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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCACTCTGGCTTCGCCAAGCGCGGCGAGGACTACTTCCTCGTCAAGCCCGACTGCCTCCGCGTCCCCGGAGACCCTTCCTCCTCTTTCTCCGTCTTCGCTgtaggcccacttttccccctaagatattcttttggtgtctcgtttgggttcggtgatgtgatggtctgtttgtttggtttgacggatctgcggttcgcag

Basic information

species Zea mays
transcript GRMZM2G006429_T02
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G006429_T01 (Zea mays), 5'ss of exon 1
lower sequence: LOC_Os03g18970.1 (Oryza sativa), 5'ss of exon 1
CCACTCTGGCTTCGCCAAGCGCGGCGAGGACTACTTCCTCGTCAAGCCCGACTGCCTCCGCGTCCCCGGAGACCCTTCCTCCTCTTTCTCCGTCTTCGCTgtaggcccacttttccccctaagatattcttttggtgtctcgtttgggttcggtgatg-tgatggtctg------tttgtttggtttgacggatctgcggttcg-cag
|||||  ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| || |||||||||||| | |||||||||||||| ||| |  | ||   |||||   |      || |||| ||   |  || ||| |||||| ||||||  ||      ||||||    ||   |||||||||||| | |||
CCACTTCGGCTTCGCCAAGCGCGGCGAGGACTACTTCCTCGTCAAGCCCGACTGCCTCCGCGTCCCGGGCGACCCTTCCTCCGCCTTCTCCGTCTTCGCCgtacgtgccct---ccccccgtgtcgcgtttctggtctcgtctcgggattccgtgatgctgatggcgtgtcgggttttgttcttgttcttggatctgcggtttggcag
















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|26560042|gb|CA832277.1|CA832277
EST:     ACTGCCTCCGCGTCCCCGGAGACCCTTCTTCCTCTTTCTCCGTCTTCGCT                         GTATTCGACGGCCACAATGGCGTGTCGGCGGCGGTGTTCAGCAAGGAGAAA
genomic: ACTGCCTCCGCGTCCCCGGAGACCCTTCCTCCTCTTTCTCCGTCTTCGCTgtaggcccac ... cggttcgcagGTATTCGACGGCCACAATGGCGTGTCGGCGGCGGTGTTCAGCAAGGAGAAA
EST: gi|37418869|gb|CF647107.1|CF647107
EST:     ACTGCCTCCGCGTCCCCGGAGACCCTTCCTCCTCTTTCTCCGTCTTCGCT                         GTATTCGACGGCCACAATGGCGTGTCCGCGGCGGTGTTCAGCAAGGAGAAA
genomic: ACTGCCTCCGCGTCCCCGGAGACCCTTCCTCCTCTTTCTCCGTCTTCGCTgtaggcccac ... cggttcgcagGTATTCGACGGCCACAATGGCGTGTCGGCGGCGGTGTTCAGCAAGGAGAAA
EST: gi|31354352|gb|CD438709.1|CD438709
EST:     ACTGCCTCCGCGTCCCCGGAGACCCTTCCTCCTCTTTCTCCGTCTTCGCT                         GTATTCGACGGCCACAATGGCGTGTCGGCGGCGGTGTTCAGCAAGGAGAAA
genomic: ACTGCCTCCGCGTCCCCGGAGACCCTTCCTCCTCTTTCTCCGTCTTCGCTgtaggcccac ... cggttcgcagGTATTCGACGGCCACAATGGCGTGTCGGCGGCGGTGTTCAGCAAGGAGAAA
EST: gi|211035342|gb|FL198977.1|FL198977
EST:     ACTGCCTCCGCGTCCCCGGAGACCCTTCCTCCTCTTTCTCCGTCTTCGCT                         GTATTCGACGGCCACAATGGCGTGTCGGCGGCGTTGTTCAGCAAGGAGAAA
genomic: ACTGCCTCCGCGTCCCCGGAGACCCTTCCTCCTCTTTCTCCGTCTTCGCTgtaggcccac ... cggttcgcagGTATTCGACGGCCACAATGGCGTGTCGGCGGCGGTGTTCAGCAAGGAGAAA
EST: gi|76281727|gb|DV021295.1|DV021295
EST:     ACTGCCTCCGCGTCCCCGGAGACCCTTCCTCCTCTTTCTCCGTCTTCGCT                         GTATTCGACGGCCACAATGGCGTGTCGGCGGCGGTGTTCAGCAAGGAGAAA
genomic: ACTGCCTCCGCGTCCCCGGAGACCCTTCCTCCTCTTTCTCCGTCTTCGCTgtaggcccac ... cggttcgcagGTATTCGACGGCCACAATGGCGTGTCGGCGGCGGTGTTCAGCAAGGAGAAA
EST: gi|211032898|gb|FL198967.1|FL198967
EST:     ACTGCCTCCGCGTCCCCGGAGACC-TTCCTCCTCTTTCTCCGTCTTCGCT                         GTATTCGACGGTCACAATGGCGTGTCGGCGGCG
genomic: ACTGCCTCCGCGTCCCCGGAGACCCTTCCTCCTCTTTCTCCGTCTTCGCTgtaggcccac ... cggttcgcagGTATTCGACGGCCACAATGGCGTGTCGGCGGCG
EST: gi|71331543|gb|DR802616.1|DR802616
EST:     ACTGCCTCCGCGTCCCCGGAGACCCTTCCTCCTCTTTCTCCGTCTTCGCT                         GTATTCGACGGCCACAATGGCGTGTCGGCGGCGGTGTTCAGCAAGGAGAAA
genomic: ACTGCCTCCGCGTCCCCGGAGACCCTTCCTCCTCTTTCTCCGTCTTCGCTgtaggcccac ... cggttcgcagGTATTCGACGGCCACAATGGCGTGTCGGCGGCGGTGTTCAGCAAGGAGAAA
EST: gi|211035339|gb|FL198974.1|FL198974
EST:     ACTGCCTCCGCGTCCCCGGAGACC-TTCCTCCTCTTTCTCCGTCTTCGCT                         GTATTCGACGG
genomic: ACTGCCTCCGCGTCCCCGGAGACCCTTCCTCCTCTTTCTCCGTCTTCGCTgtaggcccac ... cggttcgcagGTATTCGACGG
EST: gi|50331894|gb|CO527020.1|CO527020
EST:     ACTGCCTCCGCGTCCCCGGAGACCCTTCCTCCTCTTTCTCCGTCTTCGCT                         GTATTCGACGGCCACAATGGCGTGTCGGCGGCGGTGTTCAGCAAGGAGAAA
genomic: ACTGCCTCCGCGTCCCCGGAGACCCTTCCTCCTCTTTCTCCGTCTTCGCTgtaggcccac ... cggttcgcagGTATTCGACGGCCACAATGGCGTGTCGGCGGCGGTGTTCAGCAAGGAGAAA
EST: gi|50332586|gb|CO527712.1|CO527712
EST:     ACTGCCTCCGCGTCCCCGGAGACCCTTCCTCCTCTTTCTCCGTCTTCGCT                         GTATTCGACGGCCACAATGGCGTGTCGGCGGCGGTGTTCAGCAAGGAGAAA
genomic: ACTGCCTCCGCGTCCCCGGAGACCCTTCCTCCTCTTTCTCCGTCTTCGCTgtaggcccac ... cggttcgcagGTATTCGACGGCCACAATGGCGTGTCGGCGGCGGTGTTCAGCAAGGAGAAA
EST: gi|71773439|gb|DR971341.1|DR971341
EST:     ACTGCCTCCGCGTCCCCGGAGACCCTTCCTCCTCTTTCTCCGTCTTCGCT                         GTATTCGACGGCCACAATGGCGTGTCGGCGGCGGTGTTCAGCAAGGAGAAA
genomic: ACTGCCTCCGCGTCCCCGGAGACCCTTCCTCCTCTTTCTCCGTCTTCGCTgtaggcccac ... cggttcgcagGTATTCGACGGCCACAATGGCGTGTCGGCGGCGGTGTTCAGCAAGGAGAAA
EST: gi|148995556|gb|EE034750.2|EE034750
EST:     ACTGCCTCCGCGTCCCCGGAGACCCTTCCTCCTCTTTCTCCGTCTTCGCT                         GTATTCGACGGCCACAATGGCGTGTCGGCGGCGGTGTTCAGCAAGGAGAAA
genomic: ACTGCCTCCGCGTCCCCGGAGACCCTTCCTCCTCTTTCTCCGTCTTCGCTgtaggcccac ... cggttcgcagGTATTCGACGGCCACAATGGCGTGTCGGCGGCGGTGTTCAGCAAGGAGAAA
EST: gi|211035345|gb|FL198980.1|FL198980
EST:     ACTGCCTCCGCGTCCCCGGAGACCCTTCCTCCTCTTTCTCCGTCTTCGCT                         GTATTCGACGGCCA
genomic: ACTGCCTCCGCGTCCCCGGAGACCCTTCCTCCTCTTTCTCCGTCTTCGCTgtaggcccac ... cggttcgcagGTATTCGACGGCCA
EST: gi|89106849|gb|DY577066.1|DY577066
EST:     ACTGCCTCCGCGTCCCCGGAGACCCTTCTTCCTCTTTCTCCGTCTTCGCT                         GTATTCGACGGCCACAATGGCGTGTCGGCGGCGGTGTTCAGCAAGGAGAAA
genomic: ACTGCCTCCGCGTCCCCGGAGACCCTTCCTCCTCTTTCTCCGTCTTCGCTgtaggcccac ... cggttcgcagGTATTCGACGGCCACAATGGCGTGTCGGCGGCGGTGTTCAGCAAGGAGAAA
EST: gi|211037785|gb|FL198990.1|FL198990
EST:     ACTGCCTCCGCGTCCCCGGAGACCCTTCCTCCTCTTTCTCCGTCTTCGCT                         GTATTCGACGGCCACAATGGCGTGTCGGCGGCGGTGTT
genomic: ACTGCCTCCGCGTCCCCGGAGACCCTTCCTCCTCTTTCTCCGTCTTCGCTgtaggcccac ... cggttcgcagGTATTCGACGGCCACAATGGCGTGTCGGCGGCGGTGTT
EST: gi|71428998|gb|DR810048.1|DR810048
EST:     ACTGCCTCCGCGTCCCCGGAGACCCTTCCTCCTCTTTCTCCGTCTTCGCT                         GTATTCGACGGCCACAATGGCGTGTCGGCGGCGGTGTTCAGCAAGGAGAAA
genomic: ACTGCCTCCGCGTCCCCGGAGACCCTTCCTCCTCTTTCTCCGTCTTCGCTgtaggcccac ... cggttcgcagGTATTCGACGGCCACAATGGCGTGTCGGCGGCGGTGTTCAGCAAGGAGAAA
EST: gi|71438441|gb|DR819491.1|DR819491
EST:     ACTGCCTCCGCGTCCCCGGAGACCCTTCCTCCTCTTTCTCCGTCTTCGCT                         GTATTCGACGGCCACAATGGCGTGTCGGCGGCGGTGTTCAGCAAGGAGAAA
genomic: ACTGCCTCCGCGTCCCCGGAGACCCTTCCTCCTCTTTCTCCGTCTTCGCTgtaggcccac ... cggttcgcagGTATTCGACGGCCACAATGGCGTGTCGGCGGCGGTGTTCAGCAAGGAGAAA
EST: gi|78123111|gb|DV541495.1|DV541495
EST:     ACTGCCTCCGCGTCCCCGGAGACCCTTCCTCCTCTTTCTCCGTCTTCGCT                         GTATTCGACGGCCACAATGGCGTGTCGGCGGCGGTGTTCAGCAAGGAGAAA
genomic: ACTGCCTCCGCGTCCCCGGAGACCCTTCCTCCTCTTTCTCCGTCTTCGCTgtaggcccac ... cggttcgcagGTATTCGACGGCCACAATGGCGTGTCGGCGGCGGTGTTCAGCAAGGAGAAA
EST: gi|67032963|gb|CO461712.1|CO461712
EST:     ACTGCCTCCGCGTCCCCGGAGACCCTTCCTCCTCTTTCTCCGTCTTCGCT                         GTATTCGACGGCCACAATGGCGTGTCGGCGGCGGTGTTCAGCAAGGAGAAA
genomic: ACTGCCTCCGCGTCCCCGGAGACCCTTCCTCCTCTTTCTCCGTCTTCGCTgtaggcccac ... cggttcgcagGTATTCGACGGCCACAATGGCGTGTCGGCGGCGGTGTTCAGCAAGGAGAAA
EST: gi|211037782|gb|FL198987.1|FL198987
EST:     ACTGCCTCCGCGTCCCCGGAGACCCTTCCTCCTCTTTCTCCGTCTTCGCT                         GTATTCGACGGCCACAATGGCGTGTCGGCGGCGGTGTTCAGCAGGGAGAAA
genomic: ACTGCCTCCGCGTCCCCGGAGACCCTTCCTCCTCTTTCTCCGTCTTCGCTgtaggcccac ... cggttcgcagGTATTCGACGGCCACAATGGCGTGTCGGCGGCGGTGTTCAGCAAGGAGAAA
EST: gi|149079564|gb|EE168552.2|EE168552
EST:     ACTGCCTCCGCGTCCCCGGAGACCCTTCCTCCTCTTTCTCCGTCTTCGCT                         GTATTCGACGGCCACAATGGCGTGTCGGCGGCGGTGTTCAGCAAGGAGAAA
genomic: ACTGCCTCCGCGTCCCCGGAGACCCTTCCTCCTCTTTCTCCGTCTTCGCTgtaggcccac ... cggttcgcagGTATTCGACGGCCACAATGGCGTGTCGGCGGCGGTGTTCAGCAAGGAGAAA
EST: gi|94472234|gb|EB701192.1|EB701192
EST:     ACTGCCTCCGCGTCCCCGGAGACCCTTCCTCCTCTTTCTCCGTCTTCGCT                         GTATTCGACGGCCACAATGGCGTGTCGGCGGCGGTGTTCAGCAAGGAGAAA
genomic: ACTGCCTCCGCGTCCCCGGAGACCCTTCCTCCTCTTTCTCCGTCTTCGCTgtaggcccac ... cggttcgcagGTATTCGACGGCCACAATGGCGTGTCGGCGGCGGTGTTCAGCAAGGAGAAA
EST: gi|149045413|gb|EE047836.2|EE047836
EST:     ACTGCCTCCGCGTCCCCGGAGACCCTTCCTCCTCTTTCTCCGTCTTCGCT                         GTATTCGACGGCCACAATGGCGTGTCGGCGGCGGTGTTCAGCAAGGAGAAA
genomic: ACTGCCTCCGCGTCCCCGGAGACCCTTCCTCCTCTTTCTCCGTCTTCGCTgtaggcccac ... cggttcgcagGTATTCGACGGCCACAATGGCGTGTCGGCGGCGGTGTTCAGCAAGGAGAAA
EST: gi|211035348|gb|FL198983.1|FL198983
EST:     ACTGCCTCCGCGTCCCCGGAGACCCTTCCTCCTCTTTCTCCGTCTTCGCT                         GTATTCGACGGTCACAATGGCGTGTC
genomic: ACTGCCTCCGCGTCCCCGGAGACCCTTCCTCCTCTTTCTCCGTCTTCGCTgtaggcccac ... cggttcgcagGTATTCGACGGCCACAATGGCGTGTC
EST: gi|101394557|gb|EB819213.1|EB819213
EST:     ACTGCCTCCGCGTCCCCGGAGACCCTTCCTCCTCTTTCTCCGTCTTCGCT                         GTATTCGACGGCCACAATGGCGTGTCGGCGGCGGTGTTCAGCAAGGAGAAA
genomic: ACTGCCTCCGCGTCCCCGGAGACCCTTCCTCCTCTTTCTCCGTCTTCGCTgtaggcccac ... cggttcgcagGTATTCGACGGCCACAATGGCGTGTCGGCGGCGGTGTTCAGCAAGGAGAAA
EST: gi|74233458|gb|DT641372.1|DT641372
EST:     ACTGCCTCCGCGTCCCCGGAGACCCTTCCTCCTCTTTCTCCGTCTTCGCT                         GTATTCGACGGCCACAATGGCGTGTCGGCGGCGGTGTTCAGCAAGGAGAAA
genomic: ACTGCCTCCGCGTCCCCGGAGACCCTTCCTCCTCTTTCTCCGTCTTCGCTgtaggcccac ... cggttcgcagGTATTCGACGGCCACAATGGCGTGTCGGCGGCGGTGTTCAGCAAGGAGAAA
EST: gi|71448151|gb|DR829201.1|DR829201
EST:     ACTGCCTCCGCGTCCCCGGAGACCCTTCCTCCTCTTTCTCCGTCTTCGCT                         GTATTCGACGGCCACAATGGCGTGTCGGCGGCGGTGTTCAGCAAGGAGAAA
genomic: ACTGCCTCCGCGTCCCCGGAGACCCTTCCTCCTCTTTCTCCGTCTTCGCTgtaggcccac ... cggttcgcagGTATTCGACGGCCACAATGGCGTGTCGGCGGCGGTGTTCAGCAAGGAGAAA
EST: gi|21843276|gb|BQ703857.1|BQ703857
EST:     ACTGCCTCCGCGTCCCCGGAGACCCTTCTTCCTCTTTCTCCGTCTTCGCT                         GTATTCGACGGCCACAATGGCGTGTCGGCGGCGGTGTTCAGCAAGGAGAAA
genomic: ACTGCCTCCGCGTCCCCGGAGACCCTTCCTCCTCTTTCTCCGTCTTCGCTgtaggcccac ... cggttcgcagGTATTCGACGGCCACAATGGCGTGTCGGCGGCGGTGTTCAGCAAGGAGAAA
EST: gi|211035346|gb|FL198981.1|FL198981
EST:     ACTGCCTCCGCGTCCCCGGAGACCCTTCCTCCTCTTTCTCCGTCTTCGCT                         GTATTCGACGGCCACAATGGCGTGTCGGC
genomic: ACTGCCTCCGCGTCCCCGGAGACCCTTCCTCCTCTTTCTCCGTCTTCGCTgtaggcccac ... cggttcgcagGTATTCGACGGCCACAATGGCGTGTCGGC
EST: gi|211037780|gb|FL198985.1|FL198985
EST:     ACTGCCTCCGCGTCCCCGGAGACCCTTCCTCCTCTTTCTCCGTCTTCGCT                         GTATTCGACGGTCACAATGGCGTGTCGG
genomic: ACTGCCTCCGCGTCCCCGGAGACCCTTCCTCCTCTTTCTCCGTCTTCGCTgtaggcccac ... cggttcgcagGTATTCGACGGCCACAATGGCGTGTCGG
EST: gi|211035335|gb|FL198970.1|FL198970
EST:     ACTGCCTCCGCGTCCCCGGAGACCCTTCCTCCTCTTTCTCCGTCTTCGCT                         GTATTCGACGGCCACAATGGCGTGTCGGCGGCGG
genomic: ACTGCCTCCGCGTCCCCGGAGACCCTTCCTCCTCTTTCTCCGTCTTCGCTgtaggcccac ... cggttcgcagGTATTCGACGGCCACAATGGCGTGTCGGCGGCGG
EST: gi|149108127|gb|EE292476.2|EE292476
EST:     ACTGCCTCCGCGTCCCCGGAGACCCTTCCTCCTCTTTCTCCGTCTTCGCT                         GTATTCGACGGCCACAATGGCGTGTCGGCGGCGGTGTTCAGCAAGGAGAAA
genomic: ACTGCCTCCGCGTCCCCGGAGACCCTTCCTCCTCTTTCTCCGTCTTCGCTgtaggcccac ... cggttcgcagGTATTCGACGGCCACAATGGCGTGTCGGCGGCGGTGTTCAGCAAGGAGAAA
EST: gi|211037783|gb|FL198988.1|FL198988
EST:     ACTGCCTCCGCGTCCCCGGAGACCCTTCCTCCTCTTTCTCCGTCTTCGCT                         GTATTCGACGGCCACAATGGCGTGTCGGCGGCGGTGTTCAGCAAGGAGAAA
genomic: ACTGCCTCCGCGTCCCCGGAGACCCTTCCTCCTCTTTCTCCGTCTTCGCTgtaggcccac ... cggttcgcagGTATTCGACGGCCACAATGGCGTGTCGGCGGCGGTGTTCAGCAAGGAGAAA
EST: gi|211035337|gb|FL198972.1|FL198972
EST:     ACTGCCTCCGCGTCCCCGGAGACCCTTCCTCCTCTTTCTCCGTCTTCGCT                         GTATTCGACGGTCACAATGGCGTGTCGGC
genomic: ACTGCCTCCGCGTCCCCGGAGACCCTTCCTCCTCTTTCTCCGTCTTCGCTgtaggcccac ... cggttcgcagGTATTCGACGGCCACAATGGCGTGTCGGC
EST: gi|211035344|gb|FL198979.1|FL198979
EST:     ACTGCCTCCGCGTCCCCGGAGACCCTTCCTCCTCTTTCTCCGTCTTCGCT                         GTATTCGACGGTCACAATGGCGTGTCGGCGGCGGTGTTCAGCAAGGAGAAA
genomic: ACTGCCTCCGCGTCCCCGGAGACCCTTCCTCCTCTTTCTCCGTCTTCGCTgtaggcccac ... cggttcgcagGTATTCGACGGCCACAATGGCGTGTCGGCGGCGGTGTTCAGCAAGGAGAAA
EST: gi|71323567|gb|DR798450.1|DR798450
EST:     ACTGCCTCCGCGTCCCCGGAGACCCTTCCTCCTCTTTCTCCGTCTTCGCT                         GTATTCGACGGCCACAATGGCGTGTCGGCGGCGGTGTTCAGCAAGGAGAAA
genomic: ACTGCCTCCGCGTCCCCGGAGACCCTTCCTCCTCTTTCTCCGTCTTCGCTgtaggcccac ... cggttcgcagGTATTCGACGGCCACAATGGCGTGTCGGCGGCGGTGTTCAGCAAGGAGAAA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CCACTCTGGCTTCGCCAAGCGCGGCGAGGACTACTTCCTCGTCAAGCCCGACTGCCTCCGCGTCCCCGGAGACCCTTCCTCCTCTTTCTCCGTCTTCGCTgtaggcccacttttccccctaagatattcttttggtgtctcgtttgggttcggtgatgtgatggtctgtttgtttggtttgacggatctgcggttcgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC