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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaccattttgatttgagcttatgaatctagttgtcttctacgttaatgggtttatgcatgatgattgattggttgattcaagagaattgtacttagaaatggttggaattggttctttttgtgtgcagagGGTGTTTTGTTTGCTAAAAAGGATTTCAACTTACCACAACATCCTTTGATTGAGAGTGTTCCAAATCTGCAAGTTATCAAGTTGATGCAGAGTTTCAAAT

Basic information

species Arabidopsis thaliana
transcript AT5G41520.2
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G41520.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv02s0025g00310.t01 (Vitis vinifera), 3'ss of exon 2
gtaccattttgatttgagcttatgaatctagttgtcttctacgttaatgggtttatgcatgatgattgattggttgattcaagagaattgtacttagaaatggttggaattggttctttttgtgtgcagagGGTGTTTTGTTTGCTAAAAAGGATTTCAACTTACCACAACATCCTTTGATTGAGAGTGTTCCAAATCTGCAAGTTATCAAGTTGATGCAGAGTTTCAAAT-
||| | |  | |||    |   | || |  | | |  | |   | | || ||| |||  |     ||  ||  ||||||        || ||                |||  ||||| ||   | ||||||| ||||  | ||| |||||||| | |||  |  |  |||||||    || ||   ||| || |||||||| |||||||||||||||||||| ||||| | 
gtatcttacttattctctcactttaaccacgatttgctgtgattcagtgtgttcatgtttttattttattttattgatt--------ttatat---------------attttttcttgtttgcttcagAGGGAGTTTGCTATGCGAAAAAGGACTACAATCTCGCGAAACATCCCGATATCGA---TGTCCCGAATCTGCAGGTTATCAAGTTGATGCAGAGCTTCAAGTC
















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|47831362|gb|CK121046.1|CK121046
EST:     ATCATATCAGAGACTAACCGCCGTGAGATCTCCAAGTACCTCTTCAAAGAG                        
genomic: ATCATATCAGAGACTAACCGCCGTGAGATCTCCAAGTACCTCTTC-AA-AGgtaccatttt ... gtgtgcaga
EST: gi|124953707|gb|EL028864.1|EL028864
EST:     TATCAGAGACTAACCGCCGTGAGATCTCCAAGTACCTCTTCAAAGAG                        
genomic: TATCAGAGACTAACCGCCGTGAGATCTCCAAGTACCTCTTC-AA-AGgtaccatttt ... gtgtgcaga
EST: gi|116471696|gb|EG514288.1|EG514288
EST:     ATCATATCAGAGACTAACCGCCGTGAGATCTCCAAGTACCTCTTCAAAGAG                        
genomic: ATCATATCAGAGACTAACCGCCGTGAGATCTCCAAGTACCTCTTC-AA-AGgtaccatttt ... gtgtgcaga
EST: gi|116406681|gb|EG449273.1|EG449273
EST:     ATCATATCAGAGACTAACCGCCGTGAGATCTCCAAGTACCTCTTCAAAGAG                        
genomic: ATCATATCAGAGACTAACCGCCGTGAGATCTCCAAGTACCTCTTC-AA-AGgtaccatttt ... gtgtgcaga
EST: gi|163976375|gb|EL979175.1|EL979175
EST:     ATCATATCAGAGACTAACCGCCGTGAGATCTCCAAGTACCTCTTCAAAG                         A
genomic: ATCATATCAGAGACTAACCGCCGTGAGATCTCCAAGTACCTCTTCAAAGgtaccatttt ... gtgtgcagag-
EST: gi|163976375|gb|EL979175.1|EL979175
EST:     ATCATATCAGAGACTAACCGCCGTGAGATCTCCAAGTACCTCTTCAAAG                         A
genomic: ATCATATCAGAGACTAACCGCCGTGAGATCTCCAAGTACCTCTTCAAAGgtaccatttt ... gtgtgcagag-
EST: gi|125023008|gb|EL095277.1|EL095277
EST:     AGACTAACCGCCGTGAGATCTCCAAGTACCTCTTCAAAGAG                        
genomic: AGACTAACCGCCGTGAGATCTCCAAGTACCTCTTC-AA-AGgtaccatttt ... gtgtgcaga
EST: gi|116471706|gb|EG514298.1|EG514298
EST:     ATCATATCAGAGACTAACCGCCGTGAGATCTCCAAGTACCTCTTCAAAGAG                        
genomic: ATCATATCAGAGACTAACCGCCGTGAGATCTCCAAGTACCTCTTC-AA-AGgtaccatttt ... gtgtgcaga
EST: gi|124804253|gb|EH892168.1|EH892168
EST:     TCATATCAGAGACTAACCGCCGTGAGATCTCCAAGTACCTCTTCAAGGAG                         GGTGTTTTGTTTGCTAAAAAGGATTTCAA
genomic: TCATATCAGAGACTAACCGCCGTGAGATCTCCAAGTACCTCTTCAA--AGgtaccatttt ... gtgtgcagagGGTGTTTTGTTTGCTAAAAAGGATTTCAA
EST: gi|47827937|gb|CK117621.1|CK117621
EST:     CCGCCGTGAGATCTCCAAGTACCTCTTCAAAGAG                        
genomic: CCGCCGTGAGATCTCCAAGTACCTCTTC-AA-AGgtaccatttt ... gtgtgcaga
EST: gi|116476370|gb|EG518962.1|EG518962
EST:     ATCATATCAGAGACTAACCGCCGTGAGATCTCCAAGTACCTCTTCAAAGAG                        
genomic: ATCATATCAGAGACTAACCGCCGTGAGATCTCCAAGTACCTCTTC-AA-AGgtaccatttt ... gtgtgcaga
EST: gi|116406665|gb|EG449257.1|EG449257
EST:     ATCATATCAGAGACTAACCGCCGTGAGATCTCCAAGTACCTCTTCAAAGAG                        
genomic: ATCATATCAGAGACTAACCGCCGTGAGATCTCCAAGTACCTCTTC-AA-AGgtaccatttt ... gtgtgcaga
EST: gi|116471734|gb|EG514326.1|EG514326
EST:     ATCATATCAGAGACTAACCGCCGTGAGATCTCCAAGTACCTCTTCAAAGAG                        
genomic: ATCATATCAGAGACTAACCGCCGTGAGATCTCCAAGTACCTCTTC-AA-AGgtaccatttt ... gtgtgcaga
EST: gi|125013900|gb|EL086169.1|EL086169
EST:     GATCATATCAGAGACTAACCGCCGTGAGATCTCCAAGTACCTCTTCAAAGAG                        
genomic: GATCATATCAGAGACTAACCGCCGTGAGATCTCCAAGTACCTCTTC-AA-AGgtaccatttt ... gtgtgcaga
EST: gi|164107587|gb|ES170828.1|ES170828
EST:     TATCAGAGACTAACCGCCGTGAGATCTCCAAGTACCTCTTCAAAGAG                        
genomic: TATCAGAGACTAACCGCCGTGAGATCTCCAAGTACCTCTTC-AA-AGgtaccatttt ... gtgtgcaga
EST: gi|116471744|gb|EG514336.1|EG514336
EST:     ATCATATCAGAGACTAACCGCCGTGAGATCTCCAAGTACCTCTTCAAAGAG                        
genomic: ATCATATCAGAGACTAACCGCCGTGAGATCTCCAAGTACCTCTTC-AA-AGgtaccatttt ... gtgtgcaga


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attcaagagaattgtacttagaaatggttggaattggttctttttgtgtgcagagGGTGTTTTGTTTGCTAAAAAGGATTTCAACTTACCACAACATCCTTTGATTGAGAGTGTTCCAAATCTGCAAGTTATCAAGTTGATGCAGAGTTTCAAAT
 ggttgat  putative branch site (score: 5)
                                     ttctttttgt  putative PPT
                 ttagaaat  TA-rich tract