[Genome] cytogenetic banding pattern..mouse

[Hiram Clawson]

Good Morning Irina:

This same query has come up between UCSC and Ensembl recently
regarding the Human assembly.

We are currently discussing this situation with Ensembl and
how NCBI, Ensembl and UCSC derive these locations.  UCSC uses
the cytoband information as supplied to us from NCBI for
the mouse assembly from the following file:

ftp://ftp.ncbi.nih.gov/genomes/MapView/Mus_musculus/sequence/BUILD.37.1/updates/ideogram.gz

--Hiram

Tereshchenko, Irina wrote:
> Hi,
> I have question about cytogenetic banding pattern of mouse chromosomes.
> 
> I did compare the Ensemble and UCSC dbs. How it possible - to have same size of chromosome, same location of  genes, etc,  and  absolutely different location of cytogenetic bands (that seen on Giemsa-stained chromosomes).
> 
> For example, gene Psmd7
> Ensemble: Chromosome 8 at location 110,104,281-110,112,382 , Band: 8D2
> UCSC: Position: chr8:110104281-110112382 , Band: 8qD3
> 
> Cytogenetic bands:
> 
> 8A1
> Ensemble: 2999000-9040477bp (6,041,477bp)
> UCSC: 1-16,228,701 bp (16,228,701 bp)
> 
> 8A3
> Ensemble: 16776277-34188325 bp (17,412,048bp)
> UCSC: 30,070,830-34,366,662 bp (4,295,832bp)
> 
> 8D1
> Ensemble: 98852223- 107421070 (8,568,847 bp)
> UCSC: 97,372,210-105,009,245 (7,637,035 bp)
> 
> 8E2
> Ensemble: 125105471- 131738871 (6,633,400bp)
> UCSC:: 126,011,095-131,738,871 (5,727,776bp)
> 
> What is it?
> 
> Sincerely,
> 
> Irina Tereshchenko
> Rutgers, The State University of New Jersey Piscataway,
> NJ, 08854
> tereshchenko at biology.rutgers.edu