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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAGACAAGTTCGAGGCTGTTGTGCCCTTCATGGGTGAATCTGTAACTGATGGAACTCTTGCTAACTTCTTAAAGAgtatgctctctctctccctctccctctccctctctctctctctctcccctccctgtgataacattttctttttttatacag

Basic information

species Zea mays
transcript GRMZM5G807639_T03
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G807639_T02 (Zea mays), 5'ss of exon 5
lower sequence: LOC_Os04g32330.1 (Oryza sativa), 5'ss of exon 5
GAGACAAGTTCGAGGCTGTTGTGCCCTTCATGGGTGAATCTGTAACTGATGGAACTCTTGCTAACTTCTTAAAGAgtatgctctctctctccctctccctctccctctctctc-tctctctcccctccctgtgataacattttctttttttatacag
||||| || | || |||||||| || |||||||||||||||||||||||||||||||||||||||||||| ||||||||| | |||||||| ||||| ||||| | | | | | ||    ||   | | |   || |   || ||||    ||||||
GAGACCAGGTTGAAGCTGTTGTCCCTTTCATGGGTGAATCTGTAACTGATGGAACTCTTGCTAACTTCTTGAAGAgtatgatttctctctctctctctctctcacacacacacatcaggttcatttgcttacaattaaccttccttta---atacag
















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|211347968|gb|FL368837.1|FL368837
EST:     CTTCATGGGTGAATCTGTAACTGATGGAACTCTTGCTAACTTCTTAAAGA                         AGCCTGGAGACAGAGTCGAGGCCGATGAACCCATAGCGCAGATTGAAACTG
genomic: CTTCATGGGTGAATCTGTAACTGATGGAACTCTTGCTAACTTCTTAAAGAgtatgctctc ... ttttatacagAGCCTGGAGACAGAGTCGAGGCCGATGAACCCATAGCGCAGATTGAAACTG
EST: gi|211126388|gb|FL388997.1|FL388997
EST:     CTTCATGGGTGAATCTGTAACTGATGGAACTCTTGCTAACTTCTTAAAGA                         AGCCTGGAGACAGAGTCGAGGCCGATGAACCCATAGCGC
genomic: CTTCATGGGTGAATCTGTAACTGATGGAACTCTTGCTAACTTCTTAAAGAgtatgctctc ... ttttatacagAGCCTGGAGACAGAGTCGAGGCCGATGAACCCATAGCGC
EST: gi|211511665|gb|FL408091.1|FL408091
EST:     CTTCATGGGTGAATCTGTAACTGATGGAACTCTTGCTAACTTCTTAAAGA                         -GCCTGGAGACAGAGTCGAGGCCGATGAACCCATAGCGCAGATTGAAACTG
genomic: CTTCATGGGTGAATCTGTAACTGATGGAACTCTTGCTAACTTCTTAAAGAgtatgctctc ... ttttatacagAGCCTGGAGACAGAGTCGAGGCCGATGAACCCATAGCGCAGATTGAAACTG
EST: gi|211042919|gb|FL416910.1|FL416910
EST:     CTTCATGGGTGAATCTGTAACTGATGGAACTCTTGCTAACTTCTTAAAGA                         AGC-TGGAGACAGAGTCGAGGCCGATGAAACCATAGCGCAGATTGAAACTG
genomic: CTTCATGGGTGAATCTGTAACTGATGGAACTCTTGCTAACTTCTTAAAGAgtatgctctc ... ttttatacagAGCCTGGAGACAGAGTCGAGGCCGATGAACCCATAGCGCAGATTGAAACTG
EST: gi|211011070|gb|FL374939.1|FL374939
EST:     CTTCATGGGTGAATCTGTAACTGATGGAACTCTTGCTAACTTCTTAAAGA                         AGCCTGGAGACAGAGTCGAGGCCGATGAACCCATAGCGCAGATTGAAACTG
genomic: CTTCATGGGTGAATCTGTAACTGATGGAACTCTTGCTAACTTCTTAAAGAgtatgctctc ... ttttatacagAGCCTGGAGACAGAGTCGAGGCCGATGAACCCATAGCGCAGATTGAAACTG
EST: gi|211150258|gb|FL395029.1|FL395029
EST:     CTTCATGGGTGAATCTGTAACTGATGGAACTCTTGCTAACTTCTTAAAGA                         AGCCTGGAGACAGAGTCGAGGCCGATGAACCCATAGCGCAGATTGAAACTG
genomic: CTTCATGGGTGAATCTGTAACTGATGGAACTCTTGCTAACTTCTTAAAGAgtatgctctc ... ttttatacagAGCCTGGAGACAGAGTCGAGGCCGATGAACCCATAGCGCAGATTGAAACTG
EST: gi|211479894|gb|FL423794.1|FL423794
EST:     CTTCATGGGTGAATCTGTAACTGATGGAACTCTTGCTAACTTCTTAAAGA                         AGCCTGGAGACAGAGTCGAGGCCGATGAACCCATAGCGCAGATTGAAACTG
genomic: CTTCATGGGTGAATCTGTAACTGATGGAACTCTTGCTAACTTCTTAAAGAgtatgctctc ... ttttatacagAGCCTGGAGACAGAGTCGAGGCCGATGAACCCATAGCGCAGATTGAAACTG
EST: gi|67025111|gb|CO453860.1|CO453860
EST:     CTTCATGGGTGAATCTGTAACTGATGGAACTCTTGCTAACTTCTTAAAGA                         AGCCTGGAGACAGAGTCGAGGCCGATGAACCCATAGCGCAGATTGAAACTG
genomic: CTTCATGGGTGAATCTGTAACTGATGGAACTCTTGCTAACTTCTTAAAGAgtatgctctc ... ttttatacagAGCCTGGAGACAGAGTCGAGGCCGATGAACCCATAGCGCAGATTGAAACTG
EST: gi|211137577|gb|FL389523.1|FL389523
EST:     CTTCATGGGTGAATCTGTAACTGATGGAACTCTTGCTAACTTCTTAAAGA                         AGCCTGGAGACAGAGTCGAGGCCGATGAACCCATAGCGCAGATTGAAACTG
genomic: CTTCATGGGTGAATCTGTAACTGATGGAACTCTTGCTAACTTCTTAAAGAgtatgctctc ... ttttatacagAGCCTGGAGACAGAGTCGAGGCCGATGAACCCATAGCGCAGATTGAAACTG
EST: gi|211461966|gb|FL427684.1|FL427684
EST:     CTTCATGGGTGAATCTGTAACTGATGGAACTCTTGCTAACTTCTTAAAGA                         AGCCTGGAGACAGAGTCGAGGCCGATGAACCCATAGCGCAGATTGAAACTG
genomic: CTTCATGGGTGAATCTGTAACTGATGGAACTCTTGCTAACTTCTTAAAGAgtatgctctc ... ttttatacagAGCCTGGAGACAGAGTCGAGGCCGATGAACCCATAGCGCAGATTGAAACTG
EST: gi|32862756|gb|CF002438.1|CF002438
EST:     CTTCATGGGTGAATCTGTAACTGATGGAACTCTTGCTAACTTCTTAAAGA                         AGCCTGGAGACAGAGTCGAGGCCGATGAACCCATAGCGCAGATTGAAACTG
genomic: CTTCATGGGTGAATCTGTAACTGATGGAACTCTTGCTAACTTCTTAAAGAgtatgctctc ... ttttatacagAGCCTGGAGACAGAGTCGAGGCCGATGAACCCATAGCGCAGATTGAAACTG
EST: gi|30306817|gb|CD001490.1|CD001490
EST:     CTTCATGGGTGAATCTGTAACTGATGGAACTCTTGCTAACTTCTTAAAGA                         AGCCTGGAGACAGAGTCGAGGCCGATGAACCCATAGCGCAGATTGAAACTG
genomic: CTTCATGGGTGAATCTGTAACTGATGGAACTCTTGCTAACTTCTTAAAGAgtatgctctc ... ttttatacagAGCCTGGAGACAGAGTCGAGGCCGATGAACCCATAGCGCAGATTGAAACTG
EST: gi|211518170|gb|FL380292.1|FL380292
EST:     CTTCATGGGTGAATCTGTAACTGATGGAACTCTTGCTAACTTCTTAAAGA                         AGCCTGGAGACAGAGTCGAGGCCGATGAACCCATAGCGCAGATTGAAACTG
genomic: CTTCATGGGTGAATCTGTAACTGATGGAACTCTTGCTAACTTCTTAAAGAgtatgctctc ... ttttatacagAGCCTGGAGACAGAGTCGAGGCCGATGAACCCATAGCGCAGATTGAAACTG
EST: gi|211494399|gb|FL426463.1|FL426463
EST:     TTCATGGGTGAATCTGTAACTGATGGAACTCTTGCTAACTTCTTAAAAGA                         AGCCTGGAGACAGAGTCGAGGCCGATGAACCCATAGCGCAGATTGAAACT
genomic: TTCATGGGTGAATCTGTAACTGATGGAACTCTTGCTAACTTCTTAAA-GAgtatgctctc ... ttttatacagAGCCTGGAGACAGAGTCGAGGCCGATGAACCCATAGCGCAGATTGAAACT
EST: gi|211418591|gb|FL407188.1|FL407188
EST:     CTTCATGGGTGAATCTGTAACTGATGGAACTCTTGCTAACTTCTTAAAGA                         AGCCTGGAGACAGAGTC
genomic: CTTCATGGGTGAATCTGTAACTGATGGAACTCTTGCTAACTTCTTAAAGAgtatgctctc ... ttttatacagAGCCTGGAGACAGAGTC
EST: gi|211490936|gb|FL402016.1|FL402016
EST:     CTTCATGGGTGAATCTGTAACTGATGGAACTCTTGCTAACTTCTTAAAGA                         AGCCTGGAGACAGAGTCGAGGCCGATGAACCCATAGCGCAGATTGAAACTG
genomic: CTTCATGGGTGAATCTGTAACTGATGGAACTCTTGCTAACTTCTTAAAGAgtatgctctc ... ttttatacagAGCCTGGAGACAGAGTCGAGGCCGATGAACCCATAGCGCAGATTGAAACTG
EST: gi|31349005|gb|CD433362.1|CD433362
EST:     CTTCATGGGTGAATCTGTAACTGATGGAACTCTTGCTAACTTCTTAAAGA                         AGCCTGGAGACAGAGTCGAGGCCGATGAACCCATAGCGCAGATTGAAACTG
genomic: CTTCATGGGTGAATCTGTAACTGATGGAACTCTTGCTAACTTCTTAAAGAgtatgctctc ... ttttatacagAGCCTGGAGACAGAGTCGAGGCCGATGAACCCATAGCGCAGATTGAAACTG
EST: gi|211157939|gb|FL380349.1|FL380349
EST:     CTTCATGGGTGAATCTGTAACTGATGGAACTCTTGCTAACTTCTTAAAGA                         AGCCTGGAGACAGAGTCGANGGCCGATGAACCCATAGCGCAGATTGAAACT
genomic: CTTCATGGGTGAATCTGTAACTGATGGAACTCTTGCTAACTTCTTAAAGAgtatgctctc ... ttttatacagAGCCTGGAGACAGAGTCGA-GGCCGATGAACCCATAGCGCAGATTGAAACT
EST: gi|28187901|gb|CB179511.1|CB179511
EST:     CTTCATGGGTGAATCTGTAACTGATGGAACTCTTGCTAACTTCTTAAAGA                         AGCCTGGAGACAGAGTCGAGGCCGATGAACCCATAGCGCAGATTGAAACTG
genomic: CTTCATGGGTGAATCTGTAACTGATGGAACTCTTGCTAACTTCTTAAAGAgtatgctctc ... ttttatacagAGCCTGGAGACAGAGTCGAGGCCGATGAACCCATAGCGCAGATTGAAACTG
EST: gi|211437186|gb|FL418966.1|FL418966
EST:     CTTCATGGGTGAATCTGTAACTGATGGAACTCTTGCTAACTTCTTAAAGA                         AGCCTGGAGACAGAGTCGRGGCCGATGAACCCATAGCGCAGATTGAWACTG
genomic: CTTCATGGGTGAATCTGTAACTGATGGAACTCTTGCTAACTTCTTAAAGAgtatgctctc ... ttttatacagAGCCTGGAGACAGAGTCGAGGCCGATGAACCCATAGCGCAGATTGAAACTG
EST: gi|37420219|gb|CF647798.1|CF647798
EST:     CTTCATGGGTGAATCTGTAACTGATGGAACTCTTGCTAACTTCTTAAAGA                         AGCCTGGAGACAGAGTCGAGGCCGATGAACCCATAGCGCAGATTGAAACTG
genomic: CTTCATGGGTGAATCTGTAACTGATGGAACTCTTGCTAACTTCTTAAAGAgtatgctctc ... ttttatacagAGCCTGGAGACAGAGTCGAGGCCGATGAACCCATAGCGCAGATTGAAACTG
EST: gi|93017175|gb|EB642695.1|EB642695
EST:     CTTCATGGGTGAATCTGTAACTGATGGAACTCTTGCTAACTTCTTAAAGA                         AGCCTGGAGACAGAGTCGAGGCCGATGAACCCATAGCGCAGATTGAAACTG
genomic: CTTCATGGGTGAATCTGTAACTGATGGAACTCTTGCTAACTTCTTAAAGAgtatgctctc ... ttttatacagAGCCTGGAGACAGAGTCGAGGCCGATGAACCCATAGCGCAGATTGAAACTG
EST: gi|211305586|gb|FL419218.1|FL419218
EST:     CTTCATGGGTGAATCTGTAACTGATGGAACTCTTGCTAACTTCTTAAAGA                         AGCCTGGAGACAGAGTCGAGGCCGATGAACCCATAGCGCAGATTGAAACTG
genomic: CTTCATGGGTGAATCTGTAACTGATGGAACTCTTGCTAACTTCTTAAAGAgtatgctctc ... ttttatacagAGCCTGGAGACAGAGTCGAGGCCGATGAACCCATAGCGCAGATTGAAACTG
EST: gi|211002857|gb|FL384096.1|FL384096
EST:     CTTCATGGGTGAATCTGTAACTGATGGAACTCTTGCTAACTTCTTAAAGA                         AGCCTGGAGACAGAGTCGAGGCCGATGAACCCATAGCGCAGATTGAAACTG
genomic: CTTCATGGGTGAATCTGTAACTGATGGAACTCTTGCTAACTTCTTAAAGAgtatgctctc ... ttttatacagAGCCTGGAGACAGAGTCGAGGCCGATGAACCCATAGCGCAGATTGAAACTG
EST: gi|211142865|gb|FL377125.1|FL377125
EST:     CTTCATGGGTGAATCTGTAACTGATGGAACTCTTGCTAACTTCTTAAAGA                         AGCCTGGAGACAGAGTCGAGGCCGATGAACCCATAGCGCAGATTGAAACTG
genomic: CTTCATGGGTGAATCTGTAACTGATGGAACTCTTGCTAACTTCTTAAAGAgtatgctctc ... ttttatacagAGCCTGGAGACAGAGTCGAGGCCGATGAACCCATAGCGCAGATTGAAACTG
EST: gi|211530093|gb|FL390761.1|FL390761
EST:     CTTCATGGGTGAATCTGTAACTGATGGAACTCTTGCTAACTTCTTAAAGA                         AGCCTGGAGACAGAGTCGAGGCCGATGAACCCATAGCGCAGATTGAAACTG
genomic: CTTCATGGGTGAATCTGTAACTGATGGAACTCTTGCTAACTTCTTAAAGAgtatgctctc ... ttttatacagAGCCTGGAGACAGAGTCGAGGCCGATGAACCCATAGCGCAGATTGAAACTG
EST: gi|211235901|gb|FL373720.1|FL373720
EST:     CTTCATGGGTGAATCTGTAACTGATGGAACTCTTGCTAACTTCTTAAAGA                         AGCCTGGAGACAGAGTCGAGGCCGATGAACCCATAGCGCAGATTGAAACTG
genomic: CTTCATGGGTGAATCTGTAACTGATGGAACTCTTGCTAACTTCTTAAAGAgtatgctctc ... ttttatacagAGCCTGGAGACAGAGTCGAGGCCGATGAACCCATAGCGCAGATTGAAACTG
EST: gi|211431976|gb|FL418926.1|FL418926
EST:     CTTCATGGGTGAATCTGTAACTGATGGAACTCTTGCTAACTTCTTAAAGA                         AGCCTGGAGACAGAGTCGAGGCCGATGAACCCATAGCGCAGATTGAAACTG
genomic: CTTCATGGGTGAATCTGTAACTGATGGAACTCTTGCTAACTTCTTAAAGAgtatgctctc ... ttttatacagAGCCTGGAGACAGAGTCGAGGCCGATGAACCCATAGCGCAGATTGAAACTG
EST: gi|211063833|gb|FL423073.1|FL423073
EST:     CTTCATGGGTGAATCTGTAACTGATGGAACTCTTGCTAACTTCTTAAAGA                         AGCCTGGAGACAGAGTCGAGGCCGATGAACCCATAGCGCAGATTGAAACTG
genomic: CTTCATGGGTGAATCTGTAACTGATGGAACTCTTGCTAACTTCTTAAAGAgtatgctctc ... ttttatacagAGCCTGGAGACAGAGTCGAGGCCGATGAACCCATAGCGCAGATTGAAACTG
EST: gi|211441962|gb|FL416333.1|FL416333
EST:     CTTCATGGGTGAATCTGTAACTGATGGAACTCTTGCTAACTTCTTAAAGA                         AGCCTGGAGACAGAGTCGANGGCCGATGAACCCATAGCGCAGATTGAAACT
genomic: CTTCATGGGTGAATCTGTAACTGATGGAACTCTTGCTAACTTCTTAAAGAgtatgctctc ... ttttatacagAGCCTGGAGACAGAGTCGA-GGCCGATGAACCCATAGCGCAGATTGAAACT
EST: gi|32834807|gb|CD974485.1|CD974485
EST:     CTTCATGGGTGAATCTGTAACTGATGGAACTCTTGCTAACTTCTTAAAGA                         AGCCTGGAGACAGAGTCGAGGCCGATGAACCCATAGCGCAGATTGAAACTG
genomic: CTTCATGGGTGAATCTGTAACTGATGGAACTCTTGCTAACTTCTTAAAGAgtatgctctc ... ttttatacagAGCCTGGAGACAGAGTCGAGGCCGATGAACCCATAGCGCAGATTGAAACTG
EST: gi|211094733|gb|FL379398.1|FL379398
EST:     CTTCATGGGTGAATCTGTAACTGATGGAACTCTTGCTAACTTCTTAAAGA                         AGCCTGGAGACAGAGTCGAGGCCGATGAACCCATAGCGCAGATTGAAACTG
genomic: CTTCATGGGTGAATCTGTAACTGATGGAACTCTTGCTAACTTCTTAAAGAgtatgctctc ... ttttatacagAGCCTGGAGACAGAGTCGAGGCCGATGAACCCATAGCGCAGATTGAAACTG
EST: gi|67031724|gb|CO460473.1|CO460473
EST:     CTTCATGGGTGAATCTGTAACTGATGGAACTCTTGCTAACTTCTTAAAGA                         AGCCTGGAGACAGAGTCGAGGCCGATGAACCCATAGCGCAGATTGAAACTG
genomic: CTTCATGGGTGAATCTGTAACTGATGGAACTCTTGCTAACTTCTTAAAGAgtatgctctc ... ttttatacagAGCCTGGAGACAGAGTCGAGGCCGATGAACCCATAGCGCAGATTGAAACTG
EST: gi|211539307|gb|FL400264.1|FL400264
EST:     CTTCATGGGTGAATCTGTAACTGATGGAACTCTTGCTAACTTCTTAAAGA                         AGCCTGGAGACAGAGTCGAGGCCGATGAACCCATAGCGCAGATTGAAACTG
genomic: CTTCATGGGTGAATCTGTAACTGATGGAACTCTTGCTAACTTCTTAAAGAgtatgctctc ... ttttatacagAGCCTGGAGACAGAGTCGAGGCCGATGAACCCATAGCGCAGATTGAAACTG

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), 46 (downstream exon)
Score: 65

GAGACAAGTTCGAGGCTGTTGTGCCCTTCATGGGTGAATCTGTAACTGATGGAACTCTTGCTAACTTCTTAAAGAgtatgctctc ... ttttatacagAGCCTGGAGACAGAGTCGAGGCCGATGAACCCATAGCGCAGATTGAAACTGATAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 160

GAGACAAGTTCGAGGCTGTTGTGCCCTTCATGGGTGAATCTGTAACTGATGGAACTCTTGCTAACTTCTTAAAGAgtatgctctc ... ttttatacagAGCCTGGAGACAGAGTCGAGGCCGATGAACCCATAGCGCAGATTGAAACTGATAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 128

GAGACAAGTTCGAGGCTGTTGTGCCCTTCATGGGTGAATCTGTAACTGATGGAACTCTTGCTAACTTCTTAAAGAgtatgctctc ... ttttatacagAGCCTGGAGACAGAGTCGAGGCCGATGAACCCATAGCGCAGATTGAAACTGATAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 168

GAGACAAGTTCGAGGCTGTTGTGCCCTTCATGGGTGAATCTGTAACTGATGGAACTCTTGCTAACTTCTTAAAGAgtatgctctc ... ttttatacagAGCCTGGAGACAGAGTCGAGGCCGATGAACCCATAGCGCAGATTGAAACTGATAAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAGACAAGTTCGAGGCTGTTGTGCCCTTCATGGGTGAATCTGTAACTGATGGAACTCTTGCTAACTTCTTAAAGAgtatgctctctctctccctctccctctccctctctctctctctctcccctccctgtgataacattttctttttttatacag

- - - - - - - - - - - - - - - - - - - - - - -  GATGGA