Supplementary Materials for Guigó et al (2003)
PNAS, 100(3):1140-1145 [ Abstract ]
  IMIM * UPF * CRG * GRIB HOME DATASETS Mouse/Human GP Chr5
   
CHROMOSOME 5 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
8E1 SGP.chr5_76  9613308 - 9623327 REV 408bp / 2 1 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0
8A3 TS.chr5.24.014  23439109 - 23441083 REV 303bp / 2 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
1F5 SGP.chr5_296  26809765 - 26905774 FWD 3357bp / 19 16 0 0 0 0 0 0 0 0 1 0 0 0 1 0 0
4E2 TS.chr5.27.020  26900479 - 26905771 FWD 465bp / 4 2 1 1 1 1 1 1 1 1 1 1 1 1 1 0 0
4E3 TS.chr5.34.019  33764465 - 33794887 FWD 1515bp / 10 3 1 1 0 0 0 1 0 1 1 1 1 0 1 0 0
6C2 SGP.chr5_469  36038002 - 36109130 FWD 3474bp / 7 5 1 0 0 0 1 0 0 0 1 0 0 0 1 0 0
7A5 SGP.chr5_515  40222920 - 40241319 FWD 342bp / 2 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
7A6 SGP.chr5_516  40337044 - 40384518 FWD 909bp / 7 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
4E4 TS.chr5.44.003  43130347 - 43141724 REV 891bp / 7 2 1 1 1 1 1 1 1 1 1 1 1 1 1 0 0
1F6 SGP.chr5_559  44418879 - 44429230 FWD 699bp / 3 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
4E5 TS.chr5.52.006  51468911 - 51475256 REV 630bp / 7 4 1 1 1 1 1 1 1 1 1 1 1 1 1 0 0
4E6 TS.chr5.64.001  63000045 - 63010653 REV 784bp / 4 2 1 1 1 1 1 1 1 1 1 1 1 1 1 0 0
9G4 SGP.chr5_812  66173078 - 66174751 FWD 492bp / 2 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0
6C3 SGP.chr5_821  66471708 - 66484653 REV 624bp / 4 3 0 0 0 1 0 0 0 1 0 0 0 0 0 1 0
7B1 SGP.chr5_831  67230124 - 67253442 FWD 258bp / 3 2 0 0 0 0 0 0 0 0 1 0 0 0 1 0 0
1G1 SGP.chr5_865  71638996 - 71679252 REV 975bp / 8 3 1 0 1 1 1 1 0 1 0 0 1 0 1 0 0
8A4 TS.chr5.72.017  71689028 - 71692860 REV 1092bp / 4 1 1 0 1 1 0 0 0 0 1 0 0 1 1 0 0
4F1 TS.chr5.96.018  95857105 - 95874236 FWD 243bp / 2 1 1 0 0 1 0 1 0 1 1 1 0 1 1 0 0
1F2 SGP.chr5_1399  103956540 - 104009310 FWD 789bp / 4 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
9E4 SGP.chr5_1410  104201932 - 104207633 FWD 654bp / 4 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
11F4 SGP.chr5_1415  104242438 - 104246055 REV 384bp / 3 2 0 0 0 1 0 0 0 0 0 0 0 0 0 1 0
4D3 TS.chr5.105.012  104538081 - 104541213 REV 564bp / 5 3 1 0 0 0 0 0 0 0 1 0 0 0 1 0 0
8A2 TS.chr5.111.017  110421388 - 110432502 REV 303bp / 3 2 1 1 0 0 0 0 1 1 1 1 1 1 1 0 0
6B6 SGP.chr5_1566  110947958 - 110951826 FWD 543bp / 3 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
1F3 SGP.chr5_1652  114106821 - 114177545 REV 1263bp / 10 8 1 0 0 0 0 0 0 1 1 0 0 0 1 0 0
4D4 TS.chr5.115.004  114106824 - 114139790 REV 885bp / 7 5 1 1 0 1 0 1 1 1 1 1 1 1 1 0 0
4D5 TS.chr5.120.004  119314703 - 119429253 FWD 12783bp / 77 76 1 1 1 1 1 1 1 1 1 1 1 1 1 0 0
8D5 SGP.chr5_1942  130211636 - 130253291 REV 633bp / 5 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
8D6 SGP.chr5_1943  130263121 - 130274632 REV 738bp / 6 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
4D6 TS.chr5.140.021  139643792 - 139654670 FWD 1416bp / 6 2 0 1 0 1 0 1 0 1 1 1 0 1 1 0 0
9F4 SGP.chr5_2181  139807053 - 139819381 REV 1044bp / 5 3 0 0 0 1 0 0 0 1 1 1 0 0 1 0 0
6C1 SGP.chr5_2190  140693521 - 140748319 FWD 255bp / 3 2 0 0 0 0 0 0 ? 0 0 0 0 0 0 0 0
12A5 TS.chr5.142.013  141639804 - 141651721 FWD 1500bp / 10 5 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0
1F4 SGP.chr5_2329  147150192 - 147198340 FWD 546bp / 5 3 1 1 1 1 0 1 1 1 1 1 1 0 1 0 0
4E1 TS.chr5.150.018  149763395 - 149769336 REV 741bp / 4 2 1 0 0 0 0 0 0 0 1 0 0 1 0 1 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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