Lias (lipoic acid synthetase) - Rat Genome Database

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Gene: Lias (lipoic acid synthetase) Rattus norvegicus
Analyze
Symbol: Lias
Name: lipoic acid synthetase
RGD ID: 1307270
Description: Predicted to enable lipoate synthase activity. Predicted to be involved in lipoate biosynthetic process. Predicted to act upstream of or within several processes, including neural tube closure; response to lipopolysaccharide; and response to oxidative stress. Predicted to be active in mitochondrion. Human ortholog(s) of this gene implicated in pyruvate decarboxylase deficiency. Orthologous to human LIAS (lipoic acid synthetase); PARTICIPATES IN lipoic acid metabolic pathway; INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; bisphenol A; dibutyl phthalate.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: lip-syn; lipoate synthase; lipoic acid synthase; lipoyl synthase, mitochondrial; LOC305348; LS
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
GRCr81443,230,369 - 43,247,469 (-)NCBIGRCr8
mRatBN7.21442,876,699 - 42,893,824 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1442,876,699 - 42,893,783 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1443,230,511 - 43,247,734 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01444,530,429 - 44,547,653 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01443,010,544 - 43,027,770 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01444,507,217 - 44,524,287 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1444,507,218 - 44,524,252 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01444,326,598 - 44,343,665 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41445,575,334 - 45,592,514 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11445,577,725 - 45,594,905 (-)NCBI
Celera1442,027,393 - 42,044,418 (-)NCBICelera
Cytogenetic Map14p11NCBI
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

Cellular Component
mitochondrion  (IBA,ISO)

Molecular Function

Molecular Pathway Annotations     Click to see Annotation Detail View
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. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
3. OMIM Disease Annotation Pipeline OMIM Disease Annotation Pipeline
4. KEGG Annotation Import Pipeline Pipeline to import KEGG annotations from KEGG into RGD
5. GOA pipeline RGD automated data pipeline
6. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
7. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
8. Comprehensive gene review and curation RGD comprehensive gene curation
Additional References at PubMed
PMID:11389890   PMID:12477932   PMID:14651853   PMID:15755804   PMID:18614015   PMID:18845616  


Genomics

Comparative Map Data
Lias
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81443,230,369 - 43,247,469 (-)NCBIGRCr8
mRatBN7.21442,876,699 - 42,893,824 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1442,876,699 - 42,893,783 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1443,230,511 - 43,247,734 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01444,530,429 - 44,547,653 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01443,010,544 - 43,027,770 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01444,507,217 - 44,524,287 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1444,507,218 - 44,524,252 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01444,326,598 - 44,343,665 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41445,575,334 - 45,592,514 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11445,577,725 - 45,594,905 (-)NCBI
Celera1442,027,393 - 42,044,418 (-)NCBICelera
Cytogenetic Map14p11NCBI
LIAS
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38439,459,056 - 39,479,506 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl439,459,004 - 39,485,109 (+)EnsemblGRCh38hg38GRCh38
GRCh37439,460,676 - 39,481,126 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36439,137,060 - 39,155,668 (+)NCBINCBI36Build 36hg18NCBI36
Build 34439,283,230 - 39,301,835NCBI
Celera439,898,493 - 39,917,063 (+)NCBICelera
Cytogenetic Map4p14NCBI
HuRef438,785,637 - 38,804,275 (+)NCBIHuRef
CHM1_1439,460,097 - 39,478,701 (+)NCBICHM1_1
T2T-CHM13v2.0439,428,708 - 39,449,155 (+)NCBIT2T-CHM13v2.0
Lias
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39565,548,840 - 65,567,766 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl565,548,840 - 65,568,036 (+)EnsemblGRCm39 Ensembl
GRCm38565,391,497 - 65,410,423 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl565,391,497 - 65,410,693 (+)EnsemblGRCm38mm10GRCm38
MGSCv37565,782,736 - 65,800,446 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36565,670,632 - 65,688,342 (+)NCBIMGSCv36mm8
Celera562,668,175 - 62,685,891 (+)NCBICelera
Cytogenetic Map5C3.1NCBI
cM Map533.66NCBI
Lias
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554437,889,467 - 7,907,437 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049554437,889,274 - 7,907,560 (-)NCBIChiLan1.0ChiLan1.0
LIAS
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2339,648,364 - 39,666,896 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1439,840,401 - 39,858,931 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0433,787,804 - 33,806,289 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1439,639,960 - 39,657,805 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl439,639,960 - 39,657,805 (+)Ensemblpanpan1.1panPan2
LIAS
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1372,973,527 - 72,989,522 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl372,949,512 - 72,989,487 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha375,520,382 - 75,536,407 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0373,746,941 - 73,762,971 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl373,746,936 - 73,762,912 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1373,013,540 - 73,029,564 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0373,159,817 - 73,175,837 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0373,546,343 - 73,562,369 (-)NCBIUU_Cfam_GSD_1.0
Lias
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440528539,212,659 - 39,229,901 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049364827,068,445 - 7,084,504 (+)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049364827,068,326 - 7,085,571 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
LIAS
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl830,699,330 - 30,720,335 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1830,699,278 - 30,717,009 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2832,314,342 - 32,332,042 (+)NCBISscrofa10.2Sscrofa10.2susScr3
LIAS
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12710,832,384 - 10,850,517 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl2710,829,865 - 10,850,552 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366604757,224,471 - 57,242,633 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Lias
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046248704,809,154 - 4,825,676 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Lias
49 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:58
Count of miRNA genes:46
Interacting mature miRNAs:54
Transcripts:ENSRNOT00000003779
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
2313089Bss81Bone structure and strength QTL 813.40.0001body length (VT:0001256)body length, nose to rump (CMO:0000079)143766971982669719Rat
1581500Renag1Renal agenesis QTL 1kidney development trait (VT:0000527)percentage of study population developing unilateral renal agenesis during a period of time (CMO:0000940)14817066868298175Rat
10755459Coatc15Coat color QTL 150.01681coat/hair pigmentation trait (VT:0010463)pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)141983694464836944Rat
70214Niddm28Non-insulin dependent diabetes mellitus QTL 284.06blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)143999825175582726Rat
1300154Bp189Blood pressure QTL 1893.04arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)143088377768757901Rat
70187Pancm5Pancreatic morphology QTL 516.7pancreas mass (VT:0010144)pancreas weight to body weight ratio (CMO:0000630)143032009280829842Rat
631523Pia13Pristane induced arthritis QTL 133.3joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)144079346098037301Rat
1358296Ael3Aortic elastin QTL 33.70.00051aorta elastin amount (VT:0003905)aortic elastin14826709053267090Rat
2313100Bss82Bone structure and strength QTL 8230.0001tibia size trait (VT:0100001)tibia midshaft cross-sectional area (CMO:0001717)143766971982669719Rat
7387267Uae42Urinary albumin excretion QTL 420.61urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)142216796767167967Rat
631839Niddm37Non-insulin dependent diabetes mellitus QTL 373.37blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)141103062295876975Rat
2313397Coatc1Coat color QTL1coat/hair pigmentation trait (VT:0010463)coat/hair color measurement (CMO:0001808)141854133263541332Rat
2313048Bss84Bone structure and strength QTL 843.10.0001tibia strength trait (VT:1000284)tibia total energy absorbed before break (CMO:0001736)143766971982669719Rat
1300136Rf22Renal function QTL 223.9renal blood flow trait (VT:2000006)absolute change in renal vascular resistance (CMO:0001900)144226252995023211Rat
2302045Pia39Pristane induced arthritis QTL 394.90.001blood immunoglobulin amount (VT:0002460)serum immunoglobulin G2a level (CMO:0002116)14826709053267090Rat
738037Hcas6Hepatocarcinoma susceptibility QTL 62.93liver integrity trait (VT:0010547)liver nonremodeling tumorous lesion volume to total liver volume ratio (CMO:0001464)143905723783368335Rat
2313084Bss83Bone structure and strength QTL 832.90.0001tibia size trait (VT:0100001)tibia midshaft endosteal cross-sectional area (CMO:0001716)143766971982669719Rat


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
nervous system
renal system
reproductive system
respiratory system
9 11 49 113 91 90 59 25 59 6 218 97 93 45 60 31

Sequence


Ensembl Acc Id: ENSRNOT00000003779   ⟹   ENSRNOP00000003779
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1442,876,699 - 42,893,783 (-)Ensembl
Rnor_6.0 Ensembl1444,507,218 - 44,524,252 (-)Ensembl
RefSeq Acc Id: NM_001012037   ⟹   NP_001012037
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81443,230,374 - 43,247,423 (-)NCBI
mRatBN7.21442,876,724 - 42,893,778 (-)NCBI
Rnor_6.01444,507,217 - 44,524,252 (-)NCBI
Rnor_5.01444,326,598 - 44,343,665 (-)NCBI
RGSC_v3.41445,575,334 - 45,592,514 (-)RGD
Celera1442,027,393 - 42,044,418 (-)RGD
Sequence:
RefSeq Acc Id: XM_039091920   ⟹   XP_038947848
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81443,230,369 - 43,247,469 (-)NCBI
mRatBN7.21442,876,699 - 42,893,824 (-)NCBI
RefSeq Acc Id: XM_063273134   ⟹   XP_063129204
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81443,233,586 - 43,247,469 (-)NCBI
RefSeq Acc Id: XM_063273135   ⟹   XP_063129205
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81443,233,586 - 43,247,469 (-)NCBI
RefSeq Acc Id: XM_063273136   ⟹   XP_063129206
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81443,243,414 - 43,247,469 (-)NCBI
RefSeq Acc Id: XM_063273137   ⟹   XP_063129207
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81443,230,369 - 43,247,469 (-)NCBI
RefSeq Acc Id: NP_001012037   ⟸   NM_001012037
- Peptide Label: precursor
- UniProtKB: Q5XIH4 (UniProtKB/Swiss-Prot)
- Sequence:
Ensembl Acc Id: ENSRNOP00000003779   ⟸   ENSRNOT00000003779
RefSeq Acc Id: XP_038947848   ⟸   XM_039091920
- Peptide Label: isoform X3
RefSeq Acc Id: XP_063129207   ⟸   XM_063273137
- Peptide Label: isoform X5
RefSeq Acc Id: XP_063129205   ⟸   XM_063273135
- Peptide Label: isoform X2
RefSeq Acc Id: XP_063129204   ⟸   XM_063273134
- Peptide Label: isoform X1
RefSeq Acc Id: XP_063129206   ⟸   XM_063273136
- Peptide Label: isoform X4
Protein Domains
Radical SAM core

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q5XIH4-F1-model_v2 AlphaFold Q5XIH4 1-373 view protein structure

Transcriptome

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

Promoters
RGD ID:13699315
Promoter ID:EPDNEW_R9840
Type:initiation region
Name:Lias_1
Description:lipoic acid synthetase
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_6.01444,524,257 - 44,524,317EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1307270 AgrOrtholog
BioCyc Gene G2FUF-15745 BioCyc
BioCyc Pathway PWY0-501 [lipoate biosynthesis and incorporation I] BioCyc
BioCyc Pathway Image PWY0-501 BioCyc
Ensembl Genes ENSRNOG00000002759 Ensembl, UniProtKB/Swiss-Prot
  ENSRNOG00055017981 UniProtKB/Swiss-Prot
  ENSRNOG00060015945 UniProtKB/Swiss-Prot
  ENSRNOG00065013434 UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000003779.5 UniProtKB/Swiss-Prot
  ENSRNOT00055030457 UniProtKB/Swiss-Prot
  ENSRNOT00060027312 UniProtKB/Swiss-Prot
  ENSRNOT00065022100 UniProtKB/Swiss-Prot
Gene3D-CATH 3.20.20.70 UniProtKB/Swiss-Prot
IMAGE_CLONE IMAGE:7190554 IMAGE-MGC_LOAD
InterPro Aldolase_TIM UniProtKB/Swiss-Prot
  Elp3/MiaB/NifB UniProtKB/Swiss-Prot
  LIAS_N UniProtKB/Swiss-Prot
  Lipoyl_synth UniProtKB/Swiss-Prot
  rSAM UniProtKB/Swiss-Prot
KEGG Report rno:305348 UniProtKB/Swiss-Prot
MGC_CLONE MGC:94598 IMAGE-MGC_LOAD
NCBI Gene 305348 ENTREZGENE
PANTHER LIPOYL SYNTHASE, MITOCHONDRIAL UniProtKB/Swiss-Prot
  PTHR10949 UniProtKB/Swiss-Prot
Pfam LIAS_N UniProtKB/Swiss-Prot
  Radical_SAM UniProtKB/Swiss-Prot
PhenoGen Lias PhenoGen
PIRSF Lipoyl_synth UniProtKB/Swiss-Prot
PROSITE RADICAL_SAM UniProtKB/Swiss-Prot
RatGTEx ENSRNOG00000002759 RatGTEx
  ENSRNOG00055017981 RatGTEx
  ENSRNOG00060015945 RatGTEx
  ENSRNOG00065013434 RatGTEx
SMART Elp3 UniProtKB/Swiss-Prot
Superfamily-SCOP Radical SAM enzymes UniProtKB/Swiss-Prot
UniProt LIAS_RAT UniProtKB/Swiss-Prot, ENTREZGENE


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2005-12-06 Lias  lipoic acid synthetase  Lias_predicted  lipoic acid synthetase (predicted)  Symbol and Name updated 1559027 APPROVED
2005-01-12 Lias_predicted  lipoic acid synthetase (predicted)      Symbol and Name status set to approved 70820 APPROVED