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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttcataataaaactcttccccgttatttgcagtgctgtttttttgtaacagttaatctaatatgagttctttctttgattcaaattgtcagGGTACGTTCGTTTCCATGGGAGTATACTCCGATGGCTCTTACAGCGTTCCATCAGGACTTATCTACTCCTTCCCTGTAACTTGTCGCAATGGAGACTGGA

Basic information

species Arabidopsis thaliana
transcript AT1G04410.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G04410.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: Vv07s0005g03360.t01 (Vitis vinifera), 3'ss of exon 5
----gttcataataaaactcttcc--ccgt-tatttgcagtgctgtttttttgtaacagttaatctaatatgagttctttctttgattcaaattgtcagGGTACGTTCGTTTCCATGGGAGTATACTCCGATGGCTCTTACAGCGTTCCATCAGGACTTATCTACTCCTTCCCTGTAACTTGTCGCAATGGAGACTGGA
     ||  |  ||   || || |  | || || || ||||  |   || | ||    ||  |||| ||     |  |||  |   | ||| ||  ||||| || |  || |||||||| |||||||| ||||| || ||||  |||||| | || |||||||| |||||||||||||||||  |   |||||| ||||
gttgttttctgttagtgcttttacatctgtatacttccagtaatagattgt-gtg-tggtgtatctgatgcatttgattttctccttgcaactt--cagGGAACTTGGGTGTCCATGGGCGTATACTCTGATGGTTCATACAATGTTCCAGCGGGTCTTATCTATTCCTTCCCTGTAACTTGCTGTGCTGGAGAATGGA

upper sequence: AT1G04410.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: Vv07s0005g03350.t01 (Vitis vinifera), 3'ss of exon 6
----gttcataataaaactcttcc--ccgt-tatttgcagtgctgtttttttgtaacagttaatctaatatgagttctttctttgattcaaattgtcagGGTACGTTCGTTTCCATGGGAGTATACTCCGATGGCTCTTACAGCGTTCCATCAGGACTTATCTACTCCTTCCCTGTAACTTGTCGCAATGGAGACTGGA
     ||| |  ||   || || |  | || |  || ||||  |   || | ||    ||  |||| ||     |  |||  |   | | | ||   |||| || |  || |||||||| || ||||| ||||| || ||||  |||||| |||| |||||||| |||||||||||||| ||  |   ||| || ||||
gttgtttcttgttagtgcttttacatctgtatgcttccagtaatagattgt-gtg-tggtgtatctgatgcatttgattttctccttgcgactt--tagGGAACTTGGGTGTCCATGGGTGTGTACTCTGATGGTTCATACAATGTTCCAGCAGGGCTTATCTATTCCTTCCCTGTAACCTGCTGTGCTGGTGAATGGA
















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|124944980|gb|EL021030.1|EL021030
EST:     CTAGCCCTGCTTGTGACCACATCCGTGACTGGGTCCTTGGAACTCCAGAG                         GGTACGTTCGTTTCC
genomic: CTAGCTCTGCTTGTGACCACATCCGTGACTGGGTCCTTGGAACTCCAGAGgttcataata ... aaattgtcagGGTACGTTCGTTTCC
EST: gi|124799956|gb|EH889621.1|EH889621
EST:     CCTTGGAACTCCAGAG                         GGTACGTTCGTTTCCATGGGAGTATACTCCGATGGCTCTTACAGCGTTCCA
genomic: CCTTGGAACTCCAGAGgttcataata ... aaattgtcagGGTACGTTCGTTTCCATGGGAGTATACTCCGATGGCTCTTACAGCGTTCCA
EST: gi|124735972|gb|EH827374.1|EH827374
EST:     CTGCTTGTGACCACATCCGTGACTGGGTCCTTGGAACTCCAGAG                         GGTACGTTCGTTTCCATGGGAGTATACTCCGATGGCTCTTACAGCGTTCCA
genomic: CTGCTTGTGACCACATCCGTGACTGGGTCCTTGGAACTCCAGAGgttcataata ... aaattgtcagGGTACGTTCGTTTCCATGGGAGTATACTCCGATGGCTCTTACAGCGTTCCA
EST: gi|125271053|gb|EL285138.1|EL285138
EST:     CTAGCTCTGCTTGTGACCACATCCGTGACTGGGTCCTTGGAACTCCAGAG                         GGTACGTTCGTTTCCATGGGAGTATACTCCGATGGCT
genomic: CTAGCTCTGCTTGTGACCACATCCGTGACTGGGTCCTTGGAACTCCAGAGgttcataata ... aaattgtcagGGTACGTTCGTTTCCATGGGAGTATACTCCGATGGCT
EST: gi|125202375|gb|EL217329.1|EL217329
EST:     CTAGCTCTGCTTGTGACCACATCCGTGACTGGGTCCTTGGAACTCCAGAG                         GGTACGTTCGTTTCCATGGGAGTATACTCCGATGGCTCTTACAG
genomic: CTAGCTCTGCTTGTGACCACATCCGTGACTGGGTCCTTGGAACTCCAGAGgttcataata ... aaattgtcagGGTACGTTCGTTTCCATGGGAGTATACTCCGATGGCTCTTACAG
EST: gi|125299579|gb|EL313664.1|EL313664
EST:     CTAGCTCTGCTCGTGACCACATCCGTGACTGGGTCCTTGGAACTCCAGAG                         GGTACGTTCGTTTCCA
genomic: CTAGCTCTGCTTGTGACCACATCCGTGACTGGGTCCTTGGAACTCCAGAGgttcataata ... aaattgtcagGGTACGTTCGTTTCCA
EST: gi|116378554|gb|EG421146.1|EG421146
EST:     CTAGCTCTGCTTGTGACCACATCCGTGACTGGGTCCTTGGAACTCCAGAG                         GGTACGTTCGTTTCCATGGGAGTATACTCCGATGGCTCTTACAGCGTTCCA
genomic: CTAGCTCTGCTTGTGACCACATCCGTGACTGGGTCCTTGGAACTCCAGAGgttcataata ... aaattgtcagGGTACGTTCGTTTCCATGGGAGTATACTCCGATGGCTCTTACAGCGTTCCA
EST: gi|164153100|gb|EL993290.1|EL993290
EST:     TCCGTGACTGGGTCCTTGGAACTCCAGAG                         GGTACGTTCGTTTCCATGGGAGTATACTCCGATGGCTCTTACAGCGTTCCA
genomic: TCCGTGACTGGGTCCTTGGAACTCCAGAGgttcataata ... aaattgtcagGGTACGTTCGTTTCCATGGGAGTATACTCCGATGGCTCTTACAGCGTTCCA
EST: gi|116378552|gb|EG421144.1|EG421144
EST:     CTAGCTCTGCTTGTGACCACATCCGTGACTGGGTCCTTGGAACTCCAGAG                         GGTACGTTCGTTTCCATGGGAGTATACTCCGATGGCTCTTACAGCGTTCCA
genomic: CTAGCTCTGCTTGTGACCACATCCGTGACTGGGTCCTTGGAACTCCAGAGgttcataata ... aaattgtcagGGTACGTTCGTTTCCATGGGAGTATACTCCGATGGCTCTTACAGCGTTCCA
EST: gi|125019218|gb|EL091487.1|EL091487
EST:     TGACTGGGTCCTTGGAACTCCAGAG                         GGTACGTTCGTTTCCATGGGAAGTATACTCCGATGGCTCTTACAGCGTTCC
genomic: TGACTGGGTCCTTGGAACTCCAGAGgttcataata ... aaattgtcagGGTACGTTCGTTTCCATGGGA-GTATACTCCGATGGCTCTTACAGCGTTCC
EST: gi|124902534|gb|EH976614.1|EH976614
EST:     CTTGTGACCACATCCGTGACTGGGTCCTTGGAACTCCAGAG                         GGTACGTTCGTTTCCATGGGAGTATACTCCGATGGCTCTTAC
genomic: CTTGTGACCACATCCGTGACTGGGTCCTTGGAACTCCAGAGgttcataata ... aaattgtcagGGTACGTTCGTTTCCATGGGAGTATACTCCGATGGCTCTTAC
EST: gi|86081490|gb|DR377247.1|DR377247
EST:     CTAGCTCTGCTTGTGACCACATCCGTGACTGGGTCCTTGGAACTCCAGAG                         GGTACGTTCGTTTCCATGGGAGTATACTCCGATGGCTCTTACAGCGTTCCA
genomic: CTAGCTCTGCTTGTGACCACATCCGTGACTGGGTCCTTGGAACTCCAGAGgttcataata ... aaattgtcagGGTACGTTCGTTTCCATGGGAGTATACTCCGATGGCTCTTACAGCGTTCCA
EST: gi|116469998|gb|EG512590.1|EG512590
EST:     CTAGCTCTGCTTGTGACCACATCCGTGACTGGGTCCTTGGAACTCCAGAG                         GGTACGTTCGTTTCCATGGGAGTATACTCCGATGGCTCTTACAGCGTTCCA
genomic: CTAGCTCTGCTTGTGACCACATCCGTGACTGGGTCCTTGGAACTCCAGAGgttcataata ... aaattgtcagGGTACGTTCGTTTCCATGGGAGTATACTCCGATGGCTCTTACAGCGTTCCA
EST: gi|86080897|gb|DR376654.1|DR376654
EST:     CTAGCTCTGCTTGTGACCACATCCGTGACTGGGTCCTTGGAACTCCAGAG                         GGTACGTTCGTTTCCATGGGAGTATACTCCGATGGCTCTTACAGCGTTCCA
genomic: CTAGCTCTGCTTGTGACCACATCCGTGACTGGGTCCTTGGAACTCCAGAGgttcataata ... aaattgtcagGGTACGTTCGTTTCCATGGGAGTATACTCCGATGGCTCTTACAGCGTTCCA
EST: gi|125299265|gb|EL313350.1|EL313350
EST:     CTAGCTCTGCTTGTGACCACANCCGTGACTGGGTCCTTGGAACTCCAGAG                         GGTACGTTCGTTTCCATGGGAGTATACTCCGATGGCTCTTACAGCGTTCCA
genomic: CTAGCTCTGCTTGTGACCACATCCGTGACTGGGTCCTTGGAACTCCAGAGgttcataata ... aaattgtcagGGTACGTTCGTTTCCATGGGAGTATACTCCGATGGCTCTTACAGCGTTCCA
EST: gi|116376802|gb|EG419394.1|EG419394
EST:     CTAGCTCTGCTTGTGACCACATCCGTGACTGGGTCCTTGGAACTCCAGAG                         GGTACGTTCGTTTCCATGGGAGTATACTCCGATGGCTCTTACAGCGTTCCA
genomic: CTAGCTCTGCTTGTGACCACATCCGTGACTGGGTCCTTGGAACTCCAGAGgttcataata ... aaattgtcagGGTACGTTCGTTTCCATGGGAGTATACTCCGATGGCTCTTACAGCGTTCCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtttttttgtaacagttaatctaatatgagttctttctttgattcaaattgtcagGGTACGTTCGTTTCCATGGGAGTATACTCCGATGGCTCTTACAGCGTTCCATCAGGACTTATCTACTCCTTCCCTGTAACTTGTCGCAATGGAGACTGGA
             agttaatctaatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttcataataaaactcttccccgttatttgcagtgctgtttttttgtaacagttaatctaatatgagttctttctttgattcaaattgtcagGGTACGTTCGTTTCCATGGGAGTATACTCCGATGGCTCTTACAGCGTTCCATCAGGACTTATCTACTCCTTCCCTGTAACTTGTCGCAATGGAGACTGGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA