HCG BioInformatics || The Ohio State University

First exon and promoter annotations in the human genome

(NCBI Build 35 & hg17, May 2004)

Supplementary Table 1:

List of 49,890 first exon annotations of 28,850 genes in the human genome:

Column 1 (i.j) denotes the gene number (i) followed by alternative exon number (j) of each gene. P(P) and P(E) stand for probabilities of promoter and first exon given by FirstEF program. Column 9 gives the assembled transcript by FexAnnotator, with corresponding Gene ID & Symbols are presented in in columns 10 & 11. The last column presents the support of the prediction by each database; F-FexAnnotator; E-Ensembl; H-H-InvDB; P-PromoSer; T-trome.

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Supplementary Table 2:

List of real exons and the corresponding predictions by FexAnnotator:

Column 1: Chromosome Number

Column 2: Serial Number of the real exon

Column 3: Real first exon coordinates

Column 5: Experimental Support (GenBank record or Database)

Column 6: Predicted promoter by FirstEF

Column 7: Probability of predicted promoter

Column 8: Predicted first exon by FirstEF

Column 9: Probability of predicted first exon

Column 10: CpG-window (the CpG-window of size 201 nts that has maximum CG di-nucleotide percentage within -500 of TSS to +500 of donor site)

Column 11: Assemble transcript by FexAnnotator

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Supplementary Table 3:

List of real exons and the corresponding predictions by Ensembl:

Column 1: Chromosome Number

Column 2: Serial Number of the real exon

Column 3: Real first exon coordinates

Column 4: Strand

Column 5: Experimental Support (GenBank record or Database)

Column 6: Predicted TSS of the first exon

Column 7: Predicted donor site of the first exon

Column 8: Strand of the predicted first exon

Column 9: Corresponding transcript ID in Ensembl

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Supplementary Table 4:

List of real exons and the corresponding predictions by PromoSer:

Column 1: Chromosome Number

Column 2: Serial Number of the real exon

Column 3: Real first exon coordinates

Column 4: Strand

Column 5: Experimental Support (GenBank record or Database)

Column 6: Predicted TSS of the first exon

Column 7: +200 nts downstream of the TSS

Column 8: Strand of the predicted first exon

Column 9: Corresponding promoter ID in PromoSer

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Supplementary Table 5:

List of real exons and the corresponding predictions by H-InvDB:

Column 1: Chromosome Number

Column 2: Serial Number of the real exon

Column 3: Real first exon coordinates

Column 4: Strand

Column 5: Experimental Support (GenBank record or Database)

Column 6: Predicted TSS of the first exon

Column 7: Predicted donor site of the first exon

Column 8: Strand of the predicted first exon

Column 9: Corresponding cDNA ID in H-InvDB

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Supplementary Table 6:

List of real exons and the corresponding predictions by trome database:

Column 1: Chromosome Number

Column 2: Serial Number of the real exon

Column 3: Real first exon coordinates

Column 4: Strand

Column 5: Experimental Support (GenBank record or Database)

Column 6: Predicted TSS of the first exon

Column 7: Predicted donor site of the first exon

Column 8: Strand of the predicted first exon

Column 9: Corresponding first exon ID in trome database

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Using First Exon Annotation Browser to check the first exon annoation data