Lratd1 (LRAT domain containing 1) - Rat Genome Database

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Gene: Lratd1 (LRAT domain containing 1) Rattus norvegicus
Analyze
Symbol: Lratd1
Name: LRAT domain containing 1
RGD ID: 1305779
Description: Predicted to be involved in cell morphogenesis and cell motility. Orthologous to human LRATD1 (LRAT domain containing 1); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 2,3,7,8-Tetrachlorodibenzofuran; acrylamide.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: Fam84a; family with sequence similarity 84, member A; LOC313969; RGD1305779; similar to NSE1
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8642,646,515 - 42,650,988 (-)NCBIGRCr8
mRatBN7.2636,916,969 - 36,922,143 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl636,913,469 - 36,922,319 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx637,229,678 - 37,234,169 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0637,544,351 - 37,548,842 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0636,994,065 - 36,998,553 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0639,358,285 - 39,363,458 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl639,358,985 - 39,363,458 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0648,123,155 - 48,128,472 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4637,782,015 - 37,786,488 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.1637,785,856 - 37,789,250 (-)NCBI
Celera636,259,766 - 36,264,239 (-)NCBICelera
Cytogenetic Map6q15NCBI
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
cell morphogenesis  (IBA,ISO)
cell motility  (IBA,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:12477932   PMID:16820875  


Genomics

Comparative Map Data
Lratd1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8642,646,515 - 42,650,988 (-)NCBIGRCr8
mRatBN7.2636,916,969 - 36,922,143 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl636,913,469 - 36,922,319 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx637,229,678 - 37,234,169 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0637,544,351 - 37,548,842 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0636,994,065 - 36,998,553 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0639,358,285 - 39,363,458 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl639,358,985 - 39,363,458 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0648,123,155 - 48,128,472 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4637,782,015 - 37,786,488 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.1637,785,856 - 37,789,250 (-)NCBI
Celera636,259,766 - 36,264,239 (-)NCBICelera
Cytogenetic Map6q15NCBI
LRATD1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38214,632,717 - 14,651,916 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl214,632,700 - 14,650,814 (+)EnsemblGRCh38hg38GRCh38
GRCh37214,772,841 - 14,792,040 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36214,690,307 - 14,693,898 (+)NCBINCBI36Build 36hg18NCBI36
Celera214,690,800 - 14,698,160 (+)NCBICelera
Cytogenetic Map2p24.3NCBI
HuRef214,623,272 - 14,630,632 (+)NCBIHuRef
CHM1_1214,702,276 - 14,709,636 (+)NCBICHM1_1
T2T-CHM13v2.0214,663,504 - 14,682,703 (+)NCBIT2T-CHM13v2.0
Lratd1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391214,197,599 - 14,202,039 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1214,196,831 - 14,202,055 (-)EnsemblGRCm39 Ensembl
GRCm381214,147,598 - 14,152,038 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1214,146,830 - 14,152,054 (-)EnsemblGRCm38mm10GRCm38
MGSCv371214,154,404 - 14,158,844 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361214,173,138 - 14,177,578 (-)NCBIMGSCv36mm8
Celera1214,497,016 - 14,501,453 (-)NCBICelera
Cytogenetic Map12A1.1NCBI
cM Map126.93NCBI
Lratd1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554878,452,621 - 8,454,585 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049554878,452,413 - 8,454,585 (+)NCBIChiLan1.0ChiLan1.0
LOC100974506
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v212111,875,720 - 111,877,735 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan12A111,879,692 - 111,881,707 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v02A14,632,469 - 14,634,528 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.12A14,765,550 - 14,770,290 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl2A14,767,049 - 14,767,927 (+)Ensemblpanpan1.1panPan2
LRATD1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11710,658,511 - 10,660,730 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1710,659,777 - 10,660,685 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha1710,601,907 - 10,610,106 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.01710,781,633 - 10,789,835 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl1710,782,798 - 10,783,706 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.11710,646,902 - 10,655,099 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.01710,657,481 - 10,665,043 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.01710,679,556 - 10,687,756 (+)NCBIUU_Cfam_GSD_1.0
Lratd1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440629255,149,649 - 55,150,748 (+)NCBIHiC_Itri_2
SpeTri2.0NW_00493735985,928 - 86,755 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
LRATD1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl3122,716,040 - 122,731,791 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.13122,716,029 - 122,720,957 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.23143,905,448 - 143,910,293 (-)NCBISscrofa10.2Sscrofa10.2susScr3
LRATD1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11493,016,709 - 93,022,670 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl1493,020,404 - 93,021,282 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366604519,244,941 - 19,251,510 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Lratd1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046248651,721,911 - 1,724,115 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046248651,719,711 - 1,724,056 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Lratd1
17 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:380
Count of miRNA genes:212
Interacting mature miRNAs:277
Transcripts:ENSRNOT00000065531
Prediction methods:Miranda, Rnahybrid, Targetscan
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
1578758Tcas9Tongue tumor susceptibility QTL 93.29tongue integrity trait (VT:0010553)number of squamous cell tumors of the tongue with diameter greater than 3 mm (CMO:0001950)6137618905Rat
1598843Cm63Cardiac mass QTL 632.6heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)6139036266Rat
7411603Foco13Food consumption QTL 135.50.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)6141223769Rat
8552962Pigfal16Plasma insulin-like growth factor 1 level QTL 169.4blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)6141223769Rat
7411542Bw127Body weight QTL 1275.50.001body mass (VT:0001259)body weight gain (CMO:0000420)6141223769Rat
9589129Insul24Insulin level QTL 2419.060.001blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)6141223769Rat
9589048Scfw3Subcutaneous fat weight QTL 34.570.001subcutaneous adipose mass (VT:1000472)abdominal subcutaneous fat pad weight (CMO:0002069)6141223769Rat
2293709Bss23Bone structure and strength QTL 235.180.0001femur morphology trait (VT:0000559)femur cross-sectional area (CMO:0001661)6142487980Rat
2293650Bss31Bone structure and strength QTL 315.050.0001femur strength trait (VT:0010010)femur midshaft polar moment of inertia (CMO:0001669)6142487980Rat
2293656Bss28Bone structure and strength QTL 286.790.0001femur morphology trait (VT:0000559)femur midshaft cortical cross-sectional area (CMO:0001663)6142487980Rat
7411584Foco4Food consumption QTL 44.30.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)6142838846Rat
738024Sach5Saccharine consumption QTL 53.90.00039consumption behavior trait (VT:0002069)saccharin intake volume to total fluid intake volume ratio (CMO:0001601)6143394190Rat
2301972Bp325Blood pressure QTL 3254.8arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)6172227641Rat
1300164Rf15Renal function QTL 153.12renal blood flow trait (VT:2000006)absolute change in renal blood flow rate (CMO:0001168)6507449754641141Rat
4145119Mcs25Mammary carcinoma susceptibility QTL 250.0001mammary gland integrity trait (VT:0010552)ratio of deaths to total study population during a period of time (CMO:0001023)610894415110548006Rat
1578665Bss16Bone structure and strength QTL 164.4femur morphology trait (VT:0000559)bone trabecular cross-sectional area (CMO:0002311)61173566972593685Rat
1578668Bmd14Bone mineral density QTL 143.8femur mineral mass (VT:0010011)total volumetric bone mineral density (CMO:0001728)61173566972593685Rat
10401812Kidm54Kidney mass QTL 54kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)61436878859368788Rat
10401800Kidm49Kidney mass QTL 49kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)61436878859368788Rat
1576309Emca7Estrogen-induced mammary cancer QTL 74mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)615107216107351382Rat
2292589Emca10Estrogen-induced mammary cancer QTL 100.048mammary gland integrity trait (VT:0010552)post-insult time to mammary tumor formation (CMO:0000345)61653614061536140Rat
1354664Slep2Serum leptin concentration QTL 24.49blood leptin amount (VT:0005667)serum leptin level (CMO:0000780)61653614071636405Rat
1641898Colcr4Colorectal carcinoma resistance QTL43.710.0007intestine integrity trait (VT:0010554)well differentiated malignant colorectal tumor surface area measurement (CMO:0002077)62033877762613667Rat
2293839Kiddil2Kidney dilation QTL 24.8kidney pelvis morphology trait (VT:0004194)hydronephrosis severity score (CMO:0001208)62086642281133036Rat
2293841Kiddil4Kidney dilation QTL 44.4kidney pelvis morphology trait (VT:0004194)hydronephrosis severity score (CMO:0001208)62086642281133036Rat
1331779Rf38Renal function QTL 382.876kidney blood vessel physiology trait (VT:0100012)absolute change in renal vascular resistance (CMO:0001900)63207442872227641Rat
634318Bw118Body weight QTL 1183.55abdominal fat pad mass (VT:1000711)abdominal fat pad weight (CMO:0000088)63330954957730294Rat
6893340Cm77Cardiac mass QTL 770.260.57heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)63330954981132889Rat
1300143Rf14Renal function QTL 142.92renal blood flow trait (VT:2000006)absolute change in renal blood flow rate (CMO:0001168)63443413777102317Rat
1354632Scl29Serum cholesterol level QTL 293.74blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)63509870971636405Rat
634307Bp141Blood pressure QTL 1414arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)63523041780230417Rat
70199Coreg1Compensatory renal growth QTL 111.8kidney mass (VT:0002707)compensatory renal growth score (CMO:0001894)63569161857730540Rat

Markers in Region
RH142890  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2636,916,970 - 36,917,070 (+)MAPPERmRatBN7.2
Rnor_6.0639,358,287 - 39,358,386NCBIRnor6.0
Rnor_5.0648,123,157 - 48,123,256UniSTSRnor5.0
RGSC_v3.4637,781,317 - 37,781,416UniSTSRGSC3.4
Celera636,259,068 - 36,259,167UniSTS
RH 3.4 Map6147.5UniSTS
Cytogenetic Map6q15UniSTS
RH141825  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2636,917,961 - 36,918,144 (+)MAPPERmRatBN7.2
Rnor_6.0639,359,278 - 39,359,460NCBIRnor6.0
Rnor_5.0648,124,148 - 48,124,330UniSTSRnor5.0
RGSC_v3.4637,782,308 - 37,782,490UniSTSRGSC3.4
Celera636,260,059 - 36,260,241UniSTS
RH 3.4 Map6144.2UniSTS
Cytogenetic Map6q15UniSTS


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 70 24 24 4
Low 3 20 16 4 7 4 1 1 4 11 17 7 1
Below cutoff 20 30 26 7 26 7 9 7

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000065531   ⟹   ENSRNOP00000060795
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl636,917,669 - 36,922,143 (-)Ensembl
Rnor_6.0 Ensembl639,358,985 - 39,363,458 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000088687   ⟹   ENSRNOP00000069863
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl636,913,469 - 36,922,319 (-)Ensembl
Rnor_6.0 Ensembl639,359,118 - 39,363,367 (-)Ensembl
RefSeq Acc Id: NM_001127299   ⟹   NP_001120771
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8642,646,515 - 42,650,988 (-)NCBI
mRatBN7.2636,917,669 - 36,922,143 (-)NCBI
Rnor_6.0639,358,985 - 39,363,458 (-)NCBI
Rnor_5.0648,123,155 - 48,128,472 (-)NCBI
RGSC_v3.4637,782,015 - 37,786,488 (-)RGD
Celera636,259,766 - 36,264,239 (-)RGD
Sequence:
Protein Sequences
Protein RefSeqs NP_001120771 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAI66716 (Get FASTA)   NCBI Sequence Viewer  
  EDM03123 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000060795
  ENSRNOP00000060795.1
  ENSRNOP00000069863.1
Reference Protein Sequences
RefSeq Acc Id: NP_001120771   ⟸   NM_001127299
- UniProtKB: G3V9V1 (UniProtKB/TrEMBL),   A6HAR8 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000060795   ⟸   ENSRNOT00000065531
RefSeq Acc Id: ENSRNOP00000069863   ⟸   ENSRNOT00000088687
Protein Domains
LRAT

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-G3V9V1-F1-model_v2 AlphaFold G3V9V1 1-320 view protein structure

Transcriptome

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

Promoters
RGD ID:13694505
Promoter ID:EPDNEW_R5026
Type:single initiation site
Name:Fam84a_1
Description:family with sequence similarity 84, member A
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0639,363,374 - 39,363,434EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1305779 AgrOrtholog
BioCyc Gene G2FUF-38111 BioCyc
Ensembl Genes ENSRNOG00000004084 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000065531 ENTREZGENE
  ENSRNOT00000065531.2 UniProtKB/TrEMBL
  ENSRNOT00000088687.2 UniProtKB/TrEMBL
Gene3D-CATH endopeptidase domain like (from Nostoc punctiforme) UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:7930888 IMAGE-MGC_LOAD
InterPro LRAT_dom UniProtKB/TrEMBL
  LRATD1_LRATD2 UniProtKB/TrEMBL
KEGG Report rno:313969 UniProtKB/TrEMBL
MGC_CLONE MGC:188417 IMAGE-MGC_LOAD
NCBI Gene 313969 ENTREZGENE
PANTHER PROTEIN LRATD1 UniProtKB/TrEMBL
  PTHR46341 UniProtKB/TrEMBL
Pfam LRAT UniProtKB/TrEMBL
PhenoGen Lratd1 PhenoGen
PROSITE LRAT UniProtKB/TrEMBL
RatGTEx ENSRNOG00000004084 RatGTEx
UniProt A6HAR8 ENTREZGENE, UniProtKB/TrEMBL
  B2RYB4_RAT UniProtKB/TrEMBL
  G3V9V1 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2019-04-10 Lratd1  LRAT domain containing 1  Fam84a  family with sequence similarity 84, member A  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-03-06 Fam84a  family with sequence similarity 84, member A  RGD1305779_predicted  similar to NSE1 (predicted)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2005-01-20 RGD1305779_predicted  similar to NSE1 (predicted)  LOC313969_predicted    Symbol and Name status set to approved 1331353 APPROVED
2005-01-12 LOC313969_predicted  similar to NSE1 (predicted)      Symbol and Name status set to provisional 70820 PROVISIONAL