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Category   Symbol Source: HGNC EntrezGene Ensembl GeneCards RNA genes CroW21
GIFtS

FENDRR Gene

RNA gene   GIFtS: 19
GCID: GC16M086511

FOXF1 Adjacent Non-Coding Developmental Regulatory RNA

(Previous name: FOXF1 antisense RNA 1 (head to head))
(Previous symbol: FOXF1-AS1)
  Search for FENDRR
at  

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, 10fRNAdb, 12H-InvDB, 13NCBI, 14NONCODE, and/or 15RNAdb)
About This Section

Subcategory (RNA class): lncRNA

Quality score for this RNA gene is 9

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

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, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
About This Section

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 73), Regulatory elements and Epigenetics data according to QIAGEN, SABiosciences, and/or SwitchGear Genomics)
About This Section
RefSeq DNA sequence:
NC_000016.9  NC_018927.2  NT_010498.15  
Regulatory elements:
   Search SABiosciences Regulatory transcription factor binding sites for FENDRR
         Other transcription factors

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Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays 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 UniProtKB, HORDE, neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MAXQB 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, and/or Cloud-Clone Corp.,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Cloud-Clone Corp., Ontologies according to Gene Ontology Consortium 01 Oct 2013 and Entrez Gene, Antibodies by EMD Millipore, R&D Systems, GenScript, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, and/or Cloud-Clone Corp.)
About This Section

UniProtKB: --


(According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
About This Section
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,
bound targets from SABiosciences, miRNA Gene Targets from miRTarBase, shRNA from OriGene, RNAi from EMD Millipore, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, Gene Editing from DNA2.0, Sirion Biotech, Clones from EMD Millipore, OriGene, SwitchGear Genomics, GenScript, Sino Biological, DNA2.0, Vector BioLabs, and Sirion Biotech, Cell Lines from GenScript, LifeMap BioReagents, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Oct 2013 via Entrez Gene.)
About This Section

Animal Models:
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(Pathways according to EMD Millipore, 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 SABiosciences, 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 Oct 2013 via Entrez Gene).
About This Section



Interactions:

    Search SABiosciences Gene Network CentralTM Interacting Genes and Proteins Networks for FENDRR

(Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB, with drugs/clinical trials/news search links to CenterWatch)
About This Section
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Search CenterWatch for drugs/clinical trials and news about FENDRR

(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,
Conferences by KenesGroup, exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
RNAi Products from EMD Millipore,
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Tagged/untagged cDNA clones from OriGene, SwitchGear Genomics, GenScript, DNA2.0, Vector BioLabs, Sirion Biotech, Primers from OriGene, SABiosciences, and/or QIAGEN )
About This Section

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 

24/75 AceView cDNA sequences (see all 75):

CR605298 CB104576 BQ671722 BQ668915 BQ360836 CB104596 AK097312 AK091834 
BX391914 AI680624 CB104606 AW886953 BU180479 AW268824 BQ671983 AI471952 
BQ004920 AI198798 BM922208 BQ081921 AL833740 AL542731 BX479864 BM998122 

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™, plus additional links to Genevestigator, and/or SOURCE, and/or BioGPS, and/or UniProtKB,
PCR Arrays from SABiosciences, Primers from OriGene, SABiosciences, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
About This Section

Expression evidence for FENDRR:H-invDB

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


Genevestigator expression for FENDRR

SOURCE GeneReport for Unigene cluster: Hs.448825
    SABiosciences Custom PCR Arrays for FENDRR
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In Situ
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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)
About This Section
  --

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)
About This Section
  --

(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) and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers from QIAGEN, Cancer Mutation PCR Arrays and Assays and Copy Number PCR Arrays from SABiosciences)
About This Section

10/1011 SNPs in FENDRR are shown (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: --
SABiosciences Cancer Mutation 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, Conferences by KenesGroup, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
About This Section

FENDRR for disorders           About MalaCards
OMIM gene information: 614975    OMIM disorders: --


FENDRR for disorders           About GeneDecksing


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)
About This Section

PubMed articles for FENDRR gene integrated from 9 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 Regu lator of Heart and Body Wall Development in the Mouse. (PubMed id 23369715)1, 3 Grote P....Herrmann B.G. (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. (2013)
  3. Many human large intergenic noncoding RNAs associate w ith chromatin-modifying complexes and affect gene expression. (PubMed id 19571010)1, 3 Khalil A.M....Rinn J.L. (2009)
  4. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)1 Ota T.... Sugano S. (2004)
  5. (PubMed id 17451645)10 
  6. (PubMed id 15103394)10 
  7. (PubMed id 18089548)10 

(in PubMed, OMIM, and NCBI Bookshelf)
About This Section
 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)
About This Section
Entrez Gene: 400550 HGNC: 43894 AceView: LOC400550 Ensembl:ENSG00000268388 euGenes: HUgn400550
ECgene: FENDRR H-InvDB: FENDRR

(According to HUGE)
About This Section
  --

(According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL,
Wikipedia and/or GeneReviews via UniProtKB/Swiss-Prot)
About This Section
  --

(Patent information from GeneIP,
Licensable technologies from WIS Yeda, Salk, Tufts,
IP news from LifeMap Sciences, Inc.)
About This Section
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, SABiosciences, Novus Biologicals, Sino Biological, Enzo Life Sciences, Abcam, ProSpec, Cloud-Clone Corp., Thermo Fisher Scientific, LSBio, Gene Editing from DNA2.0 and Sirion Biotech, Clones from EMD Millipore, OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Sirion Biotech, Cell lines from GenScript, and LifeMap BioReagents, PCR Arrays from SABiosciences, Drugs and/or compounds from EMD Millipore, Tocris Bioscience, and/or Enzo Life Sciences, In Situ Hybridization Assays from
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