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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagaaaattcccccattctctagtttggttgccaagaaaacaaaatttccaatcatcaaacattgttccaatacactttcaacacacagagttttcatattagtattgtgatcgcaagataatcactcatatagtctcctctttctcggcatttttctacttcaaatcttgttgcagCATGCAATTCCATTGTCTCAACAATTAGAGTACTACAAGGAGTACCAAGCTAAGCTAGCAAAGGTAGCAGGTAGTCAAAAAGCGGCCACCATTATCAAGG

Basic information

species Vitis vinifera
transcript Vv09s0002g03140.t01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv09s0002g03140.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: LOC_Os06g05550.1 (Oryza sativa), 3'ss of exon 2
gtaagaaaattcccccattctctagtttggttgccaagaaaacaaaatttccaatcatcaaacattgttccaatacactttcaacacacagagttttcatattagtattgtgatcgcaagataatcactcatatagtctcctctttctcggcatttttctacttcaaatcttgt--tgcagCATGCAATTCCATTGTCTCAACAATTAGAGTACTACAAGGAGTACCAAGCTAAGCTAGCAAAGGTAGCAGGTAGTCAAAAAGCGGCCACCATTATCAAGG
                                                                            |  |  | ||     | |||||  |       |||    ||||    |||  |      || |      ||||   | |    |     |||   |||  |||||||||| ||||| ||||| |||||||| ||||||| ||||||||||||| ||||||| |||   || || || ||     | ||     | || ||||| |
----------------------------------------------------------------------------aactctatcattgctatttttcggac-gtcggtgtacctgcaa----atccatgtggcggtgtaaatgatctcttaactaacttggacaaaactgtgtaatgcagCATGCTATTCCTTTGTCCCAACAATTGGAGTACTTCAAGGAGTACCAATCTAAGCTGGCAGCCGTGGCCGGAAGCAGCCAGGCCCAGTCAATCATCAACG

upper sequence: Vv09s0002g03140.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA15G02430.1 (Glycine max), 3'ss of exon 2
gtaagaaaattcccccattctctagtttggttgccaagaaaacaaaatttccaatcatcaaacattgttccaatacactttcaacacacagagttttcatattagtattgtgatcgcaagataatcactcatatagtctcctctttctcggcatttttctacttcaaatct-tgttgcagCATGCAATTCCATTGTCTCAACAATTAGAGTACTACAAGGAGTACCAAGCTAAGCTAGCAAAGGTAGCAGGTAGTCAAAAAGCGGCCACCATTATCAAGG
                                                                         ||   |   ||   ||||    | |          |     | |||   | |||| |||||   || |      |     |||||  ||||    | | | ||||||||||| ||||||||||| ||||| ||| | || |||||||| |||||||  ||||| || |||                                     
------------------------------------------------------------------------gtaagttaggaatgaacagtacatccgcgcgccccct-----cacaa---attcacacatat---ctgcgaaaattaatggttttttaactttgtttttcttttgcagCATGCGATTCCATTGTCCCAACAGTTAAAATATTACAAGGAATACCAAGGCAAGCTGGCCAAG-------------------------------------
















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|110708453|gb|EE086014.1|EE086014
EST:     ACTTTGCCTCTGCTGGCTCTGGTTATGATGACAAAACAGCCATCTTAAGT                         CATGCAATTCCATTGTCTCAACAATTAGAGTACTACAAGGAGTACCAAGC-
genomic: ACTTTGCCTCTGCTGGCTCTGGTTATGATGACAAAACAGCCATCTTAAGTgtaagaaaat ... cttgttgcagCATGCAATTCCATTGTCTCAACAATTAGAGTACTACAAGGAGTACCAAGCT
EST: gi|87584379|gb|DY473580.1|DY473580
EST:     ACTTTGCCTCTGCTGGCTCTGGTTATGATGACAAAACAGCCATCTTAAGT                         CATGCAATTCCATTGTCTCAACAATTAGAGTACTACAAGGAGTACCAAGCT
genomic: ACTTTGCCTCTGCTGGCTCTGGTTATGATGACAAAACAGCCATCTTAAGTgtaagaaaat ... cttgttgcagCATGCAATTCCATTGTCTCAACAATTAGAGTACTACAAGGAGTACCAAGCT
EST: gi|110690654|gb|EE068002.1|EE068002
EST:     ACTTTGCCTCTGCTGGCTCTGGTTATGATGACAAAACAGCCATCTTAAGT                         CATGCAATTCCATTGTCTCAACAATTAGAGTACTACAAGGAGTACCAAGCT
genomic: ACTTTGCCTCTGCTGGCTCTGGTTATGATGACAAAACAGCCATCTTAAGTgtaagaaaat ... cttgttgcagCATGCAATTCCATTGTCTCAACAATTAGAGTACTACAAGGAGTACCAAGCT
EST: gi|77578102|gb|DV217820.1|DV217820
EST:     ACTTTGCCTCTGCTGGCTCTGGTTATGATGACAAAACAGCCATCTTAAGT                         CATGCAATTCCATTGTCTCAACAATTAGAGTACTACAAGGAGTACCAAGCT
genomic: ACTTTGCCTCTGCTGGCTCTGGTTATGATGACAAAACAGCCATCTTAAGTgtaagaaaat ... cttgttgcagCATGCAATTCCATTGTCTCAACAATTAGAGTACTACAAGGAGTACCAAGCT
EST: gi|110699841|gb|EE077205.1|EE077205
EST:     ACTTTGCCTCTGCTGGCTCTGGTTATGATGACAAAACAGCCATCTTAAGT                         CATGCAATTCCATTGTCTCAACAATTAGAGTACTACAAGGAGTACCAAGCT
genomic: ACTTTGCCTCTGCTGGCTCTGGTTATGATGACAAAACAGCCATCTTAAGTgtaagaaaat ... cttgttgcagCATGCAATTCCATTGTCTCAACAATTAGAGTACTACAAGGAGTACCAAGCT
EST: gi|30297185|gb|CB973979.1|CB973979
EST:     ACTTTGCCTCTGCTGGCTCTGGTTATGATGACAAAACAGCCATCTTAAGT                         CATGCAATTCCATTGTCTCAACAATTAGAGTACTACAAGGAGTACCAAGCT
genomic: ACTTTGCCTCTGCTGGCTCTGGTTATGATGACAAAACAGCCATCTTAAGTgtaagaaaat ... cttgttgcagCATGCAATTCCATTGTCTCAACAATTAGAGTACTACAAGGAGTACCAAGCT
EST: gi|351026188|gb|FQ428200.1|FQ428200
EST:     ACTTTGCCTCTGCTGGCTCTGGTTATGATGACAAAACAGCCATCTTAAGT                         CATGCAATTCCATTGTCTCAACAATTAGAGTACTACAAGGAGTACCAAGCT
genomic: ACTTTGCCTCTGCTGGCTCTGGTTATGATGACAAAACAGCCATCTTAAGTgtaagaaaat ... cttgttgcagCATGCAATTCCATTGTCTCAACAATTAGAGTACTACAAGGAGTACCAAGCT
EST: gi|351036838|gb|FQ459360.1|FQ459360
EST:     ACTTTGCCTCTGCTGGCTCTGGTTATGATGACAAAACAGCCATCTTAAGT                         CATGCAATTCCATTGTCTCAACAATTAGAGTACTACAAGGAGTACCAAGCT
genomic: ACTTTGCCTCTGCTGGCTCTGGTTATGATGACAAAACAGCCATCTTAAGTgtaagaaaat ... cttgttgcagCATGCAATTCCATTGTCTCAACAATTAGAGTACTACAAGGAGTACCAAGCT
EST: gi|110699441|gb|EE076440.1|EE076440
EST:     ACTTTGCCTCTGCTGGCTCTGGTTATGATGACAAAACAGCCATCTTAAGT                         CATGCAATTCCATTGTCTCAACAATTAGAGTACTACAAGGAGTACCAAGCT
genomic: ACTTTGCCTCTGCTGGCTCTGGTTATGATGACAAAACAGCCATCTTAAGTgtaagaaaat ... cttgttgcagCATGCAATTCCATTGTCTCAACAATTAGAGTACTACAAGGAGTACCAAGCT
EST: gi|110398746|gb|EC965220.1|EC965220
EST:     GCCATCTTAAGT                         CATGCAATTCCATTGTCTCAACAATTAGAGTACTACAAGGAGTACCAAGCT
genomic: GCCATCTTAAGTgtaagaaaat ... cttgttgcagCATGCAATTCCATTGTCTCAACAATTAGAGTACTACAAGGAGTACCAAGCT
EST: gi|349820296|gb|FQ403912.1|FQ403912
EST:     ACTTTGCCTCTGCTGGCTCTGGTTATGATGACAAAACAGCCATCTTAAGT                         CATGCAATTCCATTGTCTCAACAATTAGAGTACTACAAGGAGTACCAAGCT
genomic: ACTTTGCCTCTGCTGGCTCTGGTTATGATGACAAAACAGCCATCTTAAGTgtaagaaaat ... cttgttgcagCATGCAATTCCATTGTCTCAACAATTAGAGTACTACAAGGAGTACCAAGCT
EST: gi|110693430|gb|EE069653.1|EE069653
EST:     ACTTTGCCTCTGCTGGCTCTGGTTATGATGACAAAACAGCCATCTTAAGT                         CATGCAATTCCATTGTCTCAACAATTAGAGTACTACAAGGAGTACCAAGCT
genomic: ACTTTGCCTCTGCTGGCTCTGGTTATGATGACAAAACAGCCATCTTAAGTgtaagaaaat ... cttgttgcagCATGCAATTCCATTGTCTCAACAATTAGAGTACTACAAGGAGTACCAAGCT
EST: gi|110688538|gb|EE067202.1|EE067202
EST:     ACTTTGCCTCTGCTGGCTCTGGTTATGATGACAAAACAGCCATCTTAAGT                         CATGCAATTCCATTGTCTCAACAATTAGAGTACTACAAGGAGTACCAAGCT
genomic: ACTTTGCCTCTGCTGGCTCTGGTTATGATGACAAAACAGCCATCTTAAGTgtaagaaaat ... cttgttgcagCATGCAATTCCATTGTCTCAACAATTAGAGTACTACAAGGAGTACCAAGCT
EST: gi|352786676|gb|FQ479883.1|FQ479883
EST:     ACTTTGCCTCTGCTGGCTCTGGTTATGATGACAAAACAGCCATCTTAAGT                         CATGCAATTCCATTGTCTCAACAATTAGAGTACTACAAGGAGTACCAAGCT
genomic: ACTTTGCCTCTGCTGGCTCTGGTTATGATGACAAAACAGCCATCTTAAGTgtaagaaaat ... cttgttgcagCATGCAATTCCATTGTCTCAACAATTAGAGTACTACAAGGAGTACCAAGCT
EST: gi|110426154|gb|EC992551.1|EC992551
EST:     ACTTTGCCTCTGCTGGCTCTGGTTATGATGACAAAACAGCCATCTTAAGT                         CATGCAATTCCATTGTCTCAACAATTAGAGTACTACAAGGAGTACCAAGCT
genomic: ACTTTGCCTCTGCTGGCTCTGGTTATGATGACAAAACAGCCATCTTAAGTgtaagaaaat ... cttgttgcagCATGCAATTCCATTGTCTCAACAATTAGAGTACTACAAGGAGTACCAAGCT
EST: gi|30252385|gb|CB969936.1|CB969936
EST:     ACTTTGCCTCTGCTGGCTCTGGTTATGATGACAAAACAGCCATCTTAAGT                         CATGCAATTCCATTGTCTCAACAATTAGAGTACTACAAGGAGTACCAAGCT
genomic: ACTTTGCCTCTGCTGGCTCTGGTTATGATGACAAAACAGCCATCTTAAGTgtaagaaaat ... cttgttgcagCATGCAATTCCATTGTCTCAACAATTAGAGTACTACAAGGAGTACCAAGCT
EST: gi|33405107|gb|CF210734.1|CF210734
EST:     ACTTTGCCTCTGCTGGCTCTGGTTATGATGACAAAACAGCCATCTTAAGT                         CATGCAATTCCATTGTCTCAACAATTAGAGTACTACAAGGAGTACCAAGCT
genomic: ACTTTGCCTCTGCTGGCTCTGGTTATGATGACAAAACAGCCATCTTAAGTgtaagaaaat ... cttgttgcagCATGCAATTCCATTGTCTCAACAATTAGAGTACTACAAGGAGTACCAAGCT
EST: gi|351032432|gb|FQ458797.1|FQ458797
EST:     ACTTTGCCTCTGCTGGCTCTGGTTATGATGACAAAACAGCCATCTTAAGT                         CATGCAATTCCATTGTCTCAACAATTAGAGTACTACAAGGAGTACCAAGCT
genomic: ACTTTGCCTCTGCTGGCTCTGGTTATGATGACAAAACAGCCATCTTAAGTgtaagaaaat ... cttgttgcagCATGCAATTCCATTGTCTCAACAATTAGAGTACTACAAGGAGTACCAAGCT
EST: gi|71877396|gb|DT026451.1|DT026451
EST:     ACTTTGCCTCTGCTGGCTCTGGTTATGATGACAAAACAGCCATCTTAAGT                         CATGCAATTCCATTGTCTCAACAATTAGAGTACTACAAGGAGTACCAAGCT
genomic: ACTTTGCCTCTGCTGGCTCTGGTTATGATGACAAAACAGCCATCTTAAGTgtaagaaaat ... cttgttgcagCATGCAATTCCATTGTCTCAACAATTAGAGTACTACAAGGAGTACCAAGCT
EST: gi|294966492|gb|GW837627.1|GW837627
EST:     ACTTTGCCTCTGCTGGCTCTGGTTATGATGACAAAACAGCCATCTTAAGT                         CATGCAATTCCATTGTCTCAACAATTAGAGTACTACAAGGAGTACCAAGCT
genomic: ACTTTGCCTCTGCTGGCTCTGGTTATGATGACAAAACAGCCATCTTAAGTgtaagaaaat ... cttgttgcagCATGCAATTCCATTGTCTCAACAATTAGAGTACTACAAGGAGTACCAAGCT
EST: gi|351030663|gb|FQ438501.1|FQ438501
EST:     ACTTTGCCTCTGCTGGCTCTGGTTATGATGACAAAACAGCCATCTTAAGT                         CATGCAATTCCATTGTCTCAACAATTAGAGTACTACAAGGAGTACCAAGCT
genomic: ACTTTGCCTCTGCTGGCTCTGGTTATGATGACAAAACAGCCATCTTAAGTgtaagaaaat ... cttgttgcagCATGCAATTCCATTGTCTCAACAATTAGAGTACTACAAGGAGTACCAAGCT
EST: gi|110697427|gb|EE074406.1|EE074406
EST:     ACTTTGCCTCTGCTGGCTCTGGTTATGATGACAAAACAGCCATCTTAAGT                         CATGCAATTCCATTGTCTCAACAATTAGAGTACTACAAGGAGTACCAAGCT
genomic: ACTTTGCCTCTGCTGGCTCTGGTTATGATGACAAAACAGCCATCTTAAGTgtaagaaaat ... cttgttgcagCATGCAATTCCATTGTCTCAACAATTAGAGTACTACAAGGAGTACCAAGCT
EST: gi|110707568|gb|EE084113.1|EE084113
EST:     ACTTTGCCTCTGCTGGCTCTGGTTATGATGACAAAACAGCCATCTTAAGT                         CATGCAATTCCATTGTCTCAACAATTAGAGTACTACAAGGAGTACCAAGCT
genomic: ACTTTGCCTCTGCTGGCTCTGGTTATGATGACAAAACAGCCATCTTAAGTgtaagaaaat ... cttgttgcagCATGCAATTCCATTGTCTCAACAATTAGAGTACTACAAGGAGTACCAAGCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcactcatatagtctcctctttctcggcatttttctacttcaaatcttgttgcagCATGCAATTCCATTGTCTCAACAATTAGAGTACTACAAGGAGTACCAAGCTAAGCTAGCAAAGGTAGCAGGTAGTCAAAAAGCGGCCACCATTATCAAGG
                                            tcttgtt  CT-rich tract
                            atttttcta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagaaaattcccccattctctagtttggttgccaagaaaacaaaatttccaatcatcaaacattgttccaatacactttcaacacacagagttttcatattagtattgtgatcgcaagataatcactcatatagtctcctctttctcggcatttttctacttcaaatcttgttgcagCATGCAATTCCATTGTCTCAACAATTAGAGTACTACAAGGAGTACCAAGCTAAGCTAGCAAAGGTAGCAGGTAGTCAAAAAGCGGCCACCATTATCAAGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG