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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatctgcatgaattttattttttttaatatataatttcacacaaactcatttccttgttctccccccgaaagtgaagtttgagttgtttcattaattcacacctcattttaagttccaaaaaccttataagatgtatatggcgtttgcctttcatcttgttgttcagCACCGGACAGGTTGCGTTGTGGGATGCTTAAGAAAATTGCAAAAATGGTGCTTGTCATCTATTTTTGATGAGTACCAGCGGTTCGCAGCTGCTAAAGCTA

Basic information

species Vitis vinifera
transcript Vv12s0059g01400.t01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv12s0059g01400.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA02G43550.2 (Glycine max), 3'ss of exon 4
gtatctgcatgaattttattttttttaatatataatttcacacaaactcatttccttgttctccccccgaaagtgaagtttgagttgtttcattaattcacacctcattttaagttccaaaaaccttataagatgtatatggcgtttgcctttcatcttgttgttcagCACCGGACAGGTTGCGTTGTGGGATGCTTAAGAAAATTGCAAAAATGGTGCTTGTCATCTATTTTTGATGAGTACCAGCGGTTCGCAGCTGCTAAAGCTA
                                            |  |  || |    || |       |||   |  ||||   |   | |||| |  |  |   |  |         | |  ||||| | | ||||      | | ||||   |||   ||| |||||||| || |||||| | || |||||||  |||||||||||||||||||||||||||||| | |||||||| ||||| || || |||||||| ||||| |
-----------------------------------------gtgagatttttgctggatttttttt---aaaaacatttttgtcataagt-attagtatatgcactaact---------atattcttattaaaagtatgcaatttcttccttctttctg--tgtgcagCACCGAACGGGTTGCTTAGTAGGATGCTATAGAAAATTGCAAAAATGGTGCTTGTCATCTGTCTTTGATGAATACCAACGCTTTGCAGCTGCCAAAGCAA

upper sequence: Vv12s0059g01400.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA14G05400.1 (Glycine max), 3'ss of exon 4
gtatctgcatgaattttattttttttaatatataatttcacacaaactcatttccttgttctccccccgaaagtgaagtttgagttgtttcattaattcacacctcattttaagttccaaaaaccttataagatgtatatggcgtttgcctttcatcttgttgttcagCACCGGACAGGTTGCGTTGTGGGATGCTTAAGAAAATTGCAAAAATGGTGCTTGTCATCTATTTTTGATGAGTACCAGCGGTTCGCAGCTGCTAAAGCTA
             |   ||||||  | | || |  ||| | |  |  |   |     ||  |     |   |   |  | | |   ||||   ||||    | | ||| | | |||        ||| | | | |||| |    | | |||||  | |     | |||||||| ||||||||| | || |||||||  |||||||||||||||||||||||||||||  | |||||||| ||||| || || ||||| || ||||| |
------------gtgagatttttgctga-attttcttttaaaatatttttgtaataagtaatagtgtcactaacaa--tataaaacgtttttgtaatatctaac-catgtgaggtttt------cttgtcaaaagtatgtaatttcttcctttattttctgcatgcagCACCGAACAGGTTGCTTGGTAGGATGCTATAGAAAATTGCAAAAATGGTGCTTGTCATCCGTCTTTGATGAATACCAACGCTTTGCAGCCGCCAAAGCAA
















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|27585879|gb|CB008574.1|CB008574
EST:     CTTGATGTAAGGAATCATCCACTTCTAATCCATTGCAAAAGAGGGAAG                         CACCGGACAGGTTGCGTTGTGGGATGCTTAAGAAAATTGCAAAAATGGTGC
genomic: CTTGATGTAAGGAATCATCCACTTCTAATCCATTGCAAAAGAGGGAAGgtatctgcat ... tgttgttcagCACCGGACAGGTTGCGTTGTGGGATGCTTAAGAAAATTGCAAAAATGGTGC
EST: gi|30256135|gb|CB971978.1|CB971978
EST:     ATGTAAGGAATCATCCACTTCTAATCCATTGCAAAAGAGGGAAG                         CACCGGACAGGTTGCGTTGTGGGATGCTTAAGAAAATTGCAAAAATGGTGC
genomic: ATGTAAGGAATCATCCACTTCTAATCCATTGCAAAAGAGGGAAGgtatctgcat ... tgttgttcagCACCGGACAGGTTGCGTTGTGGGATGCTTAAGAAAATTGCAAAAATGGTGC
EST: gi|110389980|gb|EC954860.1|EC954860
EST:     ATGTAAGGAATCATCCACTTCTAATCCATTGCAAAAGAGGGAAG                         CACCGGACAGGTTGCGTTGTGGGATGCTTAAGAAAATTGCAAAAATGGTGC
genomic: ATGTAAGGAATCATCCACTTCTAATCCATTGCAAAAGAGGGAAGgtatctgcat ... tgttgttcagCACCGGACAGGTTGCGTTGTGGGATGCTTAAGAAAATTGCAAAAATGGTGC
EST: gi|351015527|gb|FQ447356.1|FQ447356
EST:     ATGTAAGGAATCGTCCACTTCTAATCCATTGCAAAAGAGGGAAG                         CACCGGACAGGTTGCGTTGTGGGATGCTTAAGAAAATTGCAAAAATGGTGC
genomic: ATGTAAGGAATCATCCACTTCTAATCCATTGCAAAAGAGGGAAGgtatctgcat ... tgttgttcagCACCGGACAGGTTGCGTTGTGGGATGCTTAAGAAAATTGCAAAAATGGTGC
EST: gi|26258262|gb|CA809325.1|CA809325
EST:     ATGTAAGGAATCATCCACTTCTAATCCATTGCAAAAGAGGGAAG                         CACCGGACAGGTTGCGTTGTGGGATGCTTAAGAAAATTGCAAAAATGGTGC
genomic: ATGTAAGGAATCATCCACTTCTAATCCATTGCAAAAGAGGGAAGgtatctgcat ... tgttgttcagCACCGGACAGGTTGCGTTGTGGGATGCTTAAGAAAATTGCAAAAATGGTGC
EST: gi|26257485|gb|CA808548.1|CA808548
EST:     ATGTAAGGAATCATCCACTTCTAATCCATTGCAAAAGAGGGAAG                         CACCGGACAGGTTGCGTTGTGGGATGCTTAAGAAAATTGCAAAAATGGTGC
genomic: ATGTAAGGAATCATCCACTTCTAATCCATTGCAAAAGAGGGAAGgtatctgcat ... tgttgttcagCACCGGACAGGTTGCGTTGTGGGATGCTTAAGAAAATTGCAAAAATGGTGC
EST: gi|351045015|gb|FQ449269.1|FQ449269
EST:     ATGTAAGGAATCATCCACCTCTGATCCATTGCAAAAGAGGGAAG                         CACCGGACAGGTTGCGTTGTGGGATGCTTAAGAAAATTGCAAAAATGGTGC
genomic: ATGTAAGGAATCATCCACTTCTAATCCATTGCAAAAGAGGGAAGgtatctgcat ... tgttgttcagCACCGGACAGGTTGCGTTGTGGGATGCTTAAGAAAATTGCAAAAATGGTGC
EST: gi|71857429|gb|DT006484.1|DT006484
EST:     ATGTAAGGAATCATCCACTTCTAATCCATTGCAAAAGAGGGAAG                         CACCGGACAGGTTGCGTTGTGGGATGCTTAAGAAAATTGCAAAAATGGTGC
genomic: ATGTAAGGAATCATCCACTTCTAATCCATTGCAAAAGAGGGAAGgtatctgcat ... tgttgttcagCACCGGACAGGTTGCGTTGTGGGATGCTTAAGAAAATTGCAAAAATGGTGC
EST: gi|110379464|gb|EC944660.1|EC944660
EST:     ATGTAAGGAATCATCCACTTCTAATCCATTGCAAAAGAGGGAAG                         CACCGGACAGGTTGCGTTGTGGGATGCTTAAGAAAATTGCAAAAATGGTGC
genomic: ATGTAAGGAATCATCCACTTCTAATCCATTGCAAAAGAGGGAAGgtatctgcat ... tgttgttcagCACCGGACAGGTTGCGTTGTGGGATGCTTAAGAAAATTGCAAAAATGGTGC
EST: gi|30253155|gb|CB970706.1|CB970706
EST:     ATGTAAGGAATCATCCACTTCTAATCCATTGCAAAAGAGGGAAG                         CCCCGGACAGGTTGCGTTGTGGGATGCTTAAGAAAATTGCAAAAATGGTGC
genomic: ATGTAAGGAATCATCCACTTCTAATCCATTGCAAAAGAGGGAAGgtatctgcat ... tgttgttcagCACCGGACAGGTTGCGTTGTGGGATGCTTAAGAAAATTGCAAAAATGGTGC
EST: gi|351022573|gb|FQ447095.1|FQ447095
EST:     ATGTAAGGAATCATCCACTTCTAATCCATTGCAAAAGAGGGAAG                         CACCGGACAGGTTGCGTTGTGGGATGCTTAAGAAAATTGCAAAAATGGTGC
genomic: ATGTAAGGAATCATCCACTTCTAATCCATTGCAAAAGAGGGAAGgtatctgcat ... tgttgttcagCACCGGACAGGTTGCGTTGTGGGATGCTTAAGAAAATTGCAAAAATGGTGC
EST: gi|351034099|gb|FQ448017.1|FQ448017
EST:     ATGTAAGGAATCATCCACTTCTAATCCATTGCAAAAGAGGGAAG                         CACCGGACAGGTTGCGTTGTGGGATGCTTAAGAAAATTGCAAAAATGGTGC
genomic: ATGTAAGGAATCATCCACTTCTAATCCATTGCAAAAGAGGGAAGgtatctgcat ... tgttgttcagCACCGGACAGGTTGCGTTGTGGGATGCTTAAGAAAATTGCAAAAATGGTGC
EST: gi|110362858|gb|EC926416.1|EC926416
EST:     ATGTAAGGAATCATCCACTTCTAATCCATTGCAAAAGAGGGAAG                         CACCGGACAGGTTGCGTTGTGGGATGCTTAAGAAAATTGCAAAAATGGTGC
genomic: ATGTAAGGAATCATCCACTTCTAATCCATTGCAAAAGAGGGAAGgtatctgcat ... tgttgttcagCACCGGACAGGTTGCGTTGTGGGATGCTTAAGAAAATTGCAAAAATGGTGC
EST: gi|29785487|gb|CB342539.2|CB342539
EST:     ATGTAAGGAATCATCCACTTCTAACCCATTGCAAAAGAGGGAAG                         CACCGGACAGGTTGCGTTGTGGGATGCTTAAGAAAATTGCAAAAATGGTGC
genomic: ATGTAAGGAATCATCCACTTCTAATCCATTGCAAAAGAGGGAAGgtatctgcat ... tgttgttcagCACCGGACAGGTTGCGTTGTGGGATGCTTAAGAAAATTGCAAAAATGGTGC
EST: gi|30253078|gb|CB970629.1|CB970629
EST:     ATGTAAGGAATCATCCACTTCTAATCCATTGCAAAAGAGGGAAG                         CACCGGACAGGTTGCGTTGTGGGATGCTTAAGAAAATTGCAAAAATGGTGC
genomic: ATGTAAGGAATCATCCACTTCTAATCCATTGCAAAAGAGGGAAGgtatctgcat ... tgttgttcagCACCGGACAGGTTGCGTTGTGGGATGCTTAAGAAAATTGCAAAAATGGTGC
EST: gi|30329880|gb|CD013142.1|CD013142
EST:     CTTGATGTAAGGAATCATCCACTTCTAATCCATTGCAAAAGAGGGAAG                         CACCGGACAGGTTGCGTTGTGGGATGCTTAAGAAAATTGCAAAAATGGTGC
genomic: CTTGATGTAAGGAATCATCCACTTCTAATCCATTGCAAAAGAGGGAAGgtatctgcat ... tgttgttcagCACCGGACAGGTTGCGTTGTGGGATGCTTAAGAAAATTGCAAAAATGGTGC
EST: gi|30256204|gb|CB972047.1|CB972047
EST:     ATGTAAGGAATCATCCACTTCTAATCCATTGCAAAAGAGGGAAG                         CACCGGACAGGTTGCGTTGTGGGATGCTTAAGAAAATTGCAAAAATGGTGC
genomic: ATGTAAGGAATCATCCACTTCTAATCCATTGCAAAAGAGGGAAGgtatctgcat ... tgttgttcagCACCGGACAGGTTGCGTTGTGGGATGCTTAAGAAAATTGCAAAAATGGTGC
EST: gi|83275093|gb|DV939189.1|DV939189
EST:     ATGTAAGGAATCATCCACTTCTAATCCATTGCAAAAGAGGGAAG                         CACCGGACAGGTTGCGTTGTGGGATGCTTAAGAAAATTGCAAAAATGGTGC
genomic: ATGTAAGGAATCATCCACTTCTAATCCATTGCAAAAGAGGGAAGgtatctgcat ... tgttgttcagCACCGGACAGGTTGCGTTGTGGGATGCTTAAGAAAATTGCAAAAATGGTGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttccaaaaaccttataagatgtatatggcgtttgcctttcatcttgttgttcagCACCGGACAGGTTGCGTTGTGGGATGCTTAAGAAAATTGCAAAAATGGTGCTTGTCATCTATTTTTGATGAGTACCAGCGGTTCGCAGCTGCTAAAGCTA
                               tttgcctttcatctt  CT-rich tract
            ttataagatgtatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatctgcatgaattttattttttttaatatataatttcacacaaactcatttccttgttctccccccgaaagtgaagtttgagttgtttcattaattcacacctcattttaagttccaaaaaccttataagatgtatatggcgtttgcctttcatcttgttgttcagCACCGGACAGGTTGCGTTGTGGGATGCTTAAGAAAATTGCAAAAATGGTGCTTGTCATCTATTTTTGATGAGTACCAGCGGTTCGCAGCTGCTAAAGCTA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT