[Genome] Coding Sequence [hg17]

[Fan Hsu]

Hi Anton,

The knownGene table contains genomic positions
of a gene aligned to the base genome.  Positions of exons are
defined by exonStarts and exonEnds.  Please note that
UTRs are also counted as exons.  Coding exons are defined
by the portion of exons that are between cdsStart and cdsEnd.
UTRs are exon regions outside cdsStart/cdsEnd.

mysql> select * from knownGene where name='BC020953'\G
*************************** 1. row ***************************
      name: BC020953
     chrom: chr11
    strand: +
   txStart: 68100015
     txEnd: 68139375
  cdsStart: 68120240
    cdsEnd: 68137161
 exonCount: 10
exonStarts:
68100015,68112021,68114703,68115619,68120140,68124384,68125906,68127385,6813
3947,68137109,
  exonEnds:
68100087,68112068,68114758,68115750,68120262,68124538,68126013,68127536,6813
4067,68139375,
 proteinID: Q7L4R8_HUMAN
   alignID: G173459
*************************** 2. row ***************************
...

You can get mRNA sequence of a Known Gene via the knownGeneMrna
table and the AA sequence of a Known Gene via the knownGenePep
table.

I suggest you use hg18 instead of hg17.

Fan.
-----Original Message-----
From: genome-bounces at soe.ucsc.edu [mailto:genome-bounces at soe.ucsc.edu]On
Behalf Of Anton Kratz
Sent: Sunday, June 03, 2007 6:49 PM
To: genome at soe.ucsc.edu
Subject: [Genome] Coding Sequence [hg17]


Dear UCSC Team,

I'd like to ask what the definition of coding sequence in the UCSC Known
Gene table is?
Is Coding Sequence the transcribed or the translated sequence?

I wonder because often there are several exons outside the CDS, espexcially
in the non-CDS region from the beginning of the gene.

One example is BC020953:

BC020953        chr11   +       68100015        68139375
68120240        68137161        10
68100015,68112021,68114703,68115619,68120140,68124384,68125906,68127385,6813
3947,68137109,

68100087,68112068,68114758,68115750,68120262,68124538,68126013,68127536,6813
4067,68139375,
Q7L4R8_HUMAN    G173459

Best regards,
Anton
_______________________________________________
Genome maillist  -  Genome at soe.ucsc.edu
http://www.soe.ucsc.edu/mailman/listinfo/genome