Hi all,
I downloaded ensGene.txt.gz from UCSC, and found that there were 60234 records with unique ENSG...ID. Does this mean there are more than 60000 genes? However, there were only ~20000 unique gene names in the refGene.txt.gz which also downloaded from UCSC. How such discrepancy came along?
Thank you!
Emma
Those are Ensembl Genes that are not par of RefGene. Let's looks at some records (ensembl with no overlap to refGene)
$ mysql --user=genome --host=genome-mysql.cse.ucsc.edu hg19 -A
mysql> select distinct G.name2,R.name,R.name2 from ensGene as G left join refGene as R on R.chrom=G.chrom and NOT(R.txStart>=G.txEnd OR R.txEnd<G.txStart) where R.name is NULL limit 10;
+-----------------+------+-------+
| name2 | name | name2 |
+-----------------+------+-------+
| ENSG00000268020 | NULL | NULL |
| ENSG00000240361 | NULL | NULL |
| ENSG00000238009 | NULL | NULL |
| ENSG00000239945 | NULL | NULL |
| ENSG00000241860 | NULL | NULL |
| ENSG00000222623 | NULL | NULL |
| ENSG00000241599 | NULL | NULL |
| ENSG00000228463 | NULL | NULL |
| ENSG00000241670 | NULL | NULL |
| ENSG00000237094 | NULL | NULL |
+-----------------+------+-------+
10 rows in set (0.80 sec)
ENSG00000268020 : Havana Gene
ENSG00000240361 : Havana Gene
ENSG00000238009 : Havana Gene
....
•
written
by
Pierre Lindenbaum
I am sorry but I do not know where to find out the release version. But here is the link:
http://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/ensGene.txt.gz
There is a date "06-Apr-2014" with it.
I grep the unique ENSG ID with the following commend line:
less ensGene.txt.gz | awk '{print $13}' | sort | uniq |wc -l
Hope this information helps.
Thank you!
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in UCSC I found 54,210 refseq genes for hg19. Where do you download your refGene.txt.gz file ?
Here is the link:
http://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/ensGene.txt.gz