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FENDRR Gene(RNA Gene)

FOXF1 Adjacent Non-Coding Developmental Regulatory RNA

GCID:
GC16M086511
GIFtS:
22
Genes Participants
UDN Logo

Aliases for FENDRR Gene

Subcategory (RNA class) for FENDRR Gene

non-coding RNA

Quality Score for this RNA gene is

3

Aliases for FENDRR Gene

  • FOXF1 Adjacent Non-Coding Developmental Regulatory RNA 2 3 5
  • FOXF1 Antisense RNA 1 (Head To Head) 2 3
  • FOXF1 Antisense RNA 1 (Non-Protein Coding) 3
  • TCONS_00024240 3
  • Onco-LncRNA-21 3
  • LincFOXF1 3
  • FOXF1-AS1 3

External Ids for FENDRR Gene

Previous HGNC Symbols for FENDRR Gene

  • FOXF1-AS1

Summaries for FENDRR Gene

Entrez Gene Summary for FENDRR Gene

  • This gene produces a spliced long non-coding RNA transcribed bidirectionally with FOXF1 on the opposite strand. A similar gene in mouse is essential for normal development of the heart and body wall. The encoded transcript is thought to act by binding to polycomb repressive complex 2 (PRC2) and/or TrxG/MLL complexes to promote the methylation of the promoters of target genes, thus reducing their expression. It has been suggested that this transcript may play a role in the progression of gastric cancer. Alternatively spliced transcript variants have been identified. [provided by RefSeq, Mar 2015]

GeneCards Summary for FENDRR Gene

FENDRR (FOXF1 Adjacent Non-Coding Developmental Regulatory RNA) is an RNA Gene, and is affiliated with the non-coding RNA class.

No data available for CIViC summary , UniProtKB/Swiss-Prot , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for FENDRR Gene

Genomics for FENDRR Gene

Products:

  1. Regulatory Element

Regulatory Elements for FENDRR Gene

Enhancers for FENDRR Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH16G086491 1.5 FANTOM5 ENCODE dbSUPER 6.2 +4.0 3968 27.5 ARID4B SIN3A FEZF1 ZNF2 ZNF48 GLIS2 ZNF416 ZNF207 ZNF143 FOS MTHFSD FOXF1 LINC00917 FOXC2 ZCCHC14 FENDRR ENSG00000270020 LOC401864
GH16G086466 1.3 FANTOM5 ENCODE dbSUPER 0.3 +41.9 41949 1.6 GTF2F1 TBP KLF1 SUZ12 JUN MAX ZMYM3 BRCA1 RFX5 ZKSCAN1 MTHFSD ENSG00000270020 FOXF1 LOC401864 FENDRR
GH16G086477 1 ENCODE dbSUPER 0.3 +31.5 31470 0.4 ZNF263 TBP CTCF MAZ KLF1 RNF2 SUZ12 BHLHE40 CHD1 CEBPB MTHFSD FENDRR LOC401864
GH16G086478 0.9 ENCODE dbSUPER 0.3 +31.8 31770 0.2 ZNF263 TBP CTCF MAZ KLF1 RNF2 SUZ12 CHD1 CBX2 RAD21 FENDRR LOC401864
GH16G086488 0.9 ENCODE dbSUPER 0.3 +31.2 31170 0.2 RNF2 SUZ12 HLF CEBPB CBX2 STAT3 SMC3 EZH2 FENDRR LOC401864
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around FENDRR on UCSC Golden Path with GeneCards custom track

Promoters for FENDRR Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000089172 -1001 1401 ZSCAN4 KLF17 FEZF1 ZNF2 GLIS2 ZNF366 ZNF416 EGR2 ZNF263 SP3

Genomic Location for FENDRR Gene

Chromosome:
16
Start:
86,474,525 bp from pter
End:
86,509,099 bp from pter
Size:
34,575 bases
Orientation:
Minus strand

Genomic View for FENDRR Gene

Genes around FENDRR on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
FENDRR Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for FENDRR Gene
GeneLoc Logo Genomic Neighborhood • Exon Structure • Gene Density

RefSeq DNA sequence for FENDRR Gene

Proteins for FENDRR Gene

Products:

  1. Antibody
  2. Protein
  3. Assay

Post-translational modifications for FENDRR Gene

No Post-translational modifications

No data available for DME Specific Peptides for FENDRR Gene

Domains & Families for FENDRR Gene

Gene Families for FENDRR Gene

HGNC:

Graphical View of Domain Structure for InterPro Entry

genes like me logo Genes that share domains with FENDRR: view

No data available for Protein Domains , Suggested Antigen Peptide Sequences and UniProtKB/Swiss-Prot for FENDRR Gene

Function for FENDRR Gene

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  1. Animal Model
  2. CRISPR
  3. miRNA
  4. Inhibitory RNA
  5. Clone
  6. Cell Line
  7. Flow Cytometry

Phenotypes for FENDRR Gene

GenomeRNAi human phenotypes for FENDRR:
genes like me logo Genes that share phenotypes with FENDRR: view

Flow Cytometry Products

No data available for Molecular function , Enzyme Numbers (IUBMB) , Gene Ontology (GO) - Molecular Function , Human Phenotype Ontology , Animal Models , miRNA , Transcription Factor Targets and HOMER Transcription for FENDRR Gene

Localization for FENDRR Gene

No data available for Subcellular locations from UniProtKB/Swiss-Prot , Subcellular locations from COMPARTMENTS and Gene Ontology (GO) - Cellular Components for FENDRR Gene

Pathways & Interactions for FENDRR Gene

SuperPathways for FENDRR Gene

PathCards logo More details on SuperPathways for FENDRR
No Data Available

Interacting Proteins for FENDRR Gene

Gene Ontology (GO) - Biological Process for FENDRR Gene

None

No data available for Pathways by source and SIGNOR curated interactions for FENDRR Gene

Drugs & Compounds for FENDRR Gene

Products:

  1. Drug
No Compound Related Data Available

Transcripts for FENDRR Gene

Products:

  1. CRISPR
  2. miRNA
  3. Inhibitory RNA
  4. Clone
  5. Flow Cytometry

mRNA/cDNA for FENDRR Gene

(6) Additional mRNA sequences :
(75) Selected AceView cDNA sequences:
(7) Ensembl transcripts including schematic representations, and UCSC links where relevant :

Unigene Clusters for FENDRR Gene

FOXF1 adjacent non-coding developmental regulatory RNA:
Representative Sequences:

Flow Cytometry Products

Alternative Splicing Database (ASD) splice patterns (SP) for FENDRR Gene

No ASD Table

Relevant External Links for FENDRR Gene

GeneLoc Exon Structure for
FENDRR
ECgene alternative splicing isoforms for
FENDRR

Expression for FENDRR Gene

Products:

  1. Primer

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for FENDRR Gene

mRNA expression in normal human tissues for FENDRR Gene
mRNA expression by GTEx for FENDRR Gene

mRNA differential expression in normal tissues according to GTEx for FENDRR Gene

This gene is overexpressed in Colon - Sigmoid (x9.1), Esophagus - Gastroesophageal Junction (x7.5), Esophagus - Muscularis (x6.8), Bladder (x6.1), and Lung (x4.4).

NURSA nuclear receptor signaling pathways regulating expression of FENDRR Gene:

FENDRR

SOURCE GeneReport for Unigene cluster for FENDRR Gene:

Hs.448825
genes like me logo Genes that share expression patterns with FENDRR: view

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , Protein differential expression in normal tissues , Protein expression , Protein tissue co-expression partners , mRNA Expression by UniProt/SwissProt , Evidence on tissue expression from TISSUES and Phenotype-based relationships between genes and organs from Gene ORGANizer for FENDRR Gene

Orthologs for FENDRR Gene

Evolution for FENDRR Gene

ENSEMBL:
Gene Tree for FENDRR (if available)
TreeFam:
Gene Tree for FENDRR (if available)

No data available for Orthologs for FENDRR Gene

Paralogs for FENDRR Gene

No data available for Paralogs for FENDRR Gene

Variants for FENDRR Gene

Sequence variations from dbSNP and Humsavar for FENDRR Gene

SNP ID Clin Chr 16 pos Sequence Context AA Info Type
rs121909336 Pathogenic 86,510,794(+) ATCTA(A/C)CAGTT upstream-variant-2KB, reference, stop-gained
rs1057518868 Likely pathogenic 86,510,849(+) GGAAG(A/T)ACTCC upstream-variant-2KB, reference, missense
rs373503439 Likely benign 86,510,654(+) ACCCC(G/T)CGTCG upstream-variant-2KB, reference, missense
rs886052375 Likely benign 86,510,628(+) GGCGG(-/CGG)GGGAG upstream-variant-2KB, cds-indel
rs752749806 Uncertain significance 86,510,566(+) AGCCA(C/T)CCGAT upstream-variant-2KB, utr-variant-5-prime

Structural Variations from Database of Genomic Variants (DGV) for FENDRR Gene

Variant ID Type Subtype PubMed ID
dgv498n67 CNV gain 20364138
esv2758666 CNV gain+loss 17122850
esv29890 CNV loss 19812545
esv3639482 CNV loss 21293372
esv4262 OTHER complex 18987735
nsv1065605 CNV gain 25217958
nsv1070778 CNV deletion 25765185
nsv1143828 CNV deletion 24896259
nsv483044 CNV gain 15286789
nsv510430 OTHER sequence alteration 20534489
nsv525024 CNV loss 19592680
nsv527579 CNV loss 19592680
nsv9468 CNV gain 18304495

Relevant External Links for FENDRR Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
FENDRR

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot and Variation tolerance for FENDRR Gene

Disorders for FENDRR Gene

Relevant External Links for FENDRR

Atlas of Genetics and Cytogenetics in Oncology and Haematology:
FENDRR

No disorders were found for FENDRR Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for FENDRR Gene

Publications for FENDRR Gene

  1. The tissue-specific lncRNA Fendrr is an essential regulator of heart and body wall development in the mouse. (PMID: 23369715) Grote P. … Herrmann B.G. (Dev. Cell 2013) 2 3 64
  2. Small noncoding differentially methylated copy-number variants, including lncRNA genes, cause a lethal lung developmental disorder. (PMID: 23034409) Szafranski P. … Stankiewicz P. (Genome Res. 2013) 2 3 64
  3. Multiple knockout mouse models reveal lincRNAs are required for life and brain development. (PMID: 24381249) Sauvageau M. … Rinn J.L. (Elife 2013) 2 3 64
  4. Many human large intergenic noncoding RNAs associate with chromatin-modifying complexes and affect gene expression. (PMID: 19571010) Khalil A.M. … Rinn J.L. (Proc. Natl. Acad. Sci. U.S.A. 2009) 2 3 64
  5. Pan-cancer transcriptome analysis reveals long noncoding RNAs with conserved function. (PMID: 25864709) Cabanski C.R. … Maher C.A. (RNA Biol 2015) 3 64

Products for FENDRR Gene

Sources for FENDRR Gene

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