Schema for Chromosome Band - Chromosome Bands Localized by FISH Mapping Clones
  Database: hg38    Primary Table: cytoBand    Row Count: 1,433   Data last updated: 2018-08-11
Format description: Describes the positions of cytogenetic bands with a chromosome
fieldexampleSQL type info description
chrom chr1varchar(255) values Reference sequence chromosome or scaffold
chromStart 0int(10) unsigned range Start position in genoSeq
chromEnd 2300000int(10) unsigned range End position in genoSeq
name p36.33varchar(255) values Name of cytogenetic band
gieStain gnegvarchar(255) values Giemsa stain results

Sample Rows
 
chromchromStartchromEndnamegieStain
chr102300000p36.33gneg
chr123000005300000p36.32gpos25
chr153000007100000p36.31gneg
chr171000009100000p36.23gpos25
chr1910000012500000p36.22gneg
chr11250000015900000p36.21gpos50
chr11590000020100000p36.13gneg
chr12010000023600000p36.12gpos25
chr12360000027600000p36.11gneg
chr12760000029900000p35.3gpos25

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

Chromosome Band (cytoBand) Track Description
 

Description

The chromosome band track represents the approximate location of bands seen on Giemsa-stained chromosomes. Chromosomes are displayed in the browser with the short arm first. Cytologically identified bands on the chromosome are numbered outward from the centromere on the short (p) and long (q) arms. At low resolution, bands are classified using the nomenclature [chromosome][arm][band], where band is a single digit. Examples of bands on chromosome 3 include 3p2, 3p1, cen, 3q1, and 3q2. At a finer resolution, some of the bands are subdivided into sub-bands, adding a second digit to the band number, e.g. 3p26. This resolution produces about 500 bands. A final subdivision into a total of 862 sub-bands is made by adding a period and another digit to the band, resulting in 3p26.3, 3p26.2, etc.

Methods

A full description of the method by which the chromosome band locations are estimated can be found in Furey and Haussler, 2003.

Barbara Trask, Vivian Cheung, Norma Nowak and others in the BAC Resource Consortium used fluorescent in-situ hybridization (FISH) to determine a cytogenetic location for large genomic clones on the chromosomes. The results from these experiments are the primary source of information used in estimating the chromosome band locations. For more information about the process, see the paper, Cheung, et al., 2001. and the accompanying web site, Human BAC Resource.

BAC clone placements in the human sequence are determined at UCSC using a combination of full BAC clone sequence, BAC end sequence, and STS marker information.

Credits

We would like to thank all the labs that have contributed to this resource:

References

Cheung VG, Nowak N, Jang W, Kirsch IR, Zhao S, Chen XN, Furey TS, Kim UJ, Kuo WL, Olivier M et al. Integration of cytogenetic landmarks into the draft sequence of the human genome. Nature. 2001 Feb 15;409(6822):953-8. PMID: 11237021

Furey TS, Haussler D. Integration of the cytogenetic map with the draft human genome sequence. Hum Mol Genet. 2003 May 1;12(9):1037-44. PMID: 12700172