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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGAGGAAGTGTTCCACCTGCCACCAATTCTCGTCTCTCACCTCTATCACATGAACCGGCTGATTTCTACAATGTGGACATTCCTCTCGACTCATCAAAGgtacttataatctctttccatctggatcactgcacaattgaaccaaattacatttctgagaacacttcccattgagtaaaaaaaaagagttaacgagctt...

Basic information

species Zea mays
transcript GRMZM2G174730_T01
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G174730_T01 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os05g42330.2 (Oryza sativa), 5'ss of exon 2
GGAGGAAGTGTTCCACCTGCCACCAATTCTCGTCTCTCACCTCTATCACATGAACCGGCTGATTTCTACAATGTGGACATTCCTCTCGACTCATCAAAGgtacttataatctctttccatctggatcactgcacaattgaaccaaattacatttctgagaacacttcccattgagtaaaaaaaaagagttaacgagctt----------
|||||||||||||| ||||||| ||||||||| ||| ||||||| || ||||| || |||||||| |||||||||||||||||||| ||||| || ||||||| |  |||  | || ||| |  || |  | |    || ||    ||  | || ||||||   |    ||  | ||||||  |    |    ||||||          
GGAGGAAGTGTTCCTCCTGCCAACAATTCTCGACTCCCACCTCTCTCCCATGAGCCAGCTGATTTTTACAATGTGGACATTCCTCTTGACTCGTCTAAGgtacatgcaattccatttcatgttcattatcgta----tggac----ttctagttttgagaatgttat--atccactaaaaactagtgttatttgagcttcttgctgtca
















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|149076952|gb|EE165608.2|EE165608
EST:     ATGAACCGGCTGATTTCTACAATGTGGACATTCCTCTCGACTCATCAAAG                         GATCTGAAGAAAAAGGAGAAAGAACTCCAGGCTATGGAGGCTGAGCTAAAC
genomic: ATGAACCGGCTGATTTCTACAATGTGGACATTCCTCTCGACTCATCAAAGgtacttataa ... tgatatttagGATCTGAAGAAAAAGGAGAAAGAACTCCAGGCTATGGAGGCTGAGCTAAAC
EST: gi|211455821|gb|FL370764.1|FL370764
EST:     ATGAACCGGCTGATTTCTACAATGTGGACATTCCTCTCGACTCATCAAAG                         GATCTGAAGAAAAAGGAGAAAGAACTCCAGGCTATGGAGGCTGAGCTAAAC
genomic: ATGAACCGGCTGATTTCTACAATGTGGACATTCCTCTCGACTCATCAAAGgtacttataa ... tgatatttagGATCTGAAGAAAAAGGAGAAAGAACTCCAGGCTATGGAGGCTGAGCTAAAC
EST: gi|211251918|gb|FL397021.1|FL397021
EST:     ATGAACCGGCTGATTTCTACAATGTGGACATTCCTCTCGACTCATCAAAG                         GATCTGAAGAAAAAGGAGAAAGAACTCCAGGCTATGGAGGCTGAGCTAAAC
genomic: ATGAACCGGCTGATTTCTACAATGTGGACATTCCTCTCGACTCATCAAAGgtacttataa ... tgatatttagGATCTGAAGAAAAAGGAGAAAGAACTCCAGGCTATGGAGGCTGAGCTAAAC
EST: gi|31353834|gb|CD438191.1|CD438191
EST:     ATGAACCGGCTGATTTCTACAATGTGGACATTCCTCTCGACTCATCAAAG                         GATCTGAAGAAAAAGGAGAAAGAACTCCAGGCTATGGAGGCTGAGCTAAAC
genomic: ATGAACCGGCTGATTTCTACAATGTGGACATTCCTCTCGACTCATCAAAGgtacttataa ... tgatatttagGATCTGAAGAAAAAGGAGAAAGAACTCCAGGCTATGGAGGCTGAGCTAAAC
EST: gi|211137749|gb|FL292364.1|FL292364
EST:     ATGAACCGGCTGATTTCTACAATGTGGACATTCCTCTCGACTCATCAAAG                         GATCTGAAGAAAAAGGAGAAAGAACTCCAGGCTATGGAGGCTGAGCTAAAC
genomic: ATGAACCGGCTGATTTCTACAATGTGGACATTCCTCTCGACTCATCAAAGgtacttataa ... tgatatttagGATCTGAAGAAAAAGGAGAAAGAACTCCAGGCTATGGAGGCTGAGCTAAAC
EST: gi|211138691|gb|FL292374.1|FL292374
EST:     ATGAACCGGCTGATTTCTACAATGTGGACATTCCTCTCGACTCATCAAAG                         GATCTGAAGAAAAAGGAGAAAGAACTCCAGGCTATGGAGGCTGAGCTAAAC
genomic: ATGAACCGGCTGATTTCTACAATGTGGACATTCCTCTCGACTCATCAAAGgtacttataa ... tgatatttagGATCTGAAGAAAAAGGAGAAAGAACTCCAGGCTATGGAGGCTGAGCTAAAC
EST: gi|211137750|gb|FL292365.1|FL292365
EST:     ATGAACCGGCTGATTTCTACAATGTGGACATTCCTCTCGACTCATCAAAG                         GATCTGAAGAAAAAGGAGAAAGA
genomic: ATGAACCGGCTGATTTCTACAATGTGGACATTCCTCTCGACTCATCAAAGgtacttataa ... tgatatttagGATCTGAAGAAAAAGGAGAAAGA
EST: gi|211198979|gb|FL379473.1|FL379473
EST:     AATGTGGACATTCCTCTCGACTCATCAAAG                         GATCTGAAGAAAAAGGAGAAAGAACTCCAGGCTATGGAGGCTGAGCTAAAC
genomic: AATGTGGACATTCCTCTCGACTCATCAAAGgtacttataa ... tgatatttagGATCTGAAGAAAAAGGAGAAAGAACTCCAGGCTATGGAGGCTGAGCTAAAC
EST: gi|211039428|gb|FL384648.1|FL384648
EST:     ATGAACCGGCTGATTTCTACAATGTGGACATTCCTCTCGACTCATCAAAG                         GATCTGAAGAAAAAGGAGAAAGAACTCCAGGCTATGGAGGCTGAGCTAAAC
genomic: ATGAACCGGCTGATTTCTACAATGTGGACATTCCTCTCGACTCATCAAAGgtacttataa ... tgatatttagGATCTGAAGAAAAAGGAGAAAGAACTCCAGGCTATGGAGGCTGAGCTAAAC
EST: gi|91876331|gb|EB406288.1|EB406288
EST:     ATGAACCGGCTGATTTCTACAATGTGGACATTCCTCTCGACTCATCAAAG                         GATCTGAAGAAAAAGGAGAAAGAACTCCAGGCTATGGAGG
genomic: ATGAACCGGCTGATTTCTACAATGTGGACATTCCTCTCGACTCATCAAAGgtacttataa ... tgatatttagGATCTGAAGAAAAAGGAGAAAGAACTCCAGGCTATGGAGG
EST: gi|211501973|gb|FL392126.1|FL392126
EST:     ATGAACCGGCTGATTTCTACAATGTGGACATTCCTCTCGACTCATCAAAG                         GATCTGAAGAAAAAGGAGAAAGAACTCCAGGCTATGGAGGCTGAGCTAAAC
genomic: ATGAACCGGCTGATTTCTACAATGTGGACATTCCTCTCGACTCATCAAAGgtacttataa ... tgatatttagGATCTGAAGAAAAAGGAGAAAGAACTCCAGGCTATGGAGGCTGAGCTAAAC
EST: gi|149069546|gb|EE157919.2|EE157919
EST:     ATGAACCGGCTGATTTCTACAATGTGGACATTCCTCTCGACTCATCAAAG                         GATCTGAAGAAAAAGGAGAAAGAACTCCAGGCTATGGAGGCTGAGCTAAAC
genomic: ATGAACCGGCTGATTTCTACAATGTGGACATTCCTCTCGACTCATCAAAGgtacttataa ... tgatatttagGATCTGAAGAAAAAGGAGAAAGAACTCCAGGCTATGGAGGCTGAGCTAAAC
EST: gi|76927277|gb|DV171213.1|DV171213
EST:     ATGAACCGGCTGATTTCTACAATGTGGACATTCCTCTCGACTCATCAAAG                         GATCTGAAGAAAAAGGAGAAAGAACTCCAGGCTATGGAGGCTGAGCTAAAC
genomic: ATGAACCGGCTGATTTCTACAATGTGGACATTCCTCTCGACTCATCAAAGgtacttataa ... tgatatttagGATCTGAAGAAAAAGGAGAAAGAACTCCAGGCTATGGAGGCTGAGCTAAAC
EST: gi|211138685|gb|FL292368.1|FL292368
EST:     ATGAACCGGCTGATTTCTACAATGTGGACATTCCTCTCGACTCATCAAAG                         GATCTGAAGAAAAAGGAGAAAGAACTCCAGGCTATGGAGGCTGAGCTAAAC
genomic: ATGAACCGGCTGATTTCTACAATGTGGACATTCCTCTCGACTCATCAAAGgtacttataa ... tgatatttagGATCTGAAGAAAAAGGAGAAAGAACTCCAGGCTATGGAGGCTGAGCTAAAC
EST: gi|211138688|gb|FL292371.1|FL292371
EST:     ATGAACCGGCTGATTTCTACAATGTGGACATTCCTCTCGACTCATCAAAG                         GATCTGAAGAAAAAGGAGAAAGAACTCCAGGCTATGGAGGCTGAGCTAAAC
genomic: ATGAACCGGCTGATTTCTACAATGTGGACATTCCTCTCGACTCATCAAAGgtacttataa ... tgatatttagGATCTGAAGAAAAAGGAGAAAGAACTCCAGGCTATGGAGGCTGAGCTAAAC
EST: gi|211122269|gb|FL373644.1|FL373644
EST:     ATGAACCGGCTGATTTCTACAATGTGGACATTCCTCTCGACTCATCAAAG                         GATCTGAAGAAAAAGGAGAAAGAACTCCAGGCTATGGAGGCTGAGCTAAAC
genomic: ATGAACCGGCTGATTTCTACAATGTGGACATTCCTCTCGACTCATCAAAGgtacttataa ... tgatatttagGATCTGAAGAAAAAGGAGAAAGAACTCCAGGCTATGGAGGCTGAGCTAAAC
EST: gi|211138687|gb|FL292370.1|FL292370
EST:     ATGAACCGGCTGATTTCTACAATGTGGACATTCCTCTCGACTCATCAAAG                         GATCTGAAGAAAAAGGAGAAAGAACTCCAGGCTATGGAGGCTGAGCTAAAC
genomic: ATGAACCGGCTGATTTCTACAATGTGGACATTCCTCTCGACTCATCAAAGgtacttataa ... tgatatttagGATCTGAAGAAAAAGGAGAAAGAACTCCAGGCTATGGAGGCTGAGCTAAAC
EST: gi|76289053|gb|DV028621.1|DV028621
EST:     ATGAACCGGCTGATTTCTACAATGTGGACATTCCTCTCGACTCATCAAAG                         GATCTGAAGAAAAAGGAGAAAGAACTCCAGGCTATGGAGGCTGAGCTAAAC
genomic: ATGAACCGGCTGATTTCTACAATGTGGACATTCCTCTCGACTCATCAAAGgtacttataa ... tgatatttagGATCTGAAGAAAAAGGAGAAAGAACTCCAGGCTATGGAGGCTGAGCTAAAC
EST: gi|91872788|gb|EB402745.1|EB402745
EST:     ATGAACCGGCTGATTTCTACAATGTGGACATTCCTCTCGACTCATCAAAG                         GATCTGAAGAAAAAGGAGAAAGAACTCCAGGCTTTGGAGGCTGAGCTAAAC
genomic: ATGAACCGGCTGATTTCTACAATGTGGACATTCCTCTCGACTCATCAAAGgtacttataa ... tgatatttagGATCTGAAGAAAAAGGAGAAAGAACTCCAGGCTATGGAGGCTGAGCTAAAC
EST: gi|71322127|gb|DR797759.1|DR797759
EST:     ATGAACCGGCTGATTTCTACAATGGGGACATTCCTCTCGACTCATCAAAG                         GATCTGAAGAAAAAGGAGAAAGAACTCCAGGCTATGGAGGCTGAGCTAAAC
genomic: ATGAACCGGCTGATTTCTACAATGTGGACATTCCTCTCGACTCATCAAAGgtacttataa ... tgatatttagGATCTGAAGAAAAAGGAGAAAGAACTCCAGGCTATGGAGGCTGAGCTAAAC
EST: gi|211228158|gb|FL414420.1|FL414420
EST:     TGAACCMGGCTGATTTCTACAATGTGGACATTCCTCTCGACTCATCAAAG                         GATCTGAAGAAAAAGGAGAAAGAACTCCAGGCTATGGAGGCTGAGCTAAAC
genomic: TGAACC-GGCTGATTTCTACAATGTGGACATTCCTCTCGACTCATCAAAGgtacttataa ... tgatatttagGATCTGAAGAAAAAGGAGAAAGAACTCCAGGCTATGGAGGCTGAGCTAAAC
EST: gi|149079646|gb|EE168643.2|EE168643
EST:     ATGAACCGGCTGATTTCTACAATGTGGACATTCCTCTCGACTCATCAAAG                         GATCTGAAGAAAAAGGAGAAAGAACTCCAGGCTATGGAGGCTGAGCTAAAC
genomic: ATGAACCGGCTGATTTCTACAATGTGGACATTCCTCTCGACTCATCAAAGgtacttataa ... tgatatttagGATCTGAAGAAAAAGGAGAAAGAACTCCAGGCTATGGAGGCTGAGCTAAAC
EST: gi|211137751|gb|FL292366.1|FL292366
EST:     ATGAACCGGCTGATTTCTACAATGTGGACATTCCTCTCGACTCATCAAAG                         GATCTGAAGAAAAAGGAGAAAGA
genomic: ATGAACCGGCTGATTTCTACAATGTGGACATTCCTCTCGACTCATCAAAGgtacttataa ... tgatatttagGATCTGAAGAAAAAGGAGAAAGA
EST: gi|78081465|gb|DV509877.1|DV509877
EST:     ATGAACCGGCTGATTTCTACAATGTGGACATTCCTCTCGACTCATCAAAG                         GATCTGAAGAAAAAGGAGAAAGAACTCCAGGCTATGGAGGCTGAGCTAAAC
genomic: ATGAACCGGCTGATTTCTACAATGTGGACATTCCTCTCGACTCATCAAAGgtacttataa ... tgatatttagGATCTGAAGAAAAAGGAGAAAGAACTCCAGGCTATGGAGGCTGAGCTAAAC
EST: gi|211138689|gb|FL292372.1|FL292372
EST:     ATGAACCGGCTGATTTCTACAATGTGGACATTCCTCTCGACTCATCAAAG                         GATCTGAAGAAAAAGGAGAAAGA
genomic: ATGAACCGGCTGATTTCTACAATGTGGACATTCCTCTCGACTCATCAAAGgtacttataa ... tgatatttagGATCTGAAGAAAAAGGAGAAAGA
EST: gi|211138692|gb|FL292375.1|FL292375
EST:     ATGAACCGGCTGATTTCTACAATGTGGACATTCCTCTCGACTCATCAAAG                         GATCTGAAGAAAAAGGAGAAAGA
genomic: ATGAACCGGCTGATTTCTACAATGTGGACATTCCTCTCGACTCATCAAAGgtacttataa ... tgatatttagGATCTGAAGAAAAAGGAGAAAGA
EST: gi|211130112|gb|FL389065.1|FL389065
EST:     ATGAACCGGCTGATTTCTACAATGTGGACATTCCTCTCGACTCATCAAAG                         GATCTGAAGAAAAAGGAGAAAGAACTCCAGGCTATGGAGGCTGAGCTAAAC
genomic: ATGAACCGGCTGATTTCTACAATGTGGACATTCCTCTCGACTCATCAAAGgtacttataa ... tgatatttagGATCTGAAGAAAAAGGAGAAAGAACTCCAGGCTATGGAGGCTGAGCTAAAC
EST: gi|211138694|gb|FL292377.1|FL292377
EST:     ATGAACCGGCTGATTTCTACAATGTGGACATTCCTCTCGACTCATCAAAG                         GATCTGAAGAAAAAGGAGAAAGA
genomic: ATGAACCGGCTGATTTCTACAATGTGGACATTCCTCTCGACTCATCAAAGgtacttataa ... tgatatttagGATCTGAAGAAAAAGGAGAAAGA
EST: gi|78112246|gb|DV530640.1|DV530640
EST:     ATGAACCGGCTGATTTCTACAATGTGGACATTCCTCTCGACTCATCAAAG                         GATCTGAAGAAAAAGGAGAAAGAACTCCAGGCTATGGAGGCTGAGCTAAAC
genomic: ATGAACCGGCTGATTTCTACAATGTGGACATTCCTCTCGACTCATCAAAGgtacttataa ... tgatatttagGATCTGAAGAAAAAGGAGAAAGAACTCCAGGCTATGGAGGCTGAGCTAAAC
EST: gi|37417263|gb|CF646284.1|CF646284
EST:     ATGAACCGGCTGATTTCTACAATGTGGACATTCCTCTCGACTCATCAAAG                         GATCTGAAGAAAAAGGAGAAAGAACTCCAGGCTATGGAGGCTGAGCTAAAC
genomic: ATGAACCGGCTGATTTCTACAATGTGGACATTCCTCTCGACTCATCAAAGgtacttataa ... tgatatttagGATCTGAAGAAAAAGGAGAAAGAACTCCAGGCTATGGAGGCTGAGCTAAAC
EST: gi|211035296|gb|FL425638.1|FL425638
EST:     ATGAACCGGCTGATTTCTACAATGTGGACATTCCTCTCGACTCATCAAAG                         GATCTGAAGAAAAAGGAGAAAGAACTCCAGGCTATGGAGGCTGAGCTAAAC
genomic: ATGAACCGGCTGATTTCTACAATGTGGACATTCCTCTCGACTCATCAAAGgtacttataa ... tgatatttagGATCTGAAGAAAAAGGAGAAAGAACTCCAGGCTATGGAGGCTGAGCTAAAC
EST: gi|211138693|gb|FL292376.1|FL292376
EST:     ATGAACCGGCTGATTTCTACAATGTGGACATTCCTCTCGACTCATCAAAG                         GATCTGAAGAAAAAGGAGAAAGA
genomic: ATGAACCGGCTGATTTCTACAATGTGGACATTCCTCTCGACTCATCAAAGgtacttataa ... tgatatttagGATCTGAAGAAAAAGGAGAAAGA
EST: gi|211137579|gb|FL389525.1|FL389525
EST:     ATGAACCGGCTGATTTCTACAATGTGGACATTCCTCTCGACTCATCAAAG                         GATCTGAAGAAAAAGGAGAAAGAACTCCAGGCTATGGAGGCTGAGCTAAAC
genomic: ATGAACCGGCTGATTTCTACAATGTGGACATTCCTCTCGACTCATCAAAGgtacttataa ... tgatatttagGATCTGAAGAAAAAGGAGAAAGAACTCCAGGCTATGGAGGCTGAGCTAAAC
EST: gi|149104177|gb|EE289611.2|EE289611
EST:     ATGAACCGGCTGATTTCTACAATGTGGACATTCCTCTCGACTCATCAAAG                         GATCTGAAGAAAAAGGAGAAAGAACTCCAGGCTATGGAGGCTGAGCTAAAC
genomic: ATGAACCGGCTGATTTCTACAATGTGGACATTCCTCTCGACTCATCAAAGgtacttataa ... tgatatttagGATCTGAAGAAAAAGGAGAAAGAACTCCAGGCTATGGAGGCTGAGCTAAAC

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: 219

GGAGGAAGTGTTCCACCTGCCACCAATTCTCGTCTCTCACCTCTATCACATGAACCGGCTGATTTCTACAATGTGGACATTCCTCTCGACTCATCAAAGgtacttataa ... tgatatttagGATCTGAAGAAAAAGGAGAAAGAACTCCAGGCTATGGAGGCTGAGCTAAACAAAAGAGAACGG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 190

GGAGGAAGTGTTCCACCTGCCACCAATTCTCGTCTCTCACCTCTATCACATGAACCGGCTGATTTCTACAATGTGGACATTCCTCTCGACTCATCAAAGgtacttataa ... tgatatttagGATCTGAAGAAAAAGGAGAAAGAACTCCAGGCTATGGAGGCTGAGCTAAACAAAAGAGAACGG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 225

GGAGGAAGTGTTCCACCTGCCACCAATTCTCGTCTCTCACCTCTATCACATGAACCGGCTGATTTCTACAATGTGGACATTCCTCTCGACTCATCAAAGgtacttataa ... tgatatttagGATCTGAAGAAAAAGGAGAAAGAACTCCAGGCTATGGAGGCTGAGCTAAACAAAAGAGAACGG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 269

GGAGGAAGTGTTCCACCTGCCACCAATTCTCGTCTCTCACCTCTATCACATGAACCGGCTGATTTCTACAATGTGGACATTCCTCTCGACTCATCAAAGgtacttataa ... tgatatttagGATCTGAAGAAAAAGGAGAAAGAACTCCAGGCTATGGAGGCTGAGCTAAACAAAAGAGAACGG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGAGGAAGTGTTCCACCTGCCACCAATTCTCGTCTCTCACCTCTATCACATGAACCGGCTGATTTCTACAATGTGGACATTCCTCTCGACTCATCAAAGgtacttataatctctttccatctggatcactgcacaattgaaccaaattacatttctgagaacacttcccattgagtaaaaaaaaagagttaacgagctt

- - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGAT