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BPIFA4P Gene

pseudogene   GIFtS: 27
GCID: GC20P031784

BPI Fold Containing Family A, Member 4, Pseudogene

  See BPIFA4P-related disease
at  

(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
BPI Fold Containing Family A, Member 4, Pseudogene1 2
BASE2 5
Breast Cancer And Salivary Gland Expression Gene1
PLUNC Family Pseudogene1

External Ids:    HGNC: 204691   Entrez Gene: 3177162   Ensembl: ENSG000001835667   OMIM: 6076275   

Export aliases for BPIFA4P gene to outside databases


(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 BPIFA4P Gene:
BPIFA4P (BPI fold containing family A, member 4, pseudogene) is a pseudogene. Diseases associated with BPIFA4P include breast cancer.


(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:
   Search for regulatory transcription factor binding sites for BPIFA4P
         Other transcription factors

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Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat BPIFA4P


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

BPIFA4P Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
BPIFA4P gene location

GeneLoc information about chromosome 20         GeneLoc Exon Structure

GeneLoc location for GC20P031784:  view genomic region     (about GC identifiers)

Start:
31,781,391 bp from pter      End:
31,798,268 bp from pter
Size:
16,878 bases      Orientation:
plus strand
ORGUL member locations:
Legend (see complete legend)

ORGUL Member Locations for BPIFA4P

(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, LSBio, 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:
BPIF: BPI fold containing

  --

(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, 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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Phenotypes:
     1 GenomeRNAi human phenotype for BPIFA4P:
 Lamellipodia and high actin ra 

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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  --

(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 BPIFA4P

(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 BPIFA4P



(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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REFSEQ mRNAs for BPIFA4P gene: 
NM_173859.1  

Unigene Cluster for BPIFA4P:

BPI fold containing family A, member 4, pseudogene
Hs.434194  [show with all ESTs]
Unigene Representative Sequence: AY180924
4 Ensembl transcripts including schematic representations, and UCSC links where relevant:
ENST00000605211 ENST00000603168 ENST00000375465(uc010gei.1 uc002wyp.2 uc002wyq.2)
ENST00000420169
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Additional mRNA sequence: 

AY180924.1 AY389991.1 AY389992.1 BC069128.1 BC069315.1 BC128240.1 BC128241.1 NR_026760.1 

3 DOTS entries:

DT.102819968  DT.120796590  DT.101975943 

6 AceView cDNA sequences:

BC069128 BC069315 AY180924 NM_173859 BX642190 BX642280 

GeneLoc Exon Structure

4 Alternative Splicing Database (ASD) splice patterns (SP) for BPIFA4P    About this scheme

ExUns: 1a · 1b ^ 2a · 2b · 2c ^ 3a · 3b · 3c ^ 4 ^ 5 ^ 6a · 6b ^ 7 ^ 8 ^ 9
SP1:                          -     -                                                         
SP2:                          -                                                               
SP3:                          -     -     -                                                   
SP4:                                                                                          


ECgene alternative splicing isoforms for BPIFA4P

(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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BPIFA4P expression in normal human tissues (normalized intensities)
See probesets specificity/sensitivity at GeneAnnot
About this imageBioGPS <intensity>2/3
CGAP TAG: ATAACAAAAG
BPIFA4P Expression
About this image

BPIFA4P Protein expression data from MOPED1, PaxDb2 and MaxQB3 --

SOURCE GeneReport for Unigene cluster: Hs.434194
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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 chordates.

Orthologs for BPIFA4P gene from 1 species (see representative species )    About this table
Organism Taxonomic
classification
Gene Description Human
Similarity
Orthology
Type
Details
tropical clawed frog
(Xenopus tropicalis)
Amphibia 1419973932   -- 89.36(n)    141997393 


ENSEMBL Gene Tree for BPIFA4P (if available)
TreeFam Gene Tree for BPIFA4P (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 BPIFA4P (see all 423)    About this table                                 

Genomic DataTranscription Related DataAllele Frequencies
SNP IDValidClinical
significance
Chr 20 posSequence#AA
Chg
TypeMore#Allele
freq
PopTotal
sample
More
----------
rs1925351631,2
--31779520(+) ACAATA/GATAGC 1 -- us2k10--------
rs765933421,2
C,F--31779526(+) ATAGCG/ATGTAC 1 -- us2k11Minor allele frequency- A:0.14EA 120
rs61201551,2
C,F,H--31779541(+) TTCACT/CACATC 1 -- us2k15Minor allele frequency- C:0.17NS WA CSA 244
rs1498091191,2
C--31779566(+) GAAACC/TTTTAT 1 -- us2k10--------
rs1835912111,2
--31779650(+) GGGAGA/TTAATT 1 -- us2k10--------
rs61201561,2
C,F--31779660(+) TGTTAC/TACCAA 1 -- us2k1 tfbs310Minor allele frequency- T:0.31NA WA CSA 246
rs10407951,2
C,F,O,A,H--31779747(+) TAAGAA/TTTTGC 1 -- us2k114Minor allele frequency- T:0.43MN NS EA NA WA 966
rs1136919741,2
F--31779756(+) GCTTAG/TCTGGA 1 -- us2k13Minor allele frequency- T:0.06CSA WA 122
rs1883402891,2
C--31779859(+) TCTGTA/GTTAGT 1 -- us2k10--------
rs114833161,2
C--31779873(+) GCAAG-/AAAAAA 1 -- us2k1 trp30--------

HapMap Linkage Disequilibrium report for BPIFA4P (31781391 - 31798268 bp)

Structural Variations
     Database of Genomic Variants (DGV) 2 variations for BPIFA4P:    About this table    
Variant IDTypeSubtypePubMed ID
esv2751912CNV Loss17911159
nsv458964CNV Loss19166990

Site Specific Mutation Identification with PCR Assays
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(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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OMIM gene information: 607627    OMIM disorders: --

1 disease for BPIFA4P:    
About MalaCards
breast cancer


Find genes that share disorders with BPIFA4P           About GenesLikeMe


Export disorders for BPIFA4P 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 BPIFA4P gene integrated from 10 sources:
(articles sorted by number of sources associating them with BPIFA4P)
    Utopia: connect your pdf to the dynamic
world of online information

  1. Systematic nomenclature for the PLUNC/PSP/BSP30/SMGB proteins as a subfamily of the BPI fold-containing superfamily. (PubMed id 21787333)1, 3 Bingle C.D....Craven C.J. (Biochem. Soc. Trans. 2011)
  2. Discovery of the breast cancer gene BASE using a molecular approach to enrich for genes encoding membrane and secreted proteins. (PubMed id 12538848)1, 3 Egland K.A.... Pastan I. (Proc. Natl. Acad. Sci. U.S.A. 2003)
  3. Estrogen induces repression of the breast cancer and salivary gland expression gene in an estrogen receptor alpha-dependent manner. (PubMed id 18172302)1 Bretschneider N....Denger S. (Cancer Res. 2008)
  4. Expansion of the Bactericidal/Permeability Increasing-like (BPI-like) protein locus in cattle. (PubMed id 17362520)1 Wheeler T.T....Zhao S. (BMC Genomics 2007)
  5. Phylogenetic and evolutionary analysis of the PLUNC gene family. (PubMed id 14739326)1 Bingle C.D....Craven C.J. (Protein Sci. 2004)
  6. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PubMed id 15489334)1 Gerhard D.S.... Malek J. (Genome Res. 2004)
  7. 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. (Proc. Natl. Acad. Sci. U.S.A. 2002)
  8. The DNA sequence and comparative analysis of human chromosome 20. (PubMed id 11780052)1 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: 317716 HGNC: 20469 AceView: BASE Ensembl:ENSG00000183566 euGenes: HUgn317716
ECgene: BPIFA4P H-InvDB: BPIFA4P

(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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(Patent information from GeneIP,
Licensable technologies from WIS Yeda, Salk, Tufts,
IP news from LifeMap Sciences, Inc.)
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Patent Information for BPIFA4P gene:
Search GeneIP for patents involving BPIFA4P

GeneCards and IP:
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