Lyrm4 (LYR motif containing 4) - Rat Genome Database

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Gene: Lyrm4 (LYR motif containing 4) Mus musculus
Analyze
Symbol: Lyrm4
Name: LYR motif containing 4
RGD ID: 1614030
MGI Page MGI
Description: Predicted to enable protein homodimerization activity. Predicted to be involved in [2Fe-2S] cluster assembly. Located in mitochondrion. Part of mitochondrial iron-sulfur cluster assembly complex. Human ortholog(s) of this gene implicated in combined oxidative phosphorylation deficiency 19. Orthologous to human LYRM4 (LYR motif containing 4).
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: BC034664; Gm903; LYR motif-containing protein 4; MGC38622
RGD Orthologs
Human
Rat
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: GRCm39 - Mouse Genome Assembly GRCm39
Position:
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391336,162,778 - 36,301,543 (-)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
cM Map1314.44NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


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. 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.
2. OMIM Disease Annotation Pipeline OMIM Disease Annotation Pipeline
3. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
4. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:8889548   PMID:10349636   PMID:11042159   PMID:11076861   PMID:11217851   PMID:12466851   PMID:12477932   PMID:12520002   PMID:14610273   PMID:15489334   PMID:16141072   PMID:16141073  
PMID:18614015   PMID:18799693   PMID:21298097   PMID:21873635   PMID:25597503   PMID:27519411   PMID:29097656   PMID:30550785   PMID:32325033  


Genomics

Comparative Map Data
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 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
cM Map1314.44NCBI
LYRM4
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh3865,031,753 - 5,260,950 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 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-CHM13v2.064,900,453 - 5,130,157 (-)NCBIT2T-CHM13v2.0
Lyrm4
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81728,951,912 - 29,067,300 (+)NCBIGRCr8
mRatBN7.21728,746,457 - 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_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01730,210,222 - 30,325,648 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01728,582,619 - 28,697,699 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
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
(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
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 (-)Ensemblpanpan1.1panPan2
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 (+)EnsemblSpeTri2.0SpeTri2.0 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 (-)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
3972 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:367
Count of miRNA genes:280
Interacting mature miRNAs:322
Transcripts:ENSMUST00000053265
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 (GRCm39)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1301455Bmd3_mbone mineral density 3 (mouse)Not determined13347761237477820Mouse
10045624Heal24_mwound healing/regeneration (mouse)Not determined13347761237477820Mouse
10045625Heal23_mwound healing/regeneration 23 (mouse)Not determined13347761237477820Mouse
1301367Twq1_mtestis weight QTL 1 (mouse)Not determined13361551237615672Mouse
1301733Heal3_mwound healing/regeneration 3 (mouse)Not determined13368020037680343Mouse
26884393Humsd7_mhumerus midshaft diameter 7, 16 week (mouse)13395000076048119Mouse
1558898Hpi1_mhapatic PMN infiltration 1 (mouse)Not determined13441402553101640Mouse
10402494Igmsc1_mimmunoglobulin M secreting cells 1 (mouse)Not determined131716854544918560Mouse
1301984Pbd2_mpeak bone density 2 (mouse)Not determined131718950838947406Mouse
1301880Hypt_mhypertension (mouse)Not determined131815679252156924Mouse
13463469Gssq1_mglomerulosclerosis severity QTL 1 (mouse)131906090853061050Mouse
12880423V25Dq7_mvitamin D inactive form serum level QTL 7 (mouse)131958398353583983Mouse
1301015Sysbp2_msystolic blood pressure 2 (mouse)Not determined132047761259821605Mouse
4142147Mvwf4_mmodifier of von Willebrand factor 4 (mouse)Not determined20477612112898424Mouse
1357591Tesq1_mtestis weight QTL 1 (mouse)Not determined132061551255720517Mouse
4142009Pregq3_mpregnancy QTL 3 (mouse)Not determined132061551272385189Mouse
10045618Heal17_mwound healing/regeneration 17 (mouse)Not determined132074693954747056Mouse
4142489Ath25_matherosclerosis 25 (mouse)Not determined2583652959836529Mouse
10401111Pgia40_mproteoglycan induced arthritis 40 (mouse)Not determined132791846961918560Mouse
1300710Pcd4ts2_mp-glycoprotein positive CD4 T cell subset 2 (mouse)Not determined132821044262210544Mouse
1357802Vtbt15_mvertebral trabecular bone trait 15 (mouse)Not determined132821737962217515Mouse
10045621Heal21_mwound healing/regeneration 21 (mouse)Not determined132821737962217515Mouse
10755533Chol18_mcholesterol 18 (mouse)133096946764969467Mouse
10755517Chol15_mcholesterol 15 (mouse)133096946764969467Mouse
12738439Twq4_mtestis weight QTL 4 (mouse)133112911065129110Mouse
14696729Kidlq2_mkidney weight, left QTL 2 (mouse)133134473665344736Mouse
1301299Sluc23_msusceptibility to lung cancer 23 (mouse)Not determined133492194368922081Mouse
10412235Scgq5_mspontaneous crescentic glomerulonephritis QTL 5 (mouse)Not determined133606090896239162Mouse
1357587Pfat3_mpredicted fat percentage 3 (mouse)Not determined133610153070101640Mouse
1301734Acsns2_mAngiostrongylus costaricensis nematode susceptibility 2 (mouse)Not determined133610153070101640Mouse
1300561Heal7_mwound healing/regeneration 7 (mouse)Not determined133614482070144904Mouse

Markers in Region
UniSTS:236993  
Mouse AssemblyChrPosition (strand)SourceJBrowse
GRCm381335,979,630 - 35,979,842UniSTSGRCm38
MGSCv371336,071,499 - 36,071,711UniSTSGRCm37
Celera1337,095,297 - 37,095,509UniSTS
Cytogenetic Map13A3.3UniSTS
UniSTS:488776  
Mouse AssemblyChrPosition (strand)SourceJBrowse
GRCm381335,990,485 - 35,991,546UniSTSGRCm38
MGSCv371336,082,354 - 36,083,415UniSTSGRCm37
Celera1337,106,159 - 37,107,220UniSTS
Cytogenetic Map13A3.3UniSTS
Cytogenetic Map12D2UniSTS


Expression


Sequence


Reference Sequences
RefSeq Acc Id: ENSMUST00000053265   ⟹   ENSMUSP00000060779
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl1336,162,378 - 36,301,509 (-)Ensembl
GRCm38.p6 Ensembl1335,978,395 - 36,117,526 (-)Ensembl
RefSeq Acc Id: NM_201358   ⟹   NP_958746
RefSeq Status: VALIDATED
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm391336,162,778 - 36,301,543 (-)NCBI
GRCm381335,978,797 - 36,117,357 (-)ENTREZGENE
MGSCv371336,070,666 - 36,209,226 (-)RGD
Celera1337,094,464 - 37,232,801 (-)RGD
cM Map13 ENTREZGENE
Sequence:
Protein Sequences
Protein RefSeqs NP_958746 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAH34664 (Get FASTA)   NCBI Sequence Viewer  
  AAH80772 (Get FASTA)   NCBI Sequence Viewer  
  BAC34321 (Get FASTA)   NCBI Sequence Viewer  
  EDL40910 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSMUSP00000060779
  ENSMUSP00000060779.7
GenBank Protein Q8K215 (Get FASTA)   NCBI Sequence Viewer  
Reference Protein Sequences
RefSeq Acc Id: NP_958746   ⟸   NM_201358
- UniProtKB: Q8K215 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSMUSP00000060779   ⟸   ENSMUST00000053265

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q8K215-F1-model_v2 AlphaFold Q8K215 1-91 view protein structure

Promoters
RGD ID:8680100
Promoter ID:EPDNEW_M18081
Type:multiple initiation site
Name:Lyrm4_1
Description:Mus musculus LYR motif containing 4 , mRNA.
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm381336,117,270 - 36,117,330EPDNEW
RGD ID:6823893
Promoter ID:MM_KWN:13822
Type:CpG-Island
SO ACC ID:SO:0000170
Source:MPROMDB
Tissues & Cell Lines:3T3L1_Day0,   3T3L1_Day2,   3T3L1_Day3,   BoneMarrow_0Hour,   BoneMarrow_2Hour,   BoneMarrow_4Hour,   Brain,   ES_Cell,   Kidney,   Liver,   Lung,   MEF_B4,   MEF_B6,   Spleen
Transcripts:NM_001039189,   NM_024274,   NM_201358
Position:
Mouse AssemblyChrPosition (strand)Source
MGSCv361336,209,351 - 36,209,851 (+)MPROMDB

Additional Information

Database Acc Id Source(s)
AGR Gene MGI:2683538 AgrOrtholog
Ensembl Genes ENSMUSG00000046573 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENSMUST00000053265 ENTREZGENE
  ENSMUST00000053265.8 UniProtKB/Swiss-Prot
InterPro Complex1_LYR UniProtKB/Swiss-Prot
  Complex1_LYR_LYRM4 UniProtKB/Swiss-Prot
KEGG Report mmu:380840 UniProtKB/Swiss-Prot
MGD MGI:2683538 ENTREZGENE
NCBI Gene 380840 ENTREZGENE
PANTHER LYR MOTIF-CONTAINING PROTEIN 4 UniProtKB/Swiss-Prot
  PROTEIN C6ORF149 UniProtKB/Swiss-Prot
Pfam Complex1_LYR UniProtKB/Swiss-Prot
PhenoGen Lyrm4 PhenoGen
UniProt LYRM4_MOUSE UniProtKB/Swiss-Prot, ENTREZGENE