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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaaatcaacgttcacttgaaccatcgtgcatgtgtatgtcttcgccaatattataagggttcgacttggctctgactggctgaattctgtacagAAAATCCCTCTGGTGTTCGCTGGGCGAAGACCCGGAGACGCAGAGATCGTCTACGCCGCAACTGCCAAGGCAGAGAAGGAGCTCAAATGGAA

Basic information

species Zea mays
transcript GRMZM2G038598_T03
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G038598_T02 (Zea mays), 3'ss of exon 7
lower sequence: LOC_Os05g51670.2 (Oryza sativa), 3'ss of exon 7
-----------------gtaaaatcaacgtt---cacttgaaccatcgtgcatgtgta---tgtc-ttcgccaatatt----ataagggttcgacttggctctgactggctgaattctgtacagAAAATCCCTCTGGTGTTCGCTGGGCGAAGACCCGGAGACGCAGAGATCGTCTACGCCGCAACTGCCAAGGCAGAGAAGGAGCTCAAATGGAA--------
                 ||  | |     ||    |||  ||  ||| |  ||    |   |||| || ||   | ||    ||| |   ||| | |  |  | |       || | || |||||||||||| || || || ||||| ||||| || ||||| || |||||||| |||||   ||||||||| || |||||||| || ||||||||        
gtaaactaacaggacaagtgtacttcctcttaattactataataatcattaattcccaacttgtcctttgcttttgttgatcatatgatgtcgtcctaacaataataatgccaact-tgaacagAAAATCCCGCTTGTATTTGCTGGACGAAGGCCTGGAGATGCCGAGATCGTTTACGCTCAAACTGCCAAAGCTGAGAAGGAACTGAAATGGAAGTAAGTAT

upper sequence: GRMZM2G038598_T02 (Zea mays), 3'ss of exon 7
lower sequence: LOC_Os05g51670.1 (Oryza sativa), 3'ss of exon 7
-----------------gtaaaatcaacgtt---cacttgaaccatcgtgcatgtgta---tgtc-ttcgccaat----attataagggttcgacttggctctgactggctgaattctgtacagAAAATCCCTCTGGTGTTCGCTGGGCGAAGACCCGGAGACGCAGAGATCGTCTACGCCGCAACTGCCAAGGCAGAGAAGGAGCTCAAATGGAA
                 ||  | |     ||    |||  ||  ||| |  ||    |   |||| || ||   |    || ||| |   ||| | |  |  | |       || | || |||||||||||| || || || ||||| ||||| || ||||| || |||||||| |||||   ||||||||| || |||||||| || ||||||||
gtaaactaacaggacaagtgtacttcctcttaattactataataatcattaattcccaacttgtcctttgcttttgttgatcatatgatgtcgtcctaacaataataatgccaact-tgaacagAAAATCCCGCTTGTATTTGCTGGACGAAGGCCTGGAGATGCCGAGATCGTTTACGCTCAAACTGCCAAAGCTGAGAAGGAACTGAAATGGAA
















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|32845089|gb|CD984770.1|CD984770
EST:     GGACGTCCGTGTTGGAAATGGTGGCTGCATTCGAGAAGGCTTCTGGGAAG                         AAAATCCCTCTGGTGTTCGCTGGGCGAAGACCCGGAGACGCAGAGATCGTC
genomic: GGACGTCGGTGTTGGAAATGGTGGCTGCATTCGAGAAGGCTTCTGGGAAGgtaaaatcaa ... ttctgtacagAAAATCCCTCTGGTGTTCGCTGGGCGAAGACCCGGAGACGCAGAGATCGTC
EST: gi|71440043|gb|DR821093.1|DR821093
EST:     GGACGTCGGTGTTGGAAATGGTGGCTGCATTCGAGAAGGCTTCTGGGAAG                         AAAATCCCTCTGGTGTTCGCTGGGCGAAGACCCGGAGACGCAGAGATCGTT
genomic: GGACGTCGGTGTTGGAAATGGTGGCTGCATTCGAGAAGGCTTCTGGGAAGgtaaaatcaa ... ttctgtacagAAAATCCCTCTGGTGTTCGCTGGGCGAAGACCCGGAGACGCAGAGATCGTC
EST: gi|148951201|gb|EC896889.2|EC896889
EST:     GGACGTCGGTGTTGGAAATGGTGGCTGCATTCGAGAAGGCTTCTGGGAAG                         AAAATCCCTTTGGTGTTCGCTGGGCGAAGACCCGGAGACGCAGAGATCGTT
genomic: GGACGTCGGTGTTGGAAATGGTGGCTGCATTCGAGAAGGCTTCTGGGAAGgtaaaatcaa ... ttctgtacagAAAATCCCTCTGGTGTTCGCTGGGCGAAGACCCGGAGACGCAGAGATCGTC
EST: gi|71440044|gb|DR821094.1|DR821094
EST:     GGACGTCGGTGTTGGAAATGGTGGCTGCATTCGAGAAGGCTTCTGGGAAG                         AAA-TCCCTCTGGTGT
genomic: GGACGTCGGTGTTGGAAATGGTGGCTGCATTCGAGAAGGCTTCTGGGAAGgtaaaatcaa ... ttctgtacagAAAATCCCTCTGGTGT
EST: gi|31250360|gb|CD219384.1|CD219384
EST:     GGACGTCGGTGTTGGAAATGGTGGCTGCATTCGAGAAGGCTTCTGGGAAG                         AAAATCCCTCTGGTGTTCGCTGGGCGAAGACCCGGAGACGCAGAGATCGTC
genomic: GGACGTCGGTGTTGGAAATGGTGGCTGCATTCGAGAAGGCTTCTGGGAAGgtaaaatcaa ... ttctgtacagAAAATCCCTCTGGTGTTCGCTGGGCGAAGACCCGGAGACGCAGAGATCGTC
EST: gi|74240923|gb|DT648837.1|DT648837
EST:     GGACGTCGGTGTTGGAAATGGTGGCTGCATTCGAGAAGGCTTCTGGGAAG                         AAAATCCCTCTGGTGTTCGCTGGGCGAAGACCCGGAGACGCAGAGATCGTC
genomic: GGACGTCGGTGTTGGAAATGGTGGCTGCATTCGAGAAGGCTTCTGGGAAGgtaaaatcaa ... ttctgtacagAAAATCCCTCTGGTGTTCGCTGGGCGAAGACCCGGAGACGCAGAGATCGTC
EST: gi|91053192|gb|EB163610.1|EB163610
EST:     GGACGTCGGTGTTGGAAATGGTGGCTGCATTCGAGAAGGCTTCTGGGAAG                         AAAATCCCTCTGGTGTTCGCTGGGCGAAGACCCGGAGACGCAGAGATCGTC
genomic: GGACGTCGGTGTTGGAAATGGTGGCTGCATTCGAGAAGGCTTCTGGGAAGgtaaaatcaa ... ttctgtacagAAAATCCCTCTGGTGTTCGCTGGGCGAAGACCCGGAGACGCAGAGATCGTC
EST: gi|211169445|gb|FL037896.1|FL037896
EST:     GGACGTCGGTGTTGGAAATGGTGGCTGCATTCGAGAAGGCTTCTGGGAAG                         AAAATCCCTCTGGTGTTCGCTGGGCGAAGACCCGGAGACGCAGAGATCGTC
genomic: GGACGTCGGTGTTGGAAATGGTGGCTGCATTCGAGAAGGCTTCTGGGAAGgtaaaatcaa ... ttctgtacagAAAATCCCTCTGGTGTTCGCTGGGCGAAGACCCGGAGACGCAGAGATCGTC
EST: gi|74237589|gb|DT645503.1|DT645503
EST:     GGACGTCGGTGTTGGAAATGGTGGCTGCATTCGAGAAGGCTTCTGGGAAG                         AAAATCCCTCTGGTGTTCGCTGGGCGAAGACCCGGAGACGCAGAGATCGTC
genomic: GGACGTCGGTGTTGGAAATGGTGGCTGCATTCGAGAAGGCTTCTGGGAAGgtaaaatcaa ... ttctgtacagAAAATCCCTCTGGTGTTCGCTGGGCGAAGACCCGGAGACGCAGAGATCGTC
EST: gi|78085824|gb|DV514217.1|DV514217
EST:     GGACGTCGGTGTTGGAAATGGTGGCTGCATTCGAGAAGGCTTCTGGGAAG                         AAAATCCCTCTGGTGTTCGCTGGGCGAAGACCCGGAGACGCAGAGATCGTT
genomic: GGACGTCGGTGTTGGAAATGGTGGCTGCATTCGAGAAGGCTTCTGGGAAGgtaaaatcaa ... ttctgtacagAAAATCCCTCTGGTGTTCGCTGGGCGAAGACCCGGAGACGCAGAGATCGTC
EST: gi|149087171|gb|EE176707.2|EE176707
EST:     GGACGTCGGTGTTGGAAATGGTGGCTGCATTCGAGAAGGCTTCTGGGAAG                         AAAATCCCTCTGGTGTTCGCTGGGCGAAGACCCGGAGACGCAGAGATCGTT
genomic: GGACGTCGGTGTTGGAAATGGTGGCTGCATTCGAGAAGGCTTCTGGGAAGgtaaaatcaa ... ttctgtacagAAAATCCCTCTGGTGTTCGCTGGGCGAAGACCCGGAGACGCAGAGATCGTC
EST: gi|211169444|gb|FL037895.1|FL037895
EST:     GGACGTCGGTGTTGGAAATGGTGGCTGCATTCGAGAAGGCTTCTGGGAAG                         AAAATCCCTCTGGTGTTCGCTGGGCGAAGACCCGGAGACGCAGAGATCGTC
genomic: GGACGTCGGTGTTGGAAATGGTGGCTGCATTCGAGAAGGCTTCTGGGAAGgtaaaatcaa ... ttctgtacagAAAATCCCTCTGGTGTTCGCTGGGCGAAGACCCGGAGACGCAGAGATCGTC
EST: gi|18660097|gb|BM500685.1|BM500685
EST:     GGACGTCCGTGTTGGAAATGGTGGCTGCATTCGAGAAGGCTTCTGGGAAG                         AAAA-CCCTCTGG
genomic: GGACGTCGGTGTTGGAAATGGTGGCTGCATTCGAGAAGGCTTCTGGGAAGgtaaaatcaa ... ttctgtacagAAAATCCCTCTGG
EST: gi|32845045|gb|CD984726.1|CD984726
EST:     GGACGTCCGTGTTGGAAATGGTGGCTGCATTCGAGAAGGCTTCTGGGAAG                         AAAATCCCTCTGGTGTTCGCTGGGCGAAGACCCGGAGACGCAGAGATCGTC
genomic: GGACGTCGGTGTTGGAAATGGTGGCTGCATTCGAGAAGGCTTCTGGGAAGgtaaaatcaa ... ttctgtacagAAAATCCCTCTGGTGTTCGCTGGGCGAAGACCCGGAGACGCAGAGATCGTC
EST: gi|211091121|gb|FL440769.1|FL440769
EST:     GGACGTCGGTGTTGGAAATGGTGGCTGCATTCGAGAAGGCTTCTGGGAAG                         AAAATCCCTCTGGTGTTCGCTGGGCGAAGACCCGGAGACGCAGAGATCGTC
genomic: GGACGTCGGTGTTGGAAATGGTGGCTGCATTCGAGAAGGCTTCTGGGAAGgtaaaatcaa ... ttctgtacagAAAATCCCTCTGGTGTTCGCTGGGCGAAGACCCGGAGACGCAGAGATCGTC
EST: gi|32845258|gb|CD984939.1|CD984939
EST:     GGACGTCCGTGTTGGAAATGGTGGCTGCATTCGAGAAGGCTTCTGGGAAG                         AAAATCCCTCTGGTGTTCGCTGGGCGAAGACCCGGAGACGCAGAGATCGTC
genomic: GGACGTCGGTGTTGGAAATGGTGGCTGCATTCGAGAAGGCTTCTGGGAAGgtaaaatcaa ... ttctgtacagAAAATCCCTCTGGTGTTCGCTGGGCGAAGACCCGGAGACGCAGAGATCGTC
EST: gi|71429156|gb|DR810206.1|DR810206
EST:     GGACGTCGGTGTTGGAAATGGTGGCTGCATTCGAGAAGGCTTCTGGGAAG                         AAAATCCCTCTGGTGTTCGCTGGGCGAAGACCCGGAGACGCAGAGATCGTC
genomic: GGACGTCGGTGTTGGAAATGGTGGCTGCATTCGAGAAGGCTTCTGGGAAGgtaaaatcaa ... ttctgtacagAAAATCCCTCTGGTGTTCGCTGGGCGAAGACCCGGAGACGCAGAGATCGTC
EST: gi|32844790|gb|CD984471.1|CD984471
EST:     GGACGTCCGTGTTGGAAATGGTGGCTGCATTCGAGAAGGCTTCTGGGAAG                         AAAATCCCTCTGGTGTTCGCTGGGCGAAGACCCGGAGACGCAGAGATCGTC
genomic: GGACGTCGGTGTTGGAAATGGTGGCTGCATTCGAGAAGGCTTCTGGGAAGgtaaaatcaa ... ttctgtacagAAAATCCCTCTGGTGTTCGCTGGGCGAAGACCCGGAGACGCAGAGATCGTC
EST: gi|32844896|gb|CD984577.1|CD984577
EST:     GGACGTCCGTGTTGGAAATGGTGGCTGCATTCGAGAAGGCTTCTGGCAAG                         AAAATCCCTCTGGTGTTCGCTGGGCGAAGACCCGGAGACGCAGAGATCGTC
genomic: GGACGTCGGTGTTGGAAATGGTGGCTGCATTCGAGAAGGCTTCTGGGAAGgtaaaatcaa ... ttctgtacagAAAATCCCTCTGGTGTTCGCTGGGCGAAGACCCGGAGACGCAGAGATCGTC
EST: gi|69351133|gb|DR452031.1|DR452031
EST:     GGACGTCGGTGTTGGAAATGGTGGCTGCATTCGAGAAGGCTTCTGGGAAN                         AAAATCCCTCTGGTGTTCGCTGGGCGAAGACCCGGAGAC
genomic: GGACGTCGGTGTTGGAAATGGTGGCTGCATTCGAGAAGGCTTCTGGGAAGgtaaaatcaa ... ttctgtacagAAAATCCCTCTGGTGTTCGCTGGGCGAAGACCCGGAGAC
EST: gi|58029768|gb|CX725195.1|CX725195
EST:     GGACGTCGGTGTTGGAAATGGTGGCTGCATTCGAGAAGGCTTCTGGGAAG                         AAAATCCCTCTGGTGTTCGCTGGGCGAANACCCGGAAACGCANANATCGTC
genomic: GGACGTCGGTGTTGGAAATGGTGGCTGCATTCGAGAAGGCTTCTGGGAAGgtaaaatcaa ... ttctgtacagAAAATCCCTCTGGTGTTCGCTGGGCGAAGACCCGGAGACGCAGAGATCGTC
EST: gi|116828756|gb|EC860854.1|EC860854
EST:     GGACGTCGGTGTTGGAAATGGTGGCTGCATTCGAGAAGGCTTCTGGGAAG                         AAAATCCCTCTGGTGTTCGCTGGGCGAAGACCCGGAGACGCAGAGATCGTC
genomic: GGACGTCGGTGTTGGAAATGGTGGCTGCATTCGAGAAGGCTTCTGGGAAGgtaaaatcaa ... ttctgtacagAAAATCCCTCTGGTGTTCGCTGGGCGAAGACCCGGAGACGCAGAGATCGTC
EST: gi|50335983|gb|CO531109.1|CO531109
EST:     GGACGTCGGTGTTGGAAATGGTGGCTGCATTCGAGAAGGCTTTTGGGAAG                         AAAATCCCTCTGGTGTTCGCTGGGCGAAGACCCGGAGACGCAGAGATCGTT
genomic: GGACGTCGGTGTTGGAAATGGTGGCTGCATTCGAGAAGGCTTCTGGGAAGgtaaaatcaa ... ttctgtacagAAAATCCCTCTGGTGTTCGCTGGGCGAAGACCCGGAGACGCAGAGATCGTC
EST: gi|18163517|gb|BM333356.1|BM333356
EST:     GGACGTCGGTGTTGGAAATGGTGGCTGCATTCGAGAAGGCTTCTGGGAAG                         AAAATCCCTCTGGTGTTCGCTGGGCGAAGACCCGGAGACGCAGAGATCGTC
genomic: GGACGTCGGTGTTGGAAATGGTGGCTGCATTCGAGAAGGCTTCTGGGAAGgtaaaatcaa ... ttctgtacagAAAATCCCTCTGGTGTTCGCTGGGCGAAGACCCGGAGACGCAGAGATCGTC
EST: gi|78121122|gb|DV539506.1|DV539506
EST:     GGACGTCGGTGTTGGAAATGGTGGCTGCATTCGAGAAGGCTTCTGGGAAG                         AAAATCCCTCTGGTGTTCGCTGGGCGAAGACCCGGAGACGCAGAGATCGTT
genomic: GGACGTCGGTGTTGGAAATGGTGGCTGCATTCGAGAAGGCTTCTGGGAAGgtaaaatcaa ... ttctgtacagAAAATCCCTCTGGTGTTCGCTGGGCGAAGACCCGGAGACGCAGAGATCGTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttcgccaatattataagggttcgacttggctctgactggctgaattctgtacagAAAATCCCTCTGGTGTTCGCTGGGCGAAGACCCGGAGACGCAGAGATCGTCTACGCCGCAACTGCCAAGGCAGAGAAGGAGCTCAAATGGAA
                              ctctgac  putative branch site (score: 3)
       aatattataa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaaatcaacgttcacttgaaccatcgtgcatgtgtatgtcttcgccaatattataagggttcgacttggctctgactggctgaattctgtacagAAAATCCCTCTGGTGTTCGCTGGGCGAAGACCCGGAGACGCAGAGATCGTCTACGCCGCAACTGCCAAGGCAGAGAAGGAGCTCAAATGGAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTCA