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DEFB122 Gene

pseudogene   GIFtS: 25
GCID: GC20P030003

Defensin, Beta 122 (Pseudogene)

(Previous names: defensin, beta 122)
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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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This gene clusters with an RNA gene
Subcategory (RNA class): lncRNA

Quality score for the ORGUL clustered with this gene is 3

Aliases
Defensin, Beta 122 (Pseudogene)1 2
Defensin, Beta 1221
DEFB-222
DEFB122P2

External Ids:    HGNC: 181021   Entrez Gene: 2459352   Ensembl: ENSG000002045477   
ORGUL members:         

Export aliases for DEFB122 gene to outside databases

Previous GC identifers: GC20U990237 GC20P029466 GC20P026791


(According to Entrez Gene, GeneCards, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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GeneCards Summary for DEFB122 Gene:
DEFB122 (defensin, beta 122 (pseudogene)) is a pseudogene, and is affiliated with the lncRNA class.


(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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RefSeq DNA sequence at NCBI GenBank:
NC_000020.10  NC_018931.2  NT_011362.11  
Regulatory elements:
   Regulatory transcription factor binding sites in the DEFB122 gene promoter:
         COUP-TF1   COUP   HNF-4alpha2   HNF-4alpha1   PPAR-gamma1   COUP-TF   PPAR-gamma2   ATF6   
         Other transcription factors

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Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat DEFB122


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

Entrez Gene cytogenetic band: 20q11.21   Ensembl cytogenetic band:  20q11.21   HGNC cytogenetic band: 20q11.21

DEFB122 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
DEFB122 gene location

GeneLoc information about chromosome 20         GeneLoc Exon Structure

GeneLoc location for GC20P030003:  view genomic region     (about GC identifiers)

Start:
30,003,051 bp from pter      End:
30,016,977 bp from pter
Size:
13,927 bases      Orientation:
plus strand

1 alternative location:
Chr20- 30,009,239-30,016,983     

(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, Cloud-Clone Corp., eBioscience, and/or antibodies-online,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, Cloud-Clone Corp., eBioscience, and/or antibodies-online, Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, Abcam, Cloud-Clone Corp, antibodies-online, and/or others.)
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UniProtKB: --


(According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
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HGNC Gene Families:
DEFB: Defensins, beta

  --

(According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, 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, Vector BioLabs and/or Addgene, Cell Lines from GenScript, ESI BIO, In Situ Hybridization Assays from Advanced Cell Diagnostics, Flow cytometry from eBioscience, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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Animal Models:
   genOway: Develop your customized and physiologically relevant rodent model for DEFB122

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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:

    Search GeneGlobe Interaction Network for DEFB122

(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 drugs & compounds from Enzo Life Sciences
  Browse compounds at ApexBio 

Browse Tocris compounds for DEFB122



(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,
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, and/or Addgene, Primers from OriGene, and/or QIAGEN, Flow cytometry from eBioscience )
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Unigene Cluster for DEFB122:

Defensin, beta 122 (pseudogene)
Hs.526624  [show with all ESTs]
Unigene Representative Sequence: AY122474
3 Ensembl transcripts including schematic representations, and UCSC links where relevant:
ENST00000433453(uc002wvx.1) ENST00000569013 ENST00000545884
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Additional mRNA sequence: 

AY122474.1 AY500999.1 NR_045677.1 

1 DOTS entry:

DT.99928015 

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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DEFB122 expression in normal human tissues (normalized intensities)
See probesets specificity/sensitivity at GeneAnnot
About this imageBioGPS <intensity>2/3
CGAP TAG: TTGGAATTTT
DEFB122 Expression
About this image

DEFB122 Protein expression data from MOPED1, PaxDb2 and MaxQB3 --

SOURCE GeneReport for Unigene cluster: Hs.526624
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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 mouse.

Orthologs for DEFB122 gene from 1 species (see representative species )    About this table
Organism Taxonomic
classification
Gene Description Human
Similarity
Orthology
Type
Details
mouse
(Mus musculus)
Mammalia Defb455 defensin beta 45   --   2 (75.41 cM) 152593191 


ENSEMBL Gene Tree for DEFB122 (if available)
TreeFam Gene Tree for DEFB122 (if available)

(Paralogs according to 1HomoloGene,
2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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  --

(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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Selected SNPs for DEFB122 (see all 195)    About this table                                 

Genomic DataTranscription Related DataAllele Frequencies
SNP IDValidClinical
significance
Chr 20 posSequence#AA
Chg
TypeMore#Allele
freq
PopTotal
sample
More
----------
rs49111211,2
C,F,A,H--30008851(+) CCTGCC/TTATAA 1 -- ds50018Minor allele frequency- T:0.43NA WA EA 374
rs1895168541,2
--30008941(+) CCTCAC/TCTCTA 1 -- ds50010--------
rs1813303031,2
--30009088(+) GACTCC/TATCTC 1 -- ds50010--------
rs1859841391,2
--30009115(+) AAATAA/GAAAGG 1 -- ds50010--------
rs1489168741,2
--30009145(+) AGCACA/GTAGTA 1 -- ds50010--------
rs1906604351,2
--30009227(+) AGAGAC/TAAACA 1 -- ds50010--------
rs1438441191,2
C--30009232(+) CAAACA/GCAGAA 1 -- ds50010--------
rs1385344511,2
C--30009250(+) AAAGAG/TGTTTT 1 -- nc-transcript-variant0--------
rs61413841,2
H--30009683(+) cctttC/Gtaaag 1 -- int14Minor allele frequency- G:0.00NS EA 418
rs1832546351,2
--30009823(+) TATATA/GTTCTG 1 -- int10--------

HapMap Linkage Disequilibrium report for DEFB122 (30003051 - 30016977 bp)

Structural Variations
     Database of Genomic Variants (DGV) 3 variations for DEFB122:    About this table    
Variant IDTypeSubtypePubMed ID
nsv458961CNV Gain19166990
nsv912835CNV Gain21882294
nsv470546CNV Gain18288195

Site Specific Mutation Identification with PCR Assays
Search QIAGEN SeqTarget long-range PCR primers for resequencing DEFB122
DNA2.0 Custom Variant and Variant Library Synthesis for DEFB122

(in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
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Find genes that share disorders with DEFB122           About GenesLikeMe

Genetic Association Database (GAD): DEFB122

Export disorders for DEFB122 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)
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PubMed articles for DEFB122 gene integrated from 10 sources:
(articles sorted by number of sources associating them with DEFB122)
    Utopia: connect your pdf to the dynamic
world of online information

  1. Identification, characterization, and evolution of a primate beta- defensin gene cluster. (PubMed id 15772680)1, 3 Radhakrishnan Y....Hall S.H. (Genes Immun. 2005)
  2. Discovery of five conserved beta-defensin gene clusters using a computational search strategy. (PubMed id 11854508)1, 3 Schutte B.C.... McCray P.B. Jr. (Proc. Natl. Acad. Sci. U.S.A. 2002)
  3. Genome-wide association of echocardiographic dimensions, brachial artery endothelial function and treadmill exercise responses in the Framingham Heart Study. (PubMed id 17903301)4 Vasan R.S....Benjamin E.J. (BMC Med. Genet. 2007)

(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: 245935 HGNC: 18102 Ensembl:ENSG00000204547 euGenes: HUgn245935 ECgene: DEFB122
H-InvDB: DEFB122

(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 DEFB122 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 DEFB122 gene:
Search GeneIP for patents involving DEFB122

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, Novus Biologicals, Sino Biological, Enzo Life Sciences, Abcam, ProSpec, Cloud-Clone Corp., Thermo Fisher Scientific, eBioscience, antibodies-online, and/or others, Gene Editing from DNA2.0. Clones from OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Addgene, Cell lines from GenScript, and ESI BIO, Flow cytometery from eBioscience, PCR Arrays from QIAGEN, Drugs and/or compounds from EMD Millipore, Tocris Bioscience, Enzo Life Sciences, and/or ApexBio, In Situ Hybridization Assays from
Advanced Cell Diagnostics, Animal models from genOway)
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