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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgattattttaccttctctctatccttcttctggttgggagggaaaaatatatgattctttttgcagttttattatatagcatgactaagatttgatatgcagGTGCGGAGGCTATCTGCTTGCGAGACAATGGGCTCTGCCACCACTATTTGCAGCGATAAAACTGGAACACTAACTCTGAATCAG

Basic information

species Arabidopsis thaliana
transcript AT5G57110.1
intron # 17
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G57110.2 (Arabidopsis thaliana), 3'ss of exon 17
lower sequence: GLYMA17G06520.1 (Glycine max), 3'ss of exon 18
gtatgattattttaccttctctctat-ccttcttctggttgggagggaaaaatatatgattctttttgcagttttattatatagcatgactaagatttgatatgcagGTGCGGAGGCTATCTGCTTGCGAGACAATGGGCTCTGCCACCACTATTTGCAGCGATAAAACTGGAACACTAACTCTGAATCAG
                       ||| ||  ||| || ||| |    |  | | |   ||   | ||  ||   |  | | |   || ||  |   ||||  |||||||| ||||||| ||||| || ||||||||||| || ||||| || |||||||| ||||| ||||||||| | ||| ||||||||
----------------------gtatgccaacttttgtttgtgctataggattttggcatatctatttgagaaatgctgtttgatataacaca---ttgaattgcagGTGAGGAGGCTTTCTGCCTGTGAGACAATGGGGTCAGCCACAACCATTTGCAGTGATAAGACTGGAACATTGACTATGAATCAG

upper sequence: AT5G57110.2 (Arabidopsis thaliana), 3'ss of exon 17
lower sequence: GLYMA13G00420.1 (Glycine max), 3'ss of exon 15
gtatgattattttaccttctctctatccttcttctggttgggagggaaaaatatatg-attctttttgcagttttattatatagcatgactaagatttgatatgcagGTGCGGAGGCTATCTGCTTGCGAGACAATGGGCTCTGCCACCACTATTTGCAGCGATAAAACTGGAACACTAACTCTGAATCAG----
                       ||| |   || | ||| |      |  || | || ||   | ||  ||   |  | | ||  || ||  |   ||||  | |||||| ||||||| ||||| || ||||||||||| || ||||| || |||||||| ||||| ||||||||| | ||| ||||||||    
----------------------gtatgccaatttttgtttgtgctttaggatttttgcatatctatttgagaaatgctgtttaatataacaca---ttgaattacagGTGAGGAGGCTTTCTGCCTGTGAGACAATGGGGTCAGCCACAACCATTTGCAGTGATAAGACTGGAACATTGACTATGAATCAGGTTA

upper sequence: AT5G57110.2 (Arabidopsis thaliana), 3'ss of exon 17
lower sequence: GLYMA15G18180.1 (Glycine max), 3'ss of exon 15
gtatgattattttaccttctctctatccttctt-ctggttgggagggaaaaatatatgattctttttgcagttttattatatagcatgactaagatttgatatgcagGTGCGGAGGCTATCTGCTTGCGAGACAATGGGCTCTGCCACCACTATTTGCAGCGATAAAACTGGAACACTAACTCTGAATCAG
       |||   |  |  | | | | ||| |    ||||  ||   ||| | || |||  |||| |      ||||  | || |||          |||  || ||||  ||||||| ||||| |||||||| |||||||||||||| || || ||||| ||||| ||||| ||| | ||| ||||||||
------gtatgccaattgatgtttgtacttttagtcggttttgacataaatacatgtgaaactttgt------ttatattgtaacat----------tgaattgtagGTAAGGAGGCTTTCTGCCTGCGAGACCATGGGCTCTGCCACAACCATATGCAGTGATAAGACTGGTACATTGACTATGAATCAG

upper sequence: AT5G57110.2 (Arabidopsis thaliana), 3'ss of exon 17
lower sequence: Vv11s0052g00320.t01 (Vitis vinifera), 3'ss of exon 18
----gtatgattattttaccttctctctatccttcttctggttgggagggaaaaata---tatgattcttt-ttgcagttttattatatagcatgactaagatttgatatgcagGTGCGGAGGCTATCTGCTTGCGAGACAATGGGCTCTGCCACCACTATTTGCAGCGATAAAACTGGAACACTAACTCTGAATCAG
    ||||||  | | |  ||   ||  | | | |    | ||      |  |  |     |||| | | | ||  |  |  ||    | |  | || |  | ||||  ||||||| |||||||| |||||||| ||||| ||||||||| |||| ||||||||||| ||||| || ||||| |||||| ||||||||
gtatgtatgacaaatatttctgaacta-agcttccacaagattatatatgttatgtgggtcatgagtatatgttatatatgcatcgggtggtttaac-agcagttgaactgcagGTACGGAGGCTTTCTGCTTGTGAGACCATGGGCTCTTCCACGACTATTTGCAGTGATAAGACAGGAACTCTAACTTTGAATCAG

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|124813608|gb|EH898474.1|EH898474
EST:     CTTTAACCCTTGCCTATTCAATGAGGAAAATGATGGCAGATAAGGCTTTG                         GTGCGGAGGCTATCTGCTTGCGAGACAATGGGCTCTGCCACCACT
genomic: CTTTAACCCTTGCCTATTCAATGAGGAAAATGATGGCAGATAAGGCTTTGgtatgattat ... tgatatgcagGTGCGGAGGCTATCTGCTTGCGAGACAATGGGCTCTGCCACCACT
EST: gi|116481548|gb|EG524140.1|EG524140
EST:     CCTTGCCTATTCAATGAGGAAAATGATGGCAGATAAGGCTTTG                         GTGCGGAGGCTATCTGCTTGCGAGACAATGGGCTCTGCCACCACTATTTGC
genomic: CCTTGCCTATTCAATGAGGAAAATGATGGCAGATAAGGCTTTGgtatgattat ... tgatatgcagGTGCGGAGGCTATCTGCTTGCGAGACAATGGGCTCTGCCACCACTATTTGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatatgattctttttgcagttttattatatagcatgactaagatttgatatgcagGTGCGGAGGCTATCTGCTTGCGAGACAATGGGCTCTGCCACCACTATTTGCAGCGATAAAACTGGAACACTAACTCTGAATCAG
                                          atttgat  putative branch site (score: 5)
          tttttgcagttttatt  TA-rich tract