Description

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

Feature types include:

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.

Griffiths-Jones S. The microRNA Registry. Nucleic Acids Res. 2004 Jan 1;32(Database issue):D109-11. PMID: 14681370; PMC: PMC308757

Griffiths-Jones S, Bateman A, Marshall M, Khanna A, Eddy SR. Rfam: an RNA family database. Nucleic Acids Res. 2003 Jan 1;31(1):439-41. PMID: 12520045; PMC: PMC165453

Lowe TM, Eddy SR. tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res. 1997 Mar 1;25(5):955-64. PMID: 9023104; PMC: PMC146525