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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGATACCGGTCCTTCCTTTTGCGAGATTTGCCATTTGATGCTATACAGTTCTGCATATATGAGCAGCTTTGCTTGGGGTATAAAAAAGCCgtaagtttctttgtaaaataagtggcatttcttctatatgtaatatctttggataaggtatcggaaaaaaaaacgcatgataacttctgatgtactgatattttgcatgagatttactttggtcaactctttggcag

Basic information

species Arabidopsis thaliana
transcript AT4G39460.2
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G39460.1 (Arabidopsis thaliana), 5'ss of exon 9
lower sequence: LOC_Os07g19460.1 (Oryza sativa), 5'ss of exon 8
GGATACCGGTCCTTCCTTTTGCGAGATTTGCCATTTGATGCTATACAGTTCTGCATATATGAGCAGCTTTGCTTGGGGTATAAAAAAGCCgtaagtttctttgtaaaataagtggcatttcttctatatgtaatatctttggataaggtatcggaaaaaaaaacgcatgataacttctgatgtactgatat-tttgcatgagatttactttggtcaactctttggcag
|| ||  | ||||| || ||||||||| | |||||||||||||| ||||| |||||||||||||| ||| |  | || ||||||   || |||  | |||          | |      | ||||||| |    | | |    | |    || ||   |||   |  |   || |     | ||   | ||   ||| |||                           
GGCTATGGTTCCTTTCTGTTGCGAGATCTACCATTTGATGCTATTCAGTTTTGCATATATGAGCAACTTCGAATAGGCTATAAACTGGCGgtatttatctc---------atttatccctattctataggcgtaagcctcttctcat---tctgatgtaaatttgactatcaattatgtttctatgaaaatgcctgcctgac--------------------------

upper sequence: AT4G39460.1 (Arabidopsis thaliana), 5'ss of exon 9
lower sequence: GRMZM2G169914_T01 (Zea mays), 5'ss of exon 8
GGATACCGGTCCTTCCTTTTGCGAGATTTGCCATTTGATGCTATACAGTTCTGCATATATGAGCAGCTTTGCTTGGGGTATAAAAAAGCCgtaagtttctttgtaaaataagtggcatttcttctatatgtaatatctttggataaggtatcggaaaaaaaaacgcatgataacttctgatgtactgatattttgcatgagatttactttggtcaactctttggcag
|| ||  | ||||| ||  |||||||| ||||||||||||| || || || |||||||||||||| ||  |  | || |||  |  | | |||  | |||   |   ||     | ||         ||||| | |  ||| |||       |        ||| ||| |    ||||||  ||||||| | ||   | ||                          
GGCTATGGTTCCTTTCTCCTGCGAGATCTGCCATTTGATGCCATTCAATTTTGCATATATGAGCAACTCCGAATTGGTTATCGATTAACGgtatttatctcacttttatttaatgaatcca------atgtattgttcttgaatagttccgtgttcttttgaac-catcacg--ttctga-atactgat-tgttaattcag--------------------------

upper sequence: AT4G39460.1 (Arabidopsis thaliana), 5'ss of exon 9
lower sequence: PP1S450_16V6.1 (Physcomitrella patens), 5'ss of exon 9
GGATACCGGTCCTTCCTTTTGCGAGATTTGCCATTTGATGCTATACAGTTCTGCATATATGAGCAGCTTTGCTTGGGGTATAAAAAAGCCgtaagtttctttgtaaaat---------aagtggcatttcttctatat-------gtaatatctttggataaggtatcggaaaaaaaaacgcatgataact-tctgatgt-actgatattttgcatgagatttactttggtc---aactctttggcag------------------------------
|| |   | || |||||  | |||||||| |||||||||||||| ||||| ||||| || ||||||||| | ||||| |  || ||||  |||||||   || |  |           | || | |   | ||| |||       || |    ||||  | |  | |    | || ||  | |  | || | | ||   | || |   | ||  |||   ||    ||| ||    |    ||| |                                
GGTTTTGGATCTTTCCTCCTTCGAGATTTACCATTTGATGCTATCCAGTTTTGCATTTACGAGCAGCTTAGATTGGGCTTGAAGAAAGTGgtaagttaacttatggatagctttttcaaggttggaacacatctgtatacgcacagttacgattttgttttaaatcttaagagaagaatagaactaaaagtgtgtgtcatcaccgggctgttctatgtatttatagttgctctcagaggagttgacgttgaattaatgcttgtttttcactctttcag

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|124960330|gb|EL035005.1|EL035005
EST:     CTATACAGTTCTGCATATATGAGCAGCTTTGCTTGGGGTATAAAAAAGCC                         GCGCGTAGAGAGCTTAGTGAT
genomic: CTATACAGTTCTGCATATATGAGCAGCTTTGCTTGGGGTATAAAAAAGCCgtaagtttct ... tctttggcagGCGCGTAGAGAGCTTAGTGAT
EST: gi|86037538|gb|DR333293.1|DR333293
EST:     CTATACAGTTCTGCATATATGAGCAGCTTTGCTTGGGGTATAAAANAGCC                         GCGCGTAGAGAGCTTAGTGATCCTGAGAACGCTCTAATCGGTGCATTTGCT
genomic: CTATACAGTTCTGCATATATGAGCAGCTTTGCTTGGGGTATAAAAAAGCCgtaagtttct ... tctttggcagGCGCGTAGAGAGCTTAGTGATCCTGAGAACGCTCTAATCGGTGCATTTGCT
EST: gi|125089220|gb|EL147670.1|EL147670
EST:     AGTTCTGCATATATGAGCAGCTTTGCTTGGGGTATAAAAAAGCC                         GCGCGTAGAGAGCTTAGTGATCCTGAGAACGCTCTAATCGGTGCATTTG
genomic: AGTTCTGCATATATGAGCAGCTTTGCTTGGGGTATAAAAAAGCCgtaagtttct ... tctttggcagGCGCGTAGAGAGCTTAGTGATCCTGAGAACGCTCTAATCGGTGCATTTG
EST: gi|125212681|gb|EL227635.1|EL227635
EST:     CTTGGGGTATAAAAAAGCC                         GCGCGTAGAGAGCTTAGTGATCCTGAGAACGCTCTAATCGGTGCATTTGCT
genomic: CTTGGGGTATAAAAAAGCCgtaagtttct ... tctttggcagGCGCGTAGAGAGCTTAGTGATCCTGAGAACGCTCTAATCGGTGCATTTGCT
EST: gi|86082868|gb|DR378627.1|DR378627
EST:     CTATACAGTTCTGCATATATGAGCAGCTTTGCTTGGGGTATAAAAAAGCC                         GCGCGTAGAGAGCTTAGTGATCCTGAGAACGCTCTAATCGGTGCATTTGCT
genomic: CTATACAGTTCTGCATATATGAGCAGCTTTGCTTGGGGTATAAAAAAGCCgtaagtttct ... tctttggcagGCGCGTAGAGAGCTTAGTGATCCTGAGAACGCTCTAATCGGTGCATTTGCT
EST: gi|124727293|gb|EH818695.1|EH818695
EST:     CTTTGCTTGGGGTATAAAAAAGCC                         GCGCGTAGAGAGCTTAGTGATCCTGAGAACGCTCTAATCGGTGCATTTGCT
genomic: CTTTGCTTGGGGTATAAAAAAGCCgtaagtttct ... tctttggcagGCGCGTAGAGAGCTTAGTGATCCTGAGAACGCTCTAATCGGTGCATTTGCT
EST: gi|163994833|gb|ES152733.1|ES152733
EST:     TTTGCTTGGGGTATAAAAAAGCC                         GCGCGTAGAGAGCTTAGTGATCCTGAGAACGCTCTAATCGGT
genomic: TTTGCTTGGGGTATAAAAAAGCCgtaagtttct ... tctttggcagGCGCGTAGAGAGCTTAGTGATCCTGAGAACGCTCTAATCGGT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGATACCGGTCCTTCCTTTTGCGAGATTTGCCATTTGATGCTATACAGTTCTGCATATATGAGCAGCTTTGCTTGGGGTATAAAAAAGCCgtaagtttctttgtaaaataagtggcatttcttctatatgtaatatctttggataaggtatcggaaaaaaaaacgcatgataacttctgatgtactgatattttgcatgagatttactttggtcaactctttggcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT