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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagttttttatttcaattggtttttctttctttctttcgcctttggtataatgcagagtttcaatttgtaattgttcttttatgttttgcagGTATGCTGGAAACATTCATACGCAGGTCACAGAGATTCTTCTTCAAGAGATTTTTGCAAGTACTGGTCCTATTGAAAGCTGTAAACTCATCAGAAAGGAT

Basic information

species Arabidopsis thaliana
transcript AT1G54080.2
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G54080.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv09s0002g00880.t01 (Vitis vinifera), 3'ss of exon 2
gtgagtttttt----atttcaattggtttttctttctttctttcgcctttggtataatgcagagtttcaatttgtaattgttcttttatgttt-------tgcagGTATGCTGGAAACATTCATACGCAGGTCACAGAGATTCTTCTTCAAGAGATTTTTGCAAGTACTGGTCCTATTGAAAGCTGTAAACTCATCAGAAAGGAT
     ||||||    |||  ||  || ||||| || || ||   || |||  |           |||| |    | || |||  ||||| |||       |||||||||| ||| |||||||||||||||||  | ||    |||||||||||| |||||||||||||||||||| ||||| |||| || ||| | |||||||| 
-----ttttttggggattcaaaggggattttcctttttgctcaagcttttctttgttcttttcttttctagaatttatagtttctttatctttgaggaaatgcagGTATGTTGGGAACATTCATACGCAGGTATCGGAACCACTTCTTCAAGAGGTTTTTGCAAGTACTGGTCCTGTTGAAGGCTGCAAGCTCGTTAGAAAGGAA
















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|125144645|gb|EL180203.1|EL180203
EST:     CCAAGTGGAAACCTTCCTCCTGGTTTTGATCCAACTACTTGCCGTAGTGT                         GTATGCTGGAAACATTCATACGCA
genomic: CCAAGTGGAAACCTTCCTCCTGGTTTTGATCCAACTACTTGCCGTAGTGTgtgagttttt ... tgttttgcagGTATGCTGGAAACATTCATACGCA
EST: gi|125055193|gb|EL125537.1|EL125537
EST:     CCAAGTGGAAACCTTCCTCCTGGTTTTGATCCAACTACTTGCCGTAGTGT                         GTATGCTGGAAACATTCATACGCAGGTCACAGAGATTCTTCTTCAAGAGAT
genomic: CCAAGTGGAAACCTTCCTCCTGGTTTTGATCCAACTACTTGCCGTAGTGTgtgagttttt ... tgttttgcagGTATGCTGGAAACATTCATACGCAGGTCACAGAGATTCTTCTTCAAGAGAT
EST: gi|125104975|gb|EL158892.1|EL158892
EST:     CCAAGTGGAAACCTTCCTCCTGGTTTTGATCCAACTACTTGCCGTAGTGT                         GTATGCTGGAAACATTCATACGCAGGTCACAGAGATT
genomic: CCAAGTGGAAACCTTCCTCCTGGTTTTGATCCAACTACTTGCCGTAGTGTgtgagttttt ... tgttttgcagGTATGCTGGAAACATTCATACGCAGGTCACAGAGATT
EST: gi|124882852|gb|EH961754.1|EH961754
EST:     CCAAGTGGAAACCTTCCTCCTGGTTTTGATCCAACTACTTGCCGTAGTGT                         GTATGCTGGAAACATTCATACGCAGGTCACAGAGATTCTTCTTCAAGAGAT
genomic: CCAAGTGGAAACCTTCCTCCTGGTTTTGATCCAACTACTTGCCGTAGTGTgtgagttttt ... tgttttgcagGTATGCTGGAAACATTCATACGCAGGTCACAGAGATTCTTCTTCAAGAGAT
EST: gi|125269206|gb|EL283291.1|EL283291
EST:     ATCCAACTACTTGCCGTAGTGT                         GTATGCTGGAAACATTCATACGCAGGTCACAGAGATTCTTCTTCAAGAGAT
genomic: ATCCAACTACTTGCCGTAGTGTgtgagttttt ... tgttttgcagGTATGCTGGAAACATTCATACGCAGGTCACAGAGATTCTTCTTCAAGAGAT
EST: gi|125227260|gb|EL241345.1|EL241345
EST:     CCAAGTGGAAACCTTCCTCCTGGTTTTGATCCAACTACTTGCCGTAGTGT                         GTATGCTGGAAACATTCATACGCAGGTCACAGAGATTCTTCTTCAAGAGTA
genomic: CCAAGTGGAAACCTTCCTCCTGGTTTTGATCCAACTACTTGCCGTAGTGTgtgagttttt ... tgttttgcagGTATGCTGGAAACATTCATACGCAGGTCACAGAGATTCTTCTTCAAGAG-A


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cgcctttggtataatgcagagtttcaatttgtaattgttcttttatgttttgcagGTATGCTGGAAACATTCATACGCAGGTCACAGAGATTCTTCTTCAAGAGATTTTTGCAAGTACTGGTCCTATTGAAAGCTGTAAACTCATCAGAAAGGAT
                                     ttcttttatgtttt  CT-rich tract
                         aatttgtaattgttct  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagttttttatttcaattggtttttctttctttctttcgcctttggtataatgcagagtttcaatttgtaattgttcttttatgttttgcagGTATGCTGGAAACATTCATACGCAGGTCACAGAGATTCTTCTTCAAGAGATTTTTGCAAGTACTGGTCCTATTGAAAGCTGTAAACTCATCAGAAAGGAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG