Lage3 (L antigen family, member 3) - Rat Genome Database

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Gene: Lage3 (L antigen family, member 3) Rattus norvegicus
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Symbol: Lage3
Name: L antigen family, member 3
RGD ID: 1562476
Description: Predicted to be involved in tRNA threonylcarbamoyladenosine metabolic process. Predicted to be located in cytoplasm and nuclear body. Predicted to be part of EKC/KEOPS complex. Human ortholog(s) of this gene implicated in Galloway-Mowat syndrome 2. Orthologous to human LAGE3 (L antigen family member 3); INTERACTS WITH (+)-schisandrin B; 2,3,7,8-tetrachlorodibenzodioxine; bisphenol A.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: EKC/KEOPS complex subunit LAGE3; L antigen family member 3; LOC293863; RGD1562476; similar to Eso3 protein
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8X157,289,497 - 157,290,920 (-)NCBIGRCr8
mRatBN7.2X152,138,209 - 152,139,632 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 EnsemblX152,138,218 - 152,139,632 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_UtxX154,279,337 - 154,280,760 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0X157,842,563 - 157,843,986 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0X155,514,361 - 155,515,790 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0X156,355,376 - 156,356,799 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 EnsemblX156,355,376 - 156,356,799 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01152,095,511 - 152,096,934 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4X160,253,757 - 160,255,180 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera1135,757,019 - 135,758,442 (+)NCBICelera
Cytogenetic MapXq37NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component
cytoplasm  (ISO)
EKC/KEOPS complex  (IBA,ISO)
nuclear body  (ISO)
nucleoplasm  (ISO)
nucleus  (ISO)

Molecular Function

References

References - curated
# Reference Title Reference Citation
1. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
2. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:27903914   PMID:28805828  


Genomics

Comparative Map Data
Lage3
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8X157,289,497 - 157,290,920 (-)NCBIGRCr8
mRatBN7.2X152,138,209 - 152,139,632 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 EnsemblX152,138,218 - 152,139,632 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_UtxX154,279,337 - 154,280,760 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0X157,842,563 - 157,843,986 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0X155,514,361 - 155,515,790 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0X156,355,376 - 156,356,799 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 EnsemblX156,355,376 - 156,356,799 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01152,095,511 - 152,096,934 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4X160,253,757 - 160,255,180 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera1135,757,019 - 135,758,442 (+)NCBICelera
Cytogenetic MapXq37NCBI
LAGE3
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38X154,477,775 - 154,479,281 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 EnsemblX154,477,775 - 154,479,281 (-)EnsemblGRCh38hg38GRCh38
GRCh37X153,706,114 - 153,707,620 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36X153,358,435 - 153,360,790 (-)NCBINCBI36Build 36hg18NCBI36
CeleraX153,866,292 - 153,868,647 (-)NCBICelera
Cytogenetic MapXq28NCBI
HuRefX142,282,633 - 142,284,801 (-)NCBIHuRef
CHM1_1X153,616,885 - 153,619,241 (-)NCBICHM1_1
T2T-CHM13v2.0X152,714,284 - 152,715,790 (-)NCBIT2T-CHM13v2.0
Lage3
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39X73,395,768 - 73,397,224 (-)NCBIGRCm39GRCm39mm39
GRCm39 EnsemblX73,394,882 - 73,397,224 (-)EnsemblGRCm39 Ensembl
GRCm38X74,352,162 - 74,353,618 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 EnsemblX74,351,276 - 74,353,618 (-)EnsemblGRCm38mm10GRCm38
MGSCv37X71,597,501 - 71,598,957 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36X70,604,882 - 70,606,338 (-)NCBIMGSCv36mm8
CeleraX65,605,935 - 65,607,391 (-)NCBICelera
Cytogenetic MapXA7.3NCBI
cM MapX38.0NCBI
Lage3
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_004955580992,190 - 993,617 (-)EnsemblChiLan1.0
ChiLan1.0NW_004955580992,190 - 993,617 (-)NCBIChiLan1.0ChiLan1.0
LAGE3
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2X154,452,148 - 154,454,230 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1X154,455,753 - 154,457,259 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0X143,919,519 - 143,921,001 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1X153,790,497 - 153,791,581 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 EnsemblX153,790,672 - 153,792,549 (-)Ensemblpanpan1.1panPan2
LAGE3
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1X122,185,300 - 122,186,498 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
ROS_Cfam_1.0X125,326,940 - 125,328,145 (-)NCBIROS_Cfam_1.0
UMICH_Zoey_3.1X121,095,948 - 121,097,132 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0X123,611,147 - 123,612,224 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0X123,372,790 - 123,373,977 (-)NCBIUU_Cfam_GSD_1.0
Lage3
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2X119,492,159 - 119,494,582 (-)NCBIHiC_Itri_2
SpeTri2.0NW_0049368091,229,933 - 1,232,448 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
LOC100515685
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.11221,086,937 - 21,088,914 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21221,508,394 - 21,510,252 (+)NCBISscrofa10.2Sscrofa10.2susScr3
LAGE3
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1X128,725,788 - 128,727,565 (-)NCBIChlSab1.1ChlSab1.1chlSab2
Vero_WHO_p1.0NW_02366606566,714,371 - 66,716,168 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Lage3
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_004624946949,343 - 953,362 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_004624946951,479 - 952,962 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Lage3
1 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:39
Count of miRNA genes:38
Interacting mature miRNAs:39
Transcripts:ENSRNOT00000056312
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 (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
10059603Bw174Body weight QTL 1743.40.025body mass (VT:0001259)body weight (CMO:0000012)X113937816152453651Rat
634346Insul4Insulin level QTL 40blood insulin amount (VT:0001560)serum insulin level (CMO:0000358)X126975089152453651Rat

Markers in Region
AI102991  
Rat AssemblyChrPosition (strand)SourceJBrowse
RH 3.4 Map1906.4UniSTS
Cytogenetic MapXq37UniSTS


Expression


RNA-SEQ Expression
High: > 1000 TPM value   Medium: Between 11 and 1000 TPM
Low: Between 0.5 and 10 TPM   Below Cutoff: < 0.5 TPM

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system appendage
High
Medium 3 43 57 41 19 41 8 11 74 35 37 11 8
Low 4
Below cutoff

Sequence


RefSeq Acc Id: ENSRNOT00000078304   ⟹   ENSRNOP00000069114
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 EnsemblX152,138,218 - 152,139,632 (-)Ensembl
Rnor_6.0 EnsemblX156,355,376 - 156,356,799 (+)Ensembl
RefSeq Acc Id: NM_001106345   ⟹   NP_001099815
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8X157,289,497 - 157,290,920 (-)NCBI
mRatBN7.2X152,138,209 - 152,139,632 (-)NCBI
Rnor_6.0X156,355,376 - 156,356,799 (+)NCBI
Rnor_5.01152,095,511 - 152,096,934 (+)NCBI
RGSC_v3.4X160,253,757 - 160,255,180 (+)RGD
Celera1135,757,019 - 135,758,442 (+)NCBI
Sequence:
Protein Sequences
Protein RefSeqs NP_001099815 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein EDL84971 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000069114.2
RefSeq Acc Id: NP_001099815   ⟸   NM_001106345
- UniProtKB: A6KRQ5 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000069114   ⟸   ENSRNOT00000078304

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D3ZPW6-F1-model_v2 AlphaFold D3ZPW6 1-148 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:1562476 AgrOrtholog
BioCyc Gene G2FUF-623 BioCyc
Ensembl Genes ENSRNOG00000053456 Ensembl, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000078304.2 UniProtKB/TrEMBL
Gene3D-CATH Alpha-D-phosphohexomutase, C-terminal domain UniProtKB/TrEMBL
InterPro EKC/KEOPS_Pcc1 UniProtKB/TrEMBL
KEGG Report rno:293863 UniProtKB/TrEMBL
NCBI Gene 293863 ENTREZGENE
PANTHER EKC/KEOPS COMPLEX SUBUNIT LAGE3 UniProtKB/TrEMBL
  PTHR31283 UniProtKB/TrEMBL
Pfam Pcc1 UniProtKB/TrEMBL
PhenoGen Lage3 PhenoGen
RatGTEx ENSRNOG00000053456 RatGTEx
UniProt A6KRQ5 ENTREZGENE, UniProtKB/TrEMBL
  D3ZPW6_RAT UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-02-29 Lage3  L antigen family, member 3  RGD1562476_predicted  similar to Eso3 protein (predicted)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-03-07 RGD1562476_predicted  similar to Eso3 protein (predicted)  LOC293863  similar to Eso3 protein  Symbol and Name status set to approved 1299863 APPROVED
2006-02-09 LOC293863  similar to Eso3 protein      Symbol and Name status set to provisional 70820 PROVISIONAL