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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagttcacttcaggaaattaaaaattgaagattccttcaaaattagcataccccatgtcatttccctcttatatttttcaatgtcacatagagaagtttccatctcactctggttccttcaacagTAAGTGATGAAGGCGAGAATTGGAGCGCCGGGCAACGCCAGCTCTTCTGTCTTGGAAGAGTCCTACTTAAGAGAAACAGAATCCTTGTTCTAGATGAAGC

Basic information

species Vitis vinifera
transcript Vv09s0002g02430.t01
intron # 21
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv09s0002g02430.t01 (Vitis vinifera), 3'ss of exon 21
lower sequence: LOC_Os05g10730.2 (Oryza sativa), 3'ss of exon 9
gtgagttc-acttcaggaaattaaaaattgaagattccttcaaaattagcataccccatgtcatttccctcttatatttttcaatgtcacatagagaagtttccatctcactctggttccttcaacagTAAGTGATGAAGGCGAGAATTGGAGCGCCGGGCAACGCCAGCTCTTCTGTCTTGGAAGAGTCCTACTTAAGAGAAACAGAATCCTTGTTCTAGATGAAGC
|||||  |   |||||   |||    | || | |     |||| ||   || |     |||||      | |  |    | || ||  |   | | |   |    |||  |  |  |||  ||  |||| || || || |||||||| ||||||||||| ||||| ||||||||||| || |   | ||||| ||    || ||||  ||||| || || || || ||
gtgagccctgattcag---attccctagtgcataccttctcaatatattcagaagtt-tgtcagacaagtgtggt----tgcactgaaaagaaaaaatcctcatttctggccatctttcaatctccagTGAGCGACGACGGCGAGAACTGGAGCGCCGGACAACGGCAGCTCTTCTGCCTGGCCCGGGTCCTCCTCCGCAGGAACAAGATCCTGGTCCTCGACGAGGC

upper sequence: Vv09s0002g02430.t01 (Vitis vinifera), 3'ss of exon 21
lower sequence: GLYMA08G20770.2 (Glycine max), 3'ss of exon 9
-------------------------------------------------------------------gtgagttcacttcagga--aattaaaaattgaagattccttcaaaattagcataccccatgtcatttccctcttatatttttcaat-gtcaca-tagagaagtttccatctcactctggttccttcaacagTAAGTGATGAAGGCGAGAATTGGAGCGCCGGGCAACGCCAGCTCTTCTGTCTTGGAAGAGTCCTACTTAAGAGAAACAGAATCCTTGTTCTAGATGAAGC
                                                                   | |  || |||| ||||  |||| |||||   || |    | | |  | | |      | | ||||    ||  | |||    ||| |  ||| |  ||   ||    ||| | ||||     ||  ||||| |||||||| || |  |||||||||   || || ||||| || || |||||||||||||| ||||||||||| |||||||| |||||||||||||||||
gtgagtaaacttctagccaattctctctgcagccttgggcaagaatctattgctgctttactcttttgaggtttaactttaggaggaattcaaaatcatagttgttcttacatgttgtacttttaaag-cattcaattcgcaaattaagaaattggaacaatttagctattgaagtctaattctgacaagttatacagTGAGTGATGAGGGAGGAAATTGGAGCTTGGGACAGCGCCAACTGTTTTGTCTTGGAAGAGTACTACTTAAGAGGAACAGAATTCTTGTTCTAGATGAAGC

upper sequence: Vv09s0002g02430.t01 (Vitis vinifera), 3'ss of exon 21
lower sequence: GLYMA08G20360.1 (Glycine max), 3'ss of exon 10
-------------------------------------------gtgagtt-cacttcaggaaattaaaaattgaagattccttcaaaattagcatacc-ccatgtcatttccctcttatatttttcaatgtcacatagagaagtttccatctcactctggttccttcaacagTAAGTGATGAAGGCGAGAATTGGAGCGCCGGGCAACGCCAGCTCTTCTGTCTTGGAAGAGTCCTACTTAAGAGAAACAGAATCCTTGTTCTAGATGAAGC
                                            | |||  |  |||      || || ||| |  |    | |||| | | ||||      ||   |||  | |  | || || |||   || ||| |  | ||    ||| | ||||  |  ||   |||| ||||||||||| |  |||||||||   || ||||  || || || |||||||||||||| ||||||||||| |||||||| ||||||||||| |||||
gtgagttaacaaacctgaagccaacaatctgatgtacttttatataagtcactattctactctttcaacattaagtaaaa-tacaaagtaatcatatagttctgcatttttacccaaagatcttgcaa---caaataaacca-ttgaagtctaattctgagttgttattcagTGAGTGATGAAGGTGGAAATTGGAGCTTGGGACAACAGCAACTGTTTTGTCTTGGAAGAGTACTACTTAAGAGGAACAGAATACTTGTTCTAGACGAAGC

upper sequence: Vv09s0002g02430.t01 (Vitis vinifera), 3'ss of exon 21
lower sequence: GLYMA07G01390.1 (Glycine max), 3'ss of exon 11
gtgagttcacttcaggaaattaaaaattgaagattccttcaaaattagcataccccatgtcatttccctcttatatttttcaatgtcacatagagaagtttccatctcactctggttccttcaacagTAAGTGATGAAGGCGAGAATTGGAGCGCCGGGCAACGCCAGCTCTTCTGTCTTGGAAGAGTCCTACTTAAGAGAAACAGAATCCTTGTTCTAGATGAAGC
                |  || ||| ||  |   |  |  |   |||    || | ||     ||||   ||| | ||||  |   || ||  ||   ||    ||| | ||||  |  ||  ||||| ||||||||||| |  |||||||||   || || ||||| || || |||||||||||||| ||||||||||| |||||||| || ||||| ||||||||
----------------atgttgaaacttaca---ttttgtacttttaaagcactcaat-----ttccaaattagaattttggaa--caaatt-agttattgaagtctaattctgactaattacacagTGAGTGATGAAGGTGGAAATTGGAGCTTGGGACAGCGCCAACTATTTTGTCTTGGAAGAGTACTACTTAAGAGGAACAGAATTCTAGTTCTGGATGAAGC

upper sequence: Vv09s0002g02430.t01 (Vitis vinifera), 3'ss of exon 21
lower sequence: GLYMA08G20780.1 (Glycine max), 3'ss of exon 11
gtgagttcacttcaggaaattaaaaattgaagattccttcaaaattagcataccccatgtcatttccctcttatatttttcaatgtcacatagagaagtttccatctcactctggttccttcaacagTAAGTGATGAAGGCGAGAATTGGAGCGCCGGGCAACGCCAGCTCTTCTGTCTTGGAAGAGTCCTACTTAAGAGAAACAGAATCCTTGTTCTAGATGAAGC
                         | || | |||  |   ||||||  ||    ||  | ||         | |      ||| | ||        |      ||| | ||||      | |||||| ||||||||||| || || ||||| |  || || || || ||| | ||||| |||||||| || |||||||| |||||||| |||||||| ||||||||
------------------------gactgcatattagtc--aaattaaaattttacacat-ataatgtatcaacaaacaaaaattttactcctgactgaaatagtctaattctgaccaacttaacagTGAGTGATGAAGGTGAAAACTGGAGTGTGGGACAGCGTCAACTCATATGTCTCGGAAGAGTGCTTCTTAAGAGGAACAGAATTCTTGTTCTGGATGAAGC

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|110695449|gb|EE073482.1|EE073482
EST:     TCAGCTCAAGGCAACAATCAGCAGTCTTCCAAACTTGCTAGACTCATCTG                         TAAGTGATGAAGGCGAGAATTGGAGCGCCGGGCAACGCCAGCTCTTCTGTC
genomic: TCAGCTCAAGGCAACAATCAGCAGTCTTCCAAACTTGCTAGACTCATCTGgtgagttcac ... ccttcaacagTAAGTGATGAAGGCGAGAATTGGAGCGCCGGGCAACGCCAGCTCTTCTGTC
EST: gi|110715223|gb|EE093024.1|EE093024
EST:     TCAGCTCAAGGCAACAATCAGCAGTCTTCCAAACTTGCTAGACTCATCTG                         TAAGTGATGAAGGCGAGAATTGGAGCGCCGGGCAACGCCAGCTCTTCTGTC
genomic: TCAGCTCAAGGCAACAATCAGCAGTCTTCCAAACTTGCTAGACTCATCTGgtgagttcac ... ccttcaacagTAAGTGATGAAGGCGAGAATTGGAGCGCCGGGCAACGCCAGCTCTTCTGTC
EST: gi|22011601|gb|BQ796635.1|BQ796635
EST:     TCAGCTCAAGGCAACAATCAGCAGTCTTCCAAACTTGCTAGACTCATCTG                         TAAGTGATGAAGGCGAGAATTGGAGCGCCGGGCAACGCCAGCTCTTCTGTC
genomic: TCAGCTCAAGGCAACAATCAGCAGTCTTCCAAACTTGCTAGACTCATCTGgtgagttcac ... ccttcaacagTAAGTGATGAAGGCGAGAATTGGAGCGCCGGGCAACGCCAGCTCTTCTGTC
EST: gi|30303963|gb|CB980757.1|CB980757
EST:     TCAGCTCAAGGAAACAATCAGCAGTCTTCCAAACTTGCTAGACTCATCTG                         TAAGTGATGAAGGCGAGAATTGGAGCGCCGGGCAACGCCAGCTCTTCTGTC
genomic: TCAGCTCAAGGCAACAATCAGCAGTCTTCCAAACTTGCTAGACTCATCTGgtgagttcac ... ccttcaacagTAAGTGATGAAGGCGAGAATTGGAGCGCCGGGCAACGCCAGCTCTTCTGTC
EST: gi|30300210|gb|CB977004.1|CB977004
EST:     TCAGCTCAAGGCAACAATCAGCAGTCTTCCAAACTTGCTAGACTCATCTG                         TAAGTGATGAAGGCGAGAATTGGAGCGCCGGGCAACGCCAGCTCTTCTGTC
genomic: TCAGCTCAAGGCAACAATCAGCAGTCTTCCAAACTTGCTAGACTCATCTGgtgagttcac ... ccttcaacagTAAGTGATGAAGGCGAGAATTGGAGCGCCGGGCAACGCCAGCTCTTCTGTC
EST: gi|30303898|gb|CB980692.1|CB980692
EST:     TCAGCTCAAGGCAACAATCAGCAGTCTTCCAAACTTGCTAGACTCATCTG                         TAAGTGATGAAGGCGAGAATTGGAGCGCCGGGCAACGCCAGCTCTTCTGTC
genomic: TCAGCTCAAGGCAACAATCAGCAGTCTTCCAAACTTGCTAGACTCATCTGgtgagttcac ... ccttcaacagTAAGTGATGAAGGCGAGAATTGGAGCGCCGGGCAACGCCAGCTCTTCTGTC
EST: gi|110359216|gb|EC920349.1|EC920349
EST:     TCAGCTCAAGGCAACAATCAGCAGTCTTCCAAACTTGCTAGACTCATCTG                         TAAGTGATGAAGGCGAGAATTGGAGCGCCGGGCAACGCCAGCTCTTCTGTC
genomic: TCAGCTCAAGGCAACAATCAGCAGTCTTCCAAACTTGCTAGACTCATCTGgtgagttcac ... ccttcaacagTAAGTGATGAAGGCGAGAATTGGAGCGCCGGGCAACGCCAGCTCTTCTGTC
EST: gi|219555058|gb|FG984847.1|FG984847
EST:     TCAGCTCAAGGCAACAATCAGCAGTCTTCCAAACTTGCTAGACTCATCTG                         TAAGTGATGAAGGCGAGAATTGGAGCGCCGGGCAACGCCAGCTCTTCTGTC
genomic: TCAGCTCAAGGCAACAATCAGCAGTCTTCCAAACTTGCTAGACTCATCTGgtgagttcac ... ccttcaacagTAAGTGATGAAGGCGAGAATTGGAGCGCCGGGCAACGCCAGCTCTTCTGTC
EST: gi|22011602|gb|BQ796636.1|BQ796636
EST:     TCAGCTCAAGGCAACAATCAGCAGTCTTCCAAACTTGCTAGACTCATCTG                         TAAGTGATGAAGGCGAGAATTGGAGCGCCGGGCAACGCCAGCTCTTCTGTC
genomic: TCAGCTCAAGGCAACAATCAGCAGTCTTCCAAACTTGCTAGACTCATCTGgtgagttcac ... ccttcaacagTAAGTGATGAAGGCGAGAATTGGAGCGCCGGGCAACGCCAGCTCTTCTGTC
EST: gi|219555135|gb|FG984396.1|FG984396
EST:     TCAGCTCAAGGCAACAATCAGCAGTCTTCCAAACTTGCTAGACTCATCTG                         TAAGTGATGAAGGCGAGAATTGGAGCGCCGGGCAACGCCAGCTCTTCTGTC
genomic: TCAGCTCAAGGCAACAATCAGCAGTCTTCCAAACTTGCTAGACTCATCTGgtgagttcac ... ccttcaacagTAAGTGATGAAGGCGAGAATTGGAGCGCCGGGCAACGCCAGCTCTTCTGTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atatttttcaatgtcacatagagaagtttccatctcactctggttccttcaacagTAAGTGATGAAGGCGAGAATTGGAGCGCCGGGCAACGCCAGCTCTTCTGTCTTGGAAGAGTCCTACTTAAGAGAAACAGAATCCTTGTTCTAGATGAAGC
                               atctcac  putative branch site (score: 3)
                                           ttccttc  putative PPT
     tttcaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagttcacttcaggaaattaaaaattgaagattccttcaaaattagcataccccatgtcatttccctcttatatttttcaatgtcacatagagaagtttccatctcactctggttccttcaacagTAAGTGATGAAGGCGAGAATTGGAGCGCCGGGCAACGCCAGCTCTTCTGTCTTGGAAGAGTCCTACTTAAGAGAAACAGAATCCTTGTTCTAGATGAAGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC