How I can explain the difference in gene size in hg19 and NG genome coordinates?
I was looking at the gene coordinates of LDLR for the hg19 and NG assembly in order to convert them to each other, while I do understand the length of the gene may be different in the two assemblies, I fail to understand why should there be a difference in the length of the same gene in the two assemblies. I do appreciate if someone can clarify it to me.
0 answers
No answers yet.
Log in to answer this question.
More posts like this
-
Sheep reference genome remapping coordinates
written by valentinatsar •
-
GSVA package normalization on gene-length ?
written by xanthexu •
-
genomic location convertion between hg19 and hg38
written by dentepre •
-
How do I find the same gene in two different assemblies?
written by jstevenson2256 •
-
Convert hg19 coordinates to hg38 coordinates
written by Chat-ra •
-
transform() and transfer() of Ensembl Perl API
written by DanielC
-
How To Interpret contig field Fields In Vcf Files From 1000 Genomes?
written by 2012secondseason •
-
Sequence alignment algorithm for big size genes in MATLAB
written by r.tor •
-
What is the difference between reference genomes
written by Tom
-
Inconsitency between Ensembl Assembly converter and UCSC LiftOver
written by Mo Sander •
"NG" ?
I am going to convert coordinates from RefSeqGene NG to Hg19 genome assembly and vice versa and in the case of NG, I mean is an accession number with NG_ prefix which representing genomic regions to support more comprehensive genome-level annotation.
I don't know the answer to your question, but according to RefSeq, NG_ represents an incomplete genomic region. See
https://www.ncbi.nlm.nih.gov/books/NBK21091/table/ch18.T.refseq_accession_numbers_and_mole/?report=objectonly
I would guess that since Hg19 is UCSC, and RefSeq is NCBI, they each use their own different annotation methods to decide where the genes start and end.
Thanks so much for the response anyway. I've already checked the NCBI Handbook.