Supplementary Materials for Guigó et al (2003)
PNAS, 100(3):1140-1145 [ Abstract ]
  IMIM * UPF * CRG * GRIB HOME DATASETS Mouse/Human GP Chr4
   
CHROMOSOME 4 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
6B5 SGP.chr4_66  8461162 - 8464366 REV 219bp / 2 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
1E6 SGP.chr4_224  18392822 - 18450922 REV 762bp / 7 6 0 0 0 0 0 0 0 0 1 0 0 0 1 0 0
1F1 SGP.chr4_424  32307577 - 32419147 FWD 15915bp / 97 43 1 0 1 0 0 0 0 0 0 0 0 0 1 0 0
12H6 TS.chr4.53.007  52499790 - 52505945 FWD 951bp / 3 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
9D4 SGP.chr4_869  58630581 - 58639976 FWD 1161bp / 2 1 0 0 0 0 0 0 0 1 1 0 0 0 0 1 0
8A1 TS.chr4.60.019  59814496 - 59816375 FWD 465bp / 3 1 0 0 0 0 0 0 0 0 1 0 0 0 1 0 0
12H4 TS.chr4.81.009  80305550 - 80307592 REV 372bp / 2 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
9A4 SGP.chr4_1194  81627481 - 81628957 FWD 330bp / 2 1 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0
1E5 SGP.chr4_1209  81827742 - 81844506 REV 405bp / 3 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
6A6 SGP.chr4_1327  88169605 - 88202049 REV 546bp / 3 2 0 0 0 0 0 0 0 ? 0 0 0 0 0 0 0
7A3 SGP.chr4_1374  90903745 - 90924944 REV 216bp / 2 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
7A4 SGP.chr4_1498  97435479 - 97437641 FWD 162bp / 2 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
6B1 SGP.chr4_1508  98210448 - 98299606 FWD 801bp / 8 4 1 1 1 0 1 0 0 0 1 0 0 0 1 0 0
4C4 TS.chr4.103.012  102705687 - 102732666 FWD 921bp / 11 4 1 0 1 1 1 0 1 1 1 1 1 1 1 0 0
12F4 TS.chr4.105.008  104324560 - 104334994 REV 1299bp / 10 4 0 0 0 1 0 0 0 0 1 1 0 0 1 0 0
4C5 TS.chr4.113.003  112365270 - 112371577 FWD 471bp / 3 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
6B2 SGP.chr4_1754  112562676 - 112579184 REV 291bp / 2 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
9B4 SGP.chr4_2001  120932167 - 120977018 REV 378bp / 5 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
6B3 SGP.chr4_2022  121556112 - 121614146 REV 942bp / 5 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
11E4 SGP.chr4_2073  122784035 - 122813999 FWD 405bp / 4 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
4C6 TS.chr4.134.007  133274212 - 133292298 FWD 675bp / 6 4 0 1 0 0 0 1 0 1 1 1 0 0 1 0 0
12G4 TS.chr4.145.002  144038453 - 144042156 FWD 513bp / 5 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
4D1 TS.chr4.147.015  146526702 - 146544875 REV 1782bp / 6 4 1 1 0 0 0 0 0 0 1 0 1 0 1 0 0
6B4 SGP.chr4_2686  146532744 - 146541677 REV 1551bp / 4 2 1 1 0 0 0 0 0 1 1 1 1 1 1 0 0
7H6 TS.chr4.150.005  149143192 - 149151123 FWD 585bp / 4 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
4D2 TS.chr4.150.023  149612625 - 149625093 FWD 459bp / 4 2 1 1 0 0 0 0 0 1 1 0 0 0 1 0 0
9C4 SGP.chr4_2764  149938739 - 149984207 REV 990bp / 5 2 0 0 0 0 0 0 0 0 0 0 0 0 0 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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