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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCGTCTCCCGTCTCGAGAGATTGCAGGGGGCGGCGCTCGAAGCTGGAGGAAGCGGACGGGTTCGCGATGGGGTCCGAGGGATCCTCGGGTCCGGTCGTCGgtgagtagcagtctctgtccatcatttctcccgagttgctttgttgcatatggtgtgttcgtgtgttcgtcgatccgcgggtccgagtggagaggtgggg...

Basic information

species Zea mays
transcript GRMZM2G090172_T02
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|211187615|gb|FL186093.1|FL186093
EST:     AGCGGACGGGTTCGCGATGGGGTCCGAGGGATCCTCGGGTCCGGTCGTCG                         TTCCCAGAAACTTTAGGCTGCTAGAAGAACTAGAACGTGGTGAGAAGGGCA
genomic: AGCGGACGGGTTCGCGATGGGGTCCGAGGGATCCTCGGGTCCGGTCGTCGgtgagtagca ... tcttctgcagTTCCCAGAAACTTTAGGCTGCTAGAAGAACTAGAACGTGGTGAGAAGGGCA
EST: gi|211185215|gb|FL186078.1|FL186078
EST:     AGCGGACGGGTTCGCGATGGGGTCCGAGGGATCCTCGGGTCCGGTCGTCG                         TTCCCAGAAACTTTAGGCTGCTAGAAGAACTAGAACGTGGTGAGAAGGGCA
genomic: AGCGGACGGGTTCGCGATGGGGTCCGAGGGATCCTCGGGTCCGGTCGTCGgtgagtagca ... tcttctgcagTTCCCAGAAACTTTAGGCTGCTAGAAGAACTAGAACGTGGTGAGAAGGGCA
EST: gi|211185214|gb|FL186077.1|FL186077
EST:     AGCGGACGGGTTCGCGATGGGGTCCGAGGGATCCTCGGGTCCGGTCGTCG                         TTCCCAGAAACTTTAGGCTGCTAGAAGAACTAGAACGTGGTGAGAAGGGCA
genomic: AGCGGACGGGTTCGCGATGGGGTCCGAGGGATCCTCGGGTCCGGTCGTCGgtgagtagca ... tcttctgcagTTCCCAGAAACTTTAGGCTGCTAGAAGAACTAGAACGTGGTGAGAAGGGCA
EST: gi|211187617|gb|FL186095.1|FL186095
EST:     AGCGGACGGGTTCGCGATGGGGTCCGAGGGATCCTCGGGTCCGGTCGTCG                         TTCCCAGAAACTTTAGGCTGCTAGAAGAACTAGAACGTGGTGAGAAGGGCA
genomic: AGCGGACGGGTTCGCGATGGGGTCCGAGGGATCCTCGGGTCCGGTCGTCGgtgagtagca ... tcttctgcagTTCCCAGAAACTTTAGGCTGCTAGAAGAACTAGAACGTGGTGAGAAGGGCA
EST: gi|32788418|gb|CD940654.1|CD940654
EST:     GATCCTCGGGTCCGGTCGTCG                         TTCCCAGAAACTTTAGGCTGCTAGAAGAACTAGAACGTGGTGAGAAGGGCA
genomic: GATCCTCGGGTCCGGTCGTCGgtgagtagca ... tcttctgcagTTCCCAGAAACTTTAGGCTGCTAGAAGAACTAGAACGTGGTGAGAAGGGCA
EST: gi|211187616|gb|FL186094.1|FL186094
EST:     AGCGGACGGGTTCGCGATGGGGTCCGAGGGATCCTCGGGTCCGGTCGTCG                         TTCCCAGAAACTTTAGGCTGCTAGAAGAACTAGAACGTGGTGAGAAGGGCA
genomic: AGCGGACGGGTTCGCGATGGGGTCCGAGGGATCCTCGGGTCCGGTCGTCGgtgagtagca ... tcttctgcagTTCCCAGAAACTTTAGGCTGCTAGAAGAACTAGAACGTGGTGAGAAGGGCA
EST: gi|211185223|gb|FL186086.1|FL186086
EST:     AGCGGACGGGTTCGCGATGGGGTCCGAGGGATCCTCGGGTCCGGTCGTCG                         TTCCCAGAAACTTTAGGCTGCTAGAAGAACTAGAACGTGGTGAGAAGGGCA
genomic: AGCGGACGGGTTCGCGATGGGGTCCGAGGGATCCTCGGGTCCGGTCGTCGgtgagtagca ... tcttctgcagTTCCCAGAAACTTTAGGCTGCTAGAAGAACTAGAACGTGGTGAGAAGGGCA
EST: gi|211187612|gb|FL186090.1|FL186090
EST:     AGCGGACGGGTTCGCGATGGGGTCCGAGGGATCCTCGGGTCCGGTCGTCG                         TTCCCAGAAACTTTAGGCTGCTAGAAGAACTAGAACGTGGTGAGAAGGGCA
genomic: AGCGGACGGGTTCGCGATGGGGTCCGAGGGATCCTCGGGTCCGGTCGTCGgtgagtagca ... tcttctgcagTTCCCAGAAACTTTAGGCTGCTAGAAGAACTAGAACGTGGTGAGAAGGGCA
EST: gi|31558072|gb|CD527284.1|CD527284
EST:     AGCGGACGGGTTCGCGATGGGGTCCGAGGGATCCTCGGGTCCGGTCGTCG                         TTCCCAGAAACTTTAGGCTGCTAGAAGAACTAGAACGTGGTGAGAAGGGCA
genomic: AGCGGACGGGTTCGCGATGGGGTCCGAGGGATCCTCGGGTCCGGTCGTCGgtgagtagca ... tcttctgcagTTCCCAGAAACTTTAGGCTGCTAGAAGAACTAGAACGTGGTGAGAAGGGCA
EST: gi|211185219|gb|FL186082.1|FL186082
EST:     AGCGGACGGGTTCGCGATGGGGTCCGAGGGATCCTCGGGTCCGGTCGTCG                         TTCCCAGAAACTTTAGGCTGCTAGAAGAACTAGAACGTGGTGAGAAGGGCA
genomic: AGCGGACGGGTTCGCGATGGGGTCCGAGGGATCCTCGGGTCCGGTCGTCGgtgagtagca ... tcttctgcagTTCCCAGAAACTTTAGGCTGCTAGAAGAACTAGAACGTGGTGAGAAGGGCA
EST: gi|211185221|gb|FL186084.1|FL186084
EST:     AGCGGACGGGTTCGCGATGGGGTCCGAGGGATCCTCGGGTCCGGTCGTCG                         TTCCCAGAAACTTTAGGCTGCTAGAAGAACTAGAANGTGGTGAGAAGGGCA
genomic: AGCGGACGGGTTCGCGATGGGGTCCGAGGGATCCTCGGGTCCGGTCGTCGgtgagtagca ... tcttctgcagTTCCCAGAAACTTTAGGCTGCTAGAAGAACTAGAACGTGGTGAGAAGGGCA
EST: gi|71438019|gb|DR819069.1|DR819069
EST:     AGCGGACGGGTTCGCGATGGGGTCCGAGGGATCCTCGGGTCCGGTCGTCG                         TTCCCAGAAACTTTAGGCTGCTAGAAGAACTAGAACGTGGTGAGAAGGGCA
genomic: AGCGGACGGGTTCGCGATGGGGTCCGAGGGATCCTCGGGTCCGGTCGTCGgtgagtagca ... tcttctgcagTTCCCAGAAACTTTAGGCTGCTAGAAGAACTAGAACGTGGTGAGAAGGGCA

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: 48 (upstream exon), 45 (downstream exon)
Score: 60

TCGTCTCCCGTCTCGAGAGATTGCAGGGGGCGGCGCTCGAAGCTGGAGGAAGCGGACGGGTTCGCGATGGGGTCCGAGGGATCCTCGGGTCCGGTCGTCGgtgagtagca ... tcttctgcagTTCCCAGAAACTTTAGGCTGCTAGAAGAACTAGAACGTGGTGAGAAGGGCATTGGTGATGGAACTGTGAGCTATGGGATGGATGATGCTGATGACATATA


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 76

TCGTCTCCCGTCTCGAGAGATTGCAGGGGGCGGCGCTCGAAGCTGGAGGAAGCGGACGGGTTCGCGATGGGGTCCGAGGGATCCTCGGGTCCGGTCGTCGgtgagtagca ... tcttctgcagTTCCCAGAAACTTTAGGCTGCTAGAAGAACTAGAACGTGGTGAGAAGGGCATTGGTGATGGAACTGTGAGCTATGGGATGGATGATGCTGATGACATATA


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 71

TCGTCTCCCGTCTCGAGAGATTGCAGGGGGCGGCGCTCGAAGCTGGAGGAAGCGGACGGGTTCGCGATGGGGTCCGAGGGATCCTCGGGTCCGGTCGTCGgtgagtagca ... tcttctgcagTTCCCAGAAACTTTAGGCTGCTAGAAGAACTAGAACGTGGTGAGAAGGGCATTGGTGATGGAACTGTGAGCTATGGGATGGATGATGCTGATGACATATA


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 40

TCGTCTCCCGTCTCGAGAGATTGCAGGGGGCGGCGCTCGAAGCTGGAGGAAGCGGACGGGTTCGCGATGGGGTCCGAGGGATCCTCGGGTCCGGTCGTCGgtgagtagca ... tcttctgcagTTCCCAGAAACTTTAGGCTGCTAGAAGAACTAGAACGTGGTGAGAAGGGCATTGGTGATGGAACTGTGAGCTATGGGATGGATGATGCTGATGACATATA