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Aliases for YRDC Gene

Aliases for YRDC Gene

  • YrdC N6-Threonylcarbamoyltransferase Domain Containing 2 3 5
  • Ischemia/Reperfusion-Inducible Protein Homolog 3 4
  • Ischemia/Reperfusion Inducible Protein 2 3
  • HIRIP 3 4
  • DRIP3 3 4
  • IRIP 3 4
  • YrdC N(6)-Threonylcarbamoyltransferase Domain Containing 3
  • YrdC Domain-Containing Protein, Mitochondrial 3
  • Dopamine Receptor Interacting Protein 3 3
  • Dopamine Receptor-Interacting Protein 3 4
  • YrdC Domain Containing (E. Coli) 2
  • YrdC Domain Containing (E.Coli) 2
  • YrdC Domain Containing 3
  • SUA5 3

External Ids for YRDC Gene

Previous GeneCards Identifiers for YRDC Gene

  • GC01M037938
  • GC01M038041
  • GC01M038268
  • GC01M036386

Summaries for YRDC Gene

GeneCards Summary for YRDC Gene

YRDC (YrdC N6-Threonylcarbamoyltransferase Domain Containing) is a Protein Coding gene. Diseases associated with YRDC include Ischemia. GO annotations related to this gene include double-stranded RNA binding.

UniProtKB/Swiss-Prot for YRDC Gene

  • May regulate the activity of some transporters.

Additional gene information for YRDC Gene

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

Genomics for YRDC Gene

Regulatory Elements for YRDC Gene

Enhancers for YRDC Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH01H037988 1.2 ENCODE 19 -181.6 -181595 2 ZFP64 FEZF1 DMAP1 YY1 SLC30A9 ZNF143 SP3 NFYC ZC3H11A ZFP41 SF3A3 C1orf109 INPP5B GNL2 FHL3 MYCBP FTH1P1 RSPO1 RRAGC YRDC
GH01H037552 1.1 ENCODE 19.6 +254.3 254320 2 HDGF PKNOX1 ARNT ARID4B SIN3A DMAP1 ZNF2 YY1 ZNF766 CBX5 SNIP1 C1orf109 SF3A3 GNL2 FTH1P1 YRDC INPP5B CDCA8 ZC3H12A RSPO1
GH01H037850 1.6 FANTOM5 Ensembl ENCODE dbSUPER 13.2 -43.7 -43708 3 SOX6 HLF CEBPB CEBPG ZNF316 GATA2 ZNF366 NR2C1 HMBOX1 ZNF24 MTF1 INPP5B ZC3H12A YRDC C1orf122 ENSG00000233728 SNIP1 RPS2P13
GH01H038008 1.7 Ensembl ENCODE dbSUPER 10.2 -204.7 -204717 9 MLX ZFP64 DMAP1 YY1 SLC30A9 ZNF143 SP3 NFYC MEF2D ZNF610 SF3A3 C1orf109 INPP5B SNIP1 RNU6-510P RSPO1 ENSG00000230955 MTF1 YRDC C1orf122
GH01H037845 1.2 FANTOM5 Ensembl 13 -38.2 -38208 2 PKNOX1 IRF2 ZNF316 GATA2 STAT2 TRIM24 NFE2 IKZF2 MTA2 CEBPB MTF1 ZC3H12A YRDC C1orf122 ENSG00000233728 C1orf109 CDCA8 FHL3 SNIP1 RPS2P13
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around YRDC on UCSC Golden Path with GeneCards custom track

Promoters for YRDC Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000004891 -7 2001 PKNOX1 ATF1 ARNT ARID4B SIN3A DMAP1 YY1 ETS1 GLIS2 ELK1

Genomic Location for YRDC Gene

Chromosome:
1
Start:
37,802,942 bp from pter
End:
37,808,193 bp from pter
Size:
5,252 bases
Orientation:
Minus strand

Genomic View for YRDC Gene

Genes around YRDC on UCSC Golden Path with GeneCards custom track

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

RefSeq DNA sequence for YRDC Gene

Proteins for YRDC Gene

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

    Protein Symbol:
    Q86U90-YRDC_HUMAN
    Recommended name:
    YrdC domain-containing protein, mitochondrial
    Protein Accession:
    Q86U90
    Secondary Accessions:
    • Q4W4X8
    • Q6NVW3
    • Q7L4E4
    • Q7Z2I4
    • Q9H5F8

    Protein attributes for YRDC Gene

    Size:
    279 amino acids
    Molecular mass:
    29328 Da
    Quaternary structure:
    • Interacts with RSC1A1.
    SequenceCaution:
    • Sequence=AAH08984.3; Type=Erroneous initiation; Evidence={ECO:0000305}; Sequence=AAP37053.1; Type=Erroneous initiation; Evidence={ECO:0000305}; Sequence=AAP37054.1; Type=Erroneous initiation; Evidence={ECO:0000305}; Sequence=BAB15668.1; Type=Erroneous initiation; Evidence={ECO:0000305};

neXtProt entry for YRDC Gene

Post-translational modifications for YRDC Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for YRDC Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for YRDC Gene

Domains & Families for YRDC Gene

Gene Families for YRDC Gene

Human Protein Atlas (HPA):
  • Predicted intracellular proteins

Suggested Antigen Peptide Sequences for YRDC Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

Q86U90

UniProtKB/Swiss-Prot:

YRDC_HUMAN :
  • Belongs to the SUA5 family.
Family:
  • Belongs to the SUA5 family.
genes like me logo Genes that share domains with YRDC: view

Function for YRDC Gene

Molecular function for YRDC Gene

UniProtKB/Swiss-Prot Function:
May regulate the activity of some transporters.

Phenotypes From GWAS Catalog for YRDC Gene

Gene Ontology (GO) - Molecular Function for YRDC Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000049 tRNA binding IBA --
GO:0003725 double-stranded RNA binding IEA --
GO:0016779 nucleotidyltransferase activity IBA --
genes like me logo Genes that share ontologies with YRDC: view
genes like me logo Genes that share phenotypes with YRDC: view

Animal Model Products

CRISPR Products

miRNA for YRDC Gene

miRTarBase miRNAs that target YRDC

Inhibitory RNA Products

Clone Products

  • Applied Biological Materials Clones for YRDC
  • Vectors and viruses for ORF, Lenti, Retro, Adenovirus, AAV, and more

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for YRDC Gene

Localization for YRDC Gene

Subcellular locations from UniProtKB/Swiss-Prot for YRDC Gene

Mitochondrion. Membrane; Peripheral membrane protein. Note=Predominantly localized in the plasma membrane. {ECO:0000250}.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for YRDC gene
Compartment Confidence
mitochondrion 5
extracellular 1
nucleus 1
cytosol 1

Subcellular locations from the

Human Protein Atlas (HPA)

Gene Ontology (GO) - Cellular Components for YRDC Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005737 cytoplasm IBA --
GO:0005739 mitochondrion IEA --
GO:0016020 membrane IEA --
genes like me logo Genes that share ontologies with YRDC: view

Pathways & Interactions for YRDC Gene

No Data Available

Gene Ontology (GO) - Biological Process for YRDC Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0002949 tRNA threonylcarbamoyladenosine modification IBA --
GO:0006450 regulation of translational fidelity IBA --
GO:0051051 negative regulation of transport IDA 2675563
genes like me logo Genes that share ontologies with YRDC: view

No data available for Pathways by source and SIGNOR curated interactions for YRDC Gene

Drugs & Compounds for YRDC Gene

No Compound Related Data Available

Transcripts for YRDC Gene

mRNA/cDNA for YRDC Gene

(1) REFSEQ mRNAs :
(11) Additional mRNA sequences :
(144) Selected AceView cDNA sequences:
(1) Ensembl transcripts including schematic representations, and UCSC links where relevant :

Unigene Clusters for YRDC Gene

YrdC domain containing (E. coli):
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

Clone Products

  • Applied Biological Materials Clones for YRDC
  • Vectors and viruses for ORF, Lenti, Retro, Adenovirus, AAV, and more

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

No ASD Table

Relevant External Links for YRDC Gene

GeneLoc Exon Structure for
YRDC
ECgene alternative splicing isoforms for
YRDC

Expression for YRDC Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for YRDC Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for YRDC Gene

This gene is overexpressed in Cervix (38.1), Testis (13.4), and Fetal ovary (8.0).

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



Protein tissue co-expression partners for YRDC Gene

NURSA nuclear receptor signaling pathways regulating expression of YRDC Gene:

YRDC

SOURCE GeneReport for Unigene cluster for YRDC Gene:

Hs.301564

mRNA Expression by UniProt/SwissProt for YRDC Gene:

Q86U90-YRDC_HUMAN
Tissue specificity: Ubiquitously expressed.

Evidence on tissue expression from TISSUES for YRDC Gene

  • Intestine(4.2)
  • Liver(4.1)
  • Skin(4.1)
genes like me logo Genes that share expression patterns with YRDC: view

Primer Products

No data available for mRNA differential expression in normal tissues and Phenotype-based relationships between genes and organs from Gene ORGANizer for YRDC Gene

Orthologs for YRDC Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for YRDC Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia YRDC 33 34
  • 99.4 (n)
cow
(Bos Taurus)
Mammalia YRDC 33 34
  • 89.13 (n)
dog
(Canis familiaris)
Mammalia YRDC 33 34
  • 86.49 (n)
mouse
(Mus musculus)
Mammalia Yrdc 33 16 34
  • 85.68 (n)
rat
(Rattus norvegicus)
Mammalia Yrdc 33
  • 85.2 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia YRDC 34
  • 70 (a)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia YRDC 34
  • 66 (a)
OneToOne
chicken
(Gallus gallus)
Aves YRDC 33 34
  • 68.13 (n)
lizard
(Anolis carolinensis)
Reptilia YRDC 34
  • 64 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia yrdc 33
  • 59.97 (n)
African clawed frog
(Xenopus laevis)
Amphibia LOC398509 33
zebrafish
(Danio rerio)
Actinopterygii yrdc 33 34
  • 59.19 (n)
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP007397 33
  • 54.06 (n)
fruit fly
(Drosophila melanogaster)
Insecta CG33786 33 34
  • 53.64 (n)
worm
(Caenorhabditis elegans)
Secernentea Y48C3A.18 34
  • 38 (a)
OneToOne
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes SUA5 36
thale cress
(Arabidopsis thaliana)
eudicotyledons AT5G60590 33
  • 50.34 (n)
rice
(Oryza sativa)
Liliopsida Os03g0201600 33
  • 51.76 (n)
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 35 (a)
OneToOne
Species where no ortholog for YRDC was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • 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)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for YRDC Gene

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

Paralogs for YRDC Gene

Pseudogenes.org Pseudogenes for YRDC Gene

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

No data available for Paralogs for YRDC Gene

Variants for YRDC Gene

Sequence variations from dbSNP and Humsavar for YRDC Gene

SNP ID Clin Chr 01 pos Sequence Context AA Info Type
rs1001173441 -- 37,806,473(+) CTGGG(C/G)TCACA intron-variant, upstream-variant-2KB
rs1001204513 -- 37,806,668(+) TTTGA(A/G)ATAAA intron-variant, upstream-variant-2KB
rs10015 -- 37,802,983(-) TTTTT(C/T)TTTAA utr-variant-3-prime
rs1002263352 -- 37,805,378(+) TGCGA(C/T)TCTGA intron-variant
rs1002294536 -- 37,805,119(+) GGCAT(A/G)GTGGC intron-variant

Variation tolerance for YRDC Gene

Residual Variation Intolerance Score: 41.6% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 1.03; 21.10% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for YRDC Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
YRDC

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot and Structural Variations from Database of Genomic Variants (DGV) for YRDC Gene

Disorders for YRDC Gene

MalaCards: The human disease database

(1) MalaCards diseases for YRDC Gene - From: DISEASES and GeneCards

Disorder Aliases PubMed IDs
ischemia
  • acute coronary syndrome
- elite association - COSMIC cancer census association via MalaCards
Search YRDC in MalaCards View complete list of genes associated with diseases

Relevant External Links for YRDC

Atlas of Genetics and Cytogenetics in Oncology and Haematology:
YRDC
genes like me logo Genes that share disorders with YRDC: view

No data available for UniProtKB/Swiss-Prot and Genatlas for YRDC Gene

Publications for YRDC Gene

  1. Isolation and identification of a novel cDNA that encodes human yrdC protein. (PMID: 12730717) Chen J … Mao Y (Journal of human genetics 2003) 2 3 4 60
  2. IRIP, a new ischemia/reperfusion-inducible protein that participates in the regulation of transporter activity. (PMID: 16024787) Jiang W … Mirochnitchenko O (Molecular and cellular biology 2005) 3 4 60
  3. Architecture of the human interactome defines protein communities and disease networks. (PMID: 28514442) Huttlin EL … Harper JW (Nature 2017) 3 60
  4. SR protein kinases promote splicing of nonconsensus introns. (PMID: 26167880) Lipp JJ … Guthrie C (Nature structural & molecular biology 2015) 3 60
  5. The BioPlex Network: A Systematic Exploration of the Human Interactome. (PMID: 26186194) Huttlin EL … Gygi SP (Cell 2015) 3 60

Products for YRDC Gene

Sources for YRDC Gene

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