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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttgtcttatttctctctcaaacatccacagttcttcatttgcttgttgtgtccttctcccgtgatgatgttatgtgaccataccattttctgccttgcagGCCCTTGAGTCTTTTTACGAGAAATTTGATCCAGATTTCATTGATATTAGGACAAAAGCACGTGAGGTGTTGCAGAGGGAGGACGATCTGAATGAAATTG

Basic information

species Zea mays
transcript GRMZM2G421857_T04
intron # 15
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G421857_T02 (Zea mays), 3'ss of exon 14
lower sequence: LOC_Os02g07870.1 (Oryza sativa), 3'ss of exon 14
--ttgtcttatttctctctcaaacatccacagttcttcatttgcttgttgtgtccttctcccgtgatgatgttatgtgaccataccattttctgccttgcagGCCCTTGAGTCTTTTTACGAGAAATTTGATCCAGATTTCATTGATATTAGGACAAAAGCACGTGAGGTGTTGCAGAGGGAGGACGATCTGAATGAAATTG
  || |   ||      || | |  |  | | ||   ||||| | ||||   ||    |  | |  |||||||||||||| |||| || || ||  |||||||| |||||| |    || ||||     ||||||||||||||||||||||| ||||| ||||||||||||||||||||||| || ||| | |||||||| |
tttttttcaatgaaatgctaataagtttatatttgaacattttcctgttcgttcgcatttgctt--tgatgttatgtgacaatacaatgttttgtgttgcagGCGCTTGAGCCGCACTATGAGAGGGAAGATCCAGATTTCATTGATATTAGAACAAAGGCACGTGAGGTGTTGCAGAGGGAAGATGATTTAAATGAAATAG

upper sequence: GRMZM2G421857_T02 (Zea mays), 3'ss of exon 14
lower sequence: GLYMA08G23990.1 (Glycine max), 3'ss of exon 15
-------------ttgtcttatttctctctcaaacatccacagttcttcatttgcttg--ttgtgtccttctcccgtgatgatgttatgtgaccataccattttctgccttgca------gGCCCTTGAGTCTTTTTACGAGAAATTTGATCCAGATTTCATTGATATTAGGACAAAAGCACGTGAGGTGTTGCAGAGGGAGGACGATCTGAATGAAATTG
             |||  |  ||| |  ||||  | ||||   |||| ||||||  ||  | ||||  |  | || |||   |     |      ||  |||||||   | | |      ||| |||||  | ||||| ||| |||||||||||||||| ||  | ||||||||||| || ||||| ||  |||| ||||| || || |||||||||||||
gtatgtcctaaagttggttactttgtaactcat-cctccagctttctacatttgtatgcatagtgttttggttccatgactttccc-cgaatttttaatattttctttttggtatctttagGCACTTGAAACCTTTTATGAGCAATTTGATCCAGATTTTATCAACATTAGGACAAAGGCTCGTGAAGTTCTGCAAAGGGAAGATGACCTGAATGAAATTG

upper sequence: GRMZM2G421857_T02 (Zea mays), 3'ss of exon 14
lower sequence: AT1G78900.2 (Arabidopsis thaliana), 3'ss of exon 15
ttgtcttatttctctctcaaacatccacagttcttcatttgcttgttgtgtccttctcccgtgatgatgttatgtgaccataccattttctgccttgcagGCCCTTGAGTCTTTTTACGAGAAATTTGATCCAGATTTCATTGATATTAGGACAAAAGCACGTGAGGTGTTGCAGAGGGAGGACGATCTGAATGAAATTG
               || ||| || | | ||||    ||  |||| | |     | ||  |  ||  ||| || | |  |  |   ||| ||  ||  |||| || || ||||| || ||||| || ||||||||||||||  | || |||||||| ||  | ||||||||||||||||| |||||||| ||||||||||
----------gtatgcttaaatattctcggttcaaacttgtcttggttta---ctatctagaaatcttgt-atataaa-acgctgctttttgtttt--agGCACTGGAATCTTTCTATGAGAAGTTCGATCCAGATTTCATCAACATCAGGACAAAGGCCAGAGAGGTGTTGCAGAGGGAAGACGATCTTAATGAAATTG

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|32850183|gb|CD989864.1|CD989864
EST:     AGCATTTCCCATCTGCGAATTGGCTCATTTCCTATTCGAAATACTCCAAG                         GCCCTTGAGTCTTTTTACGAGAAATTCGATCCAGATTTCATTGATATTAGG
genomic: AGCATTTCCCATCTGTGAATTGGCTCATTTCCTATTCGAAATACTCCAAGgttatttcct ... tgccttgcagGCCCTTGAGTCTTTTTACGAGAAATTTGATCCAGATTTCATTGATATTAGG
EST: gi|32921243|gb|CF026055.1|CF026055
EST:     AGCATTTCCCATCTGTGAATTGGCTCATTTCCTATTCGAAATACTCCAAG                         GCCCTTGAGTCTTTTTACGAGAAATTTGATCCAGATTTCATTGATATTAGG
genomic: AGCATTTCCCATCTGTGAATTGGCTCATTTCCTATTCGAAATACTCCAAGgttatttcct ... tgccttgcagGCCCTTGAGTCTTTTTACGAGAAATTTGATCCAGATTTCATTGATATTAGG
EST: gi|67026160|gb|CO454909.1|CO454909
EST:     AGCATTTCCCATCTGTGAATTGGCTCATTTCCTATTCGAAATACTCCAAG                         GCCCTTGAGTCTTTTTACGAGAAATTTGATCCAGATTTCATTGATATTAGG
genomic: AGCATTTCCCATCTGTGAATTGGCTCATTTCCTATTCGAAATACTCCAAGgttatttcct ... tgccttgcagGCCCTTGAGTCTTTTTACGAGAAATTTGATCCAGATTTCATTGATATTAGG
EST: gi|32845901|gb|CD985582.1|CD985582
EST:     AACATTTCCCATCTGTGAATTGGCTCATTTCCTATTCGAAATACTCCAAG                         GCCCTTGAGTCTTTTTACGAGAAATTCGATCCAGATTTCATTGATATTAGG
genomic: AGCATTTCCCATCTGTGAATTGGCTCATTTCCTATTCGAAATACTCCAAGgttatttcct ... tgccttgcagGCCCTTGAGTCTTTTTACGAGAAATTTGATCCAGATTTCATTGATATTAGG
EST: gi|6637071|gb|AW261343.1|AW261343
EST:     AGCATTTCCCATCTGTGAATTGGCTCATTTCCTATTCGAAATACTCCAAG                         GCCCTTGAGTCTTTTTACGAGAAATTTGATCCAGATTTCATTGATATTAGG
genomic: AGCATTTCCCATCTGTGAATTGGCTCATTTCCTATTCGAAATACTCCAAGgttatttcct ... tgccttgcagGCCCTTGAGTCTTTTTACGAGAAATTTGATCCAGATTTCATTGATATTAGG
EST: gi|24774168|gb|CA409422.1|CA409422
EST:     ATTGGCTCATTTCCTATTCGAAATACTCCAAG                         GCCCTTGAGTCTTTTTACGAGAAATTTGATCCAGATTTCATTGACTATTAG
genomic: ATTGGCTCATTTCCTATTCGAAATACTCCAAGgttatttcct ... tgccttgcagGCCCTTGAGTCTTTTTACGAGAAATTTGATCCAGATTTCATTGA-TATTAG
EST: gi|8368089|gb|BE051034.1|BE051034
EST:     AGCATTTCCCATCTGTGAATTGGCTCATTTCCTATTCGAAATACTCCAAG                         GCCCTTGAGTCTTTTTACGAGAAGGGTGATCTCATATTTCATTGATATTAG
genomic: AGCATTTCCCATCTGTGAATTGGCTCATTTCCTATTCGAAATACTCCAAGgttatttcct ... tgccttgcagGCCCTTGAGTCTTTTTACGAGAAATTTGATC-CAGATTTCATTGATATTAG
EST: gi|32921648|gb|CF026460.1|CF026460
EST:     AGCATTTCCCATCTGCGAATTGGCTCATTTCCTATTCGAAATACTCCAAG                         GCCCTTGAGTCTTTTTACGAGAAATTTGATCCAGATTTCATTGATATTAGG
genomic: AGCATTTCCCATCTGTGAATTGGCTCATTTCCTATTCGAAATACTCCAAGgttatttcct ... tgccttgcagGCCCTTGAGTCTTTTTACGAGAAATTTGATCCAGATTTCATTGATATTAGG
EST: gi|211529162|gb|FL123428.1|FL123428
EST:     AGCATTTCCCATCTGTGAATTGGCTCATTTCCTATTCGAAATACTCTAAG                         GCCCTTGAGTCTTTTTACGAGAAATTTGATCCAGATTTCATTGATATTAGG
genomic: AGCATTTCCCATCTGTGAATTGGCTCATTTCCTATTCGAAATACTCCAAGgttatttcct ... tgccttgcagGCCCTTGAGTCTTTTTACGAGAAATTTGATCCAGATTTCATTGATATTAGG
EST: gi|6020503|gb|AW065431.1|AW065431
EST:     AGCATTTCCCATCTGTGAATTGGCTCATTTCCTATTCGAAATACTCCAAG                         GCCCTTGAGTCTTTTTACGAGAAATTTGATCCAGATTTCATTGATATTAGG
genomic: AGCATTTCCCATCTGTGAATTGGCTCATTTCCTATTCGAAATACTCCAAGgttatttcct ... tgccttgcagGCCCTTGAGTCTTTTTACGAGAAATTTGATCCAGATTTCATTGATATTAGG
EST: gi|32849884|gb|CD989565.1|CD989565
EST:     AGCATTTCCCATCTGTGAATTGGCTCATTTCCTATTCGAAATACTCCAAG                         GCCCTTGAGTCTTTTTACGAGAAATTCGATCCAGATTTCGTTGATATTAGG
genomic: AGCATTTCCCATCTGTGAATTGGCTCATTTCCTATTCGAAATACTCCAAGgttatttcct ... tgccttgcagGCCCTTGAGTCTTTTTACGAGAAATTTGATCCAGATTTCATTGATATTAGG
EST: gi|211538183|gb|FL123481.1|FL123481
EST:     AGCATTTCCCATCTGTGAATTGGCTCATTTCCTATTCGAAATACTCCAAG                         GCCCTTGAGTCTTTTTACGAAAAATTTGATCCAGATTTCATTGATATTAGG
genomic: AGCATTTCCCATCTGTGAATTGGCTCATTTCCTATTCGAAATACTCCAAGgttatttcct ... tgccttgcagGCCCTTGAGTCTTTTTACGAGAAATTTGATCCAGATTTCATTGATATTAGG
EST: gi|32846431|gb|CD986112.1|CD986112
EST:     AGCATTTCCCATCTGTGAATTGGCTCATTTCCTATTAGAAATACTCCAAG                         GCCCTTGAGTCTTTTTACGAGAAATTCGATCCAGATTTCATTGATATTAGG
genomic: AGCATTTCCCATCTGTGAATTGGCTCATTTCCTATTCGAAATACTCCAAGgttatttcct ... tgccttgcagGCCCTTGAGTCTTTTTACGAGAAATTTGATCCAGATTTCATTGATATTAGG
EST: gi|32846734|gb|CD986415.1|CD986415
EST:     AGCATTTCCCATCTGTGAATTGGCTCATTTCCTATTCGAAATACTCCAAG                         GCCCTTGAGTCTTTTTACGAGAAATTCGATCCAGATTTCATTGATATTAGG
genomic: AGCATTTCCCATCTGTGAATTGGCTCATTTCCTATTCGAAATACTCCAAGgttatttcct ... tgccttgcagGCCCTTGAGTCTTTTTACGAGAAATTTGATCCAGATTTCATTGATATTAGG
EST: gi|8368090|gb|BE051035.1|BE051035
EST:     AGCATTTCCCATCTGTGAATTGGCTCATTTCCTATTCGAAATACTCCAAG                         GCCCTTGAGTCTTTTTACGAGAAATTTGATCCAGATTTCATTGATATTAGG
genomic: AGCATTTCCCATCTGTGAATTGGCTCATTTCCTATTCGAAATACTCCAAGgttatttcct ... tgccttgcagGCCCTTGAGTCTTTTTACGAGAAATTTGATCCAGATTTCATTGATATTAGG
EST: gi|8665370|gb|BE186186.1|BE186186
EST:     ANTTTCTCCACTCTGTGAATTGGCTCATTTCCTATTCGAAATACTCCAAG                         GCCCTTGAGTCTTTTTACGAGAAATTTGATCCAGATTTCATTGATATTAGG
genomic: A-TTTC-CCA-TCTGTGAATTGGCTCATTTCCTATTCGAAATACTCCAAGgttatttcct ... tgccttgcagGCCCTTGAGTCTTTTTACGAGAAATTTGATCCAGATTTCATTGATATTAGG
EST: gi|40334940|gb|CK369010.1|CK369010
EST:     AGCATTTCCCATCTGTGAATTGGCTCATTTCCTATTCTAAATACTCCAAG                         GCCCTTGAGTCTTTTTACGAGAAATTCGATCCACATTTCATTGATATTAGG
genomic: AGCATTTCCCATCTGTGAATTGGCTCATTTCCTATTCGAAATACTCCAAGgttatttcct ... tgccttgcagGCCCTTGAGTCTTTTTACGAGAAATTTGATCCAGATTTCATTGATATTAGG
EST: gi|22542087|gb|BU092525.1|BU092525
EST:     AGCATTTCCCATCTGTGAATTGGCTCATTTCCTATTCGAAATACTCCAAG                         GCCCTTGAGTCTTTTTACGAGAAATTTGATCCAGATTTCATTGATATTAGG
genomic: AGCATTTCCCATCTGTGAATTGGCTCATTTCCTATTCGAAATACTCCAAGgttatttcct ... tgccttgcagGCCCTTGAGTCTTTTTACGAGAAATTTGATCCAGATTTCATTGATATTAGG
EST: gi|32921742|gb|CF026554.1|CF026554
EST:     AGCATTTCCCATCTGTGAATTGGCTCATTTCCTATTCGAAATACTCCAAG                         GCCCTTGAGTCTTTTTACGAGAAATTTGATCCAGATTTCATTGATATTAGG
genomic: AGCATTTCCCATCTGTGAATTGGCTCATTTCCTATTCGAAATACTCCAAGgttatttcct ... tgccttgcagGCCCTTGAGTCTTTTTACGAGAAATTTGATCCAGATTTCATTGATATTAGG
EST: gi|32920116|gb|CF024928.1|CF024928
EST:     AGCATTTCCCATCTGTGAATTGGCTCATTTCCTATTCGAAATACTCCAAG                         GCCCTTGAGTCTTTTTACGAGAAATTTGATCCAGATTTCATTGATATTAGG
genomic: AGCATTTCCCATCTGTGAATTGGCTCATTTCCTATTCGAAATACTCCAAGgttatttcct ... tgccttgcagGCCCTTGAGTCTTTTTACGAGAAATTTGATCCAGATTTCATTGATATTAGG
EST: gi|32921546|gb|CF026358.1|CF026358
EST:     AGCATTTCCCATCTGTGAATTGGCTCATTTCCTATTCGAAATACTCCAAG                         GCCCTTGAGTCTTTTTACGAGAAATTTGATCCAGATTTCATTGATATTAGG
genomic: AGCATTTCCCATCTGTGAATTGGCTCATTTCCTATTCGAAATACTCCAAGgttatttcct ... tgccttgcagGCCCTTGAGTCTTTTTACGAGAAATTTGATCCAGATTTCATTGATATTAGG
EST: gi|60352649|gb|DN219622.1|DN219622
EST:     AGCATTTCCCATCTGTGAATTGGCTCATTTCCTATTCGAAATACTCCAAG                         GCCCTTGAGTCTTTTTACGAGAAATTTGATCCAGATTTCATTGATATTAGG
genomic: AGCATTTCCCATCTGTGAATTGGCTCATTTCCTATTCGAAATACTCCAAGgttatttcct ... tgccttgcagGCCCTTGAGTCTTTTTACGAGAAATTTGATCCAGATTTCATTGATATTAGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgtgtccttctcccgtgatgatgttatgtgaccataccattttctgccttgcagGCCCTTGAGTCTTTTTACGAGAAATTTGATCCAGATTTCATTGATATTAGGACAAAAGCACGTGAGGTGTTGCAGAGGGAGGACGATCTGAATGAAATTG
                                     ccattttctgcctt  CT-rich tract
                     atgttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttgtcttatttctctctcaaacatccacagttcttcatttgcttgttgtgtccttctcccgtgatgatgttatgtgaccataccattttctgccttgcagGCCCTTGAGTCTTTTTACGAGAAATTTGATCCAGATTTCATTGATATTAGGACAAAAGCACGTGAGGTGTTGCAGAGGGAGGACGATCTGAATGAAATTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGGA