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LYRM4 LYR motif containing 4 [ Homo sapiens (human) ]

Gene ID: 57128, updated on 4-Dec-2022

Summary

Official Symbol
LYRM4provided by HGNC
Official Full Name
LYR motif containing 4provided by HGNC
Primary source
HGNC:HGNC:21365
See related
Ensembl:ENSG00000214113 MIM:613311; AllianceGenome:HGNC:21365
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
ISD11; CGI-203; COXPD19; C6orf149
Summary
The protein encoded by this gene is found in both mitochondria and the nucleus, where it binds cysteine desulfurase and helps free inorganic sulfur for Fe/S clusters. Disruption of this gene negatively impacts mitochondrial and cytosolic iron homeostasis. [provided by RefSeq, Sep 2016]
Expression
Ubiquitous expression in ovary (RPKM 2.3), thyroid (RPKM 2.1) and 25 other tissues See more
Orthologs
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Genomic context

See LYRM4 in Genome Data Viewer
Location:
6p25.1
Exon count:
13
Annotation release Status Assembly Chr Location
110 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (5031753..5260950, complement)
110 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (4937542..5130157, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (5068561..5261183, complement)

Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124901248 Neighboring gene LYRM4 antisense RNA 1 Neighboring gene ribonuclease P/MRP subunit p40 Neighboring gene transcription factor B2, mitochondrial pseudogene Neighboring gene protein phosphatase 1 regulatory subunit 3G Neighboring gene Sharpr-MPRA regulatory region 2533 Neighboring gene microRNA 3691 Neighboring gene Sharpr-MPRA regulatory region 15549 Neighboring gene uncharacterized LOC124901249 Neighboring gene Sharpr-MPRA regulatory region 4425 Neighboring gene phenylalanyl-tRNA synthetase 2, mitochondrial Neighboring gene FARS2 antisense RNA 1

Genomic regions, transcripts, and products

Expression

  • 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

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Phenotypes

Associated conditions

Description Tests
Combined oxidative phosphorylation deficiency 19
MedGen: C3810055 OMIM: 615595 GeneReviews: Not available
Compare labs

EBI GWAS Catalog

Description
A genome-wide search for common SNP x SNP interactions on the risk of venous thrombosis.
EBI GWAS Catalog
Identification, replication, and fine-mapping of Loci associated with adult height in individuals of african ancestry.
EBI GWAS Catalog

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
enables protein homodimerization activity IDA
Inferred from Direct Assay
more info
PubMed 
Process Evidence Code Pubs
involved_in [2Fe-2S] cluster assembly IDA
Inferred from Direct Assay
more info
PubMed 
acts_upstream_of [4Fe-4S] cluster assembly ISS
Inferred from Sequence or Structural Similarity
more info
 
involved_in iron-sulfur cluster assembly IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
involved_in iron-sulfur cluster assembly IC
Inferred by Curator
more info
PubMed 
Component Evidence Code Pubs
part_of L-cysteine desulfurase complex IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
part_of iron-sulfur cluster assembly complex IC
Inferred by Curator
more info
PubMed 
part_of mitochondrial iron-sulfur cluster assembly complex IDA
Inferred from Direct Assay
more info
PubMed 
located_in mitochondrial matrix TAS
Traceable Author Statement
more info
 
is_active_in mitochondrion IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
located_in mitochondrion IC
Inferred by Curator
more info
PubMed 
located_in mitochondrion IDA
Inferred from Direct Assay
more info
PubMed 
located_in nuclear body IDA
Inferred from Direct Assay
more info
 

General protein information

Preferred Names
LYR motif-containing protein 4
Names
homolog of yeast Isd11
mitochondrial matrix Nfs1 interacting protein

NCBI Reference Sequences (RefSeq)

NEW Try the new Transcript table

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

  1. NG_051651.2 RefSeqGene

    Range
    5000..157531
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001164840.3NP_001158312.1  LYR motif-containing protein 4 isoform 2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) contains an alternate 3' coding region and 3' UTR compared to variant 1. The encoded isoform (2) has a distinct, longer C-terminus compared to isoform 1.
    Source sequence(s)
    CK819966, HY168919
    Consensus CDS
    CCDS54962.1
    UniProtKB/TrEMBL
    F5H189
    Related
    ENSP00000443900.3, ENST00000500576.4
    Conserved Domains (2) summary
    pfam13232
    Location:767
    Complex1_LYR_1; Complex1_LYR-like
    pfam13900
    Location:75122
    GVQW; Putative domain of unknown function
  2. NM_001164841.3NP_001158313.1  LYR motif-containing protein 4 isoform 3

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) includes an additional exon that results in an alternate 3' coding region and 3' UTR compared to variant 1. The encoded isoform (3) has a distinct, longer C-terminus compared to isoform 1.
    Source sequence(s)
    AF170070, AL035653, BC067762, BX353584, CA310019, HY168919
    Consensus CDS
    CCDS54961.1
    UniProtKB/Swiss-Prot
    Q9HD34
    UniProtKB/TrEMBL
    C9JRX8
    Related
    ENSP00000420026.1, ENST00000464010.5
    Conserved Domains (1) summary
    pfam13232
    Location:767
    Complex1_LYR_1; Complex1_LYR-like
  3. NM_001318782.1NP_001305711.1  LYR motif-containing protein 4 isoform 4

    Status: REVIEWED

    Description
    Transcript Variant: This variant (6) contains an alternate 3' coding region and 3' UTR compared to variant 1. The encoded isoform (4) has a distinct, shorter C-terminus compared to isoform 1.
    Source sequence(s)
    AK309661, AL035653, HY168919
    Consensus CDS
    CCDS83061.1
    UniProtKB/TrEMBL
    C9JY28
    Related
    ENSP00000419928.1, ENST00000480566.5
    Conserved Domains (1) summary
    pfam13232
    Location:767
    Complex1_LYR_1; Complex1_LYR-like
  4. NM_001318783.1NP_001305712.1  LYR motif-containing protein 4 isoform 5

    Status: REVIEWED

    Description
    Transcript Variant: This variant (7) contains an alternate 3' coding region and 3' UTR compared to variant 1. The encoded isoform (5) has a distinct, longer C-terminus compared to isoform 1.
    Source sequence(s)
    AL121978, DA114665, HY168919
    Conserved Domains (1) summary
    pfam13232
    Location:767
    Complex1_LYR_1; Complex1_LYR-like
  5. NM_020408.6NP_065141.3  LYR motif-containing protein 4 isoform 1

    See identical proteins and their annotated locations for NP_065141.3

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) encodes isoform 1.
    Source sequence(s)
    AF170070, AL035653, BC067762, CA310019, HY168919
    Consensus CDS
    CCDS4493.1
    UniProtKB/Swiss-Prot
    Q5XKP1, Q9HD34
    Related
    ENSP00000418787.1, ENST00000330636.9
    Conserved Domains (1) summary
    pfam13232
    Location:767
    Complex1_LYR_1; Complex1_LYR-like

RNA

  1. NR_104417.2 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) contains an additional exon in the 3' region compared to variant 1. This variant is represented as non-coding because use of the expected translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AF170070, AK309458, AL035653, BC067762, CA310019, HY168919
    Related
    ENST00000463032.5
  2. NR_104418.1 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AF170070, AL035653, BC067762, CA310019, HY168919
    Related
    ENST00000468929.5
  3. NR_134856.1 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (8) lacks an exon and contains two alternate 3' exons compared to variant 1. This variant is represented as non-coding because use of the expected translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    DA114665, DA222333, HY168919

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 110 details...Open this link in a new tab

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

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000006.12 Reference GRCh38.p14 Primary Assembly

    Range
    5031753..5260950 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_017011084.3XP_016866573.1  LYR motif-containing protein 4 isoform X1

  2. XM_017011083.3XP_016866572.1  LYR motif-containing protein 4 isoform X2

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060930.1 Alternate T2T-CHM13v2.0

    Range
    4937542..5130157 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)