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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgatctgatcatctgagtgatagcacttgtggttttataaatagtagattttctgagggaaaacacttgacatatgattccccttttttttttgtcctagGATATAAAATCTCCTGAGAAAAATCCAGACGCTACTCTTGAATCTGCTATTGTGCAATTTGTCCCTTGCATCCGATCTGGTAGCTTTGCTGACATTGGAC

Basic information

species Vitis vinifera
transcript Vv07s0005g02110.t01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv07s0005g02110.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA02G01210.1 (Glycine max), 3'ss of exon 1
tgatctgatcatctgagtgatagcacttgtggttttataaatagtagattttctgagggaaaacacttgacata-tgattccccttttttttttgtcct--agGATATAAAATCTCCTGAGAAAAATCCAGACGCTACTCTTGAATCTGCTATTGTGCAATTTGTCCCTTGCATCCGATCTGGTAGCTTTGCTGACATTGGAC
   | |    || |||   | |     ||     |  || ||  |||   |||     |   |  ||||   |  |||||  | |||  || |  |  |  ||||| | || ||| | || |  |   |||| ||| |||||||||||||  || |||| | | ||||||||||||| |||||||| |||||||||||||| |
--ttgtttctatgtgatgaacaagttatgcaaaatagtacatc-tagtccttcaatatgctgattcttgttttgctgatttgcatttaattatcattgtgtagGATGTTAAGTCTGCAGACAGGATCTCAGATGCTGCTCTTGAATCTGCGGTTCTGCAGTCTATCCCTTGCATCCGTTCTGGTAGTTTTGCTGACATTGGGC

upper sequence: Vv07s0005g02110.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA10G01270.1 (Glycine max), 3'ss of exon 1
tgatctgatcatctgagtgat-agcacttgtggttttataaatagtagattttctgagggaa--aacacttgacata-tgattccccttt--tttttttgtcctagGATATAAAATCTCCTGAGAAAAATCCAGACGCTACTCTTGAATCTGCTATTGTGCAATTTGTCCCTTGCATCCGATCTGGTAGCTTTGCTGACATTGGAC
       ||  | |  ||||| | ||| |   |    |||     |  | |   |||    |   |  ||||   |  |||||  | |||  || |  |    |||||| | || ||| | || |  |   |||| ||| |||| ||||||||  || |||||||| |||| |||||||| |||||||| |||||||||||||| |
------tattgtttctgtgatgaacacgttatgcaaaatagtacatctagtccttgaatatattgattcttgttttgctgatttgcgtttaattatccttgtgtagGATGTTAAGTCTGCAGACAGGATCTCAGATGCTGCTCTAGAATCTGCGGTTCTGCAATTTATCCCATGCATCCGTTCTGGTAGTTTTGCTGACATTGGGC
















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|33402946|gb|CF208573.1|CF208573
EST:     CGATTTGCGCTTCGGATTCGGTTTCGGCTGATTCATCCGGCACTCAAGTG                         GATATAAAATCTCCTGAGAAAAATCCAGACGCTACTCTTGAATCTGCTATT
genomic: CGATTTGCGCTTCGGATTCGGTTTCGGCTGATTCATCCGGCACTCAAGTGgtgagctttt ... tttgtcctagGATATAAAATCTCCTGAGAAAAATCCAGACGCTACTCTTGAATCTGCTATT
EST: gi|110700065|gb|EE077677.1|EE077677
EST:     CGATTTGCGCTTCGGATTCGGTTTCGGCTGATTCATCCGGCACTCAAGTG                         GATATAAAATCTCCTGAGAAAAATCCAGACGCTACTCTTGAATCTGCTATT
genomic: CGATTTGCGCTTCGGATTCGGTTTCGGCTGATTCATCCGGCACTCAAGTGgtgagctttt ... tttgtcctagGATATAAAATCTCCTGAGAAAAATCCAGACGCTACTCTTGAATCTGCTATT
EST: gi|37189623|gb|CF608972.1|CF608972
EST:     CGATTTGCGCTTCGGATTCGGTTTCGGCTGATTCATCCGGCACTCAAGTG                         GATATAAAATCTCCTGAGAAAAATCCAGACGCTACTCTTGAATCTGCTAAT
genomic: CGATTTGCGCTTCGGATTCGGTTTCGGCTGATTCATCCGGCACTCAAGTGgtgagctttt ... tttgtcctagGATATAAAATCTCCTGAGAAAAATCCAGACGCTACTCTTGAATCTGCTATT
EST: gi|71861291|gb|DT010346.1|DT010346
EST:     CGATTTGCGCTTCGGATTCGGTTTCGGCTGATTCATCCGGCACTCAAGTG                         GATATAAAATCTCCTGAGAAAAATCCAGACGCTACTCTTGAATCTGCTATT
genomic: CGATTTGCGCTTCGGATTCGGTTTCGGCTGATTCATCCGGCACTCAAGTGgtgagctttt ... tttgtcctagGATATAAAATCTCCTGAGAAAAATCCAGACGCTACTCTTGAATCTGCTATT
EST: gi|71860993|gb|DT010048.1|DT010048
EST:     CGATTTGCGCTTCGGATTCGGTTTCGGCTGATTCATCCGGCACTCAAGTG                         GATATAAAATCTCCTGAGAAAAATCCAGACGCTACTCTTGAATCTGCTATT
genomic: CGATTTGCGCTTCGGATTCGGTTTCGGCTGATTCATCCGGCACTCAAGTGgtgagctttt ... tttgtcctagGATATAAAATCTCCTGAGAAAAATCCAGACGCTACTCTTGAATCTGCTATT
EST: gi|71860541|gb|DT009596.1|DT009596
EST:     CGATTTGCGCTTCGGATTCGGTTTCGGCTGATTCATCCGGCACTCAAGTG                         GATATAAAATCTCCTGAGAAAAATCCAGACGCTACTCTTGAATCTGCTATT
genomic: CGATTTGCGCTTCGGATTCGGTTTCGGCTGATTCATCCGGCACTCAAGTGgtgagctttt ... tttgtcctagGATATAAAATCTCCTGAGAAAAATCCAGACGCTACTCTTGAATCTGCTATT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agattttctgagggaaaacacttgacatatgattccccttttttttttgtcctagGATATAAAATCTCCTGAGAAAAATCCAGACGCTACTCTTGAATCTGCTATTGTGCAATTTGTCCCTTGCATCCGATCTGGTAGCTTTGCTGACATTGGAC
                   acttgac  putative branch site (score: 4)
                             tgattccccttttttt  putative PPT
                                      ttttttttttgt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgatctgatcatctgagtgatagcacttgtggttttataaatagtagattttctgagggaaaacacttgacatatgattccccttttttttttgtcctagGATATAAAATCTCCTGAGAAAAATCCAGACGCTACTCTTGAATCTGCTATTGTGCAATTTGTCCCTTGCATCCGATCTGGTAGCTTTGCTGACATTGGAC

- - - - - - - - - - - gcacttg
- - - - - - - - - - - - - - - - - - ataaata
- - - - - - - - - - - - - - - - - - - - - - - - - - - - gggaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cacttga