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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGCTATCCACAAGGGTATGCCTCATAAGTTCTACCATGGTCGTACTGGTCGCATCTGGAATGTCACTAAACGTGCCGTTGGTGTTGAAGTCAACAAACAGgtttgattactcaaaacttttaatctgtttgaaagagttttttgttgttgaaattagggtttgaaattgattttgattctttcatttggggtttaattcg...

Basic information

species Arabidopsis thaliana
transcript AT1G57860.1
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G57860.1 (Arabidopsis thaliana), 5'ss of exon 1
lower sequence: GRMZM2G026216_T01 (Zea mays), 5'ss of exon 1
AGCTATCCACAAGGGTATGCCTCATAAGTTCTACCATGGTCGTACTGGTCGCATCTGGAATGTCACTAAACGTGCCGTTGGTGTTGAAGTCAACAAACAGgtttgattactcaaaacttttaatctgtttgaaagagttttttgttgttgaaattagg-gtttgaaattgatttt----gattctttcatttggggtttaattcg
 ||  |||||||||| ||||| || ||||||||||| || || || |||||| ||||||| ||||| || || ||| | || || ||  | ||||| ||||| | |  || |  | |  ||  |  | | |   |  |  |  |||| ||     |||   ||||||| | || |    |   ||| | ||| | |         
CGCCGTCCACAAGGGGATGCCGCACAAGTTCTACCACGGCCGCACCGGTCGCGTCTGGAACGTCACCAAGCGCGCCATCGGCGTCGAGATAAACAAGCAGgtat-accacacggatccctt--ttcgctagctcgc-tgataggttgctgggcgcaggcagttgaaatcgtttgtgcacggcgcttacgtttagtgcgcggacg-

upper sequence: AT1G57860.1 (Arabidopsis thaliana), 5'ss of exon 1
lower sequence: GLYMA03G36560.1 (Glycine max), 5'ss of exon 1
AGCTATCCACAAGGGTATGCCTCATAAGTTCTACCATGGTCGTACTGGTCGCATCTGGAATGTCACTAAACGTGCCGTTGGTGTTGAAGTCAACAAACAGgtttgattactcaaaacttttaatct---gtttgaaagagttttttgttgttgaaattagggtttgaaattgattttgattctttcatttggggtttaattcg
 ||  |||||||||| ||||| || |||||||||||||| || || |||||| ||||||||||||| |||||||| ||||| || ||||||||||| ||||| |    ||||    | || |  ||     |  |   | |||| || |  |  |  |    | | |  |   ||||       |  | | |  |  ||||  
CGCCGTCCACAAGGGAATGCCACACAAGTTCTACCATGGCCGCACCGGTCGCGTCTGGAATGTCACCAAACGTGCTGTTGGGGTCGAAGTCAACAAGCAGgtctcgc-actctcttccttaaccctaacactctatttacttttctgcttctcgatctgttttgttatgtcttttttatcgtgatactatcgcttccaatt--

upper sequence: AT1G57860.1 (Arabidopsis thaliana), 5'ss of exon 1
lower sequence: GLYMA19G39240.1 (Glycine max), 5'ss of exon 1
AGCTATCCACAAGGGTATGCCTCATAAGTTCTACCATGGTCGTACTGGTCGCATCTGGAATGTCACTAAACGTGCCGTTGGTGTTGAAGTCAACAAACAGgtttgattactcaaaacttttaatctgtttgaaagagttttttgttgttgaaattagggtttgaaattgattttgattctttcatttggggtttaat-tcg--
 ||  | |||||||| ||||| || || ||||||||||| || || || ||| ||||||||||||| |||||||| ||||| || ||||||||||| ||||| | |  ||||    | || |  ||      |    | |||  || |     ||  | | ||   |   || || |||||    |     | |  | |||  
TGCCGTTCACAAGGGAATGCCCCACAAATTCTACCATGGCCGCACCGGACGCGTCTGGAATGTCACCAAACGTGCTGTTGGCGTCGAAGTCAACAAGCAGgtctcac-actctt--ccttaaccctagcaccacccttctttccttttctgcttttcgatctgttgtgttttctgtttcttattgtgatattctcgtgtcgaa

upper sequence: AT1G57860.1 (Arabidopsis thaliana), 5'ss of exon 1
lower sequence: PP1S1_780V6.1 (Physcomitrella patens), 5'ss of exon 1
AGCTATCCACAAGGGTATGCCTCATAAGTTCTACCATGGTCGTACTGGTCGCATCTGGAATGTCACTAAACGTGCCGTTGGTGTTGAAGTCAACAAACAGgtttgattactcaaaacttttaatctgtttgaa--agagttttttgttgttgaaa--ttagggtttgaaattgatttt--gattctttcatttggggtttaattcg
|||  ||||||||||||||||||| ||||||||||| || || || ||   | ||||||| ||||| || |||||||| ||||| |   | ||||| ||||| |||||   |    |  |   ||      |     ||     || |  ||  |  |     ||     ||  || |  | || || | | |  || |       
AGCCGTCCACAAGGGTATGCCTCACAAGTTCTACCACGGGCGCACCGGCATCGTCTGGAACGTCACCAAGCGTGCCGTCGGTGTCGTGATGAACAAGCAGgtatgattgaccttctccctccctcccccgaagccgaagccgcctggtcgtgggagctcccccttcctgcttcgttctagggtttttccttctttggctg------

upper sequence: AT1G57860.1 (Arabidopsis thaliana), 5'ss of exon 1
lower sequence: PP1S107_181V6.1 (Physcomitrella patens), 5'ss of exon 1
AGCTATCCACAAGGGTATGCCTCATAAGTTCTACCATGGTCGTACTGGTCGCATCTGGAATGTCACTAAACGTGCCGTTGGTGTTGAAGTCAACAAACAGgtttgattactcaaaacttttaatctgtttgaaagagttttttgttgttgaaattagggtttgaaattgattttgattctttcatttggggtttaattcg--
 ||| ||||||||||||||||||| ||||||||||| || || || ||   | ||||||| ||||| || || ||||||||||| |   | ||||| ||||| || |  ||    || | |  || | |         |||| |   |     |  || ||    | |    |   |   | | | |  |     ||||   
TGCTGTCCACAAGGGTATGCCTCACAAGTTCTACCACGGACGCACCGGCATCGTCTGGAACGTCACCAAGCGCGCCGTTGGTGTCGTGATGAACAAGCAGgtatggtctctttgtacctct--tcggctgtcgtctacttttggagatgtctgtctggcttaatgactttcgtctgtgggtgcgtcttcgccactattctcg

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|152035968|gb|AU235770.2|AU235770
EST:     GCATCTGGAATGTCACTAAACGTGCCGTTGGTGTTGAAGTCAACAAACAG                         ATTGGGAACAGAATCATAAGGAAGAGGATACATGTGCGTGTGGAGCATGTG
genomic: GCATCTGGAATGTCACTAAACGTGCCGTTGGTGTTGAAGTCAACAAACAGgtttgattac ... tgggttttagATTGGGAACAGAATCATAAGGAAGAGGATACATGTGCGTGTGGAGCATGTG
EST: gi|124818960|gb|EH903826.1|EH903826
EST:     CACTAAACGTGCCGTTGGTGTTGAAGTCAACAAACAG                         ATTGGGAACAGAATCATAAGGAAGAGGATACATGTGCGTGTGGAGCATGTG
genomic: CACTAAACGTGCCGTTGGTGTTGAAGTCAACAAACAGgtttgattac ... tgggttttagATTGGGAACAGAATCATAAGGAAGAGGATACATGTGCGTGTGGAGCATGTG
EST: gi|164082750|gb|ES021201.1|ES021201
EST:     TGTCACTAAACGTGCCGTTGGTGTTGAAGTCAACAAACAG                         ATTGGGAACAGAATCATAAGGAAGAGGATACATGTGCGTGTGGAGCATGTG
genomic: TGTCACTAAACGTGCCGTTGGTGTTGAAGTCAACAAACAGgtttgattac ... tgggttttagATTGGGAACAGAATCATAAGGAAGAGGATACATGTGCGTGTGGAGCATGTG
EST: gi|164230061|gb|ES081631.1|ES081631
EST:     GCATCTGGAATGTCACTAAACGTGCCGTTGGTGTTGAAGTCAACAAACAG                         ATTGGGAACAGAATCATAAGGAAGA
genomic: GCATCTGGAATGTCACTAAACGTGCCGTTGGTGTTGAAGTCAACAAACAGgtttgattac ... tgggttttagATTGGGAACAGAATCATAAGGAAGA
EST: gi|19741180|gb|AU226533.1|AU226533
EST:     CTGGAATGTCACTAAACGTGCCGTTGGTGTTGAAGTCAACAAACAG                         ATTGGGAACAGAATCATAAGGAAGAGGATACATGTGCGTGTGGAGCATGTC
genomic: CTGGAATGTCACTAAACGTGCCGTTGGTGTTGAAGTCAACAAACAGgtttgattac ... tgggttttagATTGGGAACAGAATCATAAGGAAGAGGATACATGTGCGTGTGGAGCATGTG
EST: gi|86063269|gb|DR359026.1|DR359026
EST:     GCATCTGGAATGTCACTAAGCGTGCCGTTGGTGTTGAAGTCAACAAACAG                         ATTGGGAACAGAATCATAAGGAAGAGGATACATGTGCGTGTGGAGCATGTG
genomic: GCATCTGGAATGTCACTAAACGTGCCGTTGGTGTTGAAGTCAACAAACAGgtttgattac ... tgggttttagATTGGGAACAGAATCATAAGGAAGAGGATACATGTGCGTGTGGAGCATGTG
EST: gi|47828955|gb|CK118639.1|CK118639
EST:     GCATCTGGAATGTCACTAAACGTGCCGTTGGTGTTGAAGTCAACAAACAG                         ATTGGGAACAGAATCATAAGGAAGAGGATACATGTGCGTGTGGAGCATGTG
genomic: GCATCTGGAATGTCACTAAACGTGCCGTTGGTGTTGAAGTCAACAAACAGgtttgattac ... tgggttttagATTGGGAACAGAATCATAAGGAAGAGGATACATGTGCGTGTGGAGCATGTG
EST: gi|125298433|gb|EL312518.1|EL312518
EST:     GCATCTGGAATGTCACTAAACGTGCCGTTGGTGTTGAAGTCAACGAACAG                         ATTGGGAACAGAATCATAAGGAAG
genomic: GCATCTGGAATGTCACTAAACGTGCCGTTGGTGTTGAAGTCAACAAACAGgtttgattac ... tgggttttagATTGGGAACAGAATCATAAGGAAG
EST: gi|125226028|gb|EL240113.1|EL240113
EST:     GCATCTGGAATGTCACTAAGCGTGCCGTTGGTGTTGAAGTCAACAAACAG                         ATTGGGAACAGAATCATAAGGAAGAGGATACATGTGCGTGTGGAG
genomic: GCATCTGGAATGTCACTAAACGTGCCGTTGGTGTTGAAGTCAACAAACAGgtttgattac ... tgggttttagATTGGGAACAGAATCATAAGGAAGAGGATACATGTGCGTGTGGAG
EST: gi|164140641|gb|ES202861.1|ES202861
EST:     GGTGTTGAAGTCAACAAACAG                         ATTGGGAACAGAATCATAAGGAAGAGGATACATGTGCGTGTGGAGCATGTG
genomic: GGTGTTGAAGTCAACAAACAGgtttgattac ... tgggttttagATTGGGAACAGAATCATAAGGAAGAGGATACATGTGCGTGTGGAGCATGTG
EST: gi|116472411|gb|EG515003.1|EG515003
EST:     GCATTTGGAATGTCACTAAGCGTGCCGTTGGTGTTGAAGTCAACAAACAG                         ATTGGGAACAGAATCATAAGGAAGAGGATACATGTGCGTGTGGAGCATGTG
genomic: GCATCTGGAATGTCACTAAACGTGCCGTTGGTGTTGAAGTCAACAAACAGgtttgattac ... tgggttttagATTGGGAACAGAATCATAAGGAAGAGGATACATGTGCGTGTGGAGCATGTG
EST: gi|86063271|gb|DR359028.1|DR359028
EST:     GCATCTGGAATGTCACTAAGCGTGCCGTTGGTGTTGAAGTCAACAAACAG                         ATTGGGAACAGAATCATAAGGAAGAGGATACATGTGCGTGTGGAGCATGTG
genomic: GCATCTGGAATGTCACTAAACGTGCCGTTGGTGTTGAAGTCAACAAACAGgtttgattac ... tgggttttagATTGGGAACAGAATCATAAGGAAGAGGATACATGTGCGTGTGGAGCATGTG
EST: gi|163987899|gb|ES077522.1|ES077522
EST:     GGTGTTGAAGTCAACAAACAG                         ATTGGGAACAGAATCATAAGGAAGAGGATACATGTGCGTGTGGAGCATGTG
genomic: GGTGTTGAAGTCAACAAACAGgtttgattac ... tgggttttagATTGGGAACAGAATCATAAGGAAGAGGATACATGTGCGTGTGGAGCATGTG
EST: gi|124795098|gb|EH884777.1|EH884777
EST:     GCATCTGGAATGTCACTAAGCGTGCCGTTGGTGTTGAAGTCAACAAACAG                         ATTGGGAACAGAATCATAAGGAAGAGGATACA
genomic: GCATCTGGAATGTCACTAAACGTGCCGTTGGTGTTGAAGTCAACAAACAGgtttgattac ... tgggttttagATTGGGAACAGAATCATAAGGAAGAGGATACA
EST: gi|86063270|gb|DR359027.1|DR359027
EST:     GCATCTGGAATGTCACTAAGCGTGCCGTTGGTGTTGAAGTCAACAAACAG                         ATTGGGAACAGAATCATAAGGAAGAGGATACATGTGCGTGTGGAGCATGTG
genomic: GCATCTGGAATGTCACTAAACGTGCCGTTGGTGTTGAAGTCAACAAACAGgtttgattac ... tgggttttagATTGGGAACAGAATCATAAGGAAGAGGATACATGTGCGTGTGGAGCATGTG
EST: gi|47828492|gb|CK118176.1|CK118176
EST:     GCATCTGGAATGTCACTAAGCGTGCCGTTGGTGTTGAAGTCAACAAACAG                         ATTGGGAACAGAATCATAAGGAAGAGGATACATGTGCGTGTGGAGCATGTG
genomic: GCATCTGGAATGTCACTAAACGTGCCGTTGGTGTTGAAGTCAACAAACAGgtttgattac ... tgggttttagATTGGGAACAGAATCATAAGGAAGAGGATACATGTGCGTGTGGAGCATGTG
EST: gi|164188242|gb|ES069696.1|ES069696
EST:     GGTGTTGAAGTCAACAAACAG                         ATTGGGAACAGAATCATAAGGAAGAGGATACATGTGCGTGTGGAGCATGTG
genomic: GGTGTTGAAGTCAACAAACAGgtttgattac ... tgggttttagATTGGGAACAGAATCATAAGGAAGAGGATACATGTGCGTGTGGAGCATGTG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGCTATCCACAAGGGTATGCCTCATAAGTTCTACCATGGTCGTACTGGTCGCATCTGGAATGTCACTAAACGTGCCGTTGGTGTTGAAGTCAACAAACAGgtttgattactcaaaacttttaatctgtttgaaagagttttttgttgttgaaattagggtttgaaattgattttgattctttcatttggggtttaattcg

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - actcaaaa