Free for academic non-profit institutions. Other users need a Commercial license

Aliases for LYRM4 Gene

Aliases for LYRM4 Gene

  • LYR Motif Containing 4 2 3 5
  • C6orf149 3 4
  • ISD11 3 4
  • Mitochondrial Matrix Nfs1 Interacting Protein 3
  • Chromosome 6 Open Reading Frame 149 2
  • Homolog Of Yeast Isd11 3
  • CGI-203 3
  • COXPD19 3

External Ids for LYRM4 Gene

Previous HGNC Symbols for LYRM4 Gene

  • C6orf149

Previous GeneCards Identifiers for LYRM4 Gene

  • GC06M005049
  • GC06M005103
  • GC06M004983

Summaries for LYRM4 Gene

GeneCards Summary for LYRM4 Gene

LYRM4 (LYR Motif Containing 4) is a Protein Coding gene. Diseases associated with LYRM4 include Combined Oxidative Phosphorylation Deficiency 19 and Severe Neonatal Lactic Acidosis Due To Nfs1-Isd11 Complex Deficiency. Among its related pathways are Metabolism and Mitochondrial iron-sulfur cluster biogenesis.

UniProtKB/Swiss-Prot for LYRM4 Gene

  • Required for nuclear and mitochondrial iron-sulfur protein biosynthesis.

No data available for Entrez Gene Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for LYRM4 Gene

Genomics for LYRM4 Gene

Regulatory Elements for LYRM4 Gene

Enhancers for LYRM4 Gene
GeneHancer Identifier Score Enhancer Sources TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Other Gene Targets for Enhancer

Enhancers around LYRM4 on UCSC Golden Path with GeneCards custom track

Promoters for LYRM4 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters

ENSRs around LYRM4 on UCSC Golden Path with GeneCards custom track

Genomic Location for LYRM4 Gene

Chromosome:
6
Start:
5,031,753 bp from pter
End:
5,260,950 bp from pter
Size:
229,198 bases
Orientation:
Minus strand

Genomic View for LYRM4 Gene

Genes around LYRM4 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
LYRM4 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for LYRM4 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for LYRM4 Gene

Proteins for LYRM4 Gene

  • Protein details for LYRM4 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9HD34-LYRM4_HUMAN
    Recommended name:
    LYR motif-containing protein 4
    Protein Accession:
    Q9HD34
    Secondary Accessions:
    • A8K543
    • Q5XKP1

    Protein attributes for LYRM4 Gene

    Size:
    91 amino acids
    Molecular mass:
    10758 Da
    Quaternary structure:
    • Interacts with FXN. Interaction is increased by nickel. Interaction is inhibited by calcium, magnesium, manganese, copper, cobalt, zinc, and iron. Forms a complex with the cytosolic/nuclear form of NFS1. The complex increased the stability of NFS1.
    Miscellaneous:
    • Reduction of LYRM4 levels by siRNA increases the total iron content, and reduces cytosolic and mitochondrial aconitase activities and NFS1 protein levels.

neXtProt entry for LYRM4 Gene

Proteomics data for LYRM4 Gene at MOPED

Post-translational modifications for LYRM4 Gene

  • Ubiquitination at Lys 58
  • Modification sites at PhosphoSitePlus

No data available for DME Specific Peptides for LYRM4 Gene

Domains & Families for LYRM4 Gene

Gene Families for LYRM4 Gene

Protein Domains for LYRM4 Gene

InterPro:
Blocks:
ProtoNet:

Suggested Antigen Peptide Sequences for LYRM4 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

Q9HD34

UniProtKB/Swiss-Prot:

LYRM4_HUMAN :
  • Belongs to the complex I LYR family.
Family:
  • Belongs to the complex I LYR family.
genes like me logo Genes that share domains with LYRM4: view

Function for LYRM4 Gene

Molecular function for LYRM4 Gene

UniProtKB/Swiss-Prot Function:
Required for nuclear and mitochondrial iron-sulfur protein biosynthesis.
genes like me logo Genes that share phenotypes with LYRM4: view

Human Phenotype Ontology for LYRM4 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Model Products

miRNA for LYRM4 Gene

miRTarBase miRNAs that target LYRM4

No data available for Enzyme Numbers (IUBMB) , Gene Ontology (GO) - Molecular Function , Animal Models , Transcription Factor Targets and HOMER Transcription for LYRM4 Gene

Localization for LYRM4 Gene

Subcellular locations from UniProtKB/Swiss-Prot for LYRM4 Gene

Mitochondrion. Nucleus.

Subcellular locations from

COMPARTMENTS
Jensen Localization Image for LYRM4 Gene COMPARTMENTS Subcellular localization image for LYRM4 gene
Compartment Confidence
mitochondrion 5
nucleus 5
cytosol 2

Gene Ontology (GO) - Cellular Components for LYRM4 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005739 mitochondrion IEA --
GO:0005759 mitochondrial matrix TAS --
genes like me logo Genes that share ontologies with LYRM4: view

Pathways & Interactions for LYRM4 Gene

genes like me logo Genes that share pathways with LYRM4: view

Pathways by source for LYRM4 Gene

2 Reactome pathways for LYRM4 Gene

UniProtKB/Swiss-Prot Q9HD34-LYRM4_HUMAN

  • Pathway: Cofactor biosynthesis; iron-sulfur cluster biosynthesis.

Interacting Proteins for LYRM4 Gene

Gene Ontology (GO) - Biological Process for LYRM4 Gene

None

No data available for SIGNOR curated interactions for LYRM4 Gene

Drugs & Compounds for LYRM4 Gene

No Compound Related Data Available

Transcripts for LYRM4 Gene

Unigene Clusters for LYRM4 Gene

LYR motif containing 4:
Representative Sequences:

Alternative Splicing Database (ASD) splice patterns (SP) for LYRM4 Gene

No ASD Table

Relevant External Links for LYRM4 Gene

GeneLoc Exon Structure for
LYRM4
ECgene alternative splicing isoforms for
LYRM4

Expression for LYRM4 Gene

mRNA expression in normal human tissues for LYRM4 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for LYRM4 Gene

This gene is overexpressed in Frontal cortex (12.1), Adrenal (9.3), and Gallbladder (6.0).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MOPED, and MaxQB for LYRM4 Gene



SOURCE GeneReport for Unigene cluster for LYRM4 Gene Hs.387755

mRNA Expression by UniProt/SwissProt for LYRM4 Gene

Q9HD34-LYRM4_HUMAN
Tissue specificity: Reduced mRNA levels in Friedreich ataxia patients.
genes like me logo Genes that share expression patterns with LYRM4: view

Protein tissue co-expression partners for LYRM4 Gene

Primer Products

No data available for mRNA differential expression in normal tissues for LYRM4 Gene

Orthologs for LYRM4 Gene

This gene was present in the common ancestor of animals and fungi.

Orthologs for LYRM4 Gene

Organism Taxonomy Gene Similarity Type Details
cow
(Bos Taurus)
Mammalia LYRM4 35
  • 84.62 (n)
  • 87.91 (a)
LYRM4 36
  • 76 (a)
OneToOne
dog
(Canis familiaris)
Mammalia LYRM4 35
  • 85.99 (n)
  • 82.61 (a)
LYRM4 36
  • 83 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Lyrm4 35
  • 89.38 (n)
  • 89.01 (a)
Lyrm4 16
Lyrm4 36
  • 75 (a)
OneToOne
chimpanzee
(Pan troglodytes)
Mammalia LYRM4 35
  • 99.27 (n)
  • 98.9 (a)
LYRM4 36
  • 97 (a)
OneToOne
rat
(Rattus norvegicus)
Mammalia LOC102550385 35
  • 87.91 (n)
  • 87.91 (a)
chicken
(Gallus gallus)
Aves LYRM4 35
  • 75.29 (n)
  • 72.94 (a)
LYRM4 36
  • 62 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia LYRM4 36
  • 65 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia lyrm4 35
  • 69.35 (n)
  • 68.97 (a)
zebrafish
(Danio rerio)
Actinopterygii lyrm4 35
  • 60.32 (n)
  • 54.76 (a)
lyrm4 36
  • 46 (a)
OneToOne
fruit fly
(Drosophila melanogaster)
Insecta bcn92 36
  • 36 (a)
OneToOne
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes ISD11 36
  • 33 (a)
OneToOne
Species with no ortholog for LYRM4:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • oppossum (Monodelphis domestica)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • platypus (Ornithorhynchus anatinus)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea squirt (Ciona intestinalis)
  • sea squirt (Ciona savignyi)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)

Evolution for LYRM4 Gene

ENSEMBL:
Gene Tree for LYRM4 (if available)
TreeFam:
Gene Tree for LYRM4 (if available)

Paralogs for LYRM4 Gene

Pseudogenes.org Pseudogenes for LYRM4 Gene

genes like me logo Genes that share paralogs with LYRM4: view

No data available for Paralogs for LYRM4 Gene

Variants for LYRM4 Gene

Sequence variations from dbSNP and Humsavar for LYRM4 Gene

SNP ID Clin Chr 06 pos Sequence Context AA Info Type
VAR_024551 -
VAR_070943 Combined oxidative phosphorylation deficiency 19 (COXPD19)
rs4960075 -- 5,252,047(+) GTGTA(C/G)TACAT intron-variant
rs1570085 -- 5,252,830(+) TGAGA(A/G)GAACA intron-variant
rs1609808 -- 5,246,100(-) TATAG(G/T)TCAAC intron-variant

Structural Variations from Database of Genomic Variants (DGV) for LYRM4 Gene

Variant ID Type Subtype PubMed ID
nsv462622 CNV Gain 19166990
esv28267 CNV Gain 19812545
esv2660224 CNV Deletion 23128226
nsv5179 CNV Loss 18451855
esv2469123 CNV Deletion 19546169
esv1953097 CNV Deletion 18987734
esv2665378 CNV Deletion 23128226
esv29679 CNV Loss 19812545
esv2731512 CNV Deletion 23290073
esv1673345 CNV Deletion 17803354
esv259633 OTHER Complex 20981092
esv260071 OTHER Complex 20981092
esv2731513 CNV Deletion 23290073
esv2666766 CNV Deletion 23128226
nsv522457 CNV Loss 19592680

Variation tolerance for LYRM4 Gene

Gene Damage Index Score: 11.68; 93.21% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for LYRM4 Gene

Human Gene Mutation Database (HGMD)
LYRM4

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for LYRM4 Gene

Disorders for LYRM4 Gene

MalaCards: The human disease database

(3) MalaCards diseases for LYRM4 Gene - From: OMIM, Orphanet, Swiss-Prot, DISEASES, and GeneCards

- elite association - COSMIC cancer census association via MalaCards
Search LYRM4 in MalaCards View complete list of genes associated with diseases

UniProtKB/Swiss-Prot

LYRM4_HUMAN
  • Combined oxidative phosphorylation deficiency 19 (COXPD19) [MIM:615595]: A mitochondrial disorder characterized by respiratory distress, hypotonia, and severe lactic acidosis in the newborn period. Other features include gastroesophageal reflux and elevated liver enzymes with normal synthetic function. {ECO:0000269 PubMed:23814038}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Relevant External Links for LYRM4

Genetic Association Database (GAD)
LYRM4
Human Genome Epidemiology (HuGE) Navigator
LYRM4
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
LYRM4
genes like me logo Genes that share disorders with LYRM4: view

No data available for Genatlas for LYRM4 Gene

Publications for LYRM4 Gene

  1. Mitochondrial frataxin interacts with ISD11 of the NFS1/ISCU complex and multiple mitochondrial chaperones. (PMID: 17331979) Shan Y. … Cortopassi G. (Hum. Mol. Genet. 2007) 3 4 23 67
  2. The BioPlex Network: A Systematic Exploration of the Human Interactome. (PMID: 26186194) Huttlin E.L. … Gygi S.P. (Cell 2015) 3
  3. Mapping Key Residues of ISD11 Critical for NFS1-ISD11 Subcomplex Stability: IMPLICATIONS IN THE DEVELOPMENT OF MITOCHONDRIAL DISORDER, COXPD19. (PMID: 26342079) Saha P.P. … D'Silva P. (J. Biol. Chem. 2015) 3
  4. Panorama of ancient metazoan macromolecular complexes. (PMID: 26344197) Wan C. … Emili A. (Nature 2015) 3
  5. A human interactome in three quantitative dimensions organized by stoichiometries and abundances. (PMID: 26496610) Hein M.Y. … Mann M. (Cell 2015) 3

Products for LYRM4 Gene

Sources for LYRM4 Gene

Content