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

    Gene ID: 57128, updated on 23-Nov-2023

    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
    NEW
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    Genomic context

    See LYRM4 in Genome Data Viewer
    Location:
    6p25.1
    Exon count:
    13
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (5031753..5260950, complement)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (4900453..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 ATAC-STARR-seq lymphoblastoid silent region 16864 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16865 Neighboring gene MPRA-validated peak5630 silencer Neighboring gene uncharacterized LOC124901248 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:5027971-5028470 Neighboring gene ReSE screen-validated silencer GRCh37_chr6:5031032-5031192 Neighboring gene LYRM4 antisense RNA 1 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr6:5044856-5046055 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23899 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23900 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:5063575-5064076 Neighboring gene ribonuclease P/MRP subunit p40 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16866 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16867 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16868 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16869 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:5085857-5086546 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23901 Neighboring gene MPRA-validated peak5632 silencer Neighboring gene TFB2M pseudogene 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:5130070-5130656 Neighboring gene protein phosphatase 1 regulatory subunit 3G Neighboring gene Sharpr-MPRA regulatory region 2533 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:5193017-5193524 Neighboring gene microRNA 3691 Neighboring gene Sharpr-MPRA regulatory region 15549 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr6:5230418-5231617 Neighboring gene uncharacterized LOC124901249 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23902 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16873 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16874 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16875 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23903 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16876 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23904 Neighboring gene Sharpr-MPRA regulatory region 4425 Neighboring gene phenylalanyl-tRNA synthetase 2, mitochondrial Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr6:5368745-5369944 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23906 Neighboring gene NANOG hESC enhancer GRCh37_chr6:5412113-5412622 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr6:5438556-5439472 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr6:5439473-5440389 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:5456946-5457932 Neighboring gene FARS2 antisense RNA 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23907 Neighboring gene MPRA-validated peak5636 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23908 Neighboring gene NANOG hESC enhancer GRCh37_chr6:5529614-5530223 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr6:5541695-5542894 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr6:5581546-5582745 Neighboring gene heterogeneous nuclear ribonucleoprotein A1 pseudogene 37

    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

    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
     
    involved_in iron-sulfur cluster assembly NAS
    Non-traceable Author Statement
    more info
    PubMed 
    Component Evidence Code Pubs
    part_of L-cysteine desulfurase complex IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    part_of iron-sulfur cluster assembly complex NAS
    Non-traceable Author Statement
    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
     
    located_in mitochondrion IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in mitochondrion NAS
    Non-traceable Author Statement
    more info
    PubMed 
    located_in nuclear body IDA
    Inferred from Direct Assay
    more info
     
    located_in nucleus IDA
    Inferred from Direct Assay
    more info
    PubMed 

    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/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
      A8K543, 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: 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

    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
      4900453..5130157 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054355978.1XP_054211953.1  LYR motif-containing protein 4 isoform X1

    2. XM_054355979.1XP_054211954.1  LYR motif-containing protein 4 isoform X2