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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GACTTGCCCCGCCGACCTCGACAGCAAATGCGATGGTGGCGCGTCTGATGATGATTGGGAGGGGGAGTTCTTCCCCGGCGTCCCGAAAATCAAGTATGAGgtggggctatcaaaacccagatttttcattcagattgtcatgtcgtggtaacggcctaacgggttgttgtgaaccaaaccattgttcctgctgcag

Basic information

species Zea mays
transcript GRMZM2G081682_T02
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G081682_T02 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os07g47290.1 (Oryza sativa), 5'ss of exon 3
---GACTTGCCCCGCCGACCTCGACAGCAAATGCGATGGTGGCGCGTCTGATGATGATTGGGAGGGGGAGTTCTTCCCCGGCGTCCCGAAAATCAAGTATGAGgtgggg----ctatcaaaacccagatttttcattcagattgtcatgtcgtggt-aacggcctaacgggttgttgtgaacca-aaccattgttcctgctgcag
    || || || ||||||||||| ||||| || | || ||  || || |  |||   ||||| |||||||||||||| ||| |||| || ||||||||||||||| ||    | || ||| |  | |  ||| ||| ||||| |    |   | |        ||     ||||  || || | |||   |||  ||  |  | 
GCAAACCTGTCCGGCCGACCTCGATAGCAAGTGTGGTGATGCTGCTTCAGGGGAT---TGGGAAGGGGAGTTCTTCCCTGGCATCCCCAAGATCAAGTATGAGgtgagggaggccatgaaagcttacagctttgatt-agattattggataaagcttggaaatttatattattgtattggactataactgctgtgactctttga-
















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|211316223|gb|FL334911.1|FL334911
EST:     ATGATTGGGAGGGGGAGTTCTTCCCCGGCGTCCCGAAAATCAAGTATGAG                         GGTCCAACAAGCAAGAACCCTCTTGCTTATAAGTGGTATAACAAGGAGGAA
genomic: ATGATTGGGAGGGGGAGTTCTTCCCCGGCGTCCCGAAAATCAAGTATGAGgtggggctat ... cctgctgcagGGTCCAACAAGCAAGAACCCTCTTGCTTATAAGTGGTATAACAAGGAGGAA
EST: gi|211075605|gb|FL344132.1|FL344132
EST:     ATGATTGGGAGGGGGAGTTCTTCCCCGGCGTCCCGAAAATCAAGTATGAG                         GGTCCAACAAGCAAGAACCCTCTTGCTTATAAGTGGTATAACAAGGAGGAA
genomic: ATGATTGGGAGGGGGAGTTCTTCCCCGGCGTCCCGAAAATCAAGTATGAGgtggggctat ... cctgctgcagGGTCCAACAAGCAAGAACCCTCTTGCTTATAAGTGGTATAACAAGGAGGAA
EST: gi|211288683|gb|FL312634.1|FL312634
EST:     ATGATTGGGAGGGGGAGTTCTTCCCCGGCGTCCCGAAAATCAAGTATGAG                         GGTCCAACAAGCAAGAACCCTCTTGCTTATAAGTGGTATAACAAGGAGGAA
genomic: ATGATTGGGAGGGGGAGTTCTTCCCCGGCGTCCCGAAAATCAAGTATGAGgtggggctat ... cctgctgcagGGTCCAACAAGCAAGAACCCTCTTGCTTATAAGTGGTATAACAAGGAGGAA
EST: gi|211328969|gb|FL341564.1|FL341564
EST:     ATGATTGGGAGGGGGAGTTCTTCCCCGGCGTCCCGAAAATCAAGTATGAG                         GGTCCAACAAGCAAGAACCCTCTTGCTTATAAGTGGTATAACAAGGAGGAA
genomic: ATGATTGGGAGGGGGAGTTCTTCCCCGGCGTCCCGAAAATCAAGTATGAGgtggggctat ... cctgctgcagGGTCCAACAAGCAAGAACCCTCTTGCTTATAAGTGGTATAACAAGGAGGAA
EST: gi|71426924|gb|DR807974.1|DR807974
EST:     ATGATTGGGAGGGGGAGTTCTTCCCCGGCGTCCCGAAAATCAAGTATGAG                         GGTCCAACAAGCAAGAACCCTCTTGCTTATAAGTGGTATAACAAGGAGGAA
genomic: ATGATTGGGAGGGGGAGTTCTTCCCCGGCGTCCCGAAAATCAAGTATGAGgtggggctat ... cctgctgcagGGTCCAACAAGCAAGAACCCTCTTGCTTATAAGTGGTATAACAAGGAGGAA
EST: gi|211416745|gb|FL321410.1|FL321410
EST:     ATGATTGGGAGGGGGAGTTCTTCCCCGGCGTCCCGAAAATCAAGTATGAG                         GGTCCAACAAGCAAGAACCCTCTTGCTTATAAGTGGTATAACAAGGAGGAA
genomic: ATGATTGGGAGGGGGAGTTCTTCCCCGGCGTCCCGAAAATCAAGTATGAGgtggggctat ... cctgctgcagGGTCCAACAAGCAAGAACCCTCTTGCTTATAAGTGGTATAACAAGGAGGAA
EST: gi|74245361|gb|DT653275.1|DT653275
EST:     ATGATTGGGAGGGGGAGTTCTTCCCCGGCGTCCCGAAAATCAAGTATGAG                         GGTCCAACAAGCAAGAACCCTCTTGCTTATAAGTGGTATAACAAGGAGGAA
genomic: ATGATTGGGAGGGGGAGTTCTTCCCCGGCGTCCCGAAAATCAAGTATGAGgtggggctat ... cctgctgcagGGTCCAACAAGCAAGAACCCTCTTGCTTATAAGTGGTATAACAAGGAGGAA
EST: gi|74232804|gb|DT640718.1|DT640718
EST:     ATGATTGGGAGGGGGAGTTCTTCCCCGGCGTCCCGAAAATCAAGTATGAG                         GGTCCAACAAGCAAGAACCCTCTTGCTTATAAGTGGTATAACAAGGAGGAA
genomic: ATGATTGGGAGGGGGAGTTCTTCCCCGGCGTCCCGAAAATCAAGTATGAGgtggggctat ... cctgctgcagGGTCCAACAAGCAAGAACCCTCTTGCTTATAAGTGGTATAACAAGGAGGAA
EST: gi|211420503|gb|FL364960.1|FL364960
EST:     ATGATTGGGAGGGGGAGTTCTTCCCCGGCGTCCCGAAAATCAAGTATGAG                         GGTCCAACAAGCAAGAACCCTCTTGCTTATAAGTGGTATAACAAGGAGGAA
genomic: ATGATTGGGAGGGGGAGTTCTTCCCCGGCGTCCCGAAAATCAAGTATGAGgtggggctat ... cctgctgcagGGTCCAACAAGCAAGAACCCTCTTGCTTATAAGTGGTATAACAAGGAGGAA
EST: gi|211457434|gb|FL331063.1|FL331063
EST:     ATGATTGGGAGGGGGAGTTCTTCCCCGGCGTCCCGAAAATCAAGTATGAG                         GGTCCAACAAGCAAGAACCCTCTTGCTTATAAGTGGTATAACAAGGAGGAA
genomic: ATGATTGGGAGGGGGAGTTCTTCCCCGGCGTCCCGAAAATCAAGTATGAGgtggggctat ... cctgctgcagGGTCCAACAAGCAAGAACCCTCTTGCTTATAAGTGGTATAACAAGGAGGAA
EST: gi|32866060|gb|CF005742.1|CF005742
EST:     ATGATTGGGAGGGGGAGTTCTTCCCCGGCGTCCCGAAAATCAAGTATGAG                         GGTCCAACAAGCAAGAACCCTCTTGCTTATAAGTGGTATAACAAGGAGGAA
genomic: ATGATTGGGAGGGGGAGTTCTTCCCCGGCGTCCCGAAAATCAAGTATGAGgtggggctat ... cctgctgcagGGTCCAACAAGCAAGAACCCTCTTGCTTATAAGTGGTATAACAAGGAGGAA
EST: gi|32909379|gb|CF014191.1|CF014191
EST:     ATGATTGGGAGGGGGAGTTCTTCCCCGGCGTCCCGAAAATCAAGTATGAG                         GGTCCAACAAGCAAGAACCCTCTTGCTTATAAGTGGTATAACAAGGAGGAA
genomic: ATGATTGGGAGGGGGAGTTCTTCCCCGGCGTCCCGAAAATCAAGTATGAGgtggggctat ... cctgctgcagGGTCCAACAAGCAAGAACCCTCTTGCTTATAAGTGGTATAACAAGGAGGAA
EST: gi|211310239|gb|FL338849.1|FL338849
EST:     TGNATTGGGAGGGGGAGTTCTTCCCCGGCGTCCCGAAAATCAAGTATGAG                         GGTCCAACAAGCAAGAACCCTCTTGCTTATAAGTGGTATAACAAGGAGGAA
genomic: TG-ATTGGGAGGGGGAGTTCTTCCCCGGCGTCCCGAAAATCAAGTATGAGgtggggctat ... cctgctgcagGGTCCAACAAGCAAGAACCCTCTTGCTTATAAGTGGTATAACAAGGAGGAA
EST: gi|211149448|gb|FL325049.1|FL325049
EST:     ATGATTGGGAGGGGGAGTTCTTCCC-GGCGTCCCGAAAATCAAGTATGAG                         GGTCCAACAAGCAAGAACC-TCTTGCTTAT
genomic: ATGATTGGGAGGGGGAGTTCTTCCCCGGCGTCCCGAAAATCAAGTATGAGgtggggctat ... cctgctgcagGGTCCAACAAGCAAGAACCCTCTTGCTTAT
EST: gi|211140891|gb|FL328471.1|FL328471
EST:     ATGATTGGGAGGGGGAGTTCTTCCCCGGCGTCCCGAAAATCAAGTATGAG                         GGTCCAACAAGCAAGAACCCTCTTGCTTATAAGTGGTATAACAAGGAGGAA
genomic: ATGATTGGGAGGGGGAGTTCTTCCCCGGCGTCCCGAAAATCAAGTATGAGgtggggctat ... cctgctgcagGGTCCAACAAGCAAGAACCCTCTTGCTTATAAGTGGTATAACAAGGAGGAA
EST: gi|211320715|gb|FL358326.1|FL358326
EST:     ATGATTGGGAGGGGGAGTTCTTCCCCGGCGTCCCGAAAATCAAGTATGAG                         GGTCCAACAAGCAAGAACCCTCTTGCTTATAAGTGGTATAACAAGGAGGAA
genomic: ATGATTGGGAGGGGGAGTTCTTCCCCGGCGTCCCGAAAATCAAGTATGAGgtggggctat ... cctgctgcagGGTCCAACAAGCAAGAACCCTCTTGCTTATAAGTGGTATAACAAGGAGGAA

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: 205

GACTTGCCCCGCCGACCTCGACAGCAAATGCGATGGTGGCGCGTCTGATGATGATTGGGAGGGGGAGTTCTTCCCCGGCGTCCCGAAAATCAAGTATGAGgtggggctat ... cctgctgcagGGTCCAACAAGCAAGAACCCTCTTGCTTATAAGTGGTATAACAAGGAGGAAGTGATTCTCGGTAAGAAGATGAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 223

GACTTGCCCCGCCGACCTCGACAGCAAATGCGATGGTGGCGCGTCTGATGATGATTGGGAGGGGGAGTTCTTCCCCGGCGTCCCGAAAATCAAGTATGAGgtggggctat ... cctgctgcagGGTCCAACAAGCAAGAACCCTCTTGCTTATAAGTGGTATAACAAGGAGGAAGTGATTCTCGGTAAGAAGATGAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 243

GACTTGCCCCGCCGACCTCGACAGCAAATGCGATGGTGGCGCGTCTGATGATGATTGGGAGGGGGAGTTCTTCCCCGGCGTCCCGAAAATCAAGTATGAGgtggggctat ... cctgctgcagGGTCCAACAAGCAAGAACCCTCTTGCTTATAAGTGGTATAACAAGGAGGAAGTGATTCTCGGTAAGAAGATGAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 172

GACTTGCCCCGCCGACCTCGACAGCAAATGCGATGGTGGCGCGTCTGATGATGATTGGGAGGGGGAGTTCTTCCCCGGCGTCCCGAAAATCAAGTATGAGgtggggctat ... cctgctgcagGGTCCAACAAGCAAGAACCCTCTTGCTTATAAGTGGTATAACAAGGAGGAAGTGATTCTCGGTAAGAAGATGAAG