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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GACAACGATTTGCTGCATGAGGTCTTTGACATCAAAATTGATCGTACTGAAAACATGTCAGCCACCGAAAAGgtaaccttttcatagctattggattgtattgggcacattatattgtatcatttctaagttggttggggaaaaaaaacagtcaccagtaagataggcatcaagacatgggcatagcgacagttctctaaagaatctgtttgcatgcgttcag

Basic information

species Zea mays
transcript GRMZM2G057412_T03
intron # 11
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G057412_T04 (Zea mays), 5'ss of exon 11
lower sequence: LOC_Os03g33590.2 (Oryza sativa), 5'ss of exon 11
GACAACGATTTGCTGCATGAGGTCTTTGACATCAAAATTGATCGTACTGAAAACATGTCAGCCACCGAAAAGgtaaccttttcatagctattggattgtattgggcacattatattgtatcatttctaagttggttggggaaaaaaaacagtcaccagtaagataggcatcaagacatgggcatagcgacagttctctaaagaatctgtttgcatgcgttcag
||||| |  ||||| |||||  |||||||||||||||| |||   ||||||||||||||| |||| |||||||||| |||||||||||| | |  |||  |||    |||| |  | |||  ||| || | || |     |   | |    |     ||| |   |      |      ||                                          
GACAATGGATTGCTACATGATATCTTTGACATCAAAATGGATAAAACTGAAAACATGTCAACCACTGAAAAGgtaagcttttcatagctttggacttgctttg----cattctgat-tatgttttgtagggtgtt-----atttagagttttgtttggtatgtctgcttggcaatttccggt-----------------------------------------
















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|74240130|gb|DT648044.1|DT648044
EST:     TCTTTGACATCAAAATTGATCGTACTGAAAACATGTCAGCCACCGAAAAG                         AAAATGTTCAGATCTGGAGAAGAGAAAGGAAGAGCTCTGAAGTTGAATAAA
genomic: TCTTTGACATCAAAATTGATCGTACTGAAAACATGTCAGCCACCGAAAAGgtaacctttt ... atgcgttcagAAAATGTTCAGATCTGGAGAAGAGAAAGGAAGAGCTCTGAAGTTGAATAAA
EST: gi|93281097|gb|EB673361.1|EB673361
EST:     TTTTTGACATCAAAATTGATCGTACTGAAAACATGTCAGCCCCCGAAAAG                         AAAATGTTCAGATTTGGAGAAGAGAAAGGAAGAGCTTTGAAGTTGAATAAA
genomic: TCTTTGACATCAAAATTGATCGTACTGAAAACATGTCAGCCACCGAAAAGgtaacctttt ... atgcgttcagAAAATGTTCAGATCTGGAGAAGAGAAAGGAAGAGCTCTGAAGTTGAATAAA
EST: gi|149102607|gb|EE287965.2|EE287965
EST:     TCTTTGACATCAAAATTGATCGTACTGAAAACATGTCAGCCACCGAAAAG                         AAAATGTTCAGATCTGGAGAAGAGAAAGGAAGAGCTCTGAAGTTGAATAAA
genomic: TCTTTGACATCAAAATTGATCGTACTGAAAACATGTCAGCCACCGAAAAGgtaacctttt ... atgcgttcagAAAATGTTCAGATCTGGAGAAGAGAAAGGAAGAGCTCTGAAGTTGAATAAA
EST: gi|33467969|gb|CF245018.1|CF245018
EST:     TCTTTGACATCAAAATTGATCGTACTGAAAACATGTCAGCCACCGAAAAG                         AAAATGTTCAGATCTGGAGAAGAGAAAGGAAGAGCTCTGAAGTTGAATAAA
genomic: TCTTTGACATCAAAATTGATCGTACTGAAAACATGTCAGCCACCGAAAAGgtaacctttt ... atgcgttcagAAAATGTTCAGATCTGGAGAAGAGAAAGGAAGAGCTCTGAAGTTGAATAAA
EST: gi|60336988|gb|DN203961.1|DN203961
EST:     AACATGTCAGCCACCGAAAAG                         AAAATGTTCAGATCTGGAGAAGAGAAAGGAAGAGCTCTGAAGTTGAATAAA
genomic: AACATGTCAGCCACCGAAAAGgtaacctttt ... atgcgttcagAAAATGTTCAGATCTGGAGAAGAGAAAGGAAGAGCTCTGAAGTTGAATAAA
EST: gi|76909352|gb|DV163342.1|DV163342
EST:     TCTTTGACATCAAAATTGATCGTACTGAAAACATGTCAGCCACCGAAAAG                         AAAATGTTCAGATCTGGAGAAGAGAAAGGAAGAGCTCTGAAGTTGAATAAA
genomic: TCTTTGACATCAAAATTGATCGTACTGAAAACATGTCAGCCACCGAAAAGgtaacctttt ... atgcgttcagAAAATGTTCAGATCTGGAGAAGAGAAAGGAAGAGCTCTGAAGTTGAATAAA
EST: gi|211386247|gb|FL227579.1|FL227579
EST:     TCTTTGACATCAAAATTGATCGTACTGAAAACATGTCAGCCACCGAAAAG                         AAAATGTTCAGATCCGGAGAAGAGAAAGGAAGAGCTCTGAAGTTGAATAAA
genomic: TCTTTGACATCAAAATTGATCGTACTGAAAACATGTCAGCCACCGAAAAGgtaacctttt ... atgcgttcagAAAATGTTCAGATCTGGAGAAGAGAAAGGAAGAGCTCTGAAGTTGAATAAA
EST: gi|74242217|gb|DT650131.1|DT650131
EST:     TCTTTGACATCAAAATTGATCGTACTGAAAACATGTCAGCCCCCGAAAAG                         AAAATGTTCAGATCTGGAGAAGAGAAAGGAAGAGCTTTGAAGTTGAATAAA
genomic: TCTTTGACATCAAAATTGATCGTACTGAAAACATGTCAGCCACCGAAAAGgtaacctttt ... atgcgttcagAAAATGTTCAGATCTGGAGAAGAGAAAGGAAGAGCTCTGAAGTTGAATAAA
EST: gi|60347261|gb|DN214234.1|DN214234
EST:     TCTTTGACATCAAAATTGATCGTACTGAAAACATGTCAGCCACCGAAAAG                         AAAATGTTCAGATCTGGAGAAGAGAAAGGAAGAGCTCTGAAGTTGAATAAA
genomic: TCTTTGACATCAAAATTGATCGTACTGAAAACATGTCAGCCACCGAAAAGgtaacctttt ... atgcgttcagAAAATGTTCAGATCTGGAGAAGAGAAAGGAAGAGCTCTGAAGTTGAATAAA
EST: gi|89759386|gb|DY688239.1|DY688239
EST:     TCTTTGACATCAAAATTGATCGTACTGAAAACATGTCAGCCCCCGAAAAG                         AAAATGTTCAGATCTGGAGAAGAGAAAGGAAGAGCTCTGAAGTTGAATAAA
genomic: TCTTTGACATCAAAATTGATCGTACTGAAAACATGTCAGCCACCGAAAAGgtaacctttt ... atgcgttcagAAAATGTTCAGATCTGGAGAAGAGAAAGGAAGAGCTCTGAAGTTGAATAAA
EST: gi|86466198|gb|DY232571.1|DY232571
EST:     TCTTTGACATCAAAATTGATCGTACTGAAAACATGTCAGCCACCGAAAAG                         AAAATGTTCAGATCTGGAGAAGAGAAAGGAAGAGCTCTGAAGTTGAATAAA
genomic: TCTTTGACATCAAAATTGATCGTACTGAAAACATGTCAGCCACCGAAAAGgtaacctttt ... atgcgttcagAAAATGTTCAGATCTGGAGAAGAGAAAGGAAGAGCTCTGAAGTTGAATAAA
EST: gi|211131389|gb|FL432622.1|FL432622
EST:     TCTTTGACATCAAAATTGATCGTACTGAAAACATGTCAGCCACCGAAAAG                         AAAATGTTCAGATCTGGAGAAGAGAAAGGAAGAGCTCTGAAGTTGAATAAA
genomic: TCTTTGACATCAAAATTGATCGTACTGAAAACATGTCAGCCACCGAAAAGgtaacctttt ... atgcgttcagAAAATGTTCAGATCTGGAGAAGAGAAAGGAAGAGCTCTGAAGTTGAATAAA
EST: gi|60354297|gb|DN221270.1|DN221270
EST:     TCTTTGACATCAAAATTGATCGTACTGAAAACATGTCAGCCACCGAAAAG                         AAAATGTTCAGATCTGGAGAAGAGAAAGGAAGAGCTCTGAAGTTGAATAAA
genomic: TCTTTGACATCAAAATTGATCGTACTGAAAACATGTCAGCCACCGAAAAGgtaacctttt ... atgcgttcagAAAATGTTCAGATCTGGAGAAGAGAAAGGAAGAGCTCTGAAGTTGAATAAA
EST: gi|89249172|gb|DY620958.1|DY620958
EST:     TCTTTGACATCAAAATTGATCGTACTGAAAACATGTCAGCCACCGAAAAG                         AAAATGTTCAGATCTGGAGAAGAGAAAGGAAGAGCTCTGAAGTTGAATAAA
genomic: TCTTTGACATCAAAATTGATCGTACTGAAAACATGTCAGCCACCGAAAAGgtaacctttt ... atgcgttcagAAAATGTTCAGATCTGGAGAAGAGAAAGGAAGAGCTCTGAAGTTGAATAAA
EST: gi|211131390|gb|FL432623.1|FL432623
EST:     TTTTTGACATCAAAATTGATCGTACTGAAAACATGTCAGCCACCGAAAAG                         AAAATGTTCAGATCTGGAGAAGAGAAAGGAAGAGCTTTGAAGTTGAATAAA
genomic: TCTTTGACATCAAAATTGATCGTACTGAAAACATGTCAGCCACCGAAAAGgtaacctttt ... atgcgttcagAAAATGTTCAGATCTGGAGAAGAGAAAGGAAGAGCTCTGAAGTTGAATAAA

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), 47 (downstream exon)
Score: 42

GACAACGATTTGCTGCATGAGGTCTTTGACATCAAAATTGATCGTACTGAAAACATGTCAGCCACCGAAAAGgtaacctttt ... atgcgttcagAAAATGTTCAGATCTGGAGAAGAGAAAGGAAGAGCTCTGAAGTTGAATAAAGAGCGTCGTCTAGCTCAG


Block sizes: 39 (upstream exon), 49 (downstream exon)
Score: 42

GACAACGATTTGCTGCATGAGGTCTTTGACATCAAAATTGATCGTACTGAAAACATGTCAGCCACCGAAAAGgtaacctttt ... atgcgttcagAAAATGTTCAGATCTGGAGAAGAGAAAGGAAGAGCTCTGAAGTTGAATAAAGAGCGTCGTCTAGCTCAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 45

GACAACGATTTGCTGCATGAGGTCTTTGACATCAAAATTGATCGTACTGAAAACATGTCAGCCACCGAAAAGgtaacctttt ... atgcgttcagAAAATGTTCAGATCTGGAGAAGAGAAAGGAAGAGCTCTGAAGTTGAATAAAGAGCGTCGTCTAGCTCAG


Block sizes: 36 (upstream exon), 48 (downstream exon)
Score: 38

GACAACGATTTGCTGCATGAGGTCTTTGACATCAAAATTGATCGTACTGAAAACATGTCAGCCACCGAAAAGgtaacctttt ... atgcgttcagAAAATGTTCAGATCTGGAGAAGAGAAAGGAAGAGCTCTGAAGTTGAATAAAGAGCGTCGTCTAGCTCAG