Loxhd1 (lipoxygenase homology domains 1) - Rat Genome Database

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Gene: Loxhd1 (lipoxygenase homology domains 1) Mus musculus
Analyze
Symbol: Loxhd1
Name: lipoxygenase homology domains 1
RGD ID: 1614141
MGI Page MGI
Description: Acts upstream of or within sensory perception of sound. Located in stereocilium. Human ortholog(s) of this gene implicated in Fuchs' endothelial dystrophy; autosomal recessive nonsyndromic deafness 77; and orofacial cleft. Orthologous to human LOXHD1 (lipoxygenase homology PLAT domains 1).
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: 1700096C21Rik; 4932417K07; lipoxygenase homology domain-containing protein 1; s; sba
RGD Orthologs
Human
Rat
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: GRCm39 - Mouse Genome Assembly GRCm39
Position:
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391877,369,354 - 77,530,628 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1877,369,654 - 77,530,626 (+)EnsemblGRCm39 Ensembl
GRCm381877,281,658 - 77,442,932 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1877,281,958 - 77,442,930 (+)EnsemblGRCm38mm10GRCm38
MGSCv371877,520,697 - 77,680,996 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361877,512,200 - 77,586,778 (+)NCBIMGSCv36mm8
Celera1878,460,582 - 78,625,896 (+)NCBICelera
Cytogenetic Map18E3NCBI
cM Map1852.2NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component
cell projection  (IEA)
stereocilium  (IBA,IDA)

Phenotype Annotations     Click to see Annotation Detail View
References

References - curated
# Reference Title Reference Citation
1. Fine-Mapping of 18q21.1 Locus Identifies Single Nucleotide Polymorphisms Associated with Nonsyndromic Cleft Lip with or without Cleft Palate. Mitra AK, etal., Front Genet. 2016 May 23;7:88. doi: 10.3389/fgene.2016.00088. eCollection 2016.
2. OMIM Disease Annotation Pipeline OMIM Disease Annotation Pipeline
3. Mouse MP Annotation Import Pipeline RGD automated import 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
6. Mutations in LOXHD1, a recessive-deafness locus, cause dominant late-onset Fuchs corneal dystrophy. Riazuddin SA, etal., Am J Hum Genet. 2012 Mar 9;90(3):533-9. doi: 10.1016/j.ajhg.2012.01.013. Epub 2012 Feb 16.
Additional References at PubMed
PMID:10349636   PMID:11042159   PMID:11076861   PMID:11217851   PMID:12040188   PMID:12466851   PMID:16141072   PMID:16141073   PMID:17329413   PMID:19732867   PMID:21267068   PMID:21873635  
PMID:23217710   PMID:27534441   PMID:28378742   PMID:33087486   PMID:33707295  


Genomics

Comparative Map Data
Loxhd1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391877,369,354 - 77,530,628 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1877,369,654 - 77,530,626 (+)EnsemblGRCm39 Ensembl
GRCm381877,281,658 - 77,442,932 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1877,281,958 - 77,442,930 (+)EnsemblGRCm38mm10GRCm38
MGSCv371877,520,697 - 77,680,996 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361877,512,200 - 77,586,778 (+)NCBIMGSCv36mm8
Celera1878,460,582 - 78,625,896 (+)NCBICelera
Cytogenetic Map18E3NCBI
cM Map1852.2NCBI
LOXHD1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381846,476,961 - 46,657,220 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1846,476,972 - 46,657,220 (-)EnsemblGRCh38hg38GRCh38
GRCh371844,056,924 - 44,237,183 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361842,343,528 - 42,435,624 (-)NCBINCBI36Build 36hg18NCBI36
Build 341842,343,527 - 42,435,624NCBI
Celera1840,864,351 - 41,044,583 (-)NCBICelera
Cytogenetic Map18q21.1NCBI
HuRef1840,914,566 - 41,094,608 (-)NCBIHuRef
CHM1_11843,983,947 - 44,163,994 (-)NCBICHM1_1
T2T-CHM13v2.01846,667,522 - 46,847,775 (-)NCBIT2T-CHM13v2.0
Loxhd1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81873,093,142 - 73,245,784 (+)NCBIGRCr8
mRatBN7.21870,817,962 - 70,970,606 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1870,818,276 - 70,969,983 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1872,920,937 - 73,073,126 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01873,590,152 - 73,742,331 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01871,446,745 - 71,598,914 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01873,645,365 - 73,812,271 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1873,645,907 - 73,812,271 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01873,325,886 - 73,492,157 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41874,297,027 - 74,399,097 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11874,319,056 - 74,472,488 (+)NCBI
Celera1869,340,110 - 69,490,847 (+)NCBICelera
Cytogenetic Map18q12.3NCBI
Loxhd1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495540231,985,583 - 32,144,040 (-)EnsemblChiLan1.0
ChiLan1.0NW_00495540231,985,616 - 32,144,040 (-)NCBIChiLan1.0ChiLan1.0
LOXHD1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v21763,898,106 - 64,079,259 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan11849,590,703 - 49,771,860 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v01839,756,531 - 39,936,317 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.11843,290,361 - 43,469,923 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1843,290,579 - 43,469,921 (-)Ensemblpanpan1.1panPan2
LOXHD1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1744,662,800 - 44,828,405 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl744,663,182 - 44,826,858 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha744,145,778 - 44,310,709 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0744,615,788 - 44,781,462 (+)NCBIROS_Cfam_1.0
UMICH_Zoey_3.1744,315,651 - 44,480,579 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0744,369,642 - 44,534,212 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0744,653,348 - 44,817,946 (+)NCBIUU_Cfam_GSD_1.0
LOC101976443
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440494440,992,760 - 41,083,909 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_004936517271,909 - 409,691 (+)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_004936517271,909 - 409,818 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
LOXHD1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl196,080,824 - 96,276,992 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1196,080,751 - 96,287,034 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
LOXHD1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11834,247,584 - 34,431,038 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl1834,249,250 - 34,430,532 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_0236660508,619,822 - 8,802,681 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Loxhd1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462477810,106,975 - 10,282,085 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_00462477810,106,009 - 10,282,085 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Loxhd1
5659 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:622
Count of miRNA genes:396
Interacting mature miRNAs:466
Transcripts:ENSMUST00000035501, ENSMUST00000096547, ENSMUST00000123166, ENSMUST00000123410, ENSMUST00000148341
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
25823173Hrsq12_mhost response to SARS QTL 12, hemorrhage (mouse)182489588178339555Mouse
1357639Obsty4_mobesity 4 (mouse)Not determined183961991484638778Mouse
12904745Carcdq2_mcardiac collagen deposition QTL 2 (mouse)184642328780423287Mouse
11039493Ltpr8d_mLeishmania tropica response 8d (mouse)184687490380875042Mouse
11039494Ltpr8b_mLeishmania tropica response 8b (mouse)184687490380875042Mouse
1357630Tgq1_mtriglyceride QTL 1 (mouse)Not determined185105215685052311Mouse
11252137Modvl5_mmodifier of vacuolated lens 5 (mouse)185105215685052311Mouse
10412244Par5_mpulmonary adenoma resistance 5 (mouse)Not determined185166830085668468Mouse
1302099Hdlq30_mHDL QTL 30 (mouse)Not determined185166830085668468Mouse
1301853Heal9_mwound healing/regeneration 9 (mouse)Not determined185280527686805416Mouse
1301500Szs4_mseizure susceptibility 4 (mouse)Not determined185497587385514143Mouse
12880410V125Dq13_mvitamin D active form serum level QTL 13 (mouse)185643307190433071Mouse
12880430Fgf23lq4_mFGF23 serum level QTL 4 (mouse)185643307190433071Mouse
12880428V125Dq14_mvitamin D active form serum level QTL 14 (mouse)185743307190720763Mouse
1301353Lbw6_mlupus NZB x NZW 6 (mouse)Not determined185756233890720763Mouse
4141132Eae18_mexperimental allergic encephalomyelitis susceptibility 18 (mouse)Not determined5759055982604728Mouse
4140971Mbmq1_mmale body mass QTL 1 (mouse)Not determined5799028190720763Mouse
11049564Lmr29_mleishmaniasis resistance 29 (mouse)185918009290720763Mouse
11039495Ltpr8c_mLeishmania tropica response 8c (mouse)185918009290720763Mouse
11039492Ltpr8a_mLeishmania tropica response 8a (mouse)185918009290720763Mouse
1301103Pgia11_mproteoglycan induced arthritis 11 (mouse)Not determined185991418490720763Mouse
1302109Sluc28_msusceptibility to lung cancer 28 (mouse)Not determined185993532190720763Mouse
38455998Cdtm1_mCD62L+ CD8 TM cells 1 (mouse)186013307280043215Mouse
1558803W3q16_mweight 3 weeks QTL 16 (mouse)Not determined186127244881491831Mouse
1558782Orgwq9_morgan weight QTL 9 (mouse)Not determined186127244882604728Mouse
1301798Hdlq31_mHDL QTL 31 (mouse)Not determined186714438990720763Mouse
10401904Sicd4_mseizure-induced cell death 4 (mouse)Not determined186980527685514143Mouse
15014786Mvlq2_mmacrovesicular liver lesion QTL 2 (mouse)187156938890720763Mouse
1302183Pas7_mpulmonary adenoma susceptibility 7 (mouse)Not determined187274559484144595Mouse
4142153Idd21.1_minsulin dependent diabetes susceptibility 21.1 (mouse)Not determined187456233884144595Mouse

Markers in Region
D18Dcr2  
Mouse AssemblyChrPosition (strand)SourceJBrowse
GRCm381877,426,453 - 77,426,550UniSTSGRCm38
MGSCv371877,665,192 - 77,665,289UniSTSGRCm37
Celera1878,609,452 - 78,609,549UniSTS
Celera1878,603,455 - 78,603,552UniSTS
Cytogenetic Map18E3UniSTS
cM Map18 UniSTS


Expression


Sequence


Reference Sequences
RefSeq Acc Id: ENSMUST00000035501
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl1877,395,446 - 77,470,024 (+)Ensembl
GRCm38.p6 Ensembl1877,307,750 - 77,382,328 (+)Ensembl
RefSeq Acc Id: ENSMUST00000096547   ⟹   ENSMUSP00000094294
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl1877,369,654 - 77,529,950 (+)Ensembl
GRCm38.p6 Ensembl1877,281,958 - 77,442,254 (+)Ensembl
RefSeq Acc Id: ENSMUST00000123166
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl1877,528,392 - 77,530,626 (+)Ensembl
GRCm38.p6 Ensembl1877,440,696 - 77,442,930 (+)Ensembl
RefSeq Acc Id: ENSMUST00000123410   ⟹   ENSMUSP00000120991
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl1877,369,654 - 77,530,037 (+)Ensembl
GRCm38.p6 Ensembl1877,281,958 - 77,442,341 (+)Ensembl
RefSeq Acc Id: ENSMUST00000148341   ⟹   ENSMUSP00000114988
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl1877,369,654 - 77,529,950 (+)Ensembl
GRCm38.p6 Ensembl1877,281,958 - 77,442,254 (+)Ensembl
RefSeq Acc Id: NM_001414399   ⟹   NP_001401328
RefSeq Status: VALIDATED
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm391877,369,354 - 77,530,628 (+)NCBI
RefSeq Acc Id: NM_172834   ⟹   NP_766422
RefSeq Status: VALIDATED
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm391877,369,354 - 77,530,628 (+)NCBI
GRCm381877,281,658 - 77,442,932 (+)NCBI
MGSCv371877,520,697 - 77,680,996 (+)RGD
Celera1878,460,582 - 78,625,896 (+)RGD
cM Map18 ENTREZGENE
Sequence:
Reference Protein Sequences
RefSeq Acc Id: NP_766422   ⟸   NM_172834
- Peptide Label: isoform 1
- UniProtKB: Q8BMY5 (UniProtKB/Swiss-Prot),   C8YR32 (UniProtKB/Swiss-Prot),   F6XPZ0 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSMUSP00000114988   ⟸   ENSMUST00000148341
RefSeq Acc Id: ENSMUSP00000120991   ⟸   ENSMUST00000123410
RefSeq Acc Id: ENSMUSP00000094294   ⟸   ENSMUST00000096547
RefSeq Acc Id: NP_001401328   ⟸   NM_001414399
- Peptide Label: isoform 2
Protein Domains
PLAT

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-C8YR32-F1-model_v2 AlphaFold C8YR32 1-2068 view protein structure

Promoters
RGD ID:13678212
Promoter ID:EPDNEW_M23255
Type:single initiation site
Name:Loxhd1_2
Description:Mus musculus lipoxygenase homology domains 1 , mRNA.
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Alternative Promoters:null; see alsoEPDNEW_M23256  
Experiment Methods:Single-end sequencing.
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm381877,282,024 - 77,282,084EPDNEW
RGD ID:13678214
Promoter ID:EPDNEW_M23256
Type:single initiation site
Name:Loxhd1_1
Description:Mus musculus lipoxygenase homology domains 1 , mRNA.
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Alternative Promoters:null; see alsoEPDNEW_M23255  
Experiment Methods:Single-end sequencing.
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm381877,325,529 - 77,325,589EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene MGI:1914609 AgrOrtholog
Ensembl Genes ENSMUSG00000032818 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Ensembl Transcript ENSMUST00000096547 ENTREZGENE
  ENSMUST00000096547.11 UniProtKB/Swiss-Prot
  ENSMUST00000123410.9 UniProtKB/TrEMBL
  ENSMUST00000148341 ENTREZGENE
  ENSMUST00000148341.9 UniProtKB/TrEMBL
Gene3D-CATH Catalase core domain UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PLAT/LH2 domain UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
InterPro PLAT/LH2_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PLAT/LH2_dom_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report mmu:240411 UniProtKB/Swiss-Prot
MGD MGI:1914609 ENTREZGENE
NCBI Gene 240411 ENTREZGENE
PANTHER LIPOXYGENASE HOMOLOGY DOMAIN-CONTAINING PROTEIN 1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PROTEIN CBG12474 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam PLAT UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Loxhd1 PhenoGen
PROSITE PLAT UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
SMART LH2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF49723 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt C8YR32 ENTREZGENE
  D3YUR7_MOUSE UniProtKB/TrEMBL
  F6XPZ0 ENTREZGENE, UniProtKB/TrEMBL
  LOXH1_MOUSE UniProtKB/Swiss-Prot
  Q8BI18_MOUSE UniProtKB/TrEMBL
  Q8BMY5 ENTREZGENE
UniProt Secondary Q8BMY5 UniProtKB/Swiss-Prot