Employment Resources
Advanced Search (OLGA)
Gene: RTL6 (retrotransposon Gag like 6) Homo sapiens
Analyze
Symbol: RTL6
Name: retrotransposon Gag like 6
RGD ID: 1345067
HGNC Page HGNC:13343
Description: ASSOCIATED WITH Intellectual disability; intellectual disability; Phelan-McDermid syndrome; INTERACTS WITH 17beta-estradiol; 4,4'-sulfonyldiphenol; aflatoxin B1
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: dJ1033E15.2; dJ1033E15.C22.2; DKFZp761O17121; LDOC1 like; LDOC1L; leucine zipper down-regulated in cancer 1 like; leucine zipper protein down-regulated in cancer cells-like; leucine zipper, down-regulated in cancer 1 like; leucine zipper, down-regulated in cancer 1-like; mammalian retrotransposon-derived 6; mammalian retrotransposon-derived protein 6; Mar6; Mart6; retrotransposon Gag-like protein 6; SIRH3; Sushi-Ichi retrotransposon homolog 3
RGD Orthologs
Mouse
Rat
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Orthologs
More Info more info ...
Allele / Splice: See ClinVar data
Latest Assembly: GRCh38 - Human Genome Assembly GRCh38
Position:
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
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Phenotype Annotations     Click to see Annotation Detail View

Human 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:11230166   PMID:12477932   PMID:15461802   PMID:15716091   PMID:16093683   PMID:18029348   PMID:20562859   PMID:20811636   PMID:22658674   PMID:26186194   PMID:28514442   PMID:29507755  
PMID:30561431   PMID:33961781   PMID:35748872   PMID:37433992  


Genomics

Comparative Map Data
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
(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
15 total Variants

Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
GRCh38/hg38 22q13.2-13.33(chr22:42138114-50739836)x1 copy number loss Developmental Delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000051370]|Developmental delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000051370]|See cases [RCV000051370] Chr22:42138114..50739836 [GRCh38]
Chr22:42513525..51178264 [GRCh37]
Chr22:40843471..49525130 [NCBI36]
Chr22:22q13.2-13.33		 pathogenic
GRCh38/hg38 22q13.2-13.33(chr22:42433752-50738932)x1 copy number loss See cases [RCV000051371] Chr22:42433752..50738932 [GRCh38]
Chr22:42829758..51177360 [GRCh37]
Chr22:41159702..49524226 [NCBI36]
Chr22:22q13.2-13.33		 pathogenic
GRCh38/hg38 22q13.2-13.33(chr22:42826246-50739836)x1 copy number loss See cases [RCV000051407] Chr22:42826246..50739836 [GRCh38]
Chr22:43222252..51178264 [GRCh37]
Chr22:41552196..49525130 [NCBI36]
Chr22:22q13.2-13.33		 pathogenic
GRCh38/hg38 22q13.31-13.33(chr22:43807366-50739836)x1 copy number loss See cases [RCV000051408] Chr22:43807366..50739836 [GRCh38]
Chr22:44203246..51178264 [GRCh37]
Chr22:42534579..49525130 [NCBI36]
Chr22:22q13.31-13.33		 pathogenic
GRCh38/hg38 22q13.31-13.33(chr22:43993654-50739977)x1 copy number loss See cases [RCV000051409] Chr22:43993654..50739977 [GRCh38]
Chr22:44389534..51178405 [GRCh37]
Chr22:42720867..49525271 [NCBI36]
Chr22:22q13.31-13.33		 pathogenic
GRCh38/hg38 22q12.3-13.33(chr22:33768441-50739977)x3 copy number gain See cases [RCV000051682] Chr22:33768441..50739977 [GRCh38]
Chr22:34164428..51178405 [GRCh37]
Chr22:32494428..49525271 [NCBI36]
Chr22:22q12.3-13.33		 pathogenic
GRCh38/hg38 22q12.3-13.33(chr22:37061769-50738932)x3 copy number gain See cases [RCV000051684] Chr22:37061769..50738932 [GRCh38]
Chr22:37457809..51177360 [GRCh37]
Chr22:35787755..49524226 [NCBI36]
Chr22:22q12.3-13.33		 pathogenic
GRCh38/hg38 22q13.2-13.33(chr22:42599757-50725241)x3 copy number gain See cases [RCV000051686] Chr22:42599757..50725241 [GRCh38]
Chr22:42995763..51163669 [GRCh37]
Chr22:41325707..49510535 [NCBI36]
Chr22:22q13.2-13.33		 pathogenic
GRCh38/hg38 22q13.2-13.33(chr22:42653747-50739836)x3 copy number gain See cases [RCV000051687] Chr22:42653747..50739836 [GRCh38]
Chr22:43049753..51178264 [GRCh37]
Chr22:41379697..49525130 [NCBI36]
Chr22:22q13.2-13.33		 pathogenic
GRCh38/hg38 22q11.1-13.33(chr22:16916608-50739836)x3 copy number gain See cases [RCV000133646] Chr22:16916608..50739836 [GRCh38]
Chr22:17397498..51178264 [GRCh37]
Chr22:15777498..49525130 [NCBI36]
Chr22:22q11.1-13.33		 pathogenic
GRCh38/hg38 22q11.1-13.33(chr22:16916743-50739785)x3 copy number gain See cases [RCV000134730] Chr22:16916743..50739785 [GRCh38]
Chr22:17397633..51178213 [GRCh37]
Chr22:15777633..49525079 [NCBI36]
Chr22:22q11.1-13.33		 pathogenic
GRCh38/hg38 22q13.1-13.33(chr22:40202014-50735806)x3 copy number gain See cases [RCV000134513] Chr22:40202014..50735806 [GRCh38]
Chr22:40598018..51174234 [GRCh37]
Chr22:38927964..49521100 [NCBI36]
Chr22:22q13.1-13.33		 pathogenic
GRCh38/hg38 22q13.31-13.33(chr22:43902561-50739836)x1 copy number loss See cases [RCV000135444] Chr22:43902561..50739836 [GRCh38]
Chr22:44298441..51178264 [GRCh37]
Chr22:42629774..49525130 [NCBI36]
Chr22:22q13.31-13.33		 pathogenic
GRCh38/hg38 22q13.2-13.31(chr22:42197923-47305564)x4 copy number gain See cases [RCV000135528] Chr22:42197923..47305564 [GRCh38]
Chr22:42593929..47701314 [GRCh37]
Chr22:40923873..46079978 [NCBI36]
Chr22:22q13.2-13.31		 pathogenic
GRCh38/hg38 22q13.31-13.33(chr22:43992879-50683114)x3 copy number gain See cases [RCV000136124] Chr22:43992879..50683114 [GRCh38]
Chr22:44388759..51121542 [GRCh37]
Chr22:42720092..49468408 [NCBI36]
Chr22:22q13.31-13.33		 benign
GRCh38/hg38 22q13.2-13.33(chr22:41871143-50739836)x1 copy number loss See cases [RCV000136921] Chr22:41871143..50739836 [GRCh38]
Chr22:42267147..51178264 [GRCh37]
Chr22:40597093..49525130 [NCBI36]
Chr22:22q13.2-13.33		 pathogenic
GRCh38/hg38 22q13.2-13.33(chr22:42710276-50739836)x3 copy number gain See cases [RCV000137136] Chr22:42710276..50739836 [GRCh38]
Chr22:43106282..51178264 [GRCh37]
Chr22:41436226..49525130 [NCBI36]
Chr22:22q13.2-13.33		 pathogenic
GRCh38/hg38 22q13.2-13.33(chr22:42493445-50268479)x1 copy number loss See cases [RCV000136786] Chr22:42493445..50268479 [GRCh38]
Chr22:42889451..50706908 [GRCh37]
Chr22:41219395..49049035 [NCBI36]
Chr22:22q13.2-13.33		 pathogenic
GRCh38/hg38 22q13.2-13.33(chr22:42837094-50735806)x1 copy number loss See cases [RCV000141415] Chr22:42837094..50735806 [GRCh38]
Chr22:43233100..51174234 [GRCh37]
Chr22:41563044..49521100 [NCBI36]
Chr22:22q13.2-13.33		 pathogenic
GRCh38/hg38 22q13.2-13.33(chr22:43187980-50745444)x1 copy number loss See cases [RCV000140901] Chr22:43187980..50745444 [GRCh38]
Chr22:43583986..51183872 [GRCh37]
Chr22:41913930..49530738 [NCBI36]
Chr22:22q13.2-13.33		 pathogenic
GRCh38/hg38 22q13.2-13.33(chr22:42380961-50759410)x3 copy number gain See cases [RCV000141659] Chr22:42380961..50759410 [GRCh38]
Chr22:42776967..51197838 [GRCh37]
Chr22:41106911..49544704 [NCBI36]
Chr22:22q13.2-13.33		 pathogenic
GRCh38/hg38 22q13.2-13.33(chr22:42080077-50739836)x3 copy number gain See cases [RCV000142755] Chr22:42080077..50739836 [GRCh38]
Chr22:42476081..51178264 [GRCh37]
Chr22:40806027..49525130 [NCBI36]
Chr22:22q13.2-13.33		 pathogenic
GRCh37/hg19 22q11.1-13.33(chr22:16054691-51237518)x3 copy number gain See cases [RCV000240091] Chr22:16054691..51237518 [GRCh37]
Chr22:22q11.1-13.33		 pathogenic
GRCh37/hg19 22q12.3-13.33(chr22:35728929-51220961)x3 copy number gain See cases [RCV000240469] Chr22:35728929..51220961 [GRCh37]
Chr22:22q12.3-13.33		 pathogenic
GRCh37/hg19 22q13.1-13.33(chr22:40425714-51220961)x3 copy number gain See cases [RCV000240459] Chr22:40425714..51220961 [GRCh37]
Chr22:22q13.1-13.33		 pathogenic
GRCh37/hg19 22q11.1-13.33(chr22:16054691-51220902)x3 copy number gain See cases [RCV000446956] Chr22:16054691..51220902 [GRCh37]
Chr22:22q11.1-13.33		 pathogenic
GRCh37/hg19 22q11.1-13.33(chr22:16054691-51237463)x3 copy number gain See cases [RCV000448847] Chr22:16054691..51237463 [GRCh37]
Chr22:22q11.1-13.33		 pathogenic
GRCh37/hg19 22q13.2-13.33(chr22:43381459-51197838)x1 copy number loss See cases [RCV000512121] Chr22:43381459..51197838 [GRCh37]
Chr22:22q13.2-13.33		 pathogenic
GRCh37/hg19 22q13.31(chr22:44382852-45007914)x1 copy number loss See cases [RCV000511840] Chr22:44382852..45007914 [GRCh37]
Chr22:22q13.31		 uncertain significance
GRCh37/hg19 22q13.2-13.33(chr22:43875989-51197838)x1 copy number loss See cases [RCV000511015] Chr22:43875989..51197838 [GRCh37]
Chr22:22q13.2-13.33		 pathogenic
GRCh37/hg19 22q13.2-13.33(chr22:43050743-51197838)x1 copy number loss See cases [RCV000511256] Chr22:43050743..51197838 [GRCh37]
Chr22:22q13.2-13.33		 pathogenic
GRCh37/hg19 22q13.2-13.33(chr22:42441918-51197838)x1 copy number loss See cases [RCV000510765] Chr22:42441918..51197838 [GRCh37]
Chr22:22q13.2-13.33		 pathogenic
GRCh37/hg19 22q11.1-13.33(chr22:16888900-51197838) copy number gain See cases [RCV000510873] Chr22:16888900..51197838 [GRCh37]
Chr22:22q11.1-13.33		 pathogenic
GRCh37/hg19 22q11.1-13.33(chr22:16888900-51197838)x3 copy number gain See cases [RCV000512333] Chr22:16888900..51197838 [GRCh37]
Chr22:22q11.1-13.33		 pathogenic
GRCh37/hg19 22q13.31-13.33(chr22:44789956-51183840)x1 copy number loss not provided [RCV000684526] Chr22:44789956..51183840 [GRCh37]
Chr22:22q13.31-13.33		 pathogenic
GRCh37/hg19 22q13.2-13.33(chr22:43320284-51183840)x1 copy number loss not provided [RCV000684527] Chr22:43320284..51183840 [GRCh37]
Chr22:22q13.2-13.33		 pathogenic
GRCh37/hg19 22q13.2-13.33(chr22:43111156-51183840)x1 copy number loss not provided [RCV000684528] Chr22:43111156..51183840 [GRCh37]
Chr22:22q13.2-13.33		 pathogenic
GRCh37/hg19 22q13.2-13.33(chr22:42955616-51183840)x1 copy number loss not provided [RCV000684529] Chr22:42955616..51183840 [GRCh37]
Chr22:22q13.2-13.33		 pathogenic
GRCh37/hg19 22q11.1-13.33(chr22:16054667-51243435)x3 copy number gain not provided [RCV000741689] Chr22:16054667..51243435 [GRCh37]
Chr22:22q11.1-13.33		 pathogenic
GRCh37/hg19 22q11.1-13.33(chr22:16114244-51195728)x3 copy number gain not provided [RCV000741691] Chr22:16114244..51195728 [GRCh37]
Chr22:22q11.1-13.33		 pathogenic
GRCh37/hg19 22q13.2-13.33(chr22:42151555-51195728)x1 copy number loss not provided [RCV000741989] Chr22:42151555..51195728 [GRCh37]
Chr22:22q13.2-13.33		 pathogenic
GRCh37/hg19 22q11.1-13.33(chr22:16114244-51211392)x3 copy number gain not provided [RCV000741692] Chr22:16114244..51211392 [GRCh37]
Chr22:22q11.1-13.33		 pathogenic
GRCh37/hg19 22q13.1-13.33(chr22:40502364-51197838)x3 copy number gain not provided [RCV001007502] Chr22:40502364..51197838 [GRCh37]
Chr22:22q13.1-13.33		 pathogenic
GRCh37/hg19 22q13.2-13.33(chr22:42416026-51181759) copy number loss Phelan-McDermid syndrome [RCV000767745] Chr22:42416026..51181759 [GRCh37]
Chr22:22q13.2-13.33		 pathogenic
NM_032287.3(RTL6):c.135C>A (p.Thr45=) single nucleotide variant not provided [RCV000965507] Chr22:44497422 [GRCh38]
Chr22:44893302 [GRCh37]
Chr22:22q13.31		 benign
Single allele copy number loss 22q13.3 interstitial deletion [RCV001200047] Chr22:44850001..50850001 [GRCh37]
Chr22:22q13.31-13.33		 pathogenic
GRCh37/hg19 22q11.1-13.33(chr22:16888899-51197838)x3 copy number gain not provided [RCV000846344] Chr22:16888899..51197838 [GRCh37]
Chr22:22q11.1-13.33		 pathogenic
GRCh37/hg19 22q13.31(chr22:44485556-44933077)x3 copy number gain not provided [RCV002473690] Chr22:44485556..44933077 [GRCh37]
Chr22:22q13.31		 uncertain significance
GRCh37/hg19 22q12.2-13.33(chr22:30654764-51197838)x3 copy number gain not provided [RCV001007181] Chr22:30654764..51197838 [GRCh37]
Chr22:22q12.2-13.33		 pathogenic
GRCh37/hg19 22q13.31(chr22:44642723-45340485)x3 copy number gain See cases [RCV001007427] Chr22:44642723..45340485 [GRCh37]
Chr22:22q13.31		 uncertain significance
NC_000022.11:g.44245760_50806121del deletion Phelan-McDermid syndrome [RCV001254369] Chr22:44245760..50806121 [GRCh38]
Chr22:22q13.31-13.33		 pathogenic
NC_000022.11:g.43032129_50739836del deletion Phelan-McDermid syndrome [RCV001254356] Chr22:43032129..50739836 [GRCh38]
Chr22:22q13.2-13.33		 pathogenic
NC_000022.11:g.43802117_50806121del deletion Phelan-McDermid syndrome [RCV001254364] Chr22:43802117..50806121 [GRCh38]
Chr22:22q13.31-13.33		 pathogenic
GRCh37/hg19 22q13.31(chr22:44705738-45475334)x3 copy number gain not provided [RCV001258787] Chr22:44705738..45475334 [GRCh37]
Chr22:22q13.31		 uncertain significance
GRCh37/hg19 22q13.31(chr22:44649786-45866882)x3 copy number gain not provided [RCV001258788] Chr22:44649786..45866882 [GRCh37]
Chr22:22q13.31		 uncertain significance
GRCh37/hg19 22q13.31(chr22:44795975-45297787)x3 copy number gain not provided [RCV001258789] Chr22:44795975..45297787 [GRCh37]
Chr22:22q13.31		 uncertain significance
GRCh37/hg19 22q11.1-13.33(chr22:16197005-51224252)x3 copy number gain See cases [RCV001263056] Chr22:16197005..51224252 [GRCh37]
Chr22:22q11.1-13.33		 pathogenic
Single allele deletion Intellectual disability [RCV001293376] Chr22:42333802..51195728 [GRCh37]
Chr22:22q13.2-13.33		 pathogenic
GRCh37/hg19 22q13.2-13.33(chr22:42321321-51244066)x1 copy number loss Phelan-McDermid syndrome [RCV001801178] Chr22:42321321..51244066 [GRCh37]
Chr22:22q13.2-13.33		 pathogenic
GRCh37/hg19 22q13.2-13.33(chr22:42972719-51197838) copy number loss not specified [RCV002052757] Chr22:42972719..51197838 [GRCh37]
Chr22:22q13.2-13.33		 pathogenic
GRCh37/hg19 22q13.2-13.31(chr22:43451316-46662660) copy number loss not specified [RCV002052758] Chr22:43451316..46662660 [GRCh37]
Chr22:22q13.2-13.31		 pathogenic
GRCh37/hg19 22q13.2-13.33(chr22:44178749-51183840)x1 copy number loss not provided [RCV002472623] Chr22:44178749..51183840 [GRCh37]
Chr22:22q13.2-13.33		 pathogenic
GRCh37/hg19 22q13.31-13.33(chr22:44390702-51137629)x1 copy number loss not provided [RCV002473583] Chr22:44390702..51137629 [GRCh37]
Chr22:22q13.31-13.33		 pathogenic
GRCh37/hg19 22q13.2-13.33(chr22:43436847-51188164)x3 copy number gain not provided [RCV002468433] Chr22:43436847..51188164 [GRCh37]
Chr22:22q13.2-13.33		 pathogenic
NM_032287.3(RTL6):c.605G>C (p.Arg202Thr) single nucleotide variant not specified [RCV004314009] Chr22:44496952 [GRCh38]
Chr22:44892832 [GRCh37]
Chr22:22q13.31		 uncertain significance
NM_032287.3(RTL6):c.407G>C (p.Arg136Pro) single nucleotide variant not specified [RCV004274158] Chr22:44497150 [GRCh38]
Chr22:44893030 [GRCh37]
Chr22:22q13.31		 uncertain significance
NM_032287.3(RTL6):c.208A>T (p.Arg70Trp) single nucleotide variant not specified [RCV004277564] Chr22:44497349 [GRCh38]
Chr22:44893229 [GRCh37]
Chr22:22q13.31		 uncertain significance
GRCh38/hg38 22q13.31(chr22:44184196-45239435) copy number gain Anomalous pulmonary venous return [RCV003223579] Chr22:44184196..45239435 [GRCh38]
Chr22:22q13.31		 uncertain significance
NM_032287.3(RTL6):c.619C>T (p.Arg207Cys) single nucleotide variant not specified [RCV004350850] Chr22:44496938 [GRCh38]
Chr22:44892818 [GRCh37]
Chr22:22q13.31		 uncertain significance
NM_032287.3(RTL6):c.23A>T (p.Lys8Ile) single nucleotide variant not specified [RCV004362470] Chr22:44497534 [GRCh38]
Chr22:44893414 [GRCh37]
Chr22:22q13.31		 uncertain significance
GRCh37/hg19 22q13.2-13.33(chr22:43820992-51218654)x1 copy number loss not provided [RCV003457366] Chr22:43820992..51218654 [GRCh37]
Chr22:22q13.2-13.33		 pathogenic
GRCh37/hg19 22q13.2-13.33(chr22:43107363-51156692)x1 copy number loss not specified [RCV003986180] Chr22:43107363..51156692 [GRCh37]
Chr22:22q13.2-13.33		 pathogenic
GRCh37/hg19 22q13.2-13.31(chr22:43920110-46548382)x1 copy number loss not specified [RCV003986192] Chr22:43920110..46548382 [GRCh37]
Chr22:22q13.2-13.31		 likely pathogenic
GRCh37/hg19 22q13.31-13.33(chr22:44502872-51183871)x1 copy number loss not specified [RCV003986171] Chr22:44502872..51183871 [GRCh37]
Chr22:22q13.31-13.33		 pathogenic
GRCh37/hg19 22q13.2-13.33(chr22:44034281-51197838)x1 copy number loss not specified [RCV003986178] Chr22:44034281..51197838 [GRCh37]
Chr22:22q13.2-13.33		 pathogenic
GRCh37/hg19 22q13.1-13.31(chr22:39044105-45794212)x3 copy number gain not specified [RCV003986179] Chr22:39044105..45794212 [GRCh37]
Chr22:22q13.1-13.31		 pathogenic
NM_032287.3(RTL6):c.174G>C (p.Glu58Asp) single nucleotide variant not specified [RCV004454801] Chr22:44497383 [GRCh38]
Chr22:44893263 [GRCh37]
Chr22:22q13.31		 uncertain significance
NM_032287.3(RTL6):c.326C>G (p.Pro109Arg) single nucleotide variant not specified [RCV004454804] Chr22:44497231 [GRCh38]
Chr22:44893111 [GRCh37]
Chr22:22q13.31		 uncertain significance
NM_032287.3(RTL6):c.251C>G (p.Ser84Cys) single nucleotide variant not specified [RCV004454802] Chr22:44497306 [GRCh38]
Chr22:44893186 [GRCh37]
Chr22:22q13.31		 uncertain significance
NM_032287.3(RTL6):c.47C>T (p.Ala16Val) single nucleotide variant not specified [RCV004454805] Chr22:44497510 [GRCh38]
Chr22:44893390 [GRCh37]
Chr22:22q13.31		 uncertain significance
NM_032287.3(RTL6):c.610A>T (p.Met204Leu) single nucleotide variant not specified [RCV004454806] Chr22:44496947 [GRCh38]
Chr22:44892827 [GRCh37]
Chr22:22q13.31		 uncertain significance
NM_032287.3(RTL6):c.152C>T (p.Ala51Val) single nucleotide variant not specified [RCV004454800] Chr22:44497405 [GRCh38]
Chr22:44893285 [GRCh37]
Chr22:22q13.31		 uncertain significance
NM_032287.3(RTL6):c.295A>G (p.Thr99Ala) single nucleotide variant not specified [RCV004454803] Chr22:44497262 [GRCh38]
Chr22:44893142 [GRCh37]
Chr22:22q13.31		 uncertain significance
NM_032287.3(RTL6):c.145G>C (p.Glu49Gln) single nucleotide variant not specified [RCV004454799] Chr22:44497412 [GRCh38]
Chr22:44893292 [GRCh37]
Chr22:22q13.31		 uncertain significance
NM_032287.3(RTL6):c.154A>C (p.Asn52His) single nucleotide variant not specified [RCV004674339] Chr22:44497403 [GRCh38]
Chr22:44893283 [GRCh37]
Chr22:22q13.31		 uncertain significance
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:1868
Count of miRNA genes:984
Interacting mature miRNAs:1174
Transcripts:ENST00000341255
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 (GRCh38)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
406934165GWAS583141_Hhousehold income QTL GWAS583141 (human)8e-10household income224449536744495368Human

Markers in Region
A007A35  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh372244,888,485 - 44,888,645UniSTSGRCh37
Build 362243,267,149 - 43,267,309RGDNCBI36
Celera2228,800,386 - 28,800,546RGD
Cytogenetic Map22q13.31UniSTS
HuRef2227,837,979 - 27,838,139UniSTS
GeneMap99-GB4 RH Map22144.47UniSTS
NCBI RH Map22212.8UniSTS
WI-14034  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh372244,888,494 - 44,888,643UniSTSGRCh37
Build 362243,267,158 - 43,267,307RGDNCBI36
Celera2228,800,395 - 28,800,544RGD
Cytogenetic Map22q13.31UniSTS
HuRef2227,837,988 - 27,838,137UniSTS
GeneMap99-GB4 RH Map22143.55UniSTS
Whitehead-RH Map22171.1UniSTS
NCBI RH Map22212.8UniSTS
RH45500  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh372244,888,720 - 44,888,947UniSTSGRCh37
Build 362243,267,384 - 43,267,611RGDNCBI36
Celera2228,800,621 - 28,800,848RGD
Cytogenetic Map22q13.31UniSTS
HuRef2227,838,214 - 27,838,441UniSTS
GeneMap99-GB4 RH Map22153.37UniSTS
NCBI RH Map22210.6UniSTS


Expression

RNA-SEQ Expression

adipose tissue
alimentary part of gastrointestinal system
appendage
circulatory system
ectoderm
endocrine system
endoderm
entire extraembryonic component
exocrine system
hemolymphoid system
hepatobiliary system
integumental system
mesenchyme
mesoderm
musculoskeletal system
nervous system
pharyngeal arch
renal system
reproductive system
respiratory system
sensory system
visual system
1204 2439 2788 2240 4972 1720 2344 6 618 1885 459 2269 7245 6417 51 3734 1 852 1744 1616 174 1

Sequence


Ensembl Acc Id: ENST00000341255   ⟹   ENSP00000340434
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl2244,492,583 - 44,498,233 (-)Ensembl
RefSeq Acc Id: NM_032287   ⟹   NP_115663
RefSeq Status: VALIDATED
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh382244,492,583 - 44,498,233 (-)NCBI
GRCh372244,888,450 - 44,894,005 (-)RGD
Build 362243,267,114 - 43,272,669 (-)NCBI Archive
Celera2228,800,351 - 28,805,906 (-)RGD
HuRef2227,837,944 - 27,843,466 (-)ENTREZGENE
CHM1_12244,847,172 - 44,852,725 (-)NCBI
T2T-CHM13v2.02244,976,418 - 44,982,051 (-)NCBI
Sequence:
Protein Sequences
Protein RefSeqs NP_115663 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAH30232 (Get FASTA)   NCBI Sequence Viewer  
  BAG36437 (Get FASTA)   NCBI Sequence Viewer  
  BAG59119 (Get FASTA)   NCBI Sequence Viewer  
  CAB66488 (Get FASTA)   NCBI Sequence Viewer  
  CAG30325 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSP00000340434
  ENSP00000340434.3
GenBank Protein Q6ICC9 (Get FASTA)   NCBI Sequence Viewer  
RefSeq Acc Id: NP_115663   ⟸   NM_032287
- UniProtKB: Q6ZTR1 (UniProtKB/Swiss-Prot),   Q6ICC9 (UniProtKB/Swiss-Prot),   B4DKA7 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSP00000340434   ⟸   ENST00000341255
Protein Domains
DUF4939

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q6ICC9-F1-model_v2 AlphaFold Q6ICC9 1-239 view protein structure

Promoters
RGD ID:6800081
Promoter ID:HG_KWN:43165
Type:CpG-Island
SO ACC ID:SO:0000170
Source:MPROMDB
Tissues & Cell Lines:CD4+TCell,   CD4+TCell_12Hour,   HeLa_S3,   Jurkat,   K562,   Lymphoblastoid
Transcripts:OTTHUMT00000318222,   UC010GZS.1
Position:
Human AssemblyChrPosition (strand)Source
Build 362243,272,116 - 43,273,152 (-)MPROMDB
RGD ID:13604376
Promoter ID:EPDNEW_H28372
Type:initiation region
Name:LDOC1L_1
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Human AssemblyChrPosition (strand)Source
GRCh382244,498,217 - 44,498,277EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene HGNC:13343 AgrOrtholog
COSMIC RTL6 COSMIC
Ensembl Genes ENSG00000188636 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENST00000341255 ENTREZGENE
  ENST00000341255.4 UniProtKB/Swiss-Prot
GTEx ENSG00000188636 GTEx
HGNC ID HGNC:13343 ENTREZGENE
Human Proteome Map RTL6 Human Proteome Map
InterPro DUF4939 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  LDOC1-rel UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report hsa:84247 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
NCBI Gene RTL6 ENTREZGENE
OMIM 621006 OMIM
PANTHER LDOC1 RELATED UniProtKB/TrEMBL, UniProtKB/Swiss-Prot
  RETROTRANSPOSON GAG-LIKE PROTEIN 6 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam DUF4939 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PharmGKB PA134971270 PharmGKB
UniProt B4DKA7 ENTREZGENE, UniProtKB/TrEMBL
  Q6ICC9 ENTREZGENE
  Q6ZTR1 ENTREZGENE
  Q9BQJ3_HUMAN UniProtKB/TrEMBL
  RTL6_HUMAN UniProtKB/Swiss-Prot
UniProt Secondary Q6ZTR1 UniProtKB/Swiss-Prot


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
2016-07-12 LDOC1L  leucine zipper down-regulated in cancer 1 like    leucine zipper, down-regulated in cancer 1 like  Symbol and/or name change 5135510 APPROVED
2016-06-21 LDOC1L  leucine zipper, down-regulated in cancer 1 like    leucine zipper, down-regulated in cancer 1-like  Symbol and/or name change 5135510 APPROVED