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DEFB109P1 Gene

pseudogene   GIFtS: 20
GCID: GC08M012253

Defensin, Beta 109, Pseudogene 1

(Previous names: defensin, beta 109)
(Previous symbol: DEFB109)
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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 109, Pseudogene 11 2
DEFB1091 2 3
Defensin, Beta 1091 3
DEFB109A2 3
DEFB-92
Defensin, Beta 109, Pseudogene 1/1B3

External Ids:    HGNC: 180901   Entrez Gene: 2459122   Ensembl: ENSG000002422967   UniProtKB: Q30KR13   
ORGUL members:         

Export aliases for DEFB109P1 gene to outside databases

Previous GC identifers: GC08U900543 GC08M007887 GC08M007847 GC08M012251


(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 DEFB109P1 Gene:
DEFB109P1 (defensin, beta 109, pseudogene 1) is a pseudogene, and is affiliated with the lncRNA class.

UniProtKB/Swiss-Prot: DB109_HUMAN, Q30KR1
Function: Has antibacterial activity (By similarity)




(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:
   Regulatory transcription factor binding sites in the DEFB109P1 gene promoter:
         COUP-TF1   MEF-2   NCX/Ncx   COUP   HNF-4alpha2   HNF-4alpha1   MEF-2A   COUP-TF   aMEF-2   
         Other transcription factors

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Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat DEFB109P1


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

Entrez Gene cytogenetic band: 8p23.1   Ensembl cytogenetic band:  8p23.1   HGNC cytogenetic band: 8p23.1

DEFB109P1 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
DEFB109P1 gene location

GeneLoc information about chromosome 8         GeneLoc Exon Structure

GeneLoc location for GC08M012253:  view genomic region     (about GC identifiers)

Start:
12,250,718 bp from pter      End:
12,257,875 bp from pter
Size:
7,158 bases      Orientation:
minus 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, 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/Swiss-Prot: DB109_HUMAN, Q30KR1 (See protein sequence)
Recommended Name: Beta-defensin 109 precursor  
Size: 87 amino acids; 9886 Da

Explore the universe of human proteins at neXtProt for DEFB109P1: NX_Q30KR1


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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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HGNC Gene Families:
DEFB: Defensins, beta

2 InterPro protein domains:
 IPR025933 Beta_defensin
 IPR006080 Defensin_beta/neutrophil

Graphical View of Domain Structure for InterPro Entry Q30KR1

ProtoNet protein and cluster: Q30KR1

1 Blocks protein domain: IPB001855 Beta defensin

UniProtKB/Swiss-Prot: DB109_HUMAN, Q30KR1
Similarity: Belongs to the beta-defensin family


Find genes that share domains with DEFB109P1           About GenesLikeMe


(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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Molecular Function:

     UniProtKB/Swiss-Prot Summary: DB109_HUMAN, Q30KR1
Function: Has antibacterial activity (By similarity)

Animal Models:

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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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Subcellular locations from UniProtKB/Swiss-Prot
DB109_HUMAN, Q30KR1: Secreted (By similarity)

(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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    Custom Pathway & Disease-focused RT2 Profiler PCR Arrays for DEFB109P1
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 DEFB109P1 (DB109)



(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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1 Ensembl transcript including schematic representation, and UCSC links where relevant:
ENST00000482450(uc011kxr.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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DEFB109P1 expression in normal human tissues (normalized intensities)
See probesets specificity/sensitivity at GeneAnnot
About this imageBioGPS <intensity>2/3
CGAP TAG: --
DEFB109P1 Expression
About this image

DEFB109P1 Protein expression data from MOPED1, PaxDb2 and MaxQB3 --
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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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  --

ENSEMBL Gene Tree for DEFB109P1 (if available)
TreeFam Gene Tree for DEFB109P1 (if available)

(Paralogs according to 1HomoloGene,
2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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Paralogs for DEFB109P1 gene
4 SIMAP similar genes for DEFB109P1 using alignment to 1 protein entry:     DB109_HUMAN:
DEFB106A    DEFB106B    DEFB130    DEFB130L

Find genes that share paralogs with DEFB109P1           About GenesLikeMe



(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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1 SNPs for DEFB109P1    About this table                                 

Genomic DataTranscription Related DataAllele Frequencies
SNP IDValidClinical
significance
Chr 8 posSequence#AA
Chg
TypeMore#Allele
freq
PopTotal
sample
More
----------
rs1997649441,2
--12255121(+) TTTCT-/TTTC  
        
TTTCT
1 -- int10--------

HapMap Linkage Disequilibrium report for DEFB109P1 (12250718 - 12257875 bp)

Structural Variations
     Database of Genomic Variants (DGV) Selected variations for DEFB109P1 (see all 29):    About this table    
Variant IDTypeSubtypePubMed ID
esv2672709CNV Deletion23128226
dgv1270e199CNV Deletion23128226
esv2736614CNV Deletion23290073
nsv469553CNV Loss16826518
nsv831235CNV Loss17160897
dgv140n17CNV Loss16327808
nsv831234CNV Loss17160897
nsv821657CNV Loss15273396
nsv511387CNV Loss21212237
nsv890380CNV Gain21882294

Site Specific Mutation Identification with PCR Assays
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DNA2.0 Custom Variant and Variant Library Synthesis for DEFB109P1

(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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  --

(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 DEFB109P1 gene integrated from 10 sources:
(articles sorted by number of sources associating them with DEFB109P1)
    Utopia: connect your pdf to the dynamic
world of online information

  1. 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)
  2. Cross-species analysis of the mammalian beta-defensin gene family: presence of syntenic gene clusters and preferential expression in the male reproductive tract. (PubMed id 16033865)2 Patil A.A.... Zhang G. (Physiol. Genomics 2005)
  3. ORFeome-based search of airway epithelial cell-specific novel human beta-defensin genes. (PubMed id 12600824)1 Kao C.Y.... Wu R. (Am. J. Respir. Cell Mol. Biol. 2003)
  4. Duplication and selection in the evolution of primate beta-defensin genes. (PubMed id 12734011)1 Semple C.A.M.... Dorin J.R. (Genome Biol. 2003)

(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: 245912 HGNC: 18090 Ensembl:ENSG00000242296 euGenes: HUgn245912 ECgene: DEFB109P1
H-InvDB: DEFB109P1

(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 DEFB109P1 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 DEFB109P1 gene:
Search GeneIP for patents involving DEFB109P1

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
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