Lyrm4 (LYR motif containing 4) - Rat Genome Database

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Gene: Lyrm4 (LYR motif containing 4) Rattus norvegicus
Analyze
Symbol: Lyrm4
Name: LYR motif containing 4
RGD ID: 7672286
Description: Predicted to enable protein homodimerization activity and structural molecule activity. Predicted to be involved in [2Fe-2S] cluster assembly. Predicted to be located in nucleus. Predicted to be part of mitochondrial [2Fe-2S] assembly complex. Predicted to be active in mitochondrion. Human ortholog(s) of this gene implicated in combined oxidative phosphorylation deficiency 19. Orthologous to human LYRM4 (LYR motif containing 4); PARTICIPATES IN mitochondrial iron-sulfur cluster protein biogenesis pathway; INTERACTS WITH oxaliplatin; phosphane; tetrachloromethane.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: cDNA sequence BC034664-like; LOC100363003; LOC102550385; LYR motif-containing protein 4; LYR motif-containing protein 4-like
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Black Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: GRCr8 - GRCr8 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81728,951,912 - 29,067,300 (+)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl1728,951,924 - 29,143,177 (+)EnsemblGRCr8
mRatBN7.21728,746,457 - 28,861,849 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1728,746,469 - 28,861,750 (+)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx1728,606,677 - 28,722,099 (+)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01730,210,222 - 30,325,648 (+)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01728,582,619 - 28,697,699 (+)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.01729,439,042 - 29,552,773 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1729,438,980 - 29,552,790 (+)Ensemblrn6Rnor6.0
Rnor_5.01731,335,552 - 31,449,519 (+)NCBIRnor_5.0Rnor_5.0rn5
Celera1728,351,102 - 28,464,094 (+)NCBICelera
Cytogenetic Map17p12NCBI
JBrowse:




Disease Annotations     Click to see Annotation Detail View

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component

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. Iron-sulfur cluster biogenesis in mammalian cells: New insights into the molecular mechanisms of cluster delivery. Maio N and Rouault TA, Biochim Biophys Acta. 2015 Jun;1853(6):1493-512. doi: 10.1016/j.bbamcr.2014.09.009. Epub 2014 Sep 19.
3. OMIM Disease Annotation Pipeline OMIM Disease Annotation Pipeline
4. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
5. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:15632090   PMID:18614015  


Genomics

Comparative Map Data
Lyrm4
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81728,951,912 - 29,067,300 (+)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl1728,951,924 - 29,143,177 (+)EnsemblGRCr8
mRatBN7.21728,746,457 - 28,861,849 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1728,746,469 - 28,861,750 (+)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx1728,606,677 - 28,722,099 (+)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01730,210,222 - 30,325,648 (+)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01728,582,619 - 28,697,699 (+)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.01729,439,042 - 29,552,773 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1729,438,980 - 29,552,790 (+)Ensemblrn6Rnor6.0
Rnor_5.01731,335,552 - 31,449,519 (+)NCBIRnor_5.0Rnor_5.0rn5
Celera1728,351,102 - 28,464,094 (+)NCBICelera
Cytogenetic Map17p12NCBI
LYRM4
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh3865,031,753 - 5,260,950 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl65,102,595 - 5,260,950 (-)Ensemblhg38GRCh38
GRCh3765,068,561 - 5,261,183 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 3665,053,652 - 5,206,167 (-)NCBIBuild 36Build 36hg18NCBI36
Build 3465,053,652 - 5,206,167NCBI
Celera66,335,563 - 6,487,960 (-)NCBICelera
Cytogenetic Map6p25.1NCBI
HuRef64,983,042 - 5,135,587 (-)NCBIHuRef
CHM1_165,110,792 - 5,263,814 (-)NCBICHM1_1
T2T-CHM13v2.064,900,453 - 5,130,157 (-)NCBIT2T-CHM13v2.0
Lyrm4
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391336,162,778 - 36,301,543 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1336,162,378 - 36,301,509 (-)EnsemblGRCm39 EnsemblGRCm39
GRCm381335,978,797 - 36,117,357 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1335,978,395 - 36,117,526 (-)Ensemblmm10GRCm38
MGSCv371336,070,666 - 36,209,226 (-)NCBIMGSCv37MGSCv37mm9NCBIm37
MGSCv361335,986,262 - 36,124,795 (-)NCBIMGSCv36mm8
Celera1337,094,464 - 37,232,801 (-)NCBICelera
Cytogenetic Map13A3.3NCBI
cM Map1314.44NCBI
Lyrm4
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554658,344,965 - 8,472,816 (+)Ensembl
ChiLan1.0NW_0049554658,346,012 - 8,470,251 (+)NCBIChiLan1.0ChiLan1.0
LYRM4
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2519,660,550 - 19,890,104 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1615,684,672 - 15,894,094 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v064,887,010 - 5,096,384 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.165,126,916 - 5,279,037 (-)NCBIPanPan1.1PanPan1.1panPan2
PanPan1.1 Ensembl65,127,918 - 5,279,038 (-)EnsemblpanPan2panpan1.1
LYRM4
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1355,229,851 - 5,373,965 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha355,235,415 - 5,394,097 (-)NCBIDog10K_Boxer_TashaDog10K_Boxer_Tasha
ROS_Cfam_1.0355,299,018 - 5,458,444 (-)NCBIROS_Cfam_1.0ROS_Cfam_1.0
UMICH_Zoey_3.1355,165,491 - 5,324,206 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0355,190,998 - 5,349,956 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0356,523,175 - 6,682,769 (-)NCBIUU_Cfam_GSD_1.0UU_Cfam_GSD_1.0
Lyrm4
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440494618,936,119 - 19,081,120 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049365347,205,614 - 7,350,525 (+)EnsemblSpeTri2.0 Ensembl
SpeTri2.0NW_0049365347,205,538 - 7,350,114 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
LYRM4
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl73,070,470 - 3,192,922 (-)EnsemblsusScr11Sscrofa11.1
Sscrofa11.173,034,846 - 3,193,123 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.273,095,387 - 3,261,184 (-)NCBISscrofa10.2Sscrofa10.2susScr3
LYRM4
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11766,921,386 - 67,077,331 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl1766,921,596 - 67,076,843 (+)EnsemblChlSab1.1 EnsemblchlSab2Vervet-AGM
Vero_WHO_p1.0NW_0236660445,050,918 - 5,208,300 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Lyrm4
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462475620,017,066 - 20,152,201 (+)EnsemblHetGla_female_1.0 EnsemblhetGla2HetGla_female_1.0 Ensembl
HetGla 1.0NW_00462475620,016,773 - 20,152,201 (+)NCBIHetGla 1.0HetGla 1.0hetGla2
Lyrm4
(Rattus rattus - black rat)
Black Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rrattus_CSIRO_v11455,077,059 - 55,185,210 (-)NCBIRrattus_CSIRO_v1

Variants

.
Variants in Lyrm4
762 total Variants

QTLs in Region (GRCr8)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1354581Bp247Blood pressure QTL 2474.5arterial blood pressure trait (VT:2000000)pulse pressure (CMO:0000292)17143999106Rat
2300002Iddm36Insulin dependent diabetes mellitus QTL 361.98blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)17926675540968173Rat
8552966Pigfal18Plasma insulin-like growth factor 1 level QTL 188.7blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)171286094257860942Rat
152023626Bp403Blood pressure QTL 4033.86arterial blood pressure trait (VT:2000000)172413612784432719Rat
1300123Bp194Blood pressure QTL 1942.82arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)17212084342054133Rat
2302377Scl61Serum cholesterol level QTL 614.36blood HDL cholesterol amount (VT:0000184)serum high density lipoprotein cholesterol level (CMO:0000361)17622199858177198Rat
70157Niddm32Non-insulin dependent diabetes mellitus QTL 324.34blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)172266079955604694Rat
9589151Insul30Insulin level QTL 308.820.001blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)171286094257860942Rat
1354628Stl13Serum triglyceride level QTL 133.8blood triglyceride amount (VT:0002644)blood triglyceride level (CMO:0000118)172149899450592236Rat
1581512Cm55Cardiac mass QTL 552.80.05heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)172723344583975845Rat
10401807Kidm52Kidney mass QTL 52kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)17131706603Rat
10054088Scort28Serum corticosterone level QTL 282.040.0102blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)17473353449733534Rat
61394Bp8Blood pressure QTL 82.2arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)172328632264246472Rat
9589057Scfw6Subcutaneous fat weight QTL 68.620.001subcutaneous adipose mass (VT:1000472)abdominal subcutaneous fat pad weight (CMO:0002069)171286094257860942Rat
2317045Aia11Adjuvant induced arthritis QTL 114.06joint integrity trait (VT:0010548)left rear ankle joint diameter (CMO:0002149)172652205171522051Rat
9590154Scort9Serum corticosterone level QTL 923.570.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)171286094257860942Rat
10450503Bp386Blood pressure QTL 3860.28arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)172201970567019705Rat
1559055Bp278Blood pressure QTL 2780.04arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)172385892668858926Rat
152025238Slep14Serum leptin concentration QTL 144.62blood leptin amount (VT:0005667)172439059584432719Rat
9590088Insglur7Insulin/glucose ratio QTL 720.380.001blood insulin amount (VT:0001560)calculated plasma insulin level (CMO:0002170)171286094257860942Rat
2317053Aia25Adjuvant induced arthritis QTL 252.69joint integrity trait (VT:0010548)right rear ankle joint diameter (CMO:0002150)171060469455604694Rat
1354613Kidm14Kidney mass QTL 146.2kidney mass (VT:0002707)left kidney wet weight (CMO:0000083)17136045694Rat
1331765Hrtrt15Heart rate QTL 154.094heart pumping trait (VT:2000009)heart rate (CMO:0000002)171553702560531414Rat
7411666Foco31Food consumption QTL 3111.40.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)171286094257860942Rat
2303627Vencon8Ventilatory control QTL 80.001respiration trait (VT:0001943)tidal volume (CMO:0000222)17473353449733534Rat
12903980Cm120Cardiac mass QTL 1200.002heart right ventricle mass (VT:0007033)heart right ventricle weight to body weight ratio (CMO:0000914)172385892668858926Rat
70184BpQTLcluster14Blood pressure QTL cluster 143.38arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)17857434232199534Rat
12903981Am17Aortic mass QTL 170.001aorta mass (VT:0002845)aorta weight to aorta length to body weight ratio (CMO:0002722)172385892668858926Rat
4889955Bss93Bone structure and strength QTL 934.4tibia size trait (VT:0100001)tibia cortical bone volume to tibia total bone volume ratio (CMO:0001727)172723344565155015Rat
4889891Eae32Experimental allergic encephalomyelitis QTL 324.80.0002nervous system integrity trait (VT:0010566)experimental autoimmune encephalomyelitis severity score (CMO:0001419)172723344572233445Rat
12903982Kidm70Kidney mass QTL 700.001kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)172385892668858926Rat
631207Niddm41Non-insulin dependent diabetes mellitus QTL 41blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)17138037084Rat
12903978Cm118Cardiac mass QTL 1180.001heart mass (VT:0007028)heart wet weight to body weight ratio (CMO:0002408)172385892668858926Rat
12903979Cm119Cardiac mass QTL 1190.001heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)172385892668858926Rat
1354662Rf49Renal function QTL 492.9blood creatinine amount (VT:0005328)plasma creatinine level (CMO:0000537)17143999106Rat
152023740Bp406Blood pressure QTL 4066.06arterial blood pressure trait (VT:2000000)172413612784432719Rat
7488966Bp370Blood pressure QTL 3700.001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)172385892668858926Rat
1354658Spl8Serum phospholipid level QTL 83.8blood VLDL phospholipid amount (VT:0010507)blood very low density lipoprotein phospholipid level (CMO:0001571)17143999106Rat
152023737Bp405Blood pressure QTL 4055.06arterial blood pressure trait (VT:2000000)2413612784432719Rat
152023736Bp404Blood pressure QTL 4043.78arterial blood pressure trait (VT:2000000)172413612784432719Rat


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
musculoskeletal system
nervous system
renal system
reproductive system
respiratory system
sensory system
visual system
16 12 67 165 91 90 59 92 59 6 356 192 11 144 81 92 31 17 17

Sequence


Ensembl Acc Id: ENSRNOT00000072056   ⟹   ENSRNOP00000065815
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl1728,951,924 - 29,067,888 (+)Ensembl
mRatBN7.2 Ensembl1728,746,469 - 28,861,750 (+)Ensembl
Rnor_6.0 Ensembl1729,438,980 - 29,552,790 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000142550   ⟹   ENSRNOP00000106089
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl1728,951,926 - 29,143,177 (+)Ensembl
RefSeq Acc Id: NM_001400908   ⟹   NP_001387837
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81728,951,912 - 29,067,300 (+)NCBI
mRatBN7.21728,746,457 - 28,861,849 (+)NCBI
Protein Sequences
Protein RefSeqs NP_001387837 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein EDL98286 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000065815
  ENSRNOP00000065815.3
  ENSRNOP00000106089.1
Ensembl Acc Id: ENSRNOP00000065815   ⟸   ENSRNOT00000072056
RefSeq Acc Id: NP_001387837   ⟸   NM_001400908
- UniProtKB: A6J7D6 (UniProtKB/TrEMBL)
Ensembl Acc Id: ENSRNOP00000106089   ⟸   ENSRNOT00000142550
Protein Domains
Complex 1 LYR protein

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D3ZYM7-F1-model_v2 AlphaFold D3ZYM7 1-91 view protein structure

Transcriptome

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

Promoters
RGD ID:13700402
Promoter ID:EPDNEW_R10924
Type:initiation region
Name:Lyrm4_1
Description:LYR motif containing 4
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Alternative Promoters:null; see alsoEPDNEW_R10925  
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01729,439,046 - 29,439,106EPDNEW
RGD ID:13700403
Promoter ID:EPDNEW_R10925
Type:initiation region
Name:Lyrm4_2
Description:LYR motif containing 4
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Alternative Promoters:null; see alsoEPDNEW_R10924  
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01729,439,218 - 29,439,278EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:7672286 AgrOrtholog
BioCyc Gene G2FUF-9634 BioCyc
Ensembl Genes ENSRNOG00000047970 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000072056 ENTREZGENE
  ENSRNOT00000072056.4 UniProtKB/TrEMBL
  ENSRNOT00000142550.1 UniProtKB/TrEMBL
InterPro Complex1_LYR UniProtKB/TrEMBL
  Complex1_LYR_LYRM4 UniProtKB/TrEMBL
  ISC_assembly_LYR UniProtKB/TrEMBL
NCBI Gene LOC102550385 ENTREZGENE
PANTHER LYR MOTIF-CONTAINING PROTEIN 4 UniProtKB/TrEMBL
  PROTEIN C6ORF149 UniProtKB/TrEMBL
Pfam Complex1_LYR UniProtKB/TrEMBL
PhenoGen Lyrm4 PhenoGen
RatGTEx ENSRNOG00000047970 RatGTEx
UniProt A0ABK0LUW2_RAT UniProtKB/TrEMBL
  A6J7D6 ENTREZGENE, UniProtKB/TrEMBL
  D3ZYM7_RAT UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-10-21 Lyrm4  LYR motif containing 4  LOC102550385  LYR motif-containing protein 4-like  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2013-12-18 LOC102550385  LYR motif-containing protein 4-like      Symbol and Name status set to provisional 70820 PROVISIONAL