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FENDRR Gene

RNA gene   GIFtS: 18
GCID: GC16M086511

FOXF1 Adjacent Non-Coding Developmental Regulatory RNA

(Previous name: FOXF1 antisense RNA 1 (head to head))
(Previous symbol: FOXF1-AS1)
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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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Subcategory (RNA class): lncRNA

Quality score for this RNA gene is 4

Aliases
FOXF1 Adjacent Non-Coding Developmental Regulatory RNA1 2
FOXF1-AS11 2
TCONS_000242402 5
FOXF1 Antisense RNA 1 (Head To Head)1
lincFOXF12
FOXF1AS15

External Ids:    HGNC: 438941   Entrez Gene: 4005502   Ensembl: ENSG000002683887   OMIM: 6149755   
ORGUL members:    fRNAdb10:FR365199      
H-InvDB12:HIT000016701    
NCBI13:AK091834    
NONCODE14:n375337 n375444 n375336 n375335 n375063 see all 9    

Export aliases for FENDRR 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 FENDRR Gene:
FENDRR (FOXF1 adjacent non-coding developmental regulatory RNA) is an RNA gene, and is affiliated with the lncRNA class.

fRNAdb sequence ontology for FENDRR:
ncRNA - An RNA transcript that does not encode for a protein rather the RNA molecule is the gene product.

(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_000016.9  NC_018927.2  NT_010498.16  
Regulatory elements:
   Search for regulatory transcription factor binding sites for FENDRR
         Other transcription factors

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


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

Entrez Gene cytogenetic band: 16q24.1   Ensembl cytogenetic band:  16q24.1   HGNC cytogenetic band: 16q24.1

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

GeneLoc information about chromosome 16         GeneLoc Exon Structure

GeneLoc location for GC16M086511:  view genomic region     (about GC identifiers)

Start:
86,508,131 bp from pter      End:
86,542,705 bp from pter
Size:
34,575 bases      Orientation:
minus strand
ORGUL member locations:
Legend (see complete legend)

ORGUL Member Locations for FENDRR

(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., and/or eBioscience,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, Cloud-Clone Corp., and/or eBioscience, Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, Cloud-Clone Corp, 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:
LNCRNA: Long non-coding RNAs

  --

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

    Search GeneGlobe Interaction Network for FENDRR

(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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(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 FENDRR:

FOXF1 adjacent non-coding developmental regulatory RNA
Hs.448825  [show with all ESTs]
Unigene Representative Sequence: NR_033925
7 Ensembl transcripts including schematic representations, and UCSC links where relevant:
ENST00000595886(lincRNA) ENST00000600553(lincRNA) ENST00000598996(lincRNA) ENST00000599749(lincRNA) ENST00000597578(lincRNA)
ENST00000594398(lincRNA) ENST00000593604(lincRNA)
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Additional mRNA sequence: 

AK091834.1 AK097312.1 AL833740.1 BX538111.1 NR_033925.1 NR_036444.1 

4 DOTS entries:

DT.304449  DT.97812509  DT.100717654  DT.92415398 

Selected AceView cDNA sequences (see all 75):

BQ360836 BQ668915 CB104576 CR605298 BQ671722 BX538111 AI471952 BQ004920 
AI198798 BM922208 BQ082445 BQ081921 AL833740 AL542731 BX479864 BM998122 
AI150108 BM822408 BI771944 AK097312 AK091834 BX391914 AI680624 CB104606 

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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Expression evidence for FENDRR:H-invDB

See probesets specificity/sensitivity at GeneAnnot
CGAP TAG: --

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

SOURCE GeneReport for Unigene cluster: Hs.448825
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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 FENDRR (if available)
TreeFam Gene Tree for FENDRR (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 FENDRR (see all 1011)    About this table                                 

Genomic DataTranscription Related DataAllele Frequencies
SNP IDValidClinical
significance
Chr 16 posSequence#AA
Chg
TypeMore#Allele
freq
PopTotal
sample
More
----------
rs609709471,2
C,F--86507647(+) TTTGAC/TTTCTC 1 -- ds50015Minor allele frequency- T:0.11WA CSA 125
rs169413091,2
C,F,H--86507662(+) TCTCTA/GTTTTT 1 -- ds50018Minor allele frequency- G:0.01NA NS EA WA 672
rs1880491891,2
--86507703(+) TTATTA/GGAAGT 1 -- ds50010--------
rs563232211,2
C,F--86507725(+) CTGAGG/AGGGGC 1 -- ds50012Minor allele frequency- A:0.08NA 122
rs1477253731,2
C--86507726(+) TGAGGG/TGGGCA 1 -- ds50010--------
rs1122604851,2
F--86507798(+) GTGATG/TGTTGA 1 -- ds50012Minor allele frequency- T:0.50CSA 4
rs1925666211,2
--86507799(+) TGATGC/GTTGAA 1 -- ds50010--------
rs728165731,2
C--86507923(+) CCAAAA/GCAATG 1 -- ds50014Minor allele frequency- G:0.18NA WA EA 360
rs1822160771,2
--86507927(+) AACAAC/TGACAA 1 -- ds50010--------
rs579842361,2
C,F--86507945(+) TGCTGG/ATGAGG 1 -- ds50013Minor allele frequency- A:0.06WA CSA 122

HapMap Linkage Disequilibrium report for FENDRR (86508131 - 86542705 bp)

Structural Variations
      Database of Genomic Variants (DGV) variations for FENDRR: --
Site Specific Mutation Identification with PCR Assays
Search QIAGEN SeqTarget long-range PCR primers for resequencing FENDRR
DNA2.0 Custom Variant and Variant Library Synthesis for FENDRR

(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: 614975    OMIM disorders: --


Find genes that share disorders with FENDRR           About GenesLikeMe


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

  1. The tissue-specific lncRNA Fendrr is an essential regulator of heart and body wall development in the mouse. (PubMed id 23369715)1, 3 Grote P....Herrmann B.G. (Dev. Cell 2013)
  2. Small noncoding differentially methylated copy-number variants, including lncRNA genes, cause a lethal lung developmental disorder. (PubMed id 23034409)1, 3 Szafranski P....Stankiewicz P. (Genome Res. 2013)
  3. Multiple knockout mouse models reveal lincRNAs are required for life and brain development. (PubMed id 24381249)1, 3 Sauvageau M....Rinn J.L. (Elife 2013)
  4. Many human large intergenic noncoding RNAs associate with chromatin-modifying complexes and affect gene expression. (PubMed id 19571010)1, 3 Khalil A.M....Rinn J.L. (Proc. Natl. Acad. Sci. U.S.A. 2009)
  5. Genome-wide SNP and CNV analysis identifies common and low-frequency variants associated with severe early-onset obesity. (PubMed id 23563609)1 Wheeler E....Farooqi I.S. (Nat. Genet. 2013)
  6. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)1 Ota T.... Sugano S. (Nat. Genet. 2004)
  7. (PubMed id 17451645)10 
  8. (PubMed id 15103394)10 
  9. (PubMed id 18089548)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: 400550 HGNC: 43894 AceView: LOC400550 Ensembl:ENSG00000268388 euGenes: HUgn400550
ECgene: FENDRR H-InvDB: FENDRR

(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 FENDRR gene:
Search GeneIP for patents involving FENDRR

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, LSBio, eBioscience, 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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