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DPH3P1 Gene

pseudogene   GIFtS: 24
GCID: GC20P061477

Diphthamide Biosynthesis 3 Pseudogene 1

(Previous names: chromosome 20 open reading frame 143, zinc finger, CSL-type...)
(Previous symbols: C20orf143, ZCSL1, DPH3B)
  Search for DPH3P1
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(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, 10fRNAdb, 12H-InvDB, 13NCBI, 14NONCODE, and/or 15RNAdb)
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Aliases
Diphthamide Biosynthesis 3 Pseudogene 11 2     DPH3, KTI11 Homolog (S. Cerevisiae) Pseudogene 11
C20orf1431 2 3     DPH3B, KTI11 Homolog B (S. Cerevisiae)1
DPH3B1 2 3     Zinc Finger, CSL-Type Containing 11
ZCSL11 2 3     DPH3 Homolog B (KTI11, S. Cerevisiae)2
CSL-Type Zinc Finger-Containing Protein 12 3     Putative DPH3 Homolog B2
Chromosome 20 Open Reading Frame 1431     Zinc Finger, CSL Domain Containing 12

External Ids:    HGNC: 161361   Entrez Gene: 1001329112   Ensembl: ENSG000002338387   UniProtKB: Q9H4G83   

Export aliases for DPH3P1 gene to outside databases

Previous GC identifer: GC20P058195


(According to Entrez Gene, GeneCards, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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Entrez Gene summary for DPH3P1 Gene:
This gene may represent a processed pseudogene of DPH3, GeneID: 285381, because it lacks the exon/intron structure
found in the functional gene. However, it does contain an intact open reading frame and it has not been
established that the predicted protein is not translated. The NCBI RefSeq Project continues to treat this as a
protein coding gene in agreement with Swiss-Prot. (provided by RefSeq, Jan 2014)

GeneCards Summary for DPH3P1 Gene:
DPH3P1 (diphthamide biosynthesis 3 pseudogene 1) is a pseudogene.




(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 75), Regulatory elements and Epigenetics data according to QIAGEN, and/or SwitchGear Genomics)
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Regulatory elements:
   Search for regulatory transcription factor binding sites for DPH3P1
         Other transcription factors

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Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat DPH3P1


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

Entrez Gene cytogenetic band: 20q13.33   Ensembl cytogenetic band:  20q13.33   HGNC cytogenetic band: 20q13.33

DPH3P1 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
DPH3P1 gene location

GeneLoc information about chromosome 20         GeneLoc Exon Structure

GeneLoc location for GC20P061477:  view genomic region     (about GC identifiers)

Start:
61,476,476 bp from pter      End:
61,477,543 bp from pter
Size:
1,068 bases      Orientation:
plus strand

(According to 1UniProtKB, HORDE, 2neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, 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., Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, and/or Cloud-Clone Corp.)
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UniProtKB/Swiss-Prot: DPH3B_HUMAN, Q9H4G8 (See protein sequence)
Recommended Name: Putative DPH3 homolog B  
Size: 78 amino acids; 8721 Da
Caution: Could be the product of a pseudogene

Explore the universe of human proteins at neXtProt for DPH3P1: NX_Q9H4G8

REFSEQ proteins: NP_542788.1  

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(According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
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1 InterPro protein domain:
 IPR007872 Znf_DHP

Graphical View of Domain Structure for InterPro Entry Q9H4G8

ProtoNet protein and cluster: Q9H4G8

UniProtKB/Swiss-Prot: DPH3B_HUMAN, Q9H4G8
Similarity: Belongs to the DPH3 family
Similarity: Contains 1 DPH-type zinc finger


DPH3P1 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,
transcription factor targeting from QIAGEN and/or HOMER, miRNA Gene Targets from miRTarBase, shRNA from OriGene, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, SwitchGear Genomics, Gene Editing from DNA2.0, Clones from OriGene, GenScript, Sino Biological, DNA2.0, and Vector BioLabs, Cell Lines from GenScript, ESI BIO, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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     Gene Ontology (GO): 1 molecular function term:    About this table

GO IDQualified GO termEvidencePubMed IDs
GO:0046872metal ion binding IEA--
     
DPH3P1 for ontologies           About GeneDecksing


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(According to UniProtKB, COMPARTMENTS Subcellular localization database, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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  --

(SuperPaths according to PathCards, Pathways according to 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 QIAGEN, 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 Apr 2014 via Entrez Gene).
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Interactions:

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(Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience, ApexBio, HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB)
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Browse Tocris compounds for DPH3P1 (DPH3B)



(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,
siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN, SwitchGear Genomics,
Tagged/untagged cDNA clones from OriGene, GenScript, DNA2.0, Vector BioLabs, Primers from OriGene, and/or QIAGEN )
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REFSEQ mRNAs for DPH3P1 gene: 
NM_080750.4  

2 Ensembl transcripts including schematic representations, and UCSC links where relevant:
ENST00000486648 ENST00000502378(uc011aan.1)
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GeneLoc Exon Structure


(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™, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MaxQB, plus additional links to SOURCE, and/or BioGPS, and/or UniProtKB,
PCR Arrays from QIAGEN, Primers from OriGene, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
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DPH3P1 expression in normal human tissues (normalized intensities)      DPH3P1 embryonic expression: see
See probesets specificity/sensitivity at GeneAnnot
About this imageBioGPS <intensity>2/3
CGAP TAG: --
DPH3P1 Expression
About this image


DPH3P1 expression in embryonic tissues and stem cells    About this table
Data from LifeMap, the Embryonic Development and Stem Cells Database
 
 Testis (Reproductive System)    fully expand to see all 3 entries
         Leydig Cells Testis Interstitium
         Testis Interstitium
DPH3P1 Protein expression data from MOPED1, PaxDb2 and MaxQB3 --
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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)
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This gene was present in the common ancestor of human and chimp.

Orthologs for DPH3P1 gene from 1 species (see representative species )    About this table
Organism Taxonomic
classification
Gene Description Human
Similarity
Orthology
Type
Details
chimpanzee
(Pan troglodytes)
Mammalia DPH3P11 DPH3, KTI11 homolog (S. cerevisiae) pseudogene 1 100(n)
100(a)
  100612608  XM_003954482.1  XP_003954531.1 


ENSEMBL Gene Tree for DPH3P1 (if available)
TreeFam Gene Tree for DPH3P1 (if available)

(Paralogs according to 1HomoloGene,
2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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Paralogs for DPH3P1 gene
2 SIMAP similar genes for DPH3P1 using alignment to 1 protein entry:     DPH3B_HUMAN:
DPH3    DNAJC24

DPH3P1 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), the Human Cytochrome P450 Allele Nomenclature Database, and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers, Cancer Mutation PCR Arrays and Assays, and Copy Number PCR Arrays from QIAGEN)
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Structural Variations
     Database of Genomic Variants (DGV) 9 variations for DPH3P1:    About this table    
Variant IDTypeSubtypePubMed ID
nsv428380CNV Loss18775914
nsv913073CNV Loss21882294
dgv4614n71CNV Loss21882294
nsv834027CNV Loss17160897
nsv913127CNV Loss21882294
dgv4603n71CNV Loss21882294
nsv913124CNV Loss21882294
nsv828794CNV Loss20364138
nsv9825CNV Gain18304495

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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.)
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  --

(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)
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PubMed article for DPH3P1 gene integrated from 10 sources:
(articles sorted by number of sources associating them with DPH3P1)
    Utopia: connect your pdf to the dynamic
world of online information

  1. The DNA sequence and comparative analysis of human chromosome 20. (PubMed id 11780052)1, 2 Deloukas P....Rogers J. (Nature 2001)

(in PubMed, OMIM, and NCBI Bookshelf)
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 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)
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Entrez Gene: 100132911 HGNC: 16136 Ensembl:ENSG00000233838 euGenes: HUgn100132911 ECgene: DPH3P1
H-InvDB: DPH3P1

(According to HUGE)
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  --

(According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL, and/or others, e.g. Wikipedia and GeneReviews, via UniProtKB/Swiss-Prot)
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NameDescription
PharmGKB entry for DPH3P1 Pharmacogenomics, SNPs, Pathways

(Patent information from GeneIP,
Licensable technologies from WIS Yeda, Salk, Tufts,
IP news from LifeMap Sciences, Inc.)
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Patent Information for DPH3P1 gene:
Search GeneIP for patents involving DPH3P1

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



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Advanced Cell Diagnostics, Animal models from inGenious Targeting Laboratory, genOway)
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