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Category   Symbol Source: HGNC EntrezGene Ensembl GeneCards RNA genes CroW21
GIFtS

YBEY Gene

protein-coding   GIFtS: 43
GCID: GC21P047707

YbeY Metallopeptidase (Putative)

(Previous name: chromosome 21 open reading frame 57)
(Previous symbol: C21orf57)
Microbiology & Infectious Diseases Congress
  See related diseases
at  

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, 10fRNAdb, 12H-InvDB, 13NCBI, 14NONCODE, and/or 15RNAdb)
About This Section

Aliases
YbeY Metallopeptidase (Putative)1 2
C21orf571 2 3
Chromosome 21 Open Reading Frame 571
Putative Metalloprotease C21orf572
Putative Ribonuclease2
RRNA Maturation Factor Homolog2

External Ids:    HGNC: 12991   Entrez Gene: 540592   Ensembl: ENSG000001823627   UniProtKB: P585573   

Export aliases for YBEY gene to outside databases


(According to Entrez Gene, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
About This Section

GeneCards Summary for YBEY Gene: 
YBEY (ybeY metallopeptidase (putative)) is a protein-coding gene. Diseases associated with YBEY include pneumonia, and tuberculosis. GO annotations related to this gene include metalloendopeptidase activity and metal ion binding.


(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 37),
and/or miRBase,
Genomic Views according to UCSC (hg19) and Ensembl (release 73), Regulatory elements and Epigenetics data according to QIAGEN, SABiosciences, and/or SwitchGear Genomics)
About This Section
RefSeq DNA sequence:
NC_000021.8  NT_011515.12  NC_018932.2  
Regulatory elements:
   Search SABiosciences Regulatory transcription factor binding sites for YBEY
         Other transcription factors

Browse SwitchGear Promoter luciferase reporter plasmids
   Search SABiosciences Chromatin IP Primers for YBEY

Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat YBEY


Genomic Location:
Genomic View: UCSC Golden Path with GeneCards custom track

Entrez Gene cytogenetic band: 21q22.3   Ensembl cytogenetic band:  21q22.3   HGNC cytogenetic band: 21q22.3

YBEY Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
YBEY gene location

GeneLoc information about chromosome 21         GeneLoc Exon Structure

GeneLoc location for GC21P047707:  view genomic region     (about GC identifiers)

Start:
47,706,251 bp from pter      End:
47,717,665 bp from pter
Size:
11,415 bases      Orientation:
plus strand

(According to UniProtKB, HORDE, neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MAXQB RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from EMD Millipore, R&D Systems, GenScript, Enzo Life Sciences, OriGene, Novus Biologicals, Sino Biological, ProSpec, and/or Cloud-Clone Corp.,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Cloud-Clone Corp., Ontologies according to Gene Ontology Consortium 01 Oct 2013 and Entrez Gene, Antibodies by EMD Millipore, R&D Systems, GenScript, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, and/or Cloud-Clone Corp.)
About This Section

UniProtKB/Swiss-Prot: YBEY_HUMAN, P58557 (See protein sequence)
Recommended Name: Putative ribonuclease  
Size: 167 amino acids; 19298 Da
Cofactor: Binds 1 zinc ion (By similarity)
Subcellular location: Nucleus
Miscellaneous: A protein of the expected size has been detected by antibody binding and Western blot in at least
one of the analyzed tissues or cells (PubMed:22042635)
Sequence caution: Sequence=AAK74138.1; Type=Erroneous translation; Note=Wrong choice of CDS; Sequence=AAK74139.1;
Type=Erroneous initiation; Note=Translation N-terminally shortened; Sequence=AAK74140.1; Type=Erroneous
translation; Note=Wrong choice of CDS; Sequence=AAK74141.1; Type=Erroneous translation; Note=Wrong choice of CDS;
Secondary accessions: B7WPA9 B7WPF7 D3DSN2
Alternative splicing: 4 isoforms:  P58557-1   P58557-2   P58557-3   P58557-4   

Explore the universe of human proteins at neXtProt for YBEY: NX_P58557

Explore proteomics data for YBEY at MOPED 

YBEY Protein expression data from MOPED1, PaxDb2 and MAXQB3 :    About this image 

YBEY Protein Expression

REFSEQ proteins (2 alternative transcripts): 
NP_001006114.1  NP_478061.1  

ENSEMBL proteins: 
 ENSP00000380813   ENSP00000380808   ENSP00000329614   ENSP00000340675   ENSP00000380806  
 ENSP00000380805  

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Gene Ontology (GO): 2 cellular component terms (GO ID links to tree view):    About this table

GO IDQualified GO termEvidencePubMed IDs
GO:0005634nucleus IDA--
GO:0005739mitochondrion IEA--

YBEY for ontologies           About GeneDecksing



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(According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
About This Section
3 InterPro protein domains:
 IPR002036 YbeY
 IPR020549 YbeY_CS
 IPR023091 MetalPrtase_cat_dom_prd

Graphical View of Domain Structure for InterPro Entry P58557

ProtoNet protein and cluster: P58557

1 Blocks protein domain: IPB002036 Protein of unknown function UPF0054

UniProtKB/Swiss-Prot: YBEY_HUMAN, P58557
Similarity: Belongs to the endoribonuclease YbeY family


YBEY for domains           About GeneDecksing


(According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, inGenious Targeting Laboratory, genOway,
bound targets from SABiosciences, miRNA Gene Targets from miRTarBase, shRNA from OriGene, RNAi from EMD Millipore, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, Gene Editing from DNA2.0, Sirion Biotech, Clones from EMD Millipore, OriGene, SwitchGear Genomics, GenScript, Sino Biological, DNA2.0, Vector BioLabs, and Sirion Biotech, Cell Lines from GenScript, LifeMap BioReagents, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Oct 2013 via Entrez Gene.)
About This Section

     Gene Ontology (GO): 2 molecular function terms (GO ID links to tree view):    About this table

GO IDQualified GO termEvidencePubMed IDs
GO:0004222metalloendopeptidase activity IEA--
GO:0046872metal ion binding IEA--
     
YBEY for ontologies           About GeneDecksing


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(Pathways according to EMD Millipore, R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Sino Biological, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to SABiosciences, and/or STRING, Interactions according to 1UniProtKB, 2MINT, 3I2D, and/or 4STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Oct 2013 via Entrez Gene).
About This Section



Interactions:

    Search SABiosciences Gene Network CentralTM Interacting Genes and Proteins Networks for YBEY

STRING Interaction Network Preview (showing 3 interactants - click image to see more details)

3 Interacting proteins for YBEY (P585573 ENSP000003296144) via UniProtKB, MINT, STRING, and/or I2D
InteractantInteraction Details
GeneCardExternal ID(s)
AKTIPQ9H8T03, ENSP000003002454I2D: score=1 STRING: ENSP00000300245
GEMP550403, ENSP000002975964I2D: score=2 STRING: ENSP00000297596
MRPL17ENSP000002889374STRING: ENSP00000288937
About this table

Gene Ontology (GO): 1 biological process term (GO ID links to tree view):    About this table

GO IDQualified GO termEvidencePubMed IDs
GO:0006364rRNA processing IEA--

YBEY for ontologies           About GeneDecksing



(Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB, with drugs/clinical trials/news search links to CenterWatch)
About This Section
Browse Small Molecules at EMD Millipore
Browse drugs & compounds from Enzo Life Sciences

Browse Tocris compounds for YBEY

Search CenterWatch for drugs/clinical trials and news about YBEY

(Secondary structures according to fRNAdb,
GenBank/EMBL/DDBJ Accessions according to
Unigene (Build 236 Homo sapiens; Apr 25 2013) or GenBank,
RefSeq according to Entrez Gene,
DOTS (version 10), and/or AceView, transcript ids from Ensembl with links to UCSC,
Conferences by KenesGroup, exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
RNAi Products from EMD Millipore,
siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN,
Tagged/untagged cDNA clones from OriGene, SwitchGear Genomics, GenScript, DNA2.0, Vector BioLabs, Sirion Biotech, Primers from OriGene, SABiosciences, and/or QIAGEN )
About This Section

REFSEQ mRNAs for YBEY gene (2 alternative transcripts): 
NM_001006114.1  NM_058181.1  

Unigene Cluster for YBEY:

YbeY metallopeptidase (putative)
Hs.474066  [show with all ESTs]
Unigene Representative Sequence: AK294975
8 Ensembl transcripts including schematic representations, and UCSC links where relevant:
ENST00000397701(uc002ziw.3 uc002zix.3 uc010gqh.3) ENST00000468924
ENST00000397694 ENST00000329319(uc002ziv.3) ENST00000339195(uc002ziy.3)
ENST00000397692 ENST00000492864(uc002zit.1 uc002ziu.1) ENST00000397691

Congresses - knowledge worth sharing:  
European Congress of Clinical Microbiology and Infectious Diseases (ECCMID) 10 - 13 May 2014

miRNA
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Inhib. RNA
Products:
     
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Additional mRNA sequence: 

AK128875.1 AK294975.1 AY040873.1 AY040874.1 AY040875.1 AY040876.1 BC022828.1 BC068100.1 
BC119770.1 BC122865.1 BC131553.1 DQ786290.1 

10 DOTS entries:

DT.442093  DT.100750019  DT.121134432  DT.97823524  DT.100750018  DT.92417452  DT.91879059  DT.412085 
DT.99975493  DT.87046385 

GeneLoc Exon Structure

5/9 Alternative Splicing Database (ASD) splice patterns (SP) for YBEY (see all 9)    About this scheme

ExUns: 1a · 1b ^ 2a · 2b ^ 3a · 3b ^ 4a · 4b · 4c ^ 5 ^ 6 ^ 7
SP1:              -     -                       -     -     -               
SP2:              -     -           -           -     -     -               
SP3:                                            -     -     -               
SP4:              -     -                       -     -                     
SP5:              -     -           -     -     -     -     -               


ECgene alternative splicing isoforms for YBEY

(RNA expression data according to H-InvDB, NONCODE, miRBase, and RNAdb, Expression images according to data from BioGPS, Illumina Human BodyMap, and CGAP SAGE, Sets of similar genes according to GeneDecks, in vivo and in vitro expression data from LifeMap Discovery™, plus additional links to Genevestigator, and/or SOURCE, and/or BioGPS, and/or UniProtKB,
PCR Arrays from SABiosciences, Primers from OriGene, SABiosciences, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
About This Section

YBEY expression in normal human tissues (normalized intensities)
See probesets specificity/sensitivity at GeneAnnot
About this imageBioGPS <intensity>2/3
CGAP TAG: AGCATCTGAA
YBEY Expression
About this image


See YBEY Protein Expression from SPIRE MOPED and PaxDB
Genevestigator expression for YBEY

SOURCE GeneReport for Unigene cluster: Hs.474066
    SABiosciences Custom PCR Arrays for YBEY
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In Situ
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(Orthologs according to 1,2HomoloGene (2older version, for species not in 1newer version), 3euGenes, 4SGD , 5MGI Mar 06 2013, with possible further links to Flybase and/or WormBase, and/or 6Ensembl pan taxonomic compara , Gene Trees according to Ensembl and TreeFam)
About This Section

This gene was present in the common ancestor of chordates.

Orthologs for YBEY gene from 5/12 species (see all 12)    About this table
Organism Taxonomic
classification
Gene Description Human
Similarity
Orthology
Type
Details
mouse
(Mus musculus)
Mammalia Ybey1 , 5 ybeY metallopeptidase1, 5 82.32(n)1
77.44(a)1
  10 (38.85 cM)5
2161191  NM_172550.41  NP_766138.31 
 764595695 
chicken
(Gallus gallus)
Aves POFUT26
Uncharacterized protein
57(a)
1 ↔ 1
7(6877908-6880111)
lizard
(Anolis carolinensis)
Reptilia YBEY6
Uncharacterized protein
64(a)
1 ↔ 1
1(123000519-123009428)
African clawed frog
(Xenopus laevis)
Amphibia BG731038.12   -- 80.84(n)    BG731038.1 
zebrafish
(Danio rerio)
Actinopterygii wufb30h032 Transcribed sequence with weak similarity to protein more 72.8(n)    BG985784.1 


ENSEMBL Gene Tree for YBEY (if available)
TreeFam Gene Tree for YBEY (if available)

(Paralogs according to 1HomoloGene,
2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
About This Section
Paralogs for YBEY gene
1 SIMAP similar gene for YBEY using alignment to 1 protein entry:     YBEY_HUMAN:
C21orf57

YBEY for paralogs           About GeneDecksing



(SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, 4UniProtKB, and DNA2.0, Linkage Disequilibrium by HapMap, Structural Variations(CNVs/InDels/Inversions) from the Database of Genomic Variants, Mutations from the Human Gene Mutation Database (HGMD) and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers from QIAGEN, Cancer Mutation PCR Arrays and Assays and Copy Number PCR Arrays from SABiosciences)
About This Section

10/493 SNPs in YBEY are shown (see all 493)    About this table     
Genomic DataTranscription Related DataAllele Frequencies
SNP IDValidClinical
significance
Chr 21 posSequence#AA
Chg
TypeMore#Allele
freq
PopTotal
sample
More
----------
rs130522331,2
C,F--47707284(+) TTTTTG/TTCAGT 2 -- int18Minor allele frequency- T:0.31NA WA EA 368
rs1998190711,2
--47707284(+) TTTTT-/GTCAGT 2 -- int10--------
rs1126889591,2
C--47707339(+) CTGAA-/CC    
   T
/CTC
CTGAT
4 -- cds12CSA 4
rs672074621,2
C--47707340(+) TGAAC-/CTCTGATC 2 -- cds10--------
rs345285311,2
C--47707341(+) GAACT-/CCTGATCT 1 -- cds10--------
rs130523761,2
C,F--47707403(+) agccaG/Cagcac 2 -- int18Minor allele frequency- C:0.31NA WA CSA EA 367
rs130464941,2
C,F--47707430(+) GTATTA/CATTAT 2 -- int110Minor allele frequency- C:0.33WA NA CSA EA 371
rs130524951,2
C,F--47707474(+) tatatG/Attaca 2 -- int19Minor allele frequency- A:0.32WA NA CSA EA 369
rs1819509171,2
--47707475(+) ATATGG/TTACAG 2 -- int10--------
rs1383259741,2
C--47707488(+) ATGATG/TTTTAA 2 -- int10--------

HapMap Linkage Disequilibrium report for YBEY (47706251 - 47717665 bp)

Structural Variations
     Database of Genomic Variants (DGV) 10/14 variations for YBEY (see all 14):    About this table     
Variant IDTypeSubtypePubMed ID
esv1190668CNV Deletion17803354
esv2320022CNV Deletion18987734
nsv821184CNV Deletion20802225
esv1185684CNV Insertion17803354
nsv3547CNV Insertion18451855
nsv519904CNV Loss19592680
nsv914141CNV Loss21882294
nsv914135CNV Loss21882294
dgv4817n71CNV Loss21882294
esv27873CNV Gain19812545

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(in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Conferences by KenesGroup, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
About This Section
3 diseases for YBEY:    About MalaCards
pneumonia    tuberculosis    gastric cancer


YBEY for disorders           About GeneDecksing


Export disorders for YBEY gene to outside databases

(in PubMed. Associations of this gene to articles via 1Entrez Gene, 2UniProtKB/Swiss-Prot, 3HGNC, 4GAD, 5PharmGKB, 6HMDB, 7DrugBank, 8UniProtKB/TrEMBL, 9 Novoseek, and/or 10fRNAdb)
About This Section

PubMed articles for YBEY gene integrated from 9 sources:
(articles sorted by number of sources associating them with YBEY)
    Utopia: connect your pdf to the dynamic
world of online information

  1. From PREDs and open reading frames to cDNA isolation: revisiting the human chromosome 21 transcription map. (PubMed id 11707072)1, 2 Reymond A....Antonarakis S.E. (2001)
  2. The DNA sequence of human chromosome 21. (PubMed id 10830953)1, 2 Hattori M....Yaspo M.L. (2000)
  3. Antibody-based protein profiling of the human chromosome 21. (PubMed id 22042635)2 Uhlen M....Sivertsson A. (2012)
  4. Initial characterization of the human central proteome. (PubMed id 21269460)2 Burkard T.R.... Colinge J. (2011)
  5. Genetic variants in nuclear-encoded mitochondrial gen es influence AIDS progression. (PubMed id 20877624)1 Hendrickson S.L....O'Brien S.J. (2010)
  6. Protein interaction data set highlighted with human Ras-MAPK/PI3K signaling pathways. (PubMed id 18624398)1 Wang J....He F. (2008)
  7. Transcriptome analysis of human gastric cancer. (PubMed id 16341674)1 Oh J.H....Kim N.S. (2005)
  8. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. (PubMed id 12477932)1 Strausberg R.L....Marra M.A. (2002)

(in PubMed, OMIM, and NCBI Bookshelf)
About This Section
 ANDOR
Aliases
Free Text  

  Query String
PubMed
OMIM
NCBI Bookshelf
  (Note: In FireFox, select the above section and copy using Ctrl-C)

(According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
About This Section
Entrez Gene: 54059 HGNC: 1299 Ensembl:ENSG00000182362 euGenes: HUgn54059 ECgene: YBEY
H-InvDB: YBEY

(According to HUGE)
About This Section
  --

(According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL,
Wikipedia and/or GeneReviews via UniProtKB/Swiss-Prot)
About This Section
NameDescription
PharmGKB entry for YBEY Pharmacogenomics, SNPs, Pathways

(Patent information from GeneIP,
Licensable technologies from WIS Yeda, Salk, Tufts,
IP news from LifeMap Sciences, Inc.)
About This Section
Patent Information for YBEY gene:
Search GeneIP for patents involving YBEY

GeneCards and IP:
Japan Patent Office Licenses GeneCards     European Patent Office Licenses GeneCards     Improving the IP Search



(Antibodies, recombinant proteins, and assays from EMD Millipore, R&D Systems, OriGene, QIAGEN, GenScript, Cell Signaling Technology, SABiosciences, Novus Biologicals, Sino Biological, Enzo Life Sciences, Abcam, ProSpec, Cloud-Clone Corp., Thermo Fisher Scientific, LSBio, Gene Editing from DNA2.0 and Sirion Biotech, Clones from EMD Millipore, OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Sirion Biotech, Cell lines from GenScript, and LifeMap BioReagents, PCR Arrays from SABiosciences, Drugs and/or compounds from EMD Millipore, Tocris Bioscience, and/or Enzo Life Sciences, In Situ Hybridization Assays from
Advanced Cell Diagnostics, Animal models from inGenious Targeting Laboratory, genOway)
About This Section

 
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GeneCards Homepage - Last full update: 23 Oct 2013 - Incrementals: 3 Nov 2013 , 7 Nov 2013 , 23 Jan 2014

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Category
(GIFtS: 73)
transforming growth factor, beta 1
GIFtS Group
The GeneCards human gene database gene index: 1 3 5 6 A B C D E F G H I J K L M N O P Q R S T U V W X Y Z 


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