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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGAGGACGCCGGTGCCGTTACCGCCGCTGAAGGCGACGACGAGTCCCAGTCCACCGAGGACGACGAGCCCGTCGCGAGGGACAAGGACGATGACGACGAGgtgagcgggaggttagggtttgagtgttttaatcgcgtttttagggatttgatttaaagagggctttggaaatatactaatatttgaattttttcccgac...

Basic information

species Zea mays
transcript AC235535.1_FGT001
intron # 1
splice site 5'
intron type U2

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|14191235|gb|BG833465.1|BG833465
EST:     CCACCGAGGACGACGAGCCCGTCGCGAGGGACAAGGACGATGACGACGAG                         ACTGATGCAGTGGTTGGGAAGCGAGAGAAAGCAAGGCTAAAAGAACTCCAG
genomic: CCACCGAGGACGACGAGCCCGTCGCGAGGGACAAGGACGATGACGACGAGgtgagcggga ... tctgccgcagACTGATGCAGTGGTTGGGAAGCGAGAGAAAGCAAGGCTAAAAGAACTCCAG
EST: gi|211342489|gb|FL449460.1|FL449460
EST:     CCACCGAGGACGACGAGCCCGTCGCGAGGGACAAGGACGATGACGACGAG                         ACTGATGCAGTGGTTGGGAAGCGAGAGAAAGCAAGGCTAAAAGAACTCCAG
genomic: CCACCGAGGACGACGAGCCCGTCGCGAGGGACAAGGACGATGACGACGAGgtgagcggga ... tctgccgcagACTGATGCAGTGGTTGGGAAGCGAGAGAAAGCAAGGCTAAAAGAACTCCAG
EST: gi|149075149|gb|EE163643.2|EE163643
EST:     CCACCGAGGACGACGAGCCCGTCGCGAGGGACAAGGACGATGACGACGAG                         ACTGATGCAGTGGTTGGGAAGCGAGAGAAAGCAAGGCTAAAAGAACTCCAG
genomic: CCACCGAGGACGACGAGCCCGTCGCGAGGGACAAGGACGATGACGACGAGgtgagcggga ... tctgccgcagACTGATGCAGTGGTTGGGAAGCGAGAGAAAGCAAGGCTAAAAGAACTCCAG
EST: gi|211342491|gb|FL449462.1|FL449462
EST:     CCACCGAGGACGACGAGCCCGTCGCGAGGGACAAGGACGATGACGACGAG                         ACTGATGCAGTGGTTGGGAAGCGAGAGAAAGCAAGGCTAAAAGAACTCCAG
genomic: CCACCGAGGACGACGAGCCCGTCGCGAGGGACAAGGACGATGACGACGAGgtgagcggga ... tctgccgcagACTGATGCAGTGGTTGGGAAGCGAGAGAAAGCAAGGCTAAAAGAACTCCAG
EST: gi|161581372|gb|EY955022.1|EY955022
EST:     CCACCGAGGACGACGAGCCCGTCGCGAGGGACAAGGACGATGACGACGAG                         ACTGATGCAGT
genomic: CCACCGAGGACGACGAGCCCGTCGCGAGGGACAAGGACGATGACGACGAGgtgagcggga ... tctgccgcagACTGATGCAGT
EST: gi|18648847|gb|BM497666.1|BM497666
EST:     CCACCGAGGACGACGAGCCCGTCGCGAGGGACAAGGACGATGACGACGAG                         ACTGATGCAGTGGTTGGGAAGCGAGAGAAAGCAAGGCTAAAAGAACTCCAG
genomic: CCACCGAGGACGACGAGCCCGTCGCGAGGGACAAGGACGATGACGACGAGgtgagcggga ... tctgccgcagACTGATGCAGTGGTTGGGAAGCGAGAGAAAGCAAGGCTAAAAGAACTCCAG
EST: gi|211342490|gb|FL449461.1|FL449461
EST:     CCACCGAGGACGACGAGCCCGTCGCGAGGGACAAGGACGATGACGACGAG                         ACTGATACAGTGGTTGGGAAGCGAGAGAAAGCAAGGTTAAAAGAACTCCAG
genomic: CCACCGAGGACGACGAGCCCGTCGCGAGGGACAAGGACGATGACGACGAGgtgagcggga ... tctgccgcagACTGATGCAGTGGTTGGGAAGCGAGAGAAAGCAAGGCTAAAAGAACTCCAG
EST: gi|14191236|gb|BG833466.1|BG833466
EST:     CCACCGAGGACGACGAGCCCGTCGCGAGGGACAAGGACGATGACGACGAG                         ACTGATGCAGTGGTTGGGAAGCGAGAGAAAGCAAGGCTAAAAGAACTCCAG
genomic: CCACCGAGGACGACGAGCCCGTCGCGAGGGACAAGGACGATGACGACGAGgtgagcggga ... tctgccgcagACTGATGCAGTGGTTGGGAAGCGAGAGAAAGCAAGGCTAAAAGAACTCCAG
EST: gi|18649308|gb|BM498127.1|BM498127
EST:     CCTCCGAGGACGACGAGCCCGTCGCGAGGGACAAGGACGATGACGACGAG                         ACTGATGCAGTGGTTGGGAAGCGAGAGAAAGCAAGGCTAAAAGAACTCCAG
genomic: CCACCGAGGACGACGAGCCCGTCGCGAGGGACAAGGACGATGACGACGAGgtgagcggga ... tctgccgcagACTGATGCAGTGGTTGGGAAGCGAGAGAAAGCAAGGCTAAAAGAACTCCAG
EST: gi|32164936|gb|CD670254.1|CD670254
EST:     CCACCGAGGACGACGAGCCCGTCGCGAGGGACAAGGACGATGACGACGAG                         ACTGATGCAGTGGTTGGGAAGCGAGAGAAAGCAAGGCTAAAAGAACTCCAG
genomic: CCACCGAGGACGACGAGCCCGTCGCGAGGGACAAGGACGATGACGACGAGgtgagcggga ... tctgccgcagACTGATGCAGTGGTTGGGAAGCGAGAGAAAGCAAGGCTAAAAGAACTCCAG

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 4 RNA-Seq libraries.


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 365

GGAGGACGCCGGTGCCGTTACCGCCGCTGAAGGCGACGACGAGTCCCAGTCCACCGAGGACGACGAGCCCGTCGCGAGGGACAAGGACGATGACGACGAGgtgagcggga ... tctgccgcagACTGATGCAGTGGTTGGGAAGCGAGAGAAAGCAAGGCTAAAAGAACTCCAGAAGATGAAGAAACATAAAATCCAAGAAATATTAGATACTCAAAATGCCG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 194

GGAGGACGCCGGTGCCGTTACCGCCGCTGAAGGCGACGACGAGTCCCAGTCCACCGAGGACGACGAGCCCGTCGCGAGGGACAAGGACGATGACGACGAGgtgagcggga ... tctgccgcagACTGATGCAGTGGTTGGGAAGCGAGAGAAAGCAAGGCTAAAAGAACTCCAGAAGATGAAGAAACATAAAATCCAAGAAATATTAGATACTCAAAATGCCG


Block sizes: 47 (upstream exon), 46 (downstream exon)
Score: 122

GGAGGACGCCGGTGCCGTTACCGCCGCTGAAGGCGACGACGAGTCCCAGTCCACCGAGGACGACGAGCCCGTCGCGAGGGACAAGGACGATGACGACGAGgtgagcggga ... tctgccgcagACTGATGCAGTGGTTGGGAAGCGAGAGAAAGCAAGGCTAAAAGAACTCCAGAAGATGAAGAAACATAAAATCCAAGAAATATTAGATACTCAAAATGCCG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 246

GGAGGACGCCGGTGCCGTTACCGCCGCTGAAGGCGACGACGAGTCCCAGTCCACCGAGGACGACGAGCCCGTCGCGAGGGACAAGGACGATGACGACGAGgtgagcggga ... tctgccgcagACTGATGCAGTGGTTGGGAAGCGAGAGAAAGCAAGGCTAAAAGAACTCCAGAAGATGAAGAAACATAAAATCCAAGAAATATTAGATACTCAAAATGCCG