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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCGGAAAGCGCAATAGCTGCTCTCAACTGCAGTGGAGTTGTTCTTGGTTCTTTACCTATAAGgtcagtgaaacaaaaccgatcttcacgacacaaattcgttctctttttcggttttatgacggtttgttattctacag

Basic information

species Arabidopsis thaliana
transcript AT1G32790.1
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G32790.1 (Arabidopsis thaliana), 5'ss of exon 9
lower sequence: Vv02s0025g02740.t01 (Vitis vinifera), 5'ss of exon 10
GCGGAAAGCGCAATAGCTGCTCTCAACTGCAGTGGAGTTGTTCTTGGTTCTTTACCTATAAGgtcag--tgaaacaaaaccgatc-ttcacgacacaaattcgttctctttttcgg----ttttatgacg-gtttgttattctacag-----------------------------------
|| ||||| ||||| ||||||||||||||||| || ||||| |||||||| || || ||||||||||  |  |      |   || ||   |     || | |   | |  |  |      ||| |  |  ||||| |    |  ||                                   
GCTGAAAGTGCAATTGCTGCTCTCAACTGCAGCGGTGTTGTGCTTGGTTCCTTGCCGATAAGgtcagatttcattttgtcttctcatttctgttttcaactaggaatttcataagaaaatctttgtaccatgtttgcttgcttttagtttctaagccaacctttgctgttatgtataatcag
















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|124728675|gb|EH820077.1|EH820077
EST:     ATAGCTGCTCTCAACTGCAGTGGAGTTGTTCTTGGTTCTTTACCTATAAG                         GGTGAGTCCTTCAAAGACGCCTGTTCGTCC
genomic: ATAGCTGCTCTCAACTGCAGTGGAGTTGTTCTTGGTTCTTTACCTATAAGgtcagtgaaa ... tattctacagGGTGAGTCCTTCAAAGACGCCTGTTCGTCC
EST: gi|86081011|gb|DR376768.1|DR376768
EST:     ATAGCTGCTCTCAACTGCAGTGGAGTTGTTCTTGGTTCTTTACCTATAAG                         GGTGAGTCCTTCAAAGACGCCTGTTCGTCCGAGATCACCGAGGCATCCAAT
genomic: ATAGCTGCTCTCAACTGCAGTGGAGTTGTTCTTGGTTCTTTACCTATAAGgtcagtgaaa ... tattctacagGGTGAGTCCTTCAAAGACGCCTGTTCGTCCGAGATCACCGAGGCATCCAAT
EST: gi|164072001|gb|ES060287.1|ES060287
EST:     CAGTGGAGTTGTTCTTGGTTCTTTACCTATAAG                         GGTGAGTCCTTCAAAGACGCCTGTTCGTCCGAGATCACCGAGGCATCCAAT
genomic: CAGTGGAGTTGTTCTTGGTTCTTTACCTATAAGgtcagtgaaa ... tattctacagGGTGAGTCCTTCAAAGACGCCTGTTCGTCCGAGATCACCGAGGCATCCAAT
EST: gi|164153640|gb|ES142973.1|ES142973
EST:     ATAGCTGCTCTCAACTGCAGTGGAGTTGTTCTTGGTTCTTTACCTATAAG                         GGTGAGTCCTTCAAAGACGCCTGTTCGTCCGAG
genomic: ATAGCTGCTCTCAACTGCAGTGGAGTTGTTCTTGGTTCTTTACCTATAAGgtcagtgaaa ... tattctacagGGTGAGTCCTTCAAAGACGCCTGTTCGTCCGAG
EST: gi|125294226|gb|EL308311.1|EL308311
EST:     GCTGCTCTCAACTGCAGTGGAGTTGTTCTTGGTTCTTTACCTATAAG                         GGTGAGTCCTTCAAAGACGCCTGTTCGTCCGAGATCACCGAGGCATCCAAT
genomic: GCTGCTCTCAACTGCAGTGGAGTTGTTCTTGGTTCTTTACCTATAAGgtcagtgaaa ... tattctacagGGTGAGTCCTTCAAAGACGCCTGTTCGTCCGAGATCACCGAGGCATCCAAT
EST: gi|86051676|gb|DR347431.1|DR347431
EST:     ATAGCTGCTCTCAACTGCAGTGGAGATGTTCTTGGTTCTTTACCTATAAG                         GGTGAGTCCTTCAAAGACGCCTGTTCGTCCGAGATCACCGAGGCATCCAAT
genomic: ATAGCTGCTCTCAACTGCAGTGGAGTTGTTCTTGGTTCTTTACCTATAAGgtcagtgaaa ... tattctacagGGTGAGTCCTTCAAAGACGCCTGTTCGTCCGAGATCACCGAGGCATCCAAT
EST: gi|125304035|gb|EL318120.1|EL318120
EST:     ATAGCTGCTCTCAACTGCAGTGGAGTTGTTCTTGGTTCTTTACCTATAAG                         GGTGAGTCCTTCAAAGACGCCTGTTCGTCCGAGATCACCGAGG
genomic: ATAGCTGCTCTCAACTGCAGTGGAGTTGTTCTTGGTTCTTTACCTATAAGgtcagtgaaa ... tattctacagGGTGAGTCCTTCAAAGACGCCTGTTCGTCCGAGATCACCGAGG
EST: gi|125089080|gb|EL147586.1|EL147586
EST:     ATAGCTGCTCTCAACTGCAGTAGAGTTGTTCTTGGTTCTTTACCTATAAG                         GGTGAGTCCTTCAAAGACGCCTGTTCGTCCGAGATCACCGAGGCA
genomic: ATAGCTGCTCTCAACTGCAGTGGAGTTGTTCTTGGTTCTTTACCTATAAGgtcagtgaaa ... tattctacagGGTGAGTCCTTCAAAGACGCCTGTTCGTCCGAGATCACCGAGGCA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCGGAAAGCGCAATAGCTGCTCTCAACTGCAGTGGAGTTGTTCTTGGTTCTTTACCTATAAGgtcagtgaaacaaaaccgatcttcacgacacaaattcgttctctttttcggttttatgacggtttgttattctacag

- - - - - - - AGCTGC
- - - - - - -  GCTGCT
- - - - - - - - - - - - - CTGCAG
- - - - - - - - - - - - - - - AGTGGA
- - - - - - - - - - - - - - -  GTGGAG