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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atgtgatgtgagaatctcagacatttgattgttgatcacctatttttctttatgctattttcttgcaccaaatatgtgctgactaggggtgccttaacagATGAAGAACGCATATGCTGTTTCAAGGCTGAGGAAGAAAACTGGGTATACCAAAAATCAATTCTACGATCAAGCATTAAAAATATACAAGGAG

Basic information

species Zea mays
transcript GRMZM2G111713_T01
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G111713_T02 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os07g45300.1 (Oryza sativa), 3'ss of exon 7
atgtgatgtgagaatctcagacatttgattgttgatcacct---atttttctttatgctattttc--ttgcaccaaatatgtgctgactag--gggtgcctta---acagATGAAGAACGCATATGCTGTTTCAAGGCTGAGGAAGAAAACTGGGTATACCAAAAATCAATTCTACGATCAAGCATTAAAAATATACAAGGAG
          | |   | |   |||||||    |||  |||   ||||| |||| || ||||||   || ||| || | || ||||| |||  || ||   ||   |||||||||||| ||||||||||| |||||  |||| |||||||| || |||||||||||  ||||||| ||||||||||| || ||||||||||||
----------ataccttaatgtatttgatctgagataccctgcaattttcctttgtgatatttttattttcacgaattgtgagctgattagttggttgttatactgacagATGAAGAATGCATATGCTGTGTCAAGATTGAGAAAGAAAACAGGCTATACCAAAAAGGAATTCTATGATCAAGCATTCAAGATATACAAGGAG
















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|211131767|gb|FL358660.1|FL358660
EST:     GGTTTACACTAAGTGGCTGGAGAAGGACAAAGGAGGACATCATTTTGGAG                         ATGAAGAACGCA
genomic: GGTTTACACTAAGTGGCTGGAGAAGGACAAAGGAGGACATCATTTTGGAGgtactgaatc ... gccttaacagATGAAGAACGCA
EST: gi|211177445|gb|FL359118.1|FL359118
EST:     GGTTTACACTAAGTGGCTGGAGAAGGACAAAGGAGGACATCATTTTGGAG                         ATGAAGAACGCATATGCTGTTTCAAGGCTGAGGAAGAAAACTGGGTATACC
genomic: GGTTTACACTAAGTGGCTGGAGAAGGACAAAGGAGGACATCATTTTGGAGgtactgaatc ... gccttaacagATGAAGAACGCATATGCTGTTTCAAGGCTGAGGAAGAAAACTGGGTATACC
EST: gi|71443106|gb|DR824156.1|DR824156
EST:     GGTTTACACTAAGTGGCTGGAGAAGGACAAAGGAGGACATCATTTTGGAG                         ATGAAGAACGCATATGCTGTTTCAAGGCTGAGGAAGAAAACTGGGTATACC
genomic: GGTTTACACTAAGTGGCTGGAGAAGGACAAAGGAGGACATCATTTTGGAGgtactgaatc ... gccttaacagATGAAGAACGCATATGCTGTTTCAAGGCTGAGGAAGAAAACTGGGTATACC
EST: gi|50337823|gb|CO532949.1|CO532949
EST:     GGTTTACACTAAGTGGCTGGAGAAGGACAAAGGAGGACATCATTTTGGAG                         ATGAAGAACGCATATGCTGTTTCAAGGCTGAGGAAGAAAACTGGGTATACC
genomic: GGTTTACACTAAGTGGCTGGAGAAGGACAAAGGAGGACATCATTTTGGAGgtactgaatc ... gccttaacagATGAAGAACGCATATGCTGTTTCAAGGCTGAGGAAGAAAACTGGGTATACC
EST: gi|101389514|gb|EB816695.1|EB816695
EST:     GGTTTACACTAAGTGGCTGGAGAAGGACAAAGGAGGACATCATTTTGGAG                         ATGAAGAACGCATATGCTGTTTCAAGGCTGAGGAAGAAAACTGGGTATACC
genomic: GGTTTACACTAAGTGGCTGGAGAAGGACAAAGGAGGACATCATTTTGGAGgtactgaatc ... gccttaacagATGAAGAACGCATATGCTGTTTCAAGGCTGAGGAAGAAAACTGGGTATACC
EST: gi|61119623|gb|DN560584.1|DN560584
EST:     GGTTTACACTAAGTGGCTGGAGAAGGACAAAGGAGGACATCATTTTGGAG                         ATGAAGAACGCATATGCTGTTTCAAGGCTGAGGAAGAAAACTGGGTATACC
genomic: GGTTTACACTAAGTGGCTGGAGAAGGACAAAGGAGGACATCATTTTGGAGgtactgaatc ... gccttaacagATGAAGAACGCATATGCTGTTTCAAGGCTGAGGAAGAAAACTGGGTATACC
EST: gi|211208019|gb|FL322438.1|FL322438
EST:     GGTTTACACTAAGTGGCTGGAGAAGGACAAAGGAGGACATCATTTTGGAG                         ATGAAGAACGCATAT
genomic: GGTTTACACTAAGTGGCTGGAGAAGGACAAAGGAGGACATCATTTTGGAGgtactgaatc ... gccttaacagATGAAGAACGCATAT
EST: gi|211442630|gb|FL341621.1|FL341621
EST:     GTTTACCCTTAGTGGCTGGAGAAAGACAAAGGAGGACATCATTTTTGGAG                         ATGA-GAACGCATATGCTGGTTCA-GGCTGAGGAAGAAAACT
genomic: GTTTACACTAAGTGGCTGGAGAAGGACAAAGGAGGACATCATTTT-GGAGgtactgaatc ... gccttaacagATGAAGAACGCATATGCTGTTTCAAGGCTGAGGAAGAAAACT
EST: gi|89758224|gb|DY687488.1|DY687488
EST:     GGTTTACACTAAGTGGCTGGAGAAGGACAAAGGAGGACATCATTTTGGAG                         ATGAAGAACGCATATGCTGTTTCAAGGCTGAGGAAGAAAACTGGGTATACC
genomic: GGTTTACACTAAGTGGCTGGAGAAGGACAAAGGAGGACATCATTTTGGAGgtactgaatc ... gccttaacagATGAAGAACGCATATGCTGTTTCAAGGCTGAGGAAGAAAACTGGGTATACC
EST: gi|88758133|gb|DY542274.1|DY542274
EST:     GGTTTACACTAAGTGGCTGGAGAAGGACAAAGGAGGACATCATTTTGGAG                         ATGAAGAACGCATATGCTGTTTCAAGGCTGAGGAAGAAAACTGGGTATACC
genomic: GGTTTACACTAAGTGGCTGGAGAAGGACAAAGGAGGACATCATTTTGGAGgtactgaatc ... gccttaacagATGAAGAACGCATATGCTGTTTCAAGGCTGAGGAAGAAAACTGGGTATACC
EST: gi|211061706|gb|FL341836.1|FL341836
EST:     GTTTACACTAAGTGGCTGGAGAAAGGACAA-GGAGGACATCATTTTGGAG                         ATGAAGAACGCATATGCTGTTTCAAGGCTGAGGAAGAAA-CTGGG
genomic: GTTTACACTAAGTGGCTGGAGAA-GGACAAAGGAGGACATCATTTTGGAGgtactgaatc ... gccttaacagATGAAGAACGCATATGCTGTTTCAAGGCTGAGGAAGAAAACTGGG
EST: gi|148938688|gb|EC883024.2|EC883024
EST:     GGTTTACACTAAGTGGCTGGAGAAGGACAAAGGAGGACATCATTTTGGAG                         ATGAAGAACGCATATGCTGTTTCAAGGCTGAGGAAGAAAACTGGGTATACC
genomic: GGTTTACACTAAGTGGCTGGAGAAGGACAAAGGAGGACATCATTTTGGAGgtactgaatc ... gccttaacagATGAAGAACGCATATGCTGTTTCAAGGCTGAGGAAGAAAACTGGGTATACC
EST: gi|71420010|gb|DR804975.1|DR804975
EST:     GGTTTACACTAAGTGGCTGGAGAAGGACAAAGGAGGACATCATTTTGGAG                         ATGAAGAACGCATATGCTGTTTNCA-GGCTGAGGAAGAAAACTGGGTATAC
genomic: GGTTTACACTAAGTGGCTGGAGAAGGACAAAGGAGGACATCATTTTGGAGgtactgaatc ... gccttaacagATGAAGAACGCATATGCTGTTT-CAAGGCTGAGGAAGAAAACTGGGTATAC
EST: gi|148989211|gb|EE031705.2|EE031705
EST:     GGTTTACACTAAGTGGCTGGAGAAGGACAAAGGAGGACATCATTTTGGAG                         ATGAAGAACGCATATGCTGTTTCAAGGCTGAGGAAGAAAACTGGGTATACC
genomic: GGTTTACACTAAGTGGCTGGAGAAGGACAAAGGAGGACATCATTTTGGAGgtactgaatc ... gccttaacagATGAAGAACGCATATGCTGTTTCAAGGCTGAGGAAGAAAACTGGGTATACC
EST: gi|32913045|gb|CF017857.1|CF017857
EST:     GGTTTACACTAAGTGGCTGGAGAAGGACAAAGGAGGACATCATTTTGGAG                         ATGAAGAACGCATATGCTGTTTCAAGGCTGAGGAAGAAAACTGGGTATACC
genomic: GGTTTACACTAAGTGGCTGGAGAAGGACAAAGGAGGACATCATTTTGGAGgtactgaatc ... gccttaacagATGAAGAACGCATATGCTGTTTCAAGGCTGAGGAAGAAAACTGGGTATACC
EST: gi|91048124|gb|EB158542.1|EB158542
EST:     GGTTTACACTAAGTGGCTGGAGAAGGACAAAGGAGGACATCATTTTGGAG                         ATGAAGAACGCATATGCTGTTTCAAGGCTGAGGAAGAAAACTGGGTATACC
genomic: GGTTTACACTAAGTGGCTGGAGAAGGACAAAGGAGGACATCATTTTGGAGgtactgaatc ... gccttaacagATGAAGAACGCATATGCTGTTTCAAGGCTGAGGAAGAAAACTGGGTATACC
EST: gi|76923558|gb|DV169546.1|DV169546
EST:     GGTTTACACTAAGTGGCTGGAGAAGGACAAAGGAGGACATCATTTTGGAG                         ATGAAGAACGCATATGCTGTTTCAAGGCTGAGGAAGAAAACTGGGTATACC
genomic: GGTTTACACTAAGTGGCTGGAGAAGGACAAAGGAGGACATCATTTTGGAGgtactgaatc ... gccttaacagATGAAGAACGCATATGCTGTTTCAAGGCTGAGGAAGAAAACTGGGTATACC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttctttatgctattttcttgcaccaaatatgtgctgactaggggtgccttaacagATGAAGAACGCATATGCTGTTTCAAGGCTGAGGAAGAAAACTGGGTATACCAAAAATCAATTCTACGATCAAGCATTAAAAATATACAAGGAG
                               tgctgac  putative branch site (score: 2)
          tattttctt  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atgtgatgtgagaatctcagacatttgattgttgatcacctatttttctttatgctattttcttgcaccaaatatgtgctgactaggggtgccttaacagATGAAGAACGCATATGCTGTTTCAAGGCTGAGGAAGAAAACTGGGTATACCAAAAATCAATTCTACGATCAAGCATTAAAAATATACAAGGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG