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Protein

YrdC domain-containing protein, mitochondrial

Gene

YRDC

Organism
Homo sapiens (Human)
Status
Reviewed-Annotation score: Annotation score: 4 out of 5-Experimental evidence at protein leveli

Functioni

May regulate the activity of some transporters.By similarity

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Names & Taxonomyi

Protein namesi
Recommended name:
YrdC domain-containing protein, mitochondrial
Alternative name(s):
Dopamine receptor-interacting protein 3
Ischemia/reperfusion-inducible protein homolog
Short name:
hIRIP
Gene namesi
Name:YRDC
Synonyms:DRIP3, IRIP
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
Proteomesi
  • UP000005640 Componenti: Chromosome 1

Organism-specific databases

HGNCiHGNC:28905. YRDC.

Subcellular locationi

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Membrane, Mitochondrion

Pathology & Biotechi

Organism-specific databases

PharmGKBiPA142670553.

Polymorphism and mutation databases

BioMutaiYRDC.
DMDMi74750410.

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Transit peptidei1 – 5555MitochondrionSequence analysisAdd
BLAST
Chaini56 – 279224YrdC domain-containing protein, mitochondrialPRO_0000341402Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei60 – 601PhosphoserineCombined sources

Keywords - PTMi

Phosphoprotein

Proteomic databases

EPDiQ86U90.
MaxQBiQ86U90.
PaxDbiQ86U90.
PRIDEiQ86U90.

PTM databases

iPTMnetiQ86U90.
PhosphoSiteiQ86U90.

Expressioni

Tissue specificityi

Ubiquitously expressed.1 Publication

Gene expression databases

BgeeiQ86U90.
CleanExiHS_YRDC.
GenevisibleiQ86U90. HS.

Organism-specific databases

HPAiHPA030147.

Interactioni

Subunit structurei

Interacts with RSC1A1.By similarity

Protein-protein interaction databases

BioGridi122814. 8 interactions.
STRINGi9606.ENSP00000362135.

Structurei

3D structure databases

ProteinModelPortaliQ86U90.
SMRiQ86U90. Positions 68-245.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini67 – 257191YrdC-likePROSITE-ProRule annotationAdd
BLAST

Sequence similaritiesi

Belongs to the SUA5 family.Curated
Contains 1 YrdC-like domain.PROSITE-ProRule annotation

Keywords - Domaini

Transit peptide

Phylogenomic databases

eggNOGiKOG3051. Eukaryota.
COG0009. LUCA.
GeneTreeiENSGT00390000015364.
HOGENOMiHOG000239829.
HOVERGENiHBG055700.
InParanoidiQ86U90.
OMAiWHEQPLA.
OrthoDBiEOG7RFTJ4.
PhylomeDBiQ86U90.
TreeFamiTF314358.

Family and domain databases

Gene3Di3.90.870.10. 1 hit.
InterProiIPR017945. DHBP_synth_RibB-like_a/b_dom.
IPR006070. YrdC-like_dom.
[Graphical view]
PfamiPF01300. Sua5_yciO_yrdC. 1 hit.
[Graphical view]
SUPFAMiSSF55821. SSF55821. 1 hit.
TIGRFAMsiTIGR00057. TIGR00057. 1 hit.
PROSITEiPS51163. YRDC. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Sequence processingi: The displayed sequence is further processed into a mature form.

Q86U90-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MSPARRCRGM RAAVAASVGL SEGPAGSRSG RLFRPPSPAP AAPGARLLRL
60 70 80 90 100
PGSGAVQAAS PERAGWTEAL RAAVAELRAG AVVAVPTDTL YGLACAASCS
110 120 130 140 150
AALRAVYRLK GRSEAKPLAV CLGRVADVYR YCRVRVPEGL LKDLLPGPVT
160 170 180 190 200
LVMERSEELN KDLNPFTPLV GIRIPDHAFM QDLAQMFEGP LALTSANLSS
210 220 230 240 250
QASSLNVEEF QDLWPQLSLV IDGGQIGDGQ SPECRLGSTV VDLSVPGKFG
260 270
IIRPGCALES TTAILQQKYG LLPSHASYL
Length:279
Mass (Da):29,328
Last modified:June 1, 2003 - v1
Checksum:iF8F5C30274E2BB12
GO

Sequence cautioni

The sequence AAH08984.3 differs from that shown. Reason: Erroneous initiation. Curated
The sequence AAP37053.1 differs from that shown. Reason: Erroneous initiation. Curated
The sequence AAP37054.1 differs from that shown. Reason: Erroneous initiation. Curated
The sequence BAB15668.1 differs from that shown. Reason: Erroneous initiation. Curated

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AY172561 mRNA. Translation: AAO41711.1.
AL929472 Genomic DNA. Translation: CAH70083.1.
CH471059 Genomic DNA. Translation: EAX07317.1.
BC008984 mRNA. Translation: AAH08984.3. Different initiation.
BC067857 mRNA. Translation: AAH67857.2.
BC068057 mRNA. Translation: AAH68057.1.
BC080186 mRNA. Translation: AAH80186.2.
AY286019 mRNA. Translation: AAP37053.1. Different initiation.
AY286020 mRNA. Translation: AAP37054.1. Different initiation.
AF250397 mRNA. Translation: AAQ14263.1.
AK027129 mRNA. Translation: BAB15668.1. Different initiation.
CCDSiCCDS30675.1.
RefSeqiNP_078916.3. NM_024640.3.
UniGeneiHs.301564.

Genome annotation databases

EnsembliENST00000373044; ENSP00000362135; ENSG00000196449.
GeneIDi79693.
KEGGihsa:79693.
UCSCiuc001cca.2. human.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AY172561 mRNA. Translation: AAO41711.1.
AL929472 Genomic DNA. Translation: CAH70083.1.
CH471059 Genomic DNA. Translation: EAX07317.1.
BC008984 mRNA. Translation: AAH08984.3. Different initiation.
BC067857 mRNA. Translation: AAH67857.2.
BC068057 mRNA. Translation: AAH68057.1.
BC080186 mRNA. Translation: AAH80186.2.
AY286019 mRNA. Translation: AAP37053.1. Different initiation.
AY286020 mRNA. Translation: AAP37054.1. Different initiation.
AF250397 mRNA. Translation: AAQ14263.1.
AK027129 mRNA. Translation: BAB15668.1. Different initiation.
CCDSiCCDS30675.1.
RefSeqiNP_078916.3. NM_024640.3.
UniGeneiHs.301564.

3D structure databases

ProteinModelPortaliQ86U90.
SMRiQ86U90. Positions 68-245.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi122814. 8 interactions.
STRINGi9606.ENSP00000362135.

PTM databases

iPTMnetiQ86U90.
PhosphoSiteiQ86U90.

Polymorphism and mutation databases

BioMutaiYRDC.
DMDMi74750410.

Proteomic databases

EPDiQ86U90.
MaxQBiQ86U90.
PaxDbiQ86U90.
PRIDEiQ86U90.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000373044; ENSP00000362135; ENSG00000196449.
GeneIDi79693.
KEGGihsa:79693.
UCSCiuc001cca.2. human.

Organism-specific databases

CTDi79693.
GeneCardsiYRDC.
H-InvDBHIX0023600.
HGNCiHGNC:28905. YRDC.
HPAiHPA030147.
MIMi612276. gene.
neXtProtiNX_Q86U90.
PharmGKBiPA142670553.
GenAtlasiSearch...

Phylogenomic databases

eggNOGiKOG3051. Eukaryota.
COG0009. LUCA.
GeneTreeiENSGT00390000015364.
HOGENOMiHOG000239829.
HOVERGENiHBG055700.
InParanoidiQ86U90.
OMAiWHEQPLA.
OrthoDBiEOG7RFTJ4.
PhylomeDBiQ86U90.
TreeFamiTF314358.

Miscellaneous databases

GenomeRNAii79693.
PROiQ86U90.
SOURCEiSearch...

Gene expression databases

BgeeiQ86U90.
CleanExiHS_YRDC.
GenevisibleiQ86U90. HS.

Family and domain databases

Gene3Di3.90.870.10. 1 hit.
InterProiIPR017945. DHBP_synth_RibB-like_a/b_dom.
IPR006070. YrdC-like_dom.
[Graphical view]
PfamiPF01300. Sua5_yciO_yrdC. 1 hit.
[Graphical view]
SUPFAMiSSF55821. SSF55821. 1 hit.
TIGRFAMsiTIGR00057. TIGR00057. 1 hit.
PROSITEiPS51163. YRDC. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "Isolation and identification of a novel cDNA that encodes human yrdC protein."
    Chen J., Ji C., Gu S., Zhao E., Dai J., Huang L., Qian J., Ying K., Xie Y., Mao Y.
    J. Hum. Genet. 48:164-169(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA], TISSUE SPECIFICITY.
  2. "The DNA sequence and biological annotation of human chromosome 1."
    Gregory S.G., Barlow K.F., McLay K.E., Kaul R., Swarbreck D., Dunham A., Scott C.E., Howe K.L., Woodfine K., Spencer C.C.A., Jones M.C., Gillson C., Searle S., Zhou Y., Kokocinski F., McDonald L., Evans R., Phillips K.
    , Atkinson A., Cooper R., Jones C., Hall R.E., Andrews T.D., Lloyd C., Ainscough R., Almeida J.P., Ambrose K.D., Anderson F., Andrew R.W., Ashwell R.I.S., Aubin K., Babbage A.K., Bagguley C.L., Bailey J., Beasley H., Bethel G., Bird C.P., Bray-Allen S., Brown J.Y., Brown A.J., Buckley D., Burton J., Bye J., Carder C., Chapman J.C., Clark S.Y., Clarke G., Clee C., Cobley V., Collier R.E., Corby N., Coville G.J., Davies J., Deadman R., Dunn M., Earthrowl M., Ellington A.G., Errington H., Frankish A., Frankland J., French L., Garner P., Garnett J., Gay L., Ghori M.R.J., Gibson R., Gilby L.M., Gillett W., Glithero R.J., Grafham D.V., Griffiths C., Griffiths-Jones S., Grocock R., Hammond S., Harrison E.S.I., Hart E., Haugen E., Heath P.D., Holmes S., Holt K., Howden P.J., Hunt A.R., Hunt S.E., Hunter G., Isherwood J., James R., Johnson C., Johnson D., Joy A., Kay M., Kershaw J.K., Kibukawa M., Kimberley A.M., King A., Knights A.J., Lad H., Laird G., Lawlor S., Leongamornlert D.A., Lloyd D.M., Loveland J., Lovell J., Lush M.J., Lyne R., Martin S., Mashreghi-Mohammadi M., Matthews L., Matthews N.S.W., McLaren S., Milne S., Mistry S., Moore M.J.F., Nickerson T., O'Dell C.N., Oliver K., Palmeiri A., Palmer S.A., Parker A., Patel D., Pearce A.V., Peck A.I., Pelan S., Phelps K., Phillimore B.J., Plumb R., Rajan J., Raymond C., Rouse G., Saenphimmachak C., Sehra H.K., Sheridan E., Shownkeen R., Sims S., Skuce C.D., Smith M., Steward C., Subramanian S., Sycamore N., Tracey A., Tromans A., Van Helmond Z., Wall M., Wallis J.M., White S., Whitehead S.L., Wilkinson J.E., Willey D.L., Williams H., Wilming L., Wray P.W., Wu Z., Coulson A., Vaudin M., Sulston J.E., Durbin R.M., Hubbard T., Wooster R., Dunham I., Carter N.P., McVean G., Ross M.T., Harrow J., Olson M.V., Beck S., Rogers J., Bentley D.R.
    Nature 441:315-321(2006) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
  3. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
  4. "The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC)."
    The MGC Project Team
    Genome Res. 14:2121-2127(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
    Tissue: Lymph, Placenta and Skin.
  5. "IRIP, a new ischemia/reperfusion-inducible protein that participates in the regulation of transporter activity."
    Jiang W., Prokopenko O., Wong L., Inouye M., Mirochnitchenko O.
    Mol. Cell. Biol. 25:6496-6508(2005) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA] OF 3-279.
  6. "Cloning and characterization of DRIP3, a new protein that specifically interacts with the D1 dopamine receptor."
    Lafuente M.J., Nasir J.
    Submitted (MAR-2000) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [MRNA] OF 57-279.
  7. "Complete sequencing and characterization of 21,243 full-length human cDNAs."
    Ota T., Suzuki Y., Nishikawa T., Otsuki T., Sugiyama T., Irie R., Wakamatsu A., Hayashi K., Sato H., Nagai K., Kimura K., Makita H., Sekine M., Obayashi M., Nishi T., Shibahara T., Tanaka T., Ishii S.
    , Yamamoto J., Saito K., Kawai Y., Isono Y., Nakamura Y., Nagahari K., Murakami K., Yasuda T., Iwayanagi T., Wagatsuma M., Shiratori A., Sudo H., Hosoiri T., Kaku Y., Kodaira H., Kondo H., Sugawara M., Takahashi M., Kanda K., Yokoi T., Furuya T., Kikkawa E., Omura Y., Abe K., Kamihara K., Katsuta N., Sato K., Tanikawa M., Yamazaki M., Ninomiya K., Ishibashi T., Yamashita H., Murakawa K., Fujimori K., Tanai H., Kimata M., Watanabe M., Hiraoka S., Chiba Y., Ishida S., Ono Y., Takiguchi S., Watanabe S., Yosida M., Hotuta T., Kusano J., Kanehori K., Takahashi-Fujii A., Hara H., Tanase T.-O., Nomura Y., Togiya S., Komai F., Hara R., Takeuchi K., Arita M., Imose N., Musashino K., Yuuki H., Oshima A., Sasaki N., Aotsuka S., Yoshikawa Y., Matsunawa H., Ichihara T., Shiohata N., Sano S., Moriya S., Momiyama H., Satoh N., Takami S., Terashima Y., Suzuki O., Nakagawa S., Senoh A., Mizoguchi H., Goto Y., Shimizu F., Wakebe H., Hishigaki H., Watanabe T., Sugiyama A., Takemoto M., Kawakami B., Yamazaki M., Watanabe K., Kumagai A., Itakura S., Fukuzumi Y., Fujimori Y., Komiyama M., Tashiro H., Tanigami A., Fujiwara T., Ono T., Yamada K., Fujii Y., Ozaki K., Hirao M., Ohmori Y., Kawabata A., Hikiji T., Kobatake N., Inagaki H., Ikema Y., Okamoto S., Okitani R., Kawakami T., Noguchi S., Itoh T., Shigeta K., Senba T., Matsumura K., Nakajima Y., Mizuno T., Morinaga M., Sasaki M., Togashi T., Oyama M., Hata H., Watanabe M., Komatsu T., Mizushima-Sugano J., Satoh T., Shirai Y., Takahashi Y., Nakagawa K., Okumura K., Nagase T., Nomura N., Kikuchi H., Masuho Y., Yamashita R., Nakai K., Yada T., Nakamura Y., Ohara O., Isogai T., Sugano S.
    Nat. Genet. 36:40-45(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] OF 129-279.
    Tissue: Small intestine.
  8. "Global, in vivo, and site-specific phosphorylation dynamics in signaling networks."
    Olsen J.V., Blagoev B., Gnad F., Macek B., Kumar C., Mortensen P., Mann M.
    Cell 127:635-648(2006) [PubMed] [Europe PMC] [Abstract]
    Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    Tissue: Cervix carcinoma.
  9. "A probability-based approach for high-throughput protein phosphorylation analysis and site localization."
    Beausoleil S.A., Villen J., Gerber S.A., Rush J., Gygi S.P.
    Nat. Biotechnol. 24:1285-1292(2006) [PubMed] [Europe PMC] [Abstract]
    Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-60, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    Tissue: Cervix carcinoma.
  10. "Improved titanium dioxide enrichment of phosphopeptides from HeLa cells and high confident phosphopeptide identification by cross-validation of MS/MS and MS/MS/MS spectra."
    Yu L.R., Zhu Z., Chan K.C., Issaq H.J., Dimitrov D.S., Veenstra T.D.
    J. Proteome Res. 6:4150-4162(2007) [PubMed] [Europe PMC] [Abstract]
    Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    Tissue: Cervix carcinoma.
  11. "Kinase-selective enrichment enables quantitative phosphoproteomics of the kinome across the cell cycle."
    Daub H., Olsen J.V., Bairlein M., Gnad F., Oppermann F.S., Korner R., Greff Z., Keri G., Stemmann O., Mann M.
    Mol. Cell 31:438-448(2008) [PubMed] [Europe PMC] [Abstract]
    Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-60, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    Tissue: Cervix carcinoma.
  12. Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-60, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    Tissue: Cervix carcinoma.
  13. "Lys-N and trypsin cover complementary parts of the phosphoproteome in a refined SCX-based approach."
    Gauci S., Helbig A.O., Slijper M., Krijgsveld J., Heck A.J., Mohammed S.
    Anal. Chem. 81:4493-4501(2009) [PubMed] [Europe PMC] [Abstract]
    Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
  14. "Quantitative phosphoproteomic analysis of T cell receptor signaling reveals system-wide modulation of protein-protein interactions."
    Mayya V., Lundgren D.H., Hwang S.-I., Rezaul K., Wu L., Eng J.K., Rodionov V., Han D.K.
    Sci. Signal. 2:RA46-RA46(2009) [PubMed] [Europe PMC] [Abstract]
    Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    Tissue: Leukemic T-cell.
  15. "Quantitative phosphoproteomics reveals widespread full phosphorylation site occupancy during mitosis."
    Olsen J.V., Vermeulen M., Santamaria A., Kumar C., Miller M.L., Jensen L.J., Gnad F., Cox J., Jensen T.S., Nigg E.A., Brunak S., Mann M.
    Sci. Signal. 3:RA3-RA3(2010) [PubMed] [Europe PMC] [Abstract]
    Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-60, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    Tissue: Cervix carcinoma.
  16. Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
  17. "System-wide temporal characterization of the proteome and phosphoproteome of human embryonic stem cell differentiation."
    Rigbolt K.T., Prokhorova T.A., Akimov V., Henningsen J., Johansen P.T., Kratchmarova I., Kassem M., Mann M., Olsen J.V., Blagoev B.
    Sci. Signal. 4:RS3-RS3(2011) [PubMed] [Europe PMC] [Abstract]
    Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
  18. "An enzyme assisted RP-RPLC approach for in-depth analysis of human liver phosphoproteome."
    Bian Y., Song C., Cheng K., Dong M., Wang F., Huang J., Sun D., Wang L., Ye M., Zou H.
    J. Proteomics 96:253-262(2014) [PubMed] [Europe PMC] [Abstract]
    Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    Tissue: Liver.

Entry informationi

Entry nameiYRDC_HUMAN
AccessioniPrimary (citable) accession number: Q86U90
Secondary accession number(s): Q4W4X8
, Q6NVW3, Q7L4E4, Q7Z2I4, Q9H5F8
Entry historyi
Integrated into UniProtKB/Swiss-Prot: June 10, 2008
Last sequence update: June 1, 2003
Last modified: June 8, 2016
This is version 110 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program
DisclaimerAny medical or genetic information present in this entry is provided for research, educational and informational purposes only. It is not in any way intended to be used as a substitute for professional medical advice, diagnosis, treatment or care.

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. Human chromosome 1
    Human chromosome 1: entries, gene names and cross-references to MIM
  2. MIM cross-references
    Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot
  3. SIMILARITY comments
    Index of protein domains and families

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.