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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TACAAATTTTGTTTCCACAATCCTTATTCTACTCCTGAAACTGTCTCCTTTTATATTCATGTTGGTCATATTCCTAATGAGCATGACTTAGCCAAAGATGgttcgtttccattccccttatgtatgatcatcttcattgatgcaatctgtattttgtgcattgagcttgagctgttttgtgatgttatgttctttctgttttgttgtttggttcttag

Basic information

species Arabidopsis thaliana
transcript AT3G22845.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G22845.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: Vv05s0020g04150.t01 (Vitis vinifera), 5'ss of exon 2
TACAAATTTTGTTTCCACAATCCTTATTCTACTCCTGAAACTGTCTCCTTTTATATTCATGTTGGTCATATTCCTAATGAGCATGACTTAGCCAAAGATGgttcgtttccattccccttatgtatgatcatcttcattgatgcaatctgtattttgtgcattgagcttgagctgttttgtgatgttatgttctttctgttttgttgtttggttcttag
||||||||||||||||| ||| ||||| | || ||||| |||||||| || ||||| |||||||| |||||||| ||||||||  || | ||||||||||||  ||| | |||    || |  || ||  ||||| |||    | ||| ||| |  |      |  |  |  | |||| | || ||| || || |      ||               
TACAAATTTTGTTTCCAAAATTCTTATGCAACACCTGAGACTGTCTCTTTCTATATACATGTTGGCCATATTCCCAATGAGCACAACCTCGCCAAAGATGgtatgtt-caattttttttgtcaat-attttcttc-ttgtcatattct-tatatcttatcgctatttctatatattttataattttaagtgctattgcaaatga--------------
















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|164138454|gb|ES165709.1|ES165709
EST:     ATATTCATGTTGGTCATATTCCTAATGAGCATGACTTAGCCAAAGATG                         AACATTTGGACCCGGTAAATGTTAAGATAGCTGAGTTGAGAGAGGCTTTGG
genomic: ATATTCATGTTGGTCATATTCCTAATGAGCATGACTTAGCCAAAGATGgttcgtttcc ... tggttcttagAACATTTGGACCCGGTAAATGTTAAGATAGCTGAGTTGAGAGAGGCTTTGG
EST: gi|164015674|gb|ES141097.1|ES141097
EST:     CTTAGCCAAAGATG                         AACATTTGGTACCCGGTAAATGTTAAGATAGCTGAGTTGAGAGAGGCTTTG
genomic: CTTAGCCAAAGATGgttcgtttcc ... tggttcttagAACATTTGG-ACCCGGTAAATGTTAAGATAGCTGAGTTGAGAGAGGCTTTG
EST: gi|47828544|gb|CK118228.1|CK118228
EST:     TTATATTCATGTTGGTCATATTCCTAATGAGCATGACTTAGCCAAAGATG                         AACATTTGGACCCGGTAAATGTTAAGATAGCTGAGTTGAGAGAGGCTTTGG
genomic: TTATATTCATGTTGGTCATATTCCTAATGAGCATGACTTAGCCAAAGATGgttcgtttcc ... tggttcttagAACATTTGGACCCGGTAAATGTTAAGATAGCTGAGTTGAGAGAGGCTTTGG
EST: gi|164032319|gb|ES157058.1|ES157058
EST:     TATTCCTAATGAGCATGACTTAGCCAAAGATG                         AACATTTGGACCCGGTAAATGTTAAGATAGCTGAGTTGAGAGAGGCTTTGG
genomic: TATTCCTAATGAGCATGACTTAGCCAAAGATGgttcgtttcc ... tggttcttagAACATTTGGACCCGGTAAATGTTAAGATAGCTGAGTTGAGAGAGGCTTTGG
EST: gi|86073424|gb|DR369181.1|DR369181
EST:     TATTCCTAATGAGCATGACTTAGCCAAAGATG                         AACATTTGGACCCGGTAAATGTTAAGATAGCTGAGTTGAGAGAGGCTTTGG
genomic: TATTCCTAATGAGCATGACTTAGCCAAAGATGgttcgtttcc ... tggttcttagAACATTTGGACCCGGTAAATGTTAAGATAGCTGAGTTGAGAGAGGCTTTGG
EST: gi|164029786|gb|ES193550.1|ES193550
EST:     ATTCCTAATGAGCATGACTTAGCCAAAGATG                         AACATTTGGACCCGGTAAATGTTAAGATAGCTGAGTTGAGAGAGGCTTTGG
genomic: ATTCCTAATGAGCATGACTTAGCCAAAGATGgttcgtttcc ... tggttcttagAACATTTGGACCCGGTAAATGTTAAGATAGCTGAGTTGAGAGAGGCTTTGG
EST: gi|47828547|gb|CK118231.1|CK118231
EST:     TTATATTCATGTTGGTCATATTCCTAATGAGCATGACTTAGCCAAAGATG                         AACATTTGGACCCGGTAAATGTTAAGATAGCTGAGTTGAGAGAGGCTTTGG
genomic: TTATATTCATGTTGGTCATATTCCTAATGAGCATGACTTAGCCAAAGATGgttcgtttcc ... tggttcttagAACATTTGGACCCGGTAAATGTTAAGATAGCTGAGTTGAGAGAGGCTTTGG
EST: gi|163980529|gb|ES173764.1|ES173764
EST:     TTATATTCATGTTGGTCATATTCCTAATGAGCATGACTTAGCCAAAGATG                         AACATTTGGACCCGGTAAA
genomic: TTATATTCATGTTGGTCATATTCCTAATGAGCATGACTTAGCCAAAGATGgttcgtttcc ... tggttcttagAACATTTGGACCCGGTAAA
EST: gi|124762758|gb|EH852888.1|EH852888
EST:     TTATATTCATGTTGGTCATATTCCTAATGAGCATGACTTAGCCAAAGATG                         AACATTTGGACCCGGTAAATGTTAAGATAGCTGA
genomic: TTATATTCATGTTGGTCATATTCCTAATGAGCATGACTTAGCCAAAGATGgttcgtttcc ... tggttcttagAACATTTGGACCCGGTAAATGTTAAGATAGCTGA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TACAAATTTTGTTTCCACAATCCTTATTCTACTCCTGAAACTGTCTCCTTTTATATTCATGTTGGTCATATTCCTAATGAGCATGACTTAGCCAAAGATGgttcgtttccattccccttatgtatgatcatcttcattgatgcaatctgtattttgtgcattgagcttgagctgttttgtgatgttatgttctttctgttttgttgtttggttcttag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG