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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
  • FOXF1AS1 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.

Additional gene information for FENDRR Gene

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

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
GH16H086491 1.5 FANTOM5 ENCODE dbSUPER 6.2 +4.0 3968 27.5 ARID4B SIN3A FEZF1 ZNF2 GLIS2 ZNF416 ZNF207 ZNF143 SP3 REST MTHFSD LOC101928682 LOC101928659 FOXF1 ENSG00000269826 ENSG00000261177 ENSG00000269898 RPL39P30 C16orf95 LINC00917
GH16H086466 1.3 FANTOM5 ENCODE dbSUPER 0.3 +41.9 41949 1.6 GTF2F1 TBP KLF1 JUN MAX BRCA1 RFX5 ZKSCAN1 ZFHX2 POLR2A MTHFSD ENSG00000270020 FOXF1 LOC401864 FENDRR
GH16H086477 0.9 ENCODE dbSUPER 0.3 +31.5 31470 0.4 TBP MAZ KLF1 CEBPB RAD21 STAT3 SMC3 MAFK MTHFSD FENDRR LOC401864
GH16H086478 0.8 ENCODE dbSUPER 0.3 +31.8 31770 0.2 TBP MAZ KLF1 SMC3 RAD21 FENDRR LOC401864
GH16H086480 0.8 ENCODE dbSUPER 0.3 +31.2 31170 0.2 HLF SMC3 STAT3 CEBPB 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 SP3 ZNF398

Genomic Locations for FENDRR Gene

Genomic Locations for FENDRR Gene
chr16:86,474,525-86,509,099
(GRCh38/hg38)
Size:
34,575 bases
Orientation:
Minus strand
chr16:86,508,131-86,542,705
(GRCh37/hg19)

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 StructureGene Density

RefSeq DNA sequence for FENDRR Gene

Proteins for FENDRR Gene

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

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

Phenotypes From GWAS Catalog for FENDRR Gene

Phenotypes for FENDRR Gene

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

Animal Model 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 , Subcellular locations from the Human Protein Atlas (HPA) and Gene Ontology (GO) - Cellular Components for FENDRR Gene

Pathways & Interactions for FENDRR Gene

SuperPathways for FENDRR Gene

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

No Compound Related Data Available

Transcripts for FENDRR Gene

Unigene Clusters for FENDRR Gene

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

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

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE 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
nsv527579 CNV loss 19592680
nsv9468 CNV gain 18304495
nsv525024 CNV loss 19592680
nsv510430 OTHER sequence alteration 20534489
nsv483044 CNV gain 15286789
nsv1143828 CNV deletion 24896259
nsv1070778 CNV deletion 25765185
nsv1065605 CNV gain 25217958
esv4262 OTHER complex 18987735
esv3639482 CNV loss 21293372
esv29890 CNV loss 19812545
esv2758666 CNV gain+loss 17122850
dgv498n67 CNV gain 20364138

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. Small noncoding differentially methylated copy-number variants, including lncRNA genes, cause a lethal lung developmental disorder. (PMID: 23034409) Szafranski P … Stankiewicz P (Genome research 2013) 2 3 60
  2. The tissue-specific lncRNA Fendrr is an essential regulator of heart and body wall development in the mouse. (PMID: 23369715) Grote P … Herrmann BG (Developmental cell 2013) 2 3 60
  3. Multiple knockout mouse models reveal lincRNAs are required for life and brain development. (PMID: 24381249) Sauvageau M … Rinn JL (eLife 2013) 2 3 60
  4. Many human large intergenic noncoding RNAs associate with chromatin-modifying complexes and affect gene expression. (PMID: 19571010) Khalil AM … Rinn JL (Proceedings of the National Academy of Sciences of the United States of America 2009) 2 3 60
  5. Pan-cancer transcriptome analysis reveals long noncoding RNAs with conserved function. (PMID: 25864709) Cabanski CR … Maher CA (RNA biology 2015) 3 60

Products for FENDRR Gene

Sources for FENDRR Gene

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