Online Resource on Isochore Mapping Isochores predicted by IsoFinder Laboratorio de Genómica Evolutiva y BioInformática Universidad de Granada, Spain José L. Oliver References: GENE 276: 47-56, 2001 [Full Text] GENE 300: 117-127, 2002 [Full text] Nucl. Acids. Res. 32: W287-W292, 2004 [Full Text] Try IsoFinder

Isochore coordinates for updated genome assemblies (Feb, 2007):

Homo sapiens

Build 36.1 - hg18

Pan troglodytes

Build 2.1 - panTro2

Mus musculus

Build 36 - mm8

Rattus norvegicus

Nov. 2004 - rn4

Canis familiaris

May 2005- canFam2

Gallus gallus

May 2006 - galGal3

Danio rerio

March 2006 Zv6 freeze - danRer4

Drosophila melanogaster

Release 4 (Apr. 2004) - dm2

Caenorhabditis elegans

WS120 - cm2

Arabidopsis thaliana

2000 - Arab

Saccharomyces cerevisiae

1 Oct. 2003 - sacCer1

Isochore coordinates of Golden Path genome sequences:

Human, NCBI Build 35, UCSC version hg17, May 2004

Isochore statistics:

1	2	3	4
5	6	7	8
9	10	11	12
13	14	15	16
17	18	19	20
21	22	X	Y

Mouse, NCBI Build 33, UCSC version mm5, June 2004

1	2	3	4
5	6	7	8
9	10	11	12
13	14	15	16
17	18	19	20
X	Y

Rat, updated genome sequence produced by the Rat Genome Sequencing Consortium, UCSC version rn3, June 2003

1	2	3	4
5	6	7	8
9	10	11	12
13	14	15	16
17	18	19	20
X

Look at the integrated isochore chromosome maps using the UCSC Genome Browser

Isochore maps of genome contigs

Human genome:

NCBI Build30, August 2002 (453 contigs longer than 1.5 Mbp, amounting a total of 2.34 Gbp of human genome sequence): September 2002

Click on a chromosome tho show isochore boundaries
Image taken from The Sanger Centre

Statistics of the isochores longer than 50 kbp in this freeze:

Basic statistics

Histogram of isochore sizes

Histogram of isochore GC contents

Distribution of GC differences between adjacent isochores

Longest contig of each human chromosome (NCBI, October 2001 freeze)
MHC region (consensus sequence, Sanger Centre)
Human chromosome contigs October 2000 freeze:
- GenBank (finished, phase 3, October 2000 freeze): 1, 2, 3 , 5 , 6 , 7 , 8 , 9 , 10 , 11 , 12 , 13 , 14 , 15, 16 , 17 , 19 , 20 , 21 , 22 , X , Y
- Human Genome Project Working Draft, UCSC (7th October 2000 freeze): 1 , 2 , 3 , 4, 5 , 6 , 7 , 8 , 9 , 10 , 11 , 12 , 13 , 14 , 15 , 16 , 17 , 18 , 19 , 20 , 21 , 22 , X , Y

Drosophila: Chromosome scaffolds: X , 2L , 2R , 3L , 3R

Anopheles gambieae: The 90 longest scaffolds -- October 2002

Worm: Chromosomes: 1 , 2, 3 , 4, 5 , X

Arabidopsis: Chromosomes: 1, 2 , 3 , 4 , 5

Yeast: Chromosomes: 1 , 2 , 3 , 4 , 5 , 6 , 7 , 8 , 9 , 10 , 11 , 12 , 13 , 14 , 15 , 16

Plasmodium falciparum: Chromosomes 1-14 (sequences from PlasmoDB) -- October 2002

Leishmania major: Chromosome 1

Isochore drawings of some long genome sequences (pdf)

Human genome:

Longest contig of each chromosome, NCBI Oct 2001 freeze (Gene, 300: 117-127)

Longest contig of chromosome 21 (Gene, 300: 117-127)

Longest contig of chromosome 22 (Gene, 300: 117-127)

MHC region consensus sequence, Sanger Centre, (Gene 276: 47-56, 2001)

Longest contigs of chromosomes 21 and 22 (Gene 276: 47-56, 2001)

Drosophila

Worm

Arabidopsis

Yeast: Chrs. 1-8, Chrs. 9-16

Plasmodium