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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTGCCATCATGAACTGGAGACTGCACGCATTAATGGGCTGCTTGGGAACATTGATGCAAACACTGGTGATCCTCAAGTTGgtaagtgtcactgtttacataactcattgtgttatactggaagcatacatgcatctctttcttctctttttagagaaagaaaagtaataaaaagaatgaggcatgcatagtaacttatcttccccttatgagcag

Basic information

species Zea mays
transcript GRMZM2G005493_T01
intron # 15
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G005493_T01 (Zea mays), 5'ss of exon 15
lower sequence: LOC_Os07g47290.3 (Oryza sativa), 5'ss of exon 15
CTGCCATCATGAACTGGAGACTGCACGCATTAATGGGCTGCTTGGGAACATTGATGCAAACACTGGTGATCCTCAAGTTGgtaagtgtcactgtttacataactcattgtgttatactggaagcatacatgcatctctttcttctctttttagagaaagaaaagtaataaaaagaatgaggcatgcatagtaacttatcttccccttatgagcag
|||||| ||||| || ||||||||| | |||||||| ||||||||||| |||||||| |||||||||||||| ||  | |||| |||    ||  |   || ||| |      | | |   |  || | || |  ||||  ||   ||         |     |  ||| | || ||    |||    | |  ||||| |      ||||  |||
CTGCCACCATGAGCTTGAGACTGCAAGAATTAATGGTCTGCTTGGGAATATTGATGCCAACACTGGTGATCCCCAGATCGgtatgtgcgcatgcctt--tagctcctg-----aaagtcacattatgcctgaaattcttgtttgatttc-------gatttgtgacatacataggatataacattt-caatg-cttatata-----tatggacag

upper sequence: GRMZM2G005493_T01 (Zea mays), 5'ss of exon 15
lower sequence: GLYMA17G07380.1 (Glycine max), 5'ss of exon 15
CTGCCATCATGAACTGGAGACTGCACGCATTAATGGGCTGCTTGGGAACATTGATGCAAACACTGGTGATCCTCAAGTTGgtaagtgtcactgtttacat--aactcattgtgttatactggaagcatacatgcatct-ctttcttctctttttagagaaagaaaagtaataaaaagaatgaggcatgcatagtaacttatcttccccttatgagcag
 || |||||||| || || |||||| | || |||||  |||| || || |||||||||||||||||||||||||||||||||| || | | |  |  |||  ||   ||  ||| |   |   | |||| |  |||   ||    |  | |   | |  ||   ||||  ||| | |||   |  ||  |  | |                       
TTGTCATCATGAGCTCGAAACTGCAAGGATCAATGGATTGCTGGGTAATATTGATGCAAACACTGGTGATCCTCAAGTTGgtatgtatgaattctctcatttaataaatcatgtaaattt--taacatagaaacatgaactgaggtaacataccacaagaatggaagttgtaatatgaagctgttat-tactgcag----------------------

upper sequence: GRMZM2G005493_T01 (Zea mays), 5'ss of exon 15
lower sequence: AT5G57655.1 (Arabidopsis thaliana), 5'ss of exon 7
--------------------CTGCCATCATGAACTGGAGACTGCACGCATTAATGGGCTGCTTGGGAACATTGATGCAAACACTGGTGATCCTCAAGTTGgtaagtgt-cactgtttacataactcattgt-gttatactggaagcatac----atgcatctctttcttctctttttagagaaagaaaagtaataaaaagaatgaggcatgcatagtaacttatcttccccttatgagcag
                     || ||||| || || || |||||| | ||||||||  | ||||| |||||||||||||||||||| ||| |||||  |||||| | | || | |   |     | |||||    |      || || |     ||  | |    |  |||| || |    | ||                                                        
GCCACGCTCTCTGGTCACACTTGTCATCACGAGCTTGAAACTGCAAGAATTAATGGTTTACTTGGCAACATTGATGCAAACACTGGCGATGCTCAAACTGgtaatttttcaatttcagctctcttgattgttaacacctcctaaccagattctgattgaacaaagttctctcattctcttaacag--------------------------------------------------------

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|60337180|gb|DN204153.1|DN204153
EST:     TAATGGGCTGCTTGGAAACATTGATGCAAACACTGGTGATCCTCAAGTTG                         GCTGGGACACGGATCAGTTCATGACAGACATTGCAGAGGCTACTTTGGTTA
genomic: TAATGGGCTGCTTGGGAACATTGATGCAAACACTGGTGATCCTCAAGTTGgtaagtgtca ... ttatgagcagGCTGGGACACGGATCAGTTCATGACAGACATTGCAGAGGCTACTTTGGTTA
EST: gi|29130773|gb|CB381477.1|CB381477
EST:     GGTGATCCTCAAGTTG                         GCTGGGACACGGATCAGTTCATGACAGACATTGCAGAGGCTACTTTGGTTA
genomic: GGTGATCCTCAAGTTGgtaagtgtca ... ttatgagcagGCTGGGACACGGATCAGTTCATGACAGACATTGCAGAGGCTACTTTGGTTA
EST: gi|76286922|gb|DV026490.1|DV026490
EST:     TAATGGGCTGCTTGGGAACATTGATGCAAACACTGGTGATCCTCAAGTTG                         GCTGGGACACGGATCAGTTCATGACAGACATTGCAGAGGCTACTTTGGTTA
genomic: TAATGGGCTGCTTGGGAACATTGATGCAAACACTGGTGATCCTCAAGTTGgtaagtgtca ... ttatgagcagGCTGGGACACGGATCAGTTCATGACAGACATTGCAGAGGCTACTTTGGTTA
EST: gi|211174464|gb|FL381682.1|FL381682
EST:     TAATGGGCTGCTTGGGAACATTGATGCAAACACTGGTGATCCTCAAGTTG                         GCTGGGACACGGATCAGTTCATGACAGACATTGCAGAGGCTACTTTGGTTA
genomic: TAATGGGCTGCTTGGGAACATTGATGCAAACACTGGTGATCCTCAAGTTGgtaagtgtca ... ttatgagcagGCTGGGACACGGATCAGTTCATGACAGACATTGCAGAGGCTACTTTGGTTA
EST: gi|60344318|gb|DN211291.1|DN211291
EST:     TAATGGGCTGCTTGGGAACATTGATGCAAACACTGGTGATCCTCAAGTTG                         GCTGGGACACGGATCAGTTCATGACAGACATTGCAGAGGCTACTTTGGTTA
genomic: TAATGGGCTGCTTGGGAACATTGATGCAAACACTGGTGATCCTCAAGTTGgtaagtgtca ... ttatgagcagGCTGGGACACGGATCAGTTCATGACAGACATTGCAGAGGCTACTTTGGTTA
EST: gi|32836432|gb|CD976110.1|CD976110
EST:     TAATGGGCTGCTTGGGAACATTGATGCAAACACTGGTGATCCTCAAGTTG                         GCTGGGACACGGATCAGTTCATGACAGACATTGCAGAGGCTACTTTGGTTA
genomic: TAATGGGCTGCTTGGGAACATTGATGCAAACACTGGTGATCCTCAAGTTGgtaagtgtca ... ttatgagcagGCTGGGACACGGATCAGTTCATGACAGACATTGCAGAGGCTACTTTGGTTA
EST: gi|211379703|gb|FL400539.1|FL400539
EST:     TAATGGGCTGCTTGGGAACATTGATGCAAACACTGGTGATCCTCAAGTTG                         GCTGGGACACGGATCAGTTCATGACAGACATTGCAGAGGCTACTTTGGTTA
genomic: TAATGGGCTGCTTGGGAACATTGATGCAAACACTGGTGATCCTCAAGTTGgtaagtgtca ... ttatgagcagGCTGGGACACGGATCAGTTCATGACAGACATTGCAGAGGCTACTTTGGTTA
EST: gi|32844741|gb|CD984422.1|CD984422
EST:     TAATGGGCTGGTTGGGAACATTGATGCAAACACTGGTGATCCTCAAGTTG                         GCTGGGACACGGATCAGTTCATGACAGACATTGCAGAGGCTACTTTGGTTA
genomic: TAATGGGCTGCTTGGGAACATTGATGCAAACACTGGTGATCCTCAAGTTGgtaagtgtca ... ttatgagcagGCTGGGACACGGATCAGTTCATGACAGACATTGCAGAGGCTACTTTGGTTA
EST: gi|32845281|gb|CD984962.1|CD984962
EST:     TAATGGGCTGCTTGGGAACATTGATGCAAACACTGGTGATCCTCAAGTTG                         GCTGGGACACGGATCAGTTCATGACAGACATTGCAGAGGCTACTTTGGTTA
genomic: TAATGGGCTGCTTGGGAACATTGATGCAAACACTGGTGATCCTCAAGTTGgtaagtgtca ... ttatgagcagGCTGGGACACGGATCAGTTCATGACAGACATTGCAGAGGCTACTTTGGTTA
EST: gi|33097350|gb|CF057310.1|CF057310
EST:     GATGCAAACACTGGTGATCCTCAAGTTG                         GCTGGGACACGGATCAGTTCATGACAGACATTGCAGAGGCTACTTTGGTTA
genomic: GATGCAAACACTGGTGATCCTCAAGTTGgtaagtgtca ... ttatgagcagGCTGGGACACGGATCAGTTCATGACAGACATTGCAGAGGCTACTTTGGTTA
EST: gi|32838372|gb|CD978050.1|CD978050
EST:     TAATGGGCTGCTTGGGAACATTGATGCAAACACTGGTGATCCTCAAGTTG                         GCTGGGACACGGATCAGTTCATGACAGACATTGCAGAGGCTACTTTGGTTA
genomic: TAATGGGCTGCTTGGGAACATTGATGCAAACACTGGTGATCCTCAAGTTGgtaagtgtca ... ttatgagcagGCTGGGACACGGATCAGTTCATGACAGACATTGCAGAGGCTACTTTGGTTA
EST: gi|32845336|gb|CD985017.1|CD985017
EST:     TAATGGGCTGCTTGGGAACATTGATGCAAACACTGGTGATCCTCAAGTTG                         GCTGGGACACGGATCAGTTCATGACAGACATTGCAGAGGCTACTTTGGTTA
genomic: TAATGGGCTGCTTGGGAACATTGATGCAAACACTGGTGATCCTCAAGTTGgtaagtgtca ... ttatgagcagGCTGGGACACGGATCAGTTCATGACAGACATTGCAGAGGCTACTTTGGTTA
EST: gi|37385849|gb|CF630089.1|CF630089
EST:     TAATGGGCTGCTTGGGAACATTGATGCAAACACTGGTGATCCTCAAGTTG                         GCTGGGACACGGATCAGTTCATGACAGACATTGCAGAGGCTACTTTGGTTA
genomic: TAATGGGCTGCTTGGGAACATTGATGCAAACACTGGTGATCCTCAAGTTGgtaagtgtca ... ttatgagcagGCTGGGACACGGATCAGTTCATGACAGACATTGCAGAGGCTACTTTGGTTA
EST: gi|60346929|gb|DN213902.1|DN213902
EST:     TAATGGGCTGCTTGGGAACATTGATGCAAACACTGGTGATCCTCAAGTTG                         GCTGGGACACGGATCAGTTCATGACAGACATTGCAGAGGCTACTTTGGTTA
genomic: TAATGGGCTGCTTGGGAACATTGATGCAAACACTGGTGATCCTCAAGTTGgtaagtgtca ... ttatgagcagGCTGGGACACGGATCAGTTCATGACAGACATTGCAGAGGCTACTTTGGTTA
EST: gi|32935034|gb|CF039846.1|CF039846
EST:     TAATGGGCTGCTTGGGAACATTGATGCAAACACTGGTGATCCTCAAGTTG                         GCTGGGACACGGATCAGTTCATGACAGACATTGCAGAGGCTACTTTGGTTA
genomic: TAATGGGCTGCTTGGGAACATTGATGCAAACACTGGTGATCCTCAAGTTGgtaagtgtca ... ttatgagcagGCTGGGACACGGATCAGTTCATGACAGACATTGCAGAGGCTACTTTGGTTA
EST: gi|211459151|gb|FL411539.1|FL411539
EST:     TAATGGGCTGCTTGGGAACATTGATGCAAACACTGGTGATCCTCAAGTTG                         GCTGGGACACGGATCAGTTCATGACAGACATTGCAGAGGCTACTTTGGTTA
genomic: TAATGGGCTGCTTGGGAACATTGATGCAAACACTGGTGATCCTCAAGTTGgtaagtgtca ... ttatgagcagGCTGGGACACGGATCAGTTCATGACAGACATTGCAGAGGCTACTTTGGTTA
EST: gi|211215524|gb|FL427999.1|FL427999
EST:     TAATGGGCT--T-GGGAACATTGATGCAAACACTGGTGATCCTCAAGTTG                         GCTGGGACACGGATCAGTTCATGACAGACATTGCAGAGGCTACTT
genomic: TAATGGGCTGCTTGGGAACATTGATGCAAACACTGGTGATCCTCAAGTTGgtaagtgtca ... ttatgagcagGCTGGGACACGGATCAGTTCATGACAGACATTGCAGAGGCTACTT
EST: gi|32844417|gb|CD984098.1|CD984098
EST:     TAATGGGCTGCTTGGGAACATTGATGCAAACACTGGTGATCCTCAAGTTG                         GCTGGGACACGGATCAGTTCATGACAGACATTGCAGAGGCTACTTTGGTTA
genomic: TAATGGGCTGCTTGGGAACATTGATGCAAACACTGGTGATCCTCAAGTTGgtaagtgtca ... ttatgagcagGCTGGGACACGGATCAGTTCATGACAGACATTGCAGAGGCTACTTTGGTTA
EST: gi|211214717|gb|FL394674.1|FL394674
EST:     TAATGGGCTGCTTGGGAACATTGATGCAAACACTGGTGATCCTCAAGTTG                         GCTGGGACACGGATCAGTTCATGACAGACATTGCAGAGGCTACTTTGGTTA
genomic: TAATGGGCTGCTTGGGAACATTGATGCAAACACTGGTGATCCTCAAGTTGgtaagtgtca ... ttatgagcagGCTGGGACACGGATCAGTTCATGACAGACATTGCAGAGGCTACTTTGGTTA
EST: gi|60337495|gb|DN204468.1|DN204468
EST:     TAATGGGCTGCTTGGGAACATTGATGCAAACACTGGTGATCCTCAAGTTG                         GCTGGGACACGGATCAGTTCATGACAGACATTGCAGAGGCTACTTTGGTTA
genomic: TAATGGGCTGCTTGGGAACATTGATGCAAACACTGGTGATCCTCAAGTTGgtaagtgtca ... ttatgagcagGCTGGGACACGGATCAGTTCATGACAGACATTGCAGAGGCTACTTTGGTTA
EST: gi|67037452|gb|CO464268.1|CO464268
EST:     TAATGGGCTGCTTGGGAACATTGATGCAAACACTGGTGATCCTCAAGTTG                         GCTGGGACACGGATCAGTTCATGACAGACATTGCAGAGGCTACTTTGGTTA
genomic: TAATGGGCTGCTTGGGAACATTGATGCAAACACTGGTGATCCTCAAGTTGgtaagtgtca ... ttatgagcagGCTGGGACACGGATCAGTTCATGACAGACATTGCAGAGGCTACTTTGGTTA
EST: gi|32844874|gb|CD984555.1|CD984555
EST:     GATCCTCAAGTTG                         GCTGGGACACGGATCAGTTCATGACAGACATTGCAGAGGCTACTTTGGTTA
genomic: GATCCTCAAGTTGgtaagtgtca ... ttatgagcagGCTGGGACACGGATCAGTTCATGACAGACATTGCAGAGGCTACTTTGGTTA
EST: gi|6012630|gb|AW062067.1|AW062067
EST:     TAATGGGCTGCTTGGGAACATTGATGCAAACACTGGTGATCCTCAAGTTG                         GCTGGGACACGGATCAGTTCATGACAGACATTGCAGAGGCTACTTTGGTTA
genomic: TAATGGGCTGCTTGGGAACATTGATGCAAACACTGGTGATCCTCAAGTTGgtaagtgtca ... ttatgagcagGCTGGGACACGGATCAGTTCATGACAGACATTGCAGAGGCTACTTTGGTTA
EST: gi|32838758|gb|CD978439.1|CD978439
EST:     TAATGGGCTGCTTGGGAACATTGATGCAAACACTGGTGATCCTCAAGTTG                         GCTGGGACACGGATCAGTTCATGACAGACATTGCAGAGGCTACTTTGGTTA
genomic: TAATGGGCTGCTTGGGAACATTGATGCAAACACTGGTGATCCTCAAGTTGgtaagtgtca ... ttatgagcagGCTGGGACACGGATCAGTTCATGACAGACATTGCAGAGGCTACTTTGGTTA
EST: gi|60353702|gb|DN220675.1|DN220675
EST:     TAATGGGCTGCTTGGGAACATTGATGCAAACACTGGTGATCCTCAAGTTG                         GCTGGGACACGGATCAGTTCATGACAGACATTGCAGAGGCTACTTTGGTTA
genomic: TAATGGGCTGCTTGGGAACATTGATGCAAACACTGGTGATCCTCAAGTTGgtaagtgtca ... ttatgagcagGCTGGGACACGGATCAGTTCATGACAGACATTGCAGAGGCTACTTTGGTTA
EST: gi|110219847|gb|EC901745.1|EC901745
EST:     TAATGGGCTGCTTGGGAACATTGATGCAAACACTGGTGATCCTCAAGTTG                         GCTGGGACACGGATCAGTTCATGACAGACATTGCAGAGGCTACTTTGGTTA
genomic: TAATGGGCTGCTTGGGAACATTGATGCAAACACTGGTGATCCTCAAGTTGgtaagtgtca ... ttatgagcagGCTGGGACACGGATCAGTTCATGACAGACATTGCAGAGGCTACTTTGGTTA
EST: gi|67010832|gb|CO439581.1|CO439581
EST:     TAATGGGCTGCTTGGGAACATTGATGCAAACACTGGTGATCCTCAAGTTG                         GCTGGGACACGGATCAGTTCATGACAGACATTGCAGAGGCTACTTTGGTTA
genomic: TAATGGGCTGCTTGGGAACATTGATGCAAACACTGGTGATCCTCAAGTTGgtaagtgtca ... ttatgagcagGCTGGGACACGGATCAGTTCATGACAGACATTGCAGAGGCTACTTTGGTTA
EST: gi|32837235|gb|CD976913.1|CD976913
EST:     TAATGGGCTGCTTGGGAACATTGATGCAAACACTGGTGATCCTCAAGTTG                         GCTGGGACACGGATCAGTTCATGACAGACATTGCAGAGGCTACTTTGGTTA
genomic: TAATGGGCTGCTTGGGAACATTGATGCAAACACTGGTGATCCTCAAGTTGgtaagtgtca ... ttatgagcagGCTGGGACACGGATCAGTTCATGACAGACATTGCAGAGGCTACTTTGGTTA
EST: gi|60347419|gb|DN214392.1|DN214392
EST:     TAATGGGCTGCTTGGGAACATTGATGCAAACACTGGTGATCCTCAAGTTG                         GCTGGGACACGGATCAGTTCATGACAGACATTGCAGAGGCTACTTTGGTTA
genomic: TAATGGGCTGCTTGGGAACATTGATGCAAACACTGGTGATCCTCAAGTTGgtaagtgtca ... ttatgagcagGCTGGGACACGGATCAGTTCATGACAGACATTGCAGAGGCTACTTTGGTTA

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: 48 (upstream exon), 49 (downstream exon)
Score: 467

CTGCCATCATGAACTGGAGACTGCACGCATTAATGGGCTGCTTGGGAACATTGATGCAAACACTGGTGATCCTCAAGTTGgtaagtgtca ... ttatgagcagGCTGGGACACGGATCAGTTCATGACAGACATTGCAGAGGCTACTTTGGTTATGTCAACTGTGGTTAAGAAT


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 453

CTGCCATCATGAACTGGAGACTGCACGCATTAATGGGCTGCTTGGGAACATTGATGCAAACACTGGTGATCCTCAAGTTGgtaagtgtca ... ttatgagcagGCTGGGACACGGATCAGTTCATGACAGACATTGCAGAGGCTACTTTGGTTATGTCAACTGTGGTTAAGAAT


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 347

CTGCCATCATGAACTGGAGACTGCACGCATTAATGGGCTGCTTGGGAACATTGATGCAAACACTGGTGATCCTCAAGTTGgtaagtgtca ... ttatgagcagGCTGGGACACGGATCAGTTCATGACAGACATTGCAGAGGCTACTTTGGTTATGTCAACTGTGGTTAAGAAT


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 848

CTGCCATCATGAACTGGAGACTGCACGCATTAATGGGCTGCTTGGGAACATTGATGCAAACACTGGTGATCCTCAAGTTGgtaagtgtca ... ttatgagcagGCTGGGACACGGATCAGTTCATGACAGACATTGCAGAGGCTACTTTGGTTATGTCAACTGTGGTTAAGAAT


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTGCCATCATGAACTGGAGACTGCACGCATTAATGGGCTGCTTGGGAACATTGATGCAAACACTGGTGATCCTCAAGTTGgtaagtgtcactgtttacataactcattgtgttatactggaagcatacatgcatctctttcttctctttttagagaaagaaaagtaataaaaagaatgaggcatgcatagtaacttatcttccccttatgagcag

- - - - - - - - - - - - - - - - - - GCTGCT