Supplementary Materials for Guigó et al (2003)
PNAS, 100(3):1140-1145 [ Abstract ]
  IMIM * UPF * CRG * GRIB HOME DATASETS Mouse/Human GP Chr11
   
CHROMOSOME 11 RT-PCR SUBMITTED GENES SUMMARY

GENEVA
CODE
GENE
ID
GENE
LOCATION
CDS LEN
/ #EXONS
RTPCR
INTRON
 
BR
 
HE
 
KI
 
TH
 
LI
 
ST
 
MU
 
LU
 
TE
 
SK
 
EY
 
OV
SEQ
CNF
SEQ
WRG
DIF
SPL
11E1 SGP.chr11_3  3024135 - 3054414 REV 648bp / 6 3 1 1 0 1 1 0 0 1 0 1 1 1 1 0 0
3D1 TS.chr11.5.001  4002644 - 4010571 REV 1943bp / 9 7 1 1 1 1 1 1 0 1 1 1 1 1 1 0 0
5B4 SGP.chr11_42  4003116 - 4010571 REV 1596bp / 7 6 1 1 1 1 1 1 1 1 1 1 1 1 1 0 0
11B1 SGP.chr11_134  8731608 - 8783076 REV 2088bp / 13 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
3C6 TS.chr11.17.004  16238341 - 16245289 FWD 1254bp / 8 6 1 0 1 1 0 0 0 1 1 1 1 0 1 0 1
11A3 SGP.chr11_225  18178362 - 18189962 REV 480bp / 2 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
8B2 SGP.chr11_230  18370744 - 18380681 REV 717bp / 4 3 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0
5B3 SGP.chr11_305  21660855 - 21685943 FWD 363bp / 5 2 1 1 1 1 1 1 1 1 1 1 1 1 0 1 0
9A2 TS.chr11.33.026  32707103 - 32708999 REV 843bp / 2 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
7D4 TS.chr11.37.003  36028889 - 36034224 REV 387bp / 5 3 0 0 0 0 0 0 0 1 1 1 1 1 0 0 0
8F4 SGP.chr11_590  37423588 - 37437201 REV 438bp / 3 2 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0
5B5 SGP.chr11_669  43492028 - 43493835 FWD 474bp / 2 1 0 0 0 0 0 1 0 0 1 1 0 0 1 0 0
3D2 TS.chr11.61.011  60321561 - 60324215 REV 663bp / 2 1 0 0 0 0 1 0 0 0 1 0 0 0 1 0 0
1A3 SGP.chr11_1123  63045210 - 63087796 REV 960bp / 4 1 0 1 0 0 1 0 1 1 1 0 0 0 1 0 0
3D3 TS.chr11.64.002  63045213 - 63062545 REV 744bp / 4 2 1 1 1 1 0 1 0 1 1 1 1 1 1 0 0
5B1 SGP.chr11_1408  72992347 - 73001326 REV 399bp / 3 2 1 1 1 1 1 1 1 1 1 1 1 1 1 0 0
11F6 TS.chr11.74.031  73871134 - 73893672 FWD 1776bp / 13 7 1 1 0 0 0 1 0 1 1 1 1 0 1 0 0
3D4 TS.chr11.76.006  75245900 - 75254491 FWD 495bp / 4 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
12C3 TS.chr11.76.021  75652451 - 75659923 FWD 402bp / 4 2 1 1 1 1 1 1 1 1 1 1 1 0 1 0 0
11C1 SGP.chr11_1528  76057018 - 76069682 REV 5472bp / 11 10 1 1 1 1 1 1 1 1 1 1 1 1 1 0 0
5B2 SGP.chr11_1725  83919697 - 83925693 REV 1629bp / 3 2 1 0 0 0 0 0 0 1 1 0 0 1 1 0 0
12A6 TS.chr11.85.028  84674090 - 84681917 FWD 870bp / 6 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0 0
7D5 TS.chr11.86.023  85735307 - 85753480 REV 531bp / 4 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
8F2 SGP.chr11_1797  86309272 - 86327895 FWD 441bp / 2 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
3D5 TS.chr11.89.009  88295721 - 88301668 FWD 612bp / 3 1 0 0 0 0 0 0 0 0 1 0 0 0 1 0 0
3D6 TS.chr11.91.015  90939340 - 90947083 FWD 402bp / 2 1 0 1 0 0 0 0 0 1 0 0 0 0 0 1 0
1A4 SGP.chr11_2120  98623186 - 98648467 REV 1278bp / 9 5 1 0 1 0 1 0 0 1 1 0 0 0 1 0 0
11D1 SGP.chr11_2496  109246881 - 109419351 FWD 2091bp / 18 10 1 1 1 1 1 0 1 1 1 1 1 1 1 0 0
8F3 SGP.chr11_2583  113240184 - 113256802 REV 417bp / 2 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
7D3 TS.chr11.115.008  114333352 - 114341829 FWD 474bp / 3 1 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0
11E6 TS.chr11.116.013  115838471 - 115842257 REV 435bp / 4 1 0 1 0 0 1 0 0 1 0 1 0 1 1 0 0
12B3 TS.chr11.117.011  116171599 - 116185566 REV 1026bp / 6 2 1 0 0 1 1 1 0 1 1 1 1 0 1 0 0
3C5 TS.chr11.119.027  118770605 - 118774209 FWD 633bp / 4 3 0 0 0 0 0 0 0 0 1 0 1 0 1 0 0
1A5 SGP.chr11_2849  122560468 - 122613935 REV 861bp / 10 9 0 1 0 0 0 0 1 0 1 0 1 1 1 0 0
GENEVA
CODE
GENE
ID
GENE
LOCATION
CDS LEN
/ #EXONS
RTPCR
INTRON
BR HE KI TH LI ST MU LU TE SK EY OV SEQ
CNF
SEQ
WRG
DIF
SPL
 

TABLE COLUMNS DESCRIPTION

Here we describe what does contain each column in the previous table:

  • Geneva identifier: corresponds to an alphanumeric code for each single gene set of experiments.
  • Predicted gene identifier: the name of the given gene prediction as provided by the software. Both, this column and the previous one, are linked to a single browser page for each gene prediction that contains further information about it.
  • Gene location: the forward coordinates along the chromosome and the corresponding gene strand.
  • Length of the transcript and the number of exons.
  • The selected intron number.
  • Results on tissues: RT-PCR success on each of the mouse tissues tested in this experiment ("green" color meaning success and "red" color for failure). The tissues were: brain (BR), heart (HE), kidney (KI), thymus (TH), liver (LI), stomach (ST), muscle (MU), lung (LU), testis (TE), skin (SK), eye (EY) and ovary (OV).
  • Three extra columns summarizing RT-PCR results:
    • SEQ CNF : RT-PCR succeeded and the sequence of the predicted gene was confirmed.
    • SEQ WRG : the PCR product that was sequenced does not correspond to the predicted one (unspecific amplification).
    • DIF SPL : the RT-PCR determined a different splice site (i.e. an extra exon within the submitted intron).
    Real Positive Genes are those, and only those, having "1" in the "SEQ CNF" column.

 
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