Schema for sno/miRNA - C/D and H/ACA Box snoRNAs, scaRNAs, and microRNAs from snoRNABase and miRBase
  Database: hg38    Primary Table: wgRna    Row Count: 2,320   Data last updated: 2018-05-25
Format description: snoRNA and miRNA annotations
fieldexampleSQL type info description
bin 585smallint(6) range Indexing field to speed chromosome range queries.
chrom chr1varchar(255) values Reference sequence chromosome or scaffold
chromStart 17368int(10) unsigned range Start position in chromosome
chromEnd 17436int(10) unsigned range End position in chromosome
name hsa-mir-6859-1varchar(255) values Name of item
score 0int(10) unsigned range Score from 0-1000
strand -char(1) values + or -
thickStart 0int(10) unsigned range Start of where display should be thick (start codon)
thickEnd 0int(10) unsigned range End of where display should be thick (stop codon)
type miRNAvarchar(255) values Type of RNA

Sample Rows
 
binchromchromStartchromEndnamescorestrandthickStartthickEndtype
585chr11736817436hsa-mir-6859-10-00miRNA
585chr13036530503hsa-mir-1302-20+00miRNA
586chr1187890187958hsa-mir-6859-20-00miRNA
589chr1632614632685hsa-mir-121360-00miRNA
593chr111671031167198hsa-mir-200b0+00miRNA
593chr111678621167952hsa-mir-200a0+00miRNA
593chr111690041169087hsa-mir-4290+00miRNA
594chr112961091296170hsa-mir-67260-00miRNA
595chr113125011312566hsa-mir-67270-00miRNA
595chr113396491339708hsa-mir-68080-00miRNA

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

sno/miRNA (wgRna) Track Description
 

Description

This track displays positions of four different types of RNA in the human genome:

C/D box and H/ACA box snoRNAs are guides for the 2'O-ribose methylation and the pseudouridilation, respectively, of rRNAs and snRNAs, although many of them have no documented target RNA. The scaRNAs guide modifications of the spliceosomal snRNAs transcribed by RNA polymerase II, and often contain both C/D and H/ACA domains.

Display Conventions and Configuration

This track follows the general display conventions for gene prediction tracks.

The miRNA precursor forms (pre-miRNA) are represented by red blocks.

C/D box snoRNAs, H/ACA box snoRNAs and scaRNAs are represented by blue, green and magenta blocks, respectively. At a zoomed-in resolution, arrows superimposed on the blocks indicate the sense orientation of the snoRNAs.

Methods

Precursor miRNA genomic locations from miRBase were calculated using wublastn for sequence alignment with the requirement of 100% identity. The extents of the precursor sequences were not generally known and were predicted based on base-paired hairpin structure. miRBase is described in Griffiths-Jones, S. (2004) and Weber, M.J. (2005) in the References section below.

The snoRNAs and scaRNAs from the snoRNABase were aligned against the human genome using blat.

Credits

Genome coordinates for this track were obtained from the miRBase sequences FTP site and from snoRNABase coordinates download page.

References

When making use of these data, please cite the folowing articles in addition to the primary sources of the miRNA sequences:

Griffiths-Jones S, Saini HK, van Dongen S, Enright AJ. miRBase: tools for microRNA genomics. Nucleic Acids Res. 2008 Jan 1;36(Database issue):D154-8.

Griffiths-Jones S, Grocock RJ, van Dongen S, Bateman A, Enright AJ. miRBase: microRNA sequences, targets and gene nomenclature. Nucleic Acids Res. 2006 Jan 1;34(Database issue):D140-4.

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

Weber MJ. New human and mouse microRNA genes found by homology search.

You may also want to cite The Wellcome Trust Sanger Institute miRBase and The Laboratoire de Biologie Moleculaire Eucaryote snoRNABase.

The following publication provides guidelines on miRNA annotation: Ambros V. et al., A uniform system for microRNA annotation. RNA. 2003;9(3):277-9.