Schema for Rangan RNA - Rangan et al. RNA predictions
  Database: wuhCor1    Primary Table: rnaStructRangan    Row Count: 112   Data last updated: 2020-05-04
Format description: Browser extensible data with secondary structure string
fieldexampleSQL type info description
chrom NC_045512v2varchar(255) values Reference sequence chromosome or scaffold
chromStart 918int(10) unsigned range Start position in chromosome
chromEnd 1038int(10) unsigned range End position in chromosome
name Cons.Structure-1varchar(255) values Name of item
score 0int(10) unsigned range Score from 0-1000
strand +char(1) values + or -
size 120int(10) unsigned range Size of element.
secStr .....................((((((...longblob   Parentheses and '.'s which define the secondary structure

Sample Rows
 
chromchromStartchromEndnamescorestrandsizesecStr
NC_045512v29181038Cons.Structure-10+120.....................(((((((((...((((..(((((.((.((((((......)))))))).)))))...(((((....)))))........)))))))))))))........
NC_045512v21420614326Cons.Structure-20+120(((((((..(..(.((((((((..(((((.....))))).))))))))...........((((.((((((.......))))))..))))...........)..)..))).))))......
NC_045512v21712517245Cons.Structure-30+120((((((((...(((((((((((((((((((((((..((......)).)))))..)))))))))))))).(((((..........))))).)))).....)))))))).............
NC_045512v270117131Cons.Structure-40+120..(((((((..(((((((((...)))))))(((((((..(((((.....)))))))))))).......................))..)).)))))...(((.(((.....)))..))).
NC_045512v22613526255Cons.Structure-50+120..(((.(((((((((..((((((....((((....))))..))))))..))))))))).))).......((((((((........))))..))))(((((((((......))))))))).
NC_045512v22617526295Cons.Structure-60+120..................(((..(((((.((((((((((.....(((....)))((((((((((......)))))))))).(((((....))))))))))))))).))))).....))).
NC_045512v262516371Cons.Structure-70+120.(((......((((((.(((((((.((((......)))).))))))).).)))))..((.......((((....((((((((....))))))))))))..(((....)))))))).....
NC_045512v240158Cons.Structure-80+118....(((((.....))))).........(((((..........(((((((..((.((((.(((.....))).))))))..)))))))..((((((.....))))))...)))))....
NC_045512v22649126608Cons.Structure-90+117.((((.(((((((((..((........))))).))))))...((((((((....))))))))..(((((.....)))))...))))...((((((((....))))))))........
NC_045512v22589526015Cons.Structure-100+120..(((((((((((..((......))..((((((((.(.(..(((((((((.....)))))))))..).).)))))))))))))))))))..((((((((......)))))))).......

Note: all start coordinates in our database are 0-based, not 1-based. See explanation here.

Rangan RNA (rnaStructRangan) Track Description
 

Description

This track shows the locations of RNA structure predictions reported in Rangan et al. bioRxiv 2020 as well as recognizable matches to Rfam annotations found at https://rfam.xfam.org/search?q=coronavirus.

Display Conventions and Configuration

At zoomed out positions, RNA structure is indicated by dark (stem) and light (loops and single strands) green color bars. Zooming in to base level displays the prediction in "extended dot-bracket" notation.

Credits

This track was created by UCSC undergraduate students Justin Sim and Alinne Gonzalez Armenta with the indispensable assistance of Brian Raney.

References

Rangan Ramya, Zheludev Ivan N., Das Rhiju, 2020. RNA genome conservation and secondary structure in SARS-CoV-2 and SARS-related viruses. bioRxiv