Lyrm4 (LYR motif containing 4) - Rat Genome Database

Send us a Message



Submit Data |  Help |  Video Tutorials |  News |  Publications |  Download |  REST API |  Citing RGD |  Contact   
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. Predicted to be involved in [2Fe-2S] cluster assembly. Predicted to be located in nuclear body. Predicted to be part of L-cysteine desulfurase complex and mitochondrial iron-sulfur cluster 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
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21728,746,442 - 28,861,849 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1728,746,469 - 28,861,750 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1728,606,677 - 28,722,099 (+)NCBIRnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.01730,210,222 - 30,325,648 (+)NCBIRnor_SHRSP
UTH_Rnor_WKY_Bbb_1.01728,582,619 - 28,697,699 (+)NCBIRnor_WKY
Rnor_6.01729,439,042 - 29,552,773 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1729,438,980 - 29,552,790 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01731,335,552 - 31,449,519 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
Celera1728,351,102 - 28,464,094 (+)NCBICelera
Cytogenetic Map17p12NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene-Chemical Interaction 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
mRatBN7.21728,746,442 - 28,861,849 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1728,746,469 - 28,861,750 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1728,606,677 - 28,722,099 (+)NCBIRnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.01730,210,222 - 30,325,648 (+)NCBIRnor_SHRSP
UTH_Rnor_WKY_Bbb_1.01728,582,619 - 28,697,699 (+)NCBIRnor_WKY
Rnor_6.01729,439,042 - 29,552,773 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1729,438,980 - 29,552,790 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01731,335,552 - 31,449,519 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
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.p13 Ensembl65,103,629 - 5,260,950 (-)EnsemblGRCh38hg38GRCh38
GRCh3765,068,561 - 5,261,183 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 3665,053,652 - 5,206,167 (-)NCBINCBI36Build 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-CHM13v2.064,937,542 - 5,130,157 (-)NCBIT2T-CHM13v2.0
Lyrm4
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391336,162,780 - 36,301,340 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1336,162,378 - 36,301,509 (-)EnsemblGRCm39 Ensembl
GRCm381335,978,797 - 36,117,357 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1335,978,395 - 36,117,526 (-)EnsemblGRCm38mm10GRCm38
MGSCv371336,070,666 - 36,209,226 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361335,986,262 - 36,124,795 (-)NCBIMGSCv36mm8
Celera1337,094,464 - 37,232,801 (-)NCBICelera
Cytogenetic Map13A3.3NCBI
Lyrm4
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0NW_0049554658,346,012 - 8,470,251 (+)NCBIChiLan1.0ChiLan1.0
LYRM4
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.165,126,916 - 5,279,037 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl65,127,918 - 5,279,038 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v064,887,010 - 5,096,384 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
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_Tasha
ROS_Cfam_1.0355,299,018 - 5,458,444 (-)NCBIROS_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_1.0
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
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 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
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 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
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_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_00462475620,016,773 - 20,152,201 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Lyrm4
501 total Variants

QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
10401807Kidm52Kidney mass QTL 52kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)17131701463Rat
70184BpQTLcluster14Blood pressure QTL cluster 143.38arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)17131990913Rat
631207Niddm41Non-insulin dependent diabetes mellitus QTL 41blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)17137830672Rat
1354658Spl8Serum phospholipid level QTL 83.8blood VLDL phospholipid amount (VT:0010507)blood very low density lipoprotein phospholipid level (CMO:0001571)17160781592Rat
1354581Bp247Blood pressure QTL 2474.5arterial blood pressure trait (VT:2000000)pulse pressure (CMO:0000292)17169599340Rat
1354662Rf49Renal function QTL 492.9blood creatinine amount (VT:0005328)plasma creatinine level (CMO:0000537)17169599340Rat
1300123Bp194Blood pressure QTL 1942.82arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)17211514934551001Rat
1354613Kidm14Kidney mass QTL 146.2kidney mass (VT:0002707)left kidney wet weight (CMO:0000083)17429913035837242Rat
1354596Bw32Body weight QTL 324.5body mass (VT:0001259)body weight (CMO:0000012)17429913060781592Rat
1354630Cm34Cardiac mass QTL 348.7heart left ventricle mass (VT:0007031)heart left ventricle wet weight (CMO:0000071)17429913069599340Rat
1354638Insul1Insulin level QTL 14.8blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)17429913069599340Rat
1354651Lmblg2Limb length QTL 26tibia length (VT:0004357)tibia length (CMO:0000450)17429913069599340Rat
2303627Vencon8Ventilatory control QTL 80.001respiration trait (VT:0001943)tidal volume (CMO:0000222)17452803849528038Rat
10054088Scort28Serum corticosterone level QTL 282.040.0102blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)17452803849528038Rat
2303561Bw91Body weight QTL 912body mass (VT:0001259)body weight (CMO:0000012)17886846253868462Rat
2300002Iddm36Insulin dependent diabetes mellitus QTL 361.98blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)17999128640540197Rat
1331765Hrtrt15Heart rate QTL 154.094heart pumping trait (VT:2000009)heart rate (CMO:0000002)171533061355836425Rat
1354640Scl32Serum cholesterol level QTL 325.4blood HDL cholesterol amount (VT:0000184)blood high density lipoprotein cholesterol level (CMO:0000052)171578159260781592Rat
1354659Scl68Serum cholesterol level QTL 683.9blood VLDL cholesterol amount (VT:0005144)blood very low density lipoprotein cholesterol level (CMO:0000648)171578159260781592Rat
7394837Memor18Memory QTL 18exploratory behavior trait (VT:0010471)measurement of voluntary locomotion into, out of or within a discrete space in an experimental apparatus (CMO:0000957)171864018263640182Rat
1354628Stl13Serum triglyceride level QTL 133.8blood triglyceride amount (VT:0002644)blood triglyceride level (CMO:0000118)172129303960781592Rat
70157Niddm32Non-insulin dependent diabetes mellitus QTL 324.34blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)172245492450909196Rat
61394Bp8Blood pressure QTL 82.2arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)172308056759555013Rat
7488966Bp370Blood pressure QTL 3700.001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)172365318457246843Rat
12903978Cm118Cardiac mass QTL 1180.001heart mass (VT:0007028)heart wet weight to body weight ratio (CMO:0002408)172365318468653184Rat
12903979Cm119Cardiac mass QTL 1190.001heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)172365318468653184Rat
12903980Cm120Cardiac mass QTL 1200.002heart right ventricle mass (VT:0007033)heart right ventricle weight to body weight ratio (CMO:0000914)172365318468653184Rat
12903981Am17Aortic mass QTL 170.001aorta mass (VT:0002845)aorta weight to aorta length to body weight ratio (CMO:0002722)172365318468653184Rat
1559055Bp278Blood pressure QTL 2780.04arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)172365318468653184Rat
12903982Kidm70Kidney mass QTL 700.001kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)172365318470974005Rat
1354619Bp242Blood pressure QTL 2426.3arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)172459934069599340Rat
4889891Eae32Experimental allergic encephalomyelitis QTL 324.80.0002nervous system integrity trait (VT:0010566)experimental autoimmune encephalomyelitis severity score (CMO:0001419)172702794936146731Rat
1581512Cm55Cardiac mass QTL 552.80.05heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)172702794956836890Rat
4889955Bss93Bone structure and strength QTL 934.4tibia size trait (VT:0100001)tibia cortical bone volume to tibia total bone volume ratio (CMO:0001727)172702794960463643Rat
2302377Scl61Serum cholesterol level QTL 614.36blood HDL cholesterol amount (VT:0000184)serum high density lipoprotein cholesterol level (CMO:0000361)172738994653481766Rat
8552928Pigfal9Plasma insulin-like growth factor 1 level QTL 99blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)172840914773409147Rat
9590107Sffal7Serum free fatty acids level QTL 74.810.001blood free fatty acid amount (VT:0001553)plasma free fatty acids level (CMO:0000546)172840914773409147Rat


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 2 31 38 24 17 24 74 35 41 11
Low 1 12 19 17 2 17 8 11 8
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000072056   ⟹   ENSRNOP00000065815
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1728,746,469 - 28,861,750 (+)Ensembl
Rnor_6.0 Ensembl1729,438,980 - 29,552,790 (+)Ensembl
RefSeq Acc Id: XM_006253859   ⟹   XP_006253921
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21728,746,442 - 28,861,849 (+)NCBI
Rnor_6.01729,439,042 - 29,552,773 (+)NCBI
Rnor_5.01731,335,552 - 31,449,519 (+)NCBI
Sequence:
Protein Sequences
Protein RefSeqs NP_001387837 (Get FASTA)   NCBI Sequence Viewer  
  XP_006253921 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein EDL98286 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: XP_006253921   ⟸   XM_006253859
- UniProtKB: D3ZYM7 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000065815   ⟸   ENSRNOT00000072056

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, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000065815.2 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000072056.3 UniProtKB/TrEMBL
InterPro Complex1_LYR UniProtKB/TrEMBL
  Complex1_LYR_LYRM4 UniProtKB/TrEMBL
KEGG Report rno:102550385 UniProtKB/TrEMBL
NCBI Gene LOC102550385 ENTREZGENE
Pfam Complex1_LYR UniProtKB/TrEMBL
PhenoGen Lyrm4 PhenoGen
UniProt D3ZYM7 ENTREZGENE, 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