LOXHD1 lipoxygenase homology PLAT domains 1 [Homo sapiens (human)] - Gene

Summary

Official Symbol: LOXHD1provided by HGNC
Official Full Name: lipoxygenase homology PLAT domains 1provided by HGNC
Primary source: HGNC:HGNC:26521
See related: Ensembl:ENSG00000167210 MIM:613072; AllianceGenome:HGNC:26521
Gene type: protein coding
RefSeq status: REVIEWED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as: LH2D1; DFNB77
Summary: This gene encodes a highly conserved protein consisting entirely of PLAT (polycystin/lipoxygenase/alpha-toxin) domains, thought to be involved in targeting proteins to the plasma membrane. Studies in mice show that this gene is expressed in the mechanosensory hair cells in the inner ear, and mutations in this gene lead to auditory defects, indicating that this gene is essential for normal hair cell function. Screening of human families segregating deafness identified a mutation in this gene which causes DFNB77, a progressive form of autosomal-recessive nonsyndromic hearing loss (ARNSHL). Alternatively spliced transcript variants encoding different isoforms have been noted for this gene. [provided by RefSeq, Mar 2010]
Expression: Biased expression in testis (RPKM 2.9), bone marrow (RPKM 0.7) and 3 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 18q21.1

Exon count:: 52

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	18	NC_000018.10 (46476961..46657220, complement)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	18	NC_060942.1 (46667522..46847775, complement)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	18	NC_000018.9 (44056924..44237183, complement)

Chromosome 18 - NC_000018.10 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

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Expression

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See details

Project title: HPA RNA-seq normal tissues
Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
BioProject: PRJEB4337
Publication: PMID 24309898
Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Oncofusion-driven de novo enhancer assembly promotes malignancy in Ewing sarcoma via aberrant expression of the stereociliary protein LOXHD1.
Title: Oncofusion-driven de novo enhancer assembly promotes malignancy in Ewing sarcoma via aberrant expression of the stereociliary protein LOXHD1.
Rising of LOXHD1 as a signature causative gene of down-sloping hearing loss in people in their teens and 20s.
Title: Rising of LOXHD1 as a signature causative gene of down-sloping hearing loss in people in their teens and 20s.
Recessive LOXHD1 variants cause a prelingual down-sloping hearing loss: genotype-phenotype correlation and three additional children with novel variants.
Title: Recessive LOXHD1 variants cause a prelingual down-sloping hearing loss: genotype-phenotype correlation and three additional children with novel variants.
Five Novel Mutations in LOXHD1 Gene Were Identified to Cause Autosomal Recessive Nonsyndromic Hearing Loss in Four Chinese Families.
Title: Five Novel Mutations in LOXHD1 Gene Were Identified to Cause Autosomal Recessive Nonsyndromic Hearing Loss in Four Chinese Families.
The LOXHD1 variant c.1828G>A present in the wife had not previously been reported in individuals with congenital hearing loss.
Title: A novel LOXHD1 variant in a Chinese couple with hearing loss.
By analyzing the largest number of patients with LOXHD1 related hearing loss yet to be reported, we determined several characteristics of LOXHD1 variations, and recurrent variants
Title: Mutational Spectrum and Clinical Features of Patients with LOXHD1 Variants Identified in an 8074 Hearing Loss Patient Cohort.
We hypothesize that environmental factors or genetic modifiers are responsible for phenotypic differences. No association was found between heterozygous LOXHD1 variants and the occurrence of Fuchs corneal dystrophy in carriers.
Title: Further audiovestibular characterization of DFNB77, caused by deleterious variants in LOXHD1, and investigation into the involvement of Fuchs corneal dystrophy.
Results demonstrated that a novel missense variant, LOXHD1: c.5948C > T, was associated with non-progressive Deafness, autosomal recessive 77 in a Chinese family under consanguineous marriage.
Title: Whole-exome sequencing identifies a novel missense variant within LOXHD1 causing rare hearing loss in a Chinese family.
While mutations in ZEB1 contributed to 2% of the late-onset Fuchs' endothelial corneal dystrophy (FECD) cases, the exact role of the two variant of uncertain significance (VUS) identified in ZEB1 and LOXHD1 in FECD pathogenesis needs to be studied.
Title: Analysis of candidate genes ZEB1 and LOXHD1 in late-onset Fuchs' endothelial corneal dystrophy in an Indian cohort.
We report a Japanese family carrying compound heterozygotes of truncating and nontruncating mutations in LOXHD1 identified by targeted NGS analysis. The fact of lower degree of hearing impairment in our cases than previously reported and the molecular modeling of the missense mutant provide insight to the genotype-phenotype correlation of DFNB77.
Title: Clinical characteristics of a Japanese family with hearing loss accompanied by compound heterozygous mutations in LOXHD1.

Submit: New GeneRIF Correction See all GeneRIFs (17)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Associated conditions

Description	Tests
Autosomal recessive nonsyndromic hearing loss 77 MedGen: C2746083 OMIM: 613079 GeneReviews: Genetic Hearing Loss Overview	Compare labs

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

SHGC-146480 (e-PCR)
- UniSTS:175243

RH118914 (e-PCR)
- UniSTS:138906

Gene Ontology Provided by GOA

Process	Evidence Code	Pubs
involved_in sensory perception of sound	IBA Inferred from Biological aspect of Ancestor more info
involved_in sensory perception of sound	IMP Inferred from Mutant Phenotype more info	PubMed

Component	Evidence Code	Pubs
is_active_in stereocilium	IBA Inferred from Biological aspect of Ancestor more info
located_in stereocilium	ISS Inferred from Sequence or Structural Similarity more info

General protein information

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Preferred Names: lipoxygenase homology domain-containing protein 1

Names: lipoxygenase homology domains 1

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

NG_016646.2 RefSeqGene

Range

4814..184761

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001145472.3 → NP_001138944.1 lipoxygenase homology domain-containing protein 1 isoform 2

Status: REVIEWED

Description

Transcript Variant: This variant (2) is missing many exons from the 5' end, contains an additional in-frame coding exon, and differs at the 5' and 3' ends compared to variant 1. This results in translation initiation from an in-frame downstream AUG, and a shorter isoform (2) with a distinct C-terminus compared to isoform 1.

Source sequence(s)

AC018931, AK127869, BC041860, BG722402, BX647229

Consensus CDS

CCDS45861.1

UniProtKB/TrEMBL

J3KRE7

Related

ENSP00000300591.6, ENST00000300591.11

Conserved Domains (2) summary

cd01756
Location:64 → 184

PLAT_repeat; PLAT/LH2 domain repeats of family of proteins with unknown function. In general, PLAT/LH2 consists of an eight stranded beta-barrel and it's proposed function is to mediate interaction with lipids or membrane bound proteins.

cl00011
Location:1043 → 1102

PLAT; PLAT (Polycystin-1, Lipoxygenase, Alpha-Toxin) domain or LH2 (Lipoxygenase homology 2) domain. It consists of an eight stranded beta-barrel. The domain can be found in various domain architectures, in case of lipoxygenases, alpha toxin, lipases and ...
NM_001145473.3 → NP_001138945.1 lipoxygenase homology domain-containing protein 1 isoform 3

See identical proteins and their annotated locations for NP_001138945.1

Status: REVIEWED

Description

Transcript Variant: This variant (3) is missing many exons from the 5' end, and contains an alternate 5' terminal exon compared to variant 1. This results in translation initiation from an in-frame downstream AUG, and a shorter isoform (3) compared to isoform 1.

Source sequence(s)

AK302484, BC041860, BC047720

Consensus CDS

CCDS45862.1

UniProtKB/Swiss-Prot

Q8IVV2

UniProtKB/TrEMBL

B7Z7T7

Related

ENSP00000381676.4, ENST00000398686.8

Conserved Domains (2) summary

cd01756
Location:393 → 511

PLAT_repeat; PLAT/LH2 domain repeats of family of proteins with unknown function. In general, PLAT/LH2 consists of an eight stranded beta-barrel and it's proposed function is to mediate interaction with lipids or membrane bound proteins.

cl00011
Location:257 → 358

PLAT; PLAT (Polycystin-1, Lipoxygenase, Alpha-Toxin) domain or LH2 (Lipoxygenase homology 2) domain. It consists of an eight stranded beta-barrel. The domain can be found in various domain architectures, in case of lipoxygenases, alpha toxin, lipases and ...
NM_001173129.2 → NP_001166600.1 lipoxygenase homology domain-containing protein 1 isoform 4

See identical proteins and their annotated locations for NP_001166600.1

Status: REVIEWED

Description

Transcript Variant: This variant (4) is missing many exons from the 5' end, and differs at the 5' and 3' ends compared to variant 1. This results in translation initiation from an in-frame downstream AUG, and a shorter isoform (4) compared to isoform 1.

Source sequence(s)

AC018931, BC047720, BX647229

Consensus CDS

CCDS54184.1

UniProtKB/Swiss-Prot

Q8IVV2

Related

ENSP00000381692.2, ENST00000398705.7

Conserved Domains (2) summary

cd01756
Location:124 → 244

PLAT_repeat; PLAT/LH2 domain repeats of family of proteins with unknown function. In general, PLAT/LH2 consists of an eight stranded beta-barrel and it's proposed function is to mediate interaction with lipids or membrane bound proteins.

cl00011
Location:393 → 457

PLAT; PLAT (Polycystin-1, Lipoxygenase, Alpha-Toxin) domain or LH2 (Lipoxygenase homology 2) domain. It consists of an eight stranded beta-barrel. The domain can be found in various domain architectures, in case of lipoxygenases, alpha toxin, lipases and ...
NM_001308013.2 → NP_001294942.1 lipoxygenase homology domain-containing protein 1 isoform 5

See identical proteins and their annotated locations for NP_001294942.1

Status: REVIEWED

Description

Transcript Variant: This variant (5) is missing many exons from the 5' end, lacks an in-frame coding exon, and differs at the 5' and 3' ends compared to variant 1. This results in translation initiation from an in-frame downstream AUG, and a shorter isoform (5) with a distinct C-terminus compared to isoform 1.

Source sequence(s)

AC018931, BX647229

Consensus CDS

CCDS77182.1

UniProtKB/TrEMBL

J3KRE7, J3QKX9

Related

ENSP00000463285.1, ENST00000579038.6

Conserved Domains (2) summary

cd01756
Location:253 → 373

PLAT_repeat; PLAT/LH2 domain repeats of family of proteins with unknown function. In general, PLAT/LH2 consists of an eight stranded beta-barrel and it's proposed function is to mediate interaction with lipids or membrane bound proteins.

cl00011
Location:3 → 88

PLAT; PLAT (Polycystin-1, Lipoxygenase, Alpha-Toxin) domain or LH2 (Lipoxygenase homology 2) domain. It consists of an eight stranded beta-barrel. The domain can be found in various domain architectures, in case of lipoxygenases, alpha toxin, lipases and ...
NM_001384474.1 → NP_001371403.1 lipoxygenase homology domain-containing protein 1 isoform 6

Status: REVIEWED

Source sequence(s)

AC018931, AC064800, AC091139

Consensus CDS

CCDS92455.1

UniProtKB/Swiss-Prot

B7WNN3, B7WNT1, B7WPI9, H7BZ41, Q6ZRY7, Q86WW9, Q8IVV2, Q96DL7

UniProtKB/TrEMBL

A0A2R8Y7K4

Related

ENSP00000496347.1, ENST00000642948.1

Conserved Domains (2) summary

cd01756
Location:1022 → 1142

PLAT_repeat; PLAT/LH2 domain repeats of family of proteins with unknown function. In general, PLAT/LH2 consists of an eight stranded beta-barrel and it's proposed function is to mediate interaction with lipids or membrane bound proteins.

cl00011
Location:816 → 896

PLAT; PLAT (Polycystin-1, Lipoxygenase, Alpha-Toxin) domain or LH2 (Lipoxygenase homology 2) domain. It consists of an eight stranded beta-barrel. The domain can be found in various domain architectures, in case of lipoxygenases, alpha toxin, lipases and ...
NM_144612.7 → NP_653213.6 lipoxygenase homology domain-containing protein 1 isoform 1

Status: REVIEWED

Description

Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).

Source sequence(s)

AC018931, AC064800, AC091139, AK127869, AK302484, BC041860, BX647229, DR731345, DR731346

Consensus CDS

CCDS11929.2

UniProtKB/Swiss-Prot

B7WNN3, B7WNT1, B7WPI9, H7BZ41, Q6ZRY7, Q86WW9, Q8IVV2, Q96DL7

UniProtKB/TrEMBL

F5GZB4

Related

ENSP00000444586.1, ENST00000536736.5

Conserved Domains (2) summary

cd01756
Location:1022 → 1142

PLAT_repeat; PLAT/LH2 domain repeats of family of proteins with unknown function. In general, PLAT/LH2 consists of an eight stranded beta-barrel and it's proposed function is to mediate interaction with lipids or membrane bound proteins.

cl00011
Location:816 → 896

PLAT; PLAT (Polycystin-1, Lipoxygenase, Alpha-Toxin) domain or LH2 (Lipoxygenase homology 2) domain. It consists of an eight stranded beta-barrel. The domain can be found in various domain architectures, in case of lipoxygenases, alpha toxin, lipases and ...

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

NC_000018.10 Reference GRCh38.p14 Primary Assembly

Range

46476961..46657220 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_047437289.1 → XP_047293245.1 lipoxygenase homology domain-containing protein 1 isoform X1
XM_011525804.3 → XP_011524106.1 lipoxygenase homology domain-containing protein 1 isoform X5

Conserved Domains (2) summary

cd01756
Location:409 → 529

PLAT_repeat; PLAT/LH2 domain repeats of family of proteins with unknown function. In general, PLAT/LH2 consists of an eight stranded beta-barrel and it's proposed function is to mediate interaction with lipids or membrane bound proteins.

cl00011
Location:203 → 283

PLAT; PLAT (Polycystin-1, Lipoxygenase, Alpha-Toxin) domain or LH2 (Lipoxygenase homology 2) domain. It consists of an eight stranded beta-barrel. The domain can be found in various domain architectures, in case of lipoxygenases, alpha toxin, lipases and ...
XM_006722391.4 → XP_006722454.1 lipoxygenase homology domain-containing protein 1 isoform X11

UniProtKB/TrEMBL

B7Z7T7

Related

ENSP00000461964.1, ENST00000582408.6

Conserved Domains (2) summary

cd01756
Location:1025 → 1143

PLAT_repeat; PLAT/LH2 domain repeats of family of proteins with unknown function. In general, PLAT/LH2 consists of an eight stranded beta-barrel and it's proposed function is to mediate interaction with lipids or membrane bound proteins.

cl00011
Location:6 → 75

PLAT; PLAT (Polycystin-1, Lipoxygenase, Alpha-Toxin) domain or LH2 (Lipoxygenase homology 2) domain. It consists of an eight stranded beta-barrel. The domain can be found in various domain architectures, in case of lipoxygenases, alpha toxin, lipases and ...
XM_006722388.4 → XP_006722451.1 lipoxygenase homology domain-containing protein 1 isoform X8

UniProtKB/TrEMBL

B7Z7T7

Conserved Domains (2) summary

cd01756
Location:1087 → 1205

PLAT_repeat; PLAT/LH2 domain repeats of family of proteins with unknown function. In general, PLAT/LH2 consists of an eight stranded beta-barrel and it's proposed function is to mediate interaction with lipids or membrane bound proteins.

cl00011
Location:6 → 75

PLAT; PLAT (Polycystin-1, Lipoxygenase, Alpha-Toxin) domain or LH2 (Lipoxygenase homology 2) domain. It consists of an eight stranded beta-barrel. The domain can be found in various domain architectures, in case of lipoxygenases, alpha toxin, lipases and ...
XM_024451088.2 → XP_024306856.1 lipoxygenase homology domain-containing protein 1 isoform X12

UniProtKB/TrEMBL

J3KRE7

Conserved Domains (2) summary

cd01756
Location:947 → 1065

PLAT_repeat; PLAT/LH2 domain repeats of family of proteins with unknown function. In general, PLAT/LH2 consists of an eight stranded beta-barrel and it's proposed function is to mediate interaction with lipids or membrane bound proteins.

cl00011
Location:3 → 88

PLAT; PLAT (Polycystin-1, Lipoxygenase, Alpha-Toxin) domain or LH2 (Lipoxygenase homology 2) domain. It consists of an eight stranded beta-barrel. The domain can be found in various domain architectures, in case of lipoxygenases, alpha toxin, lipases and ...
XM_024451086.2 → XP_024306854.1 lipoxygenase homology domain-containing protein 1 isoform X12

UniProtKB/TrEMBL

J3KRE7

Conserved Domains (2) summary

cd01756
Location:947 → 1065

PLAT_repeat; PLAT/LH2 domain repeats of family of proteins with unknown function. In general, PLAT/LH2 consists of an eight stranded beta-barrel and it's proposed function is to mediate interaction with lipids or membrane bound proteins.

cl00011
Location:3 → 88

PLAT; PLAT (Polycystin-1, Lipoxygenase, Alpha-Toxin) domain or LH2 (Lipoxygenase homology 2) domain. It consists of an eight stranded beta-barrel. The domain can be found in various domain architectures, in case of lipoxygenases, alpha toxin, lipases and ...
XM_024451085.2 → XP_024306853.1 lipoxygenase homology domain-containing protein 1 isoform X10

UniProtKB/TrEMBL

J3KRE7

Conserved Domains (2) summary

cd01756
Location:1042 → 1160

PLAT_repeat; PLAT/LH2 domain repeats of family of proteins with unknown function. In general, PLAT/LH2 consists of an eight stranded beta-barrel and it's proposed function is to mediate interaction with lipids or membrane bound proteins.

cl00011
Location:517 → 632

PLAT; PLAT (Polycystin-1, Lipoxygenase, Alpha-Toxin) domain or LH2 (Lipoxygenase homology 2) domain. It consists of an eight stranded beta-barrel. The domain can be found in various domain architectures, in case of lipoxygenases, alpha toxin, lipases and ...
XM_011525810.3 → XP_011524112.1 lipoxygenase homology domain-containing protein 1 isoform X13

Conserved Domains (2) summary

cd01756
Location:410 → 528

PLAT_repeat; PLAT/LH2 domain repeats of family of proteins with unknown function. In general, PLAT/LH2 consists of an eight stranded beta-barrel and it's proposed function is to mediate interaction with lipids or membrane bound proteins.

cl00011
Location:274 → 375

PLAT; PLAT (Polycystin-1, Lipoxygenase, Alpha-Toxin) domain or LH2 (Lipoxygenase homology 2) domain. It consists of an eight stranded beta-barrel. The domain can be found in various domain architectures, in case of lipoxygenases, alpha toxin, lipases and ...
XM_011525811.3 → XP_011524113.1 lipoxygenase homology domain-containing protein 1 isoform X14

See identical proteins and their annotated locations for XP_011524113.1

UniProtKB/Swiss-Prot

Q8IVV2

Conserved Domains (2) summary

cd01756
Location:393 → 511

PLAT_repeat; PLAT/LH2 domain repeats of family of proteins with unknown function. In general, PLAT/LH2 consists of an eight stranded beta-barrel and it's proposed function is to mediate interaction with lipids or membrane bound proteins.

cl00011
Location:257 → 358

PLAT; PLAT (Polycystin-1, Lipoxygenase, Alpha-Toxin) domain or LH2 (Lipoxygenase homology 2) domain. It consists of an eight stranded beta-barrel. The domain can be found in various domain architectures, in case of lipoxygenases, alpha toxin, lipases and ...
XM_047437290.1 → XP_047293246.1 lipoxygenase homology domain-containing protein 1 isoform X2
XM_047437291.1 → XP_047293247.1 lipoxygenase homology domain-containing protein 1 isoform X3
XM_047437292.1 → XP_047293248.1 lipoxygenase homology domain-containing protein 1 isoform X4
XM_047437293.1 → XP_047293249.1 lipoxygenase homology domain-containing protein 1 isoform X6

Related

ENST00000335730.6
XM_047437295.1 → XP_047293251.1 lipoxygenase homology domain-containing protein 1 isoform X9
XM_047437294.1 → XP_047293250.1 lipoxygenase homology domain-containing protein 1 isoform X7

Alternate T2T-CHM13v2.0

Genomic

NC_060942.1 Alternate T2T-CHM13v2.0

Range

46667522..46847775 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_054318177.1 → XP_054174152.1 lipoxygenase homology domain-containing protein 1 isoform X16
XM_054318176.1 → XP_054174151.1 lipoxygenase homology domain-containing protein 1 isoform X15
XM_054318181.1 → XP_054174156.1 lipoxygenase homology domain-containing protein 1 isoform X5
XM_054318187.1 → XP_054174162.1 lipoxygenase homology domain-containing protein 1 isoform X11
XM_054318184.1 → XP_054174159.1 lipoxygenase homology domain-containing protein 1 isoform X8
XM_054318189.1 → XP_054174164.1 lipoxygenase homology domain-containing protein 1 isoform X12
XM_054318188.1 → XP_054174163.1 lipoxygenase homology domain-containing protein 1 isoform X12
XM_054318186.1 → XP_054174161.1 lipoxygenase homology domain-containing protein 1 isoform X10
XM_054318190.1 → XP_054174165.1 lipoxygenase homology domain-containing protein 1 isoform X13
XM_054318191.1 → XP_054174166.1 lipoxygenase homology domain-containing protein 1 isoform X14
XM_054318178.1 → XP_054174153.1 lipoxygenase homology domain-containing protein 1 isoform X2
XM_054318179.1 → XP_054174154.1 lipoxygenase homology domain-containing protein 1 isoform X3
XM_054318180.1 → XP_054174155.1 lipoxygenase homology domain-containing protein 1 isoform X4
XM_054318182.1 → XP_054174157.1 lipoxygenase homology domain-containing protein 1 isoform X6
XM_054318185.1 → XP_054174160.1 lipoxygenase homology domain-containing protein 1 isoform X9
XM_054318183.1 → XP_054174158.1 lipoxygenase homology domain-containing protein 1 isoform X7