Transcript: FENDRR:3

Basic information

LNCipedia transcript ID: FENDRR:3 
HGNC Gene Symbol: FENDRR    
HGNC Full Gene Name: FOXF1 adjacent non-coding developmental regulatory RNA
Ensembl Gene ID: ENSG00000268388
Ensembl Transcript ID: ENST00000597578
Location (hg19): chr16:86523789-86542482
Strand: -
Class: intergenic
Sequence Ontology term: lincRNA
Transcript size: 553 bp
Exons: 2
Sources: NONCODE v4; Ensembl release 75 - Feb 2014; Ensembl release 83 - Dec 2015; Ensembl release 87 - Dec 2016; Ensembl release 90 - Aug 2017; Ensembl release 92 - Apr 2018
Alternative transcript names: NONHSAT144213; ENST00000597578.1
Alternative gene names: ENSG00000268388.1; FENDRR; ENSG00000268388.5; lincFOXF1; onco-lncRNA-21


RNA sequence:

Structure:

Protein coding potential

Metric Raw result Interpretation
PRIDE reprocessing 2.0 0 non-coding 
Lee translation initiation sites 0 non-coding 
PhyloCSF score -28.7122 non-coding 
CPAT coding probability 1.37% non-coding 
Bazzini small ORFs 0 non-coding 

In stringent set: yes

Locus conservation

Locus conservation?
FENDRR:3 no no no no

Available literature

  1. Cabanski (2015), Pan-cancer transcriptome analysis reveals long noncoding RNAs with conserved function., RNA Biol
  2. Li (2015), Genome-Wide Analysis of Long Noncoding RNA Expression Profiles in Human Xuanwei Lung Cancer., Clin. Lab.
  3. Wei (2015), Transcriptome profiling of esophageal squamous cell carcinoma reveals a long noncoding RNA acting as a tumor suppressor., Oncotarget
  4. Yue (2015), Long non-coding RNA Fer-1-like protein 4 suppresses oncogenesis and exhibits prognostic value by associating with miR-106a-5p in colon cancer., Cancer Sci.
  5. Zhu (2015), Long noncoding RNA expression profiles of the doxorubicin-resistant human osteosarcoma cell line MG63/DXR and its parental cell line MG63 as ascertained by microarray analysis., Int J Clin Exp Pathol
  6. Marian (2014), Recent developments in cardiovascular genetics and genomics., Circ. Res.
  7. Xu (2014), Decreased expression of the long non-coding RNA FENDRR is associated with poor prognosis in gastric cancer and FENDRR regulates gastric cancer cell metastasis by affecting fibronectin1 expression., J Hematol Oncol
  8. Grote (2013), The tissue-specific lncRNA Fendrr is an essential regulator of heart and body wall development in the mouse., Dev. Cell
  9. Sauvageau (2013), Multiple knockout mouse models reveal lincRNAs are required for life and brain development., Elife
  10. Szafranski (2013), Small noncoding differentially methylated copy-number variants, including lncRNA genes, cause a lethal lung developmental disorder., Genome Res.
  11. Khalil (2009), Many human large intergenic noncoding RNAs associate with chromatin-modifying complexes and affect gene expression., Proc. Natl. Acad. Sci. U.S.A.


LNCipedia transcript ID history

LNCipedia version LNCipedia transcript ID
3.1 lnc-MTHFSD-2:13
4.0 FENDRR:3
4.1 FENDRR:3
5.0 FENDRR:3
5.1 FENDRR:3
5.2 FENDRR:3