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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaataaatcaatactcagagaactatgtgaattatttctcttttggcgacgctatataaaaaaaagatgcaaatgttgactacagGTGACATCTCCAGTCCAATGGGAGACAACAGTAAAGACTCTCTTATCCAAAGGACTTAAAAGCAGCTACGAATTGGGACCTGGAAAG

Basic information

species Arabidopsis thaliana
transcript AT2G30200.1
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT2G30200.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: Vv06s0004g07380.t01 (Vitis vinifera), 3'ss of exon 8
gtaataaatcaatactcagagaactatgtgaattatttctcttttggcgacgctatataaaaaaaagatgcaaatgttgactacagGTGACATCTCCAGTCCAATGGGAGACAACAGTAAAGACTCTCTTATCCAAAGGACTTAAAAGCAGCTACGAATTGGGACCTGGAAAG
|||| | |     |||        | | | |   ||      |  |||      ||  || |||   |  ||||      |  |||||||| || ||||| | |||||| |||||||| ||||||||| || |||||||||| ||||  || ||||||||||| |||||||||
gtaagatacttgaacttgtgatcttctatcaggaataaaaaat--ggcatgctaattcaacaaatcaactcaaa----atccccagGTGACTTCCCCAGTTCTATGGGAAACAACAGTGAAGACTCTCCTAACCAAAGGACTAAAAAAGAGTTACGAATTGGGGCCTGGAAAG
















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|86080301|gb|DR376058.1|DR376058
EST:     CACAGCCTCATGCAGATCCAGACACGATCAAGAAGATACTTGCACGCCAG                         GTGACATCTCCAGTCCAATGGGAGACAACAGTAAAGACTCTCTTATCCAAA
genomic: CACAGCCTCATGCAGATCCAGACACGATCAAGAAGATACTTGCACGCCAGgtaataaatc ... ttgactacagGTGACATCTCCAGTCCAATGGGAGACAACAGTAAAGACTCTCTTATCCAAA
EST: gi|116401255|gb|EG443847.1|EG443847
EST:     CACAGCCTCATGCAGATCCAGACACGATCAAGAAGATACTTGCACGCCAG                         GTGACATCTCCAGTCCAATGGGAGACAACAGTAAAGACTCTCTTATCCAAA
genomic: CACAGCCTCATGCAGATCCAGACACGATCAAGAAGATACTTGCACGCCAGgtaataaatc ... ttgactacagGTGACATCTCCAGTCCAATGGGAGACAACAGTAAAGACTCTCTTATCCAAA
EST: gi|116378971|gb|EG421563.1|EG421563
EST:     CACAGCCTCATGCAGATCCAGACACGATCAAGAAGATACTTGCACGCCAG                         GTGACATCTCCAGTCCAATGGGAGACAACAGTAAAGACTCTCTTATCCAAA
genomic: CACAGCCTCATGCAGATCCAGACACGATCAAGAAGATACTTGCACGCCAGgtaataaatc ... ttgactacagGTGACATCTCCAGTCCAATGGGAGACAACAGTAAAGACTCTCTTATCCAAA
EST: gi|116476496|gb|EG519088.1|EG519088
EST:     CACAGCCTCATGCAGATCCAGACACGATCAAGAAGATACTTGCACGCCAG                         GTGACATCTCCAGTCCAATGGGAGACAACAGTAAAGACTTTTTTATCCAAA
genomic: CACAGCCTCATGCAGATCCAGACACGATCAAGAAGATACTTGCACGCCAGgtaataaatc ... ttgactacagGTGACATCTCCAGTCCAATGGGAGACAACAGTAAAGACTCTCTTATCCAAA
EST: gi|86074247|gb|DR370004.1|DR370004
EST:     CACAGCCTCATGCAGATCCAGACACGATCAAGAAGATACTTGCACGCCAG                         GTGACATCTCCAGTCCAATGGGAGACAACAGTAAAGACTCTCTTATCCAAA
genomic: CACAGCCTCATGCAGATCCAGACACGATCAAGAAGATACTTGCACGCCAGgtaataaatc ... ttgactacagGTGACATCTCCAGTCCAATGGGAGACAACAGTAAAGACTCTCTTATCCAAA
EST: gi|116476495|gb|EG519087.1|EG519087
EST:     CACAGCCTCATGCAGATCCAGACACGATCAAGAAGATACTTGCACGCCAG                         GTGACATCTCCAGTCCAATGGGAGACAACAGTAAAGACTCTCTTATCCAAA
genomic: CACAGCCTCATGCAGATCCAGACACGATCAAGAAGATACTTGCACGCCAGgtaataaatc ... ttgactacagGTGACATCTCCAGTCCAATGGGAGACAACAGTAAAGACTCTCTTATCCAAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attatttctcttttggcgacgctatataaaaaaaagatgcaaatgttgactacagGTGACATCTCCAGTCCAATGGGAGACAACAGTAAAGACTCTCTTATCCAAAGGACTTAAAAGCAGCTACGAATTGGGACCTGGAAAG
                                           tgttgac  putative branch site (score: 3)
                      tatataaaaaaaagat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaataaatcaatactcagagaactatgtgaattatttctcttttggcgacgctatataaaaaaaagatgcaaatgttgactacagGTGACATCTCCAGTCCAATGGGAGACAACAGTAAAGACTCTCTTATCCAAAGGACTTAAAAGCAGCTACGAATTGGGACCTGGAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGCT