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BTF3P11 Gene

pseudogene   GIFtS: 26
GCID: GC13P077504

Basic Transcription Factor 3 Pseudogene 11

(Previous names: basic transcription factor 3, like 1, basic transcription...)
(Previous symbol: BTF3L1)
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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 3.2

Aliases
Basic Transcription Factor 3 Pseudogene 111 2     Basic Transcription Factor 3, Like 1 Pseudogene1
BTF3L11 2     Basic Transcription Factor 3-Like 1, Pseudogene1
OCIF2 5     BTF3 Homologue1
OPG2 5     Lambda H27A1
TNFRSF11B2 5     HUMBTFB2
Basic Transcription Factor 3, Like 11     

External Ids:    HGNC: 11261   Entrez Gene: 6902   Ensembl: ENSG000001189037   OMIM: 6025435   
ORGUL members:    fRNAdb10:FR395528      
RNAdb15:RNZ10343    

Export aliases for BTF3P11 gene to outside databases

Previous GC identifer: GC13P077503


(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 BTF3P11 Gene:
BTF3P11 (basic transcription factor 3 pseudogene 11) is a pseudogene, and is affiliated with the lncRNA class.

fRNAdb sequence ontology for BTF3P11:
nc_conserved_region - Non-coding region of sequence similarity by descent from a common ancestor.

View fRNAdb secondary structures for BTF3P11

(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_000013.10  NC_018924.2  NT_024524.15  
Regulatory elements:
   Search for regulatory transcription factor binding sites for BTF3P11
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidBTF3P11 promoter sequence
   Search Chromatin IP Primers for BTF3P11

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat BTF3P11


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

Entrez Gene cytogenetic band: 13q22   Ensembl cytogenetic band:  13q22.3   HGNC cytogenetic band: 13q22

BTF3P11 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
BTF3P11 gene location

GeneLoc information about chromosome 13         GeneLoc Exon Structure

GeneLoc location for GC13P077504:  view genomic region     (about GC identifiers)

Start:
77,502,200 bp from pter      End:
77,503,224 bp from pter
Size:
1,025 bases      Orientation:
plus strand
ORGUL member locations:
Legend (see complete legend)

ORGUL Member Locations for BTF3P11

(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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(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 BTF3P11

miRNA
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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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2 Downloadable PowerPoint Slides of GeneGlobe Pathway Central Maps for BTF3P11
    TRAIL Pathway
TNF Superfamily Pathway


    Custom Pathway & Disease-focused RT2 Profiler PCR Arrays for BTF3P11
Interactions:

    Search GeneGlobe Interaction Network for BTF3P11

(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 Small Molecules at EMD Millipore
   Browse drugs & compounds from Enzo Life Sciences
  Browse compounds at ApexBio 

Browse Tocris compounds for BTF3P11



(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 fRNAdb Secondary structure:


Unigene Cluster for BTF3P11:

Basic transcription factor 3 pseudogene 11
Hs.567241
Unigene Representative Sequence: NR_026983
1 Ensembl transcript including schematic representation, and UCSC links where relevant:
ENST00000426582
miRNA
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Additional mRNA sequence: 

BC106717.2 BC106718.2 BC115358.1 NR_026983.1 

1 DOTS entry:

DT.120780034 

1 AceView cDNA sequence:

NM_001208 

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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BTF3P11 expression in normal human tissues (normalized intensities)
See probesets specificity/sensitivity at GeneAnnot
About this imageBioGPS <intensity>2/3
CGAP TAG: --
BTF3P11 Expression
About this image


BTF3P11 expression in embryonic tissues and stem cells    About this table
Data from LifeMap, the Embryonic Development and Stem Cells Database
 selected tissues (see all 19) fully expand
 
 Brain (Nervous System)
         Cerebral Cortex
 
 Bone (Muscoskeletal System)
         Bone Marrow
 
 Colon (Gastrointestinal Tract)
 
 Uterus (Reproductive System)
 
 Thyroid (Endocrine System)
BTF3P11 Protein expression data from MOPED1, PaxDb2 and MaxQB3 --

SOURCE GeneReport for Unigene cluster: Hs.567241
    Custom PCR Arrays for BTF3P11
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In Situ
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Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for BTF3P11

(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 BTF3P11 (if available)
TreeFam Gene Tree for BTF3P11 (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 BTF3P11 (see all 60)    About this table                                 

Genomic DataTranscription Related DataAllele Frequencies
SNP IDValidClinical
significance
Chr 13 posSequence#AA
Chg
TypeMore#Allele
freq
PopTotal
sample
More
----------
rs6600561,2
C,F,A,H--77500593(+) ATCTGG/AAACAT 1 -- us2k1 tfbs321Minor allele frequency- A:0.20NS EA NA WA CSA 2065
rs1504394051,2
--77500723(+) GTCAAC/TAAGAA 1 -- us2k10--------
rs744630591,2
C,F--77500765(+) GTGGGG/AGACAG 1 -- us2k12Minor allele frequency- A:0.06CSA WA 120
rs6614001,2
C,F,A,H--77500888(+) CCTAAC/GAAAGG 1 -- us2k129Minor allele frequency- G:0.21EA NS NA WA CSA 1514
rs1929188791,2
--77500958(+) TGGGTC/TGCTTA 1 -- us2k10--------
rs1841393101,2
--77500969(+) TGTACG/TACAAG 1 -- us2k10--------
rs800086731,2
C,F--77501019(+) CTGCAC/TAAAGG 1 -- us2k11Minor allele frequency- T:0.13WA 118
rs356348101,2
C--77501153(+) AAAAA-/AGAAAA 1 -- us2k12Minor allele frequency- A:0.25NA CSA 4
rs3700372551,2
C--77501171(+) AAAAGA/GAAAAA 1 -- us2k10--------
rs1122364031,2
C,F--77501320(+) CAAACG/ACCGCA 1 -- us2k11Minor allele frequency- A:0.50CSA 2

HapMap Linkage Disequilibrium report for BTF3P11 (77502200 - 77503224 bp)

Structural Variations
     Database of Genomic Variants (DGV) 2 variations for BTF3P11:    About this table    
Variant IDTypeSubtypePubMed ID
nsv832651CNV Gain17160897
nsv832652CNV Gain17160897

Site Specific Mutation Identification with PCR Assays
Search QIAGEN SeqTarget long-range PCR primers for resequencing BTF3P11
DNA2.0 Custom Variant and Variant Library Synthesis for BTF3P11

(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: 602543    OMIM disorders: --


Find genes that share disorders with BTF3P11           About GenesLikeMe


Export disorders for BTF3P11 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 BTF3P11 gene integrated from 10 sources:
(articles sorted by number of sources associating them with BTF3P11)
    Utopia: connect your pdf to the dynamic
world of online information

  1. The visual assignment of genes by fiber-fish: BTF3 protein homologue gene (BTF3) and a novel pseudogene of human RNA helicase A (DDX9P) on 13q22. (PubMed id 9325059)1, 3 Klockars T....Peltonen L. (Genomics 1997)
  2. Genomic structure of the putative BTF3 transcription factor. (PubMed id 1386332)1, 3 Kanno M.... Egly J.-M. (Gene 1992)
  3. Multiple genetic loci for bone mineral density and fractures. (PubMed id 18445777)1 Styrkarsdottir U....Stefansson K. (N. Engl. J. Med. 2008)
  4. 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)
  5. (PubMed id 16273071)10 
  6. (PubMed id 15608161)10 

(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: 690 HGNC: 1126 AceView: BTF3L1 Ensembl:ENSG00000118903 euGenes: HUgn690
ECgene: BTF3P11 H-InvDB: BTF3P11

(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 BTF3P11 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 BTF3P11 gene:
Search GeneIP for patents involving BTF3P11

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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