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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaattactcatcattaatacacttctgtatcaaatttggcctagaacttattttgagaactgaccgagaacctaaaaatgttcaatttgggagactagttgctatacttcaaaatttgagttatttcacccctcagGTGGCAGATTTGGCAAGATTAAATCATGAGAATACAGGAAAATTACTGGGCTATTGTCGAGAGAGCTCTCCATTTACAAGAATGCTGGTTTTTGAATATG

Basic information

species Vitis vinifera
transcript Vv02s0025g03700.t01
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv02s0025g03700.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GLYMA01G42770.1 (Glycine max), 3'ss of exon 10
gtaattactcatcattaatacacttctgtatcaaatttggcctagaacttattttgagaactgaccgagaaccta-aaaatgttcaatttgggagactagttgctatacttcaaaatttgag--ttattt-cacccctcagGTGGCAGATTTGGCAAGATTAAATCATGAGAATACAGGAAAATTACTGGGCTATTGTCGAGAGAGCTCTCCATTTACAAGAATGCTGGTTTTTGAATATG
                                                   |   | ||| |   |     |||| |  ||| |  | || | | || | | | | | |   |   ||| |   ||||||   ||  |||||||||||| |||||||| |||||||||||||||| ||||||| |||||||||||||| |||||  | ||||||||||||| ||| |||||||||| ||||
--------------------------------------------------gtaaagggaaattttcctatgcctacagcatgctagaatttgcacacaaatagttgt-ccaaatcttttaatatttatttatgccattcagGTGGCAGACTTGGCAAGGTTAAATCATGAGAATATAGGAAAACTACTGGGCTATTGTAGAGAGGACACTCCATTTACAAGGATGTTGGTTTTTGATTATG

upper sequence: Vv02s0025g03700.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GLYMA05G37960.1 (Glycine max), 3'ss of exon 9
gtaattactcatcattaatacacttctgtatcaaatttggcctagaacttattttgagaactgaccgagaacctaaaaatgttcaatttgggagactagttgctatacttcaaaatttgagttattt-cacccctcagGTGGCAGATTTGGCAAGATTAAATCATGAGAATACAGGAAAATTACTGGGCTATTGTCGAGAGAGCTCTCCATTTACAAGAATGCTGGTTTTTGAATATG
                           |||      ||||   |   | |||  | | |  ||  | ||||   | | |     ||||      |||||    || | ||      ||  | ||||    | | |||||||||||| |||||||| ||||||||||| || ||||||||  | || || |||||| ||||||||  |||||||||||| |||||||||||||||||||
---------------------------gtaaatggattggaacatt-cctatccttacag-tgtgcaagaattgacagacaaataatt----gaactagcctttaaattt------ttctgctattgatgcacttcagGTGGCAGACTTGGCAAGGTTAAATCATGATAACACAGGAAAGCTGCTAGGATATTGTAGAGAGAGCAATCCATTTACAAGGATGCTGGTTTTTGAATATG

upper sequence: Vv02s0025g03700.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GLYMA08G01640.1 (Glycine max), 3'ss of exon 8
gtaattactcatcattaatacacttctgtatcaaatttggcctagaacttattttgagaactgaccgagaacctaaaaatgttcaatttgggagactagttgctatacttcaaaatttgagttattt-cacccctcagGTGGCAGATTTGGCAAGATTAAATCATGAGAATACAGGAAAATTACTGGGCTATTGTCGAGAGAGCTCTCCATTTACAAGAATGCTGGTTTTTGAATATG
                                  |  |||  | ||||  |||   |   ||     |      || |||   ||  |    |    ||||  | |  || |   |||  | ||||    |   |||||||||||| |||||||| ||||||||||| || ||||||||  |  | || |||||| ||||||||  |||||||||||| |||||||||||||||||||
--------------------------------gtaaatggaatggaac--attccaatgcctac---aatgttcaagaattgacagataaataattgagttagtct-tttaattttttctgctattgatgcaattcagGTGGCAGACTTGGCAAGGTTAAATCATGATAACACAGGAAAGCTGTTAGGATATTGTAGAGAGAGCAGTCCATTTACAAGGATGCTGGTTTTTGAATATG

upper sequence: Vv02s0025g03700.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GLYMA11G02690.1 (Glycine max), 3'ss of exon 9
gtaattactcatcattaatacacttctgtatcaaatttggcctagaacttattttgagaactgaccgagaacctaaaaatgttcaatttgggagactagttgctatacttcaaaatttgagttatttcacccctcagGTGGCAGATTTGGCAAGATTAAATCATGAGAATACAGGAAAATTACTGGGCTATTGTCGAGAGAGCTCTCCATTTACAAGAATGCTGGTTTTTGAATATG
                                     |    || |  ||  | ||    |  ||||    |   ||  ||  ||       | | | ||    ||   | || ||||      ||   ||  |||||||||||| |||||||| ||| || ||||||||| ||||||| | |||||||||||| |||||  | ||||||||||||| ||| |||||||||| ||||
------------------------------------gtaatgtaaattttcctatg----cctaccgcatgctagaatttgcccac----aaatagttgtccaaatctcttaatattt----ctttatgccattcagGTGGCAGACTTGGCAAGGTTAGATAATGAGAATATAGGAAAACTGCTGGGCTATTGTAGAGAGGACACTCCATTTACAAGGATGTTGGTTTTTGATTATG

upper sequence: Vv02s0025g03700.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: AT1G63430.2 (Arabidopsis thaliana), 3'ss of exon 9
gtaattactcatcattaatacacttctgtatcaaatttggcctagaacttattttgagaactgaccgagaacctaaaaatgttcaatttgggagactagttgctatacttcaaaatttgagttatttcacc-cctcagGTGGCAGATTTGGCAAGATTAAATCATGAGAATACAGGAAAATTACTGGGCTATTGTCGAGAGAGCTCTCCATTTACAAGAATGCTGGTTTTTGAATATG
               ||     ||    | | |   |   |    | |   ||    | | ||| | |     |||| || | |   ||          || ||    ||  ||||     |    ||||    |||||| ||||||||||| |||||||| || ||||| ||||  |||||||| || |||||   ||||| ||| ||||||||||||||||| |||||||| ||||
--------------gtagcttcctctcatgttatcatcatcaccaagccactt----ggattgaacaatc-tttaaacatatcctccttt---------tttctgagattttaaatcca--tctcctcactgtttcagGTTGCAGATTTGGCTAGATTAAACCACGAGAACACAGCGAAATTACTTGGATATTGCAAAGAGATCTCACCATTTACAAGAATGCTTGTTTTTGAGTATG

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|351013321|gb|FQ425026.1|FQ425026
EST:     TCAAAGAGGAGCATTGGATGGGCTATCTCGAGCTCTATTTTCAGAAGGAG                         GTGGCAGATTTGGCAAGATTAAATCATGAGAATACAGGAAAATTACTGGGC
genomic: TCAAAGAGGAGCATTGGATGGGCTATCTCGAGCTCTATTTTCAGAAGGAGgtaattactc ... cacccctcagGTGGCAGATTTGGCAAGATTAAATCATGAGAATACAGGAAAATTACTGGGC
EST: gi|161709105|gb|FC058383.1|FC058383
EST:     TCAAAGAGGAGCATTGGATGGGCTATCTCGAGCTCTATTTTCAGAAGGAG                         GTGGCAGATTTGGCAAGATTAAATCATGAGAATACAGGAAAATTACTGGGC
genomic: TCAAAGAGGAGCATTGGATGGGCTATCTCGAGCTCTATTTTCAGAAGGAGgtaattactc ... cacccctcagGTGGCAGATTTGGCAAGATTAAATCATGAGAATACAGGAAAATTACTGGGC
EST: gi|351028312|gb|FQ427208.1|FQ427208
EST:     TCAAAGAGGAGCATTGGATGGGCTATCTCGAGCTCTATTTTCAGAAGGAG                         GTGGCAGATTTGGCAAGATTAAATCATGAGAATACAGGAAAATTACTGGGC
genomic: TCAAAGAGGAGCATTGGATGGGCTATCTCGAGCTCTATTTTCAGAAGGAGgtaattactc ... cacccctcagGTGGCAGATTTGGCAAGATTAAATCATGAGAATACAGGAAAATTACTGGGC
EST: gi|32268876|gb|CD718035.1|CD718035
EST:     GGAGCATTGGATGGGCTATCTCGAGCTCTATTTTCAGAAGGAG                         GTGGCAGATTTGGCAAGATTAAATCATGAGAATACAGGAAAATTACTGGGC
genomic: GGAGCATTGGATGGGCTATCTCGAGCTCTATTTTCAGAAGGAGgtaattactc ... cacccctcagGTGGCAGATTTGGCAAGATTAAATCATGAGAATACAGGAAAATTACTGGGC
EST: gi|351024123|gb|FQ423546.1|FQ423546
EST:     TCAAAGAGGAGCATTGGATGGGCTATCTCGAGCTCTATTTTCAGAAGGAG                         GTGGCAGATTTGGCAAGATTAAATCATGAGAATACAGGAAAATTACTGGGC
genomic: TCAAAGAGGAGCATTGGATGGGCTATCTCGAGCTCTATTTTCAGAAGGAGgtaattactc ... cacccctcagGTGGCAGATTTGGCAAGATTAAATCATGAGAATACAGGAAAATTACTGGGC
EST: gi|349810552|gb|FQ402795.1|FQ402795
EST:     TCAAAGAGGAGCATTGGATGGGCTATCTCGAGCTCTATTTTCAGAAGGAG                         GTGGCAGATTTGGCAAGATTAAATCGTGAGAATACAGGAAAATTACTGGGC
genomic: TCAAAGAGGAGCATTGGATGGGCTATCTCGAGCTCTATTTTCAGAAGGAGgtaattactc ... cacccctcagGTGGCAGATTTGGCAAGATTAAATCATGAGAATACAGGAAAATTACTGGGC
EST: gi|33401750|gb|CF207377.1|CF207377
EST:     TCAAAGAGGAGCATTGGATGGGCTATCTCGAGCTCTATTTTCAGAAGGAG                         GTGGCAGATTTGGCAAGATTAAATCATGAGAATACAGGAAAATTACTGGGC
genomic: TCAAAGAGGAGCATTGGATGGGCTATCTCGAGCTCTATTTTCAGAAGGAGgtaattactc ... cacccctcagGTGGCAGATTTGGCAAGATTAAATCATGAGAATACAGGAAAATTACTGGGC
EST: gi|349808127|gb|FQ403314.1|FQ403314
EST:     TCAAAGAGGAGCATTGGATGGGCTATCTCGAGCTCTATTTTCAGAAGGAG                         GTGGCAGATTTGGCAAGATTAAATCGTGAGAATACAGGAAAATTACTGGGC
genomic: TCAAAGAGGAGCATTGGATGGGCTATCTCGAGCTCTATTTTCAGAAGGAGgtaattactc ... cacccctcagGTGGCAGATTTGGCAAGATTAAATCATGAGAATACAGGAAAATTACTGGGC
EST: gi|351021708|gb|FQ437093.1|FQ437093
EST:     TCAAAGAGGAGCATTGGATGGGCTATCTCGAGCTCTATTTTCAGAAGGAG                         GTGGCAGATTTGGCAAGATTAAATCATGAGAATACAGGAAAATTACTGGGC
genomic: TCAAAGAGGAGCATTGGATGGGCTATCTCGAGCTCTATTTTCAGAAGGAGgtaattactc ... cacccctcagGTGGCAGATTTGGCAAGATTAAATCATGAGAATACAGGAAAATTACTGGGC
EST: gi|32268886|gb|CD718045.1|CD718045
EST:     GGAGCATTGGATGGGCTATCTCGAGCTCTATTTTCAGAAGGAG                         GTGGCAGATTTGGCAAGATTAAATCATGAGAATACAGGAAAATTACTGGGC
genomic: GGAGCATTGGATGGGCTATCTCGAGCTCTATTTTCAGAAGGAGgtaattactc ... cacccctcagGTGGCAGATTTGGCAAGATTAAATCATGAGAATACAGGAAAATTACTGGGC
EST: gi|32249850|gb|CD715669.1|CD715669
EST:     GGAGCATTGGATGGGCTATCTCGAGCTCTATTTTCAGAAGGAG                         GTGGCAGATTTGGCAAGATTAAATCATGAGAATACAGGAAAATTACTGGGC
genomic: GGAGCATTGGATGGGCTATCTCGAGCTCTATTTTCAGAAGGAGgtaattactc ... cacccctcagGTGGCAGATTTGGCAAGATTAAATCATGAGAATACAGGAAAATTACTGGGC
EST: gi|351028536|gb|FQ444817.1|FQ444817
EST:     TCAAAGAGGAGCATTGGATGGGCTATCTCGAGCTCTATTTTCAGAAGGAG                         GTGGCAGATTTGGCAAGATTAAATCATGAGAATACAGGAAAATTACTGGGC
genomic: TCAAAGAGGAGCATTGGATGGGCTATCTCGAGCTCTATTTTCAGAAGGAGgtaattactc ... cacccctcagGTGGCAGATTTGGCAAGATTAAATCATGAGAATACAGGAAAATTACTGGGC
EST: gi|351031421|gb|FQ445446.1|FQ445446
EST:     TCAAAGAGGAGCATTGGATGGGCTATCTCGAGCTCTATTTTCAGAAGGAG                         GTGGCAGATTTGGCAAGATTAAATCATGAGAATACAGGAAAATTACTGGGC
genomic: TCAAAGAGGAGCATTGGATGGGCTATCTCGAGCTCTATTTTCAGAAGGAGgtaattactc ... cacccctcagGTGGCAGATTTGGCAAGATTAAATCATGAGAATACAGGAAAATTACTGGGC
EST: gi|349811570|gb|FQ409566.1|FQ409566
EST:     TCAAAGAGGAGCATTGGATGGGCTATCTCGAGCTCTATTTTCAGAAGGAG                         GTGGCAGATTTGGCAAGATTAAATCGTGAGAATACAGGAAAATTACTGGGC
genomic: TCAAAGAGGAGCATTGGATGGGCTATCTCGAGCTCTATTTTCAGAAGGAGgtaattactc ... cacccctcagGTGGCAGATTTGGCAAGATTAAATCATGAGAATACAGGAAAATTACTGGGC
EST: gi|349814064|gb|FQ414322.1|FQ414322
EST:     TCAAAGAGGAGCATTGGATGGGCTATCTCGAGCTCTATTTTCAGAAGGAG                         GTGGCAGATTTGGCAAGATTAAATCGTGAGAATACAGGAAAATTACTGGGC
genomic: TCAAAGAGGAGCATTGGATGGGCTATCTCGAGCTCTATTTTCAGAAGGAGgtaattactc ... cacccctcagGTGGCAGATTTGGCAAGATTAAATCATGAGAATACAGGAAAATTACTGGGC
EST: gi|349812384|gb|FQ406405.1|FQ406405
EST:     TCAAAGAGGAGCATTGGATGGGCTATCTCGAGCTCTATTTTCAGAAGGAG                         GTGGCAGATTTGGCAAGATTAAATCGTGAGAATACAGGAAAATTACTGGGC
genomic: TCAAAGAGGAGCATTGGATGGGCTATCTCGAGCTCTATTTTCAGAAGGAGgtaattactc ... cacccctcagGTGGCAGATTTGGCAAGATTAAATCATGAGAATACAGGAAAATTACTGGGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcaatttgggagactagttgctatacttcaaaatttgagttatttcacccctcagGTGGCAGATTTGGCAAGATTAAATCATGAGAATACAGGAAAATTACTGGGCTATTGTCGAGAGAGCTCTCCATTTACAAGAATGCTGGTTTTTGAATATG
                                       ttatttcacccctc  CT-rich tract
                             aaaatttgagttattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaattactcatcattaatacacttctgtatcaaatttggcctagaacttattttgagaactgaccgagaacctaaaaatgttcaatttgggagactagttgctatacttcaaaatttgagttatttcacccctcagGTGGCAGATTTGGCAAGATTAAATCATGAGAATACAGGAAAATTACTGGGCTATTGTCGAGAGAGCTCTCCATTTACAAGAATGCTGGTTTTTGAATATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG