Description

This track shows the location of non-protein-coding RNA genes and pseudogenes.

Feature types include:

• tRNA: Transfer RNA
• rRNA: Ribosomal RNA
• scRNA: Small cytoplasmic RNA
• snRNA: Small nuclear RNA
• snoRNA: Small nucleolar RNA
• miRNA: MicroRNA
• misc_RNA: Miscellaneous other RNA, such as RNaseP_nuc
• Intron: Group II self-splicing intron (probable contamination)
• UTR_element: cis-regulatory elements in UTRs of protein coding genes

Methods

tRNAscan-SE:
tRNAscan-SE 1.23. Score field contains tRNAscan-SE bit score; >20 is good, >50 is great.

Rfam5.0:
Rfam 5.0 covariance models and the INFERNAL 0.55 software using Rfam family specific cutoffs. The score field contains the INFERNAL bit score.

miRNA_Registry:
WU-BLASTN matches to human, mouse and rat miRNAs from the miRNA Registry 3.0. Candidate chicken miRNAs match a precursor miRNA with e-value < 1e-4, form a predicted hairpin structure with free energy of folding < -20 kJ.mol-1, and match the mature ~22 nt miRNA with 2 or fewer mismatches.

Credits

These data were kindly provided by Sam Griffiths-Jones at the Sanger Institute.

The microRNA Registry.
Sam Griffiths-Jones.
Nucleic Acids Research, 2004, 32, Database Issue, D109-D111.

Rfam: an RNA family database.
Sam Griffiths-Jones, Alex Bateman, Mhairi Marshall, Ajay Khanna and Sean R. Eddy.
Nucleic Acids Research, 2003, 31, 1, 439-441.

tRNAscan-SE: a Program For Improved Detection of Transfer RNA genes in Genomic Sequence.
T. Lowe, S.R. Eddy. Nucl. Acids Res., 25:955-964, 1997.