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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtggattcttctcactttcactctcacactttgtattttgatcatattacattccttggattttgattcattgaacaaatacctatgcttaattttcatgttattgtattggttgctgtggatgttgacttatgttattctacttgattttgttggctttgtcagTTTGTTAGTGAGTTGGCTCGAGTTGTAGCCCCAGGTGGCACAATAATACTTGTAACATGGTGCCATAGGGATCTCTCCCCTTCTGAAGAATCCTTAAAGC

Basic information

species Vitis vinifera
transcript Vv16s0039g01410.t01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv16s0039g01410.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA09G35680.1 (Glycine max), 3'ss of exon 3
gtggattcttctcactttcactctcacactttgtattttgatcatattacattccttggattttgattcattgaacaaatacctatgcttaattttcatgttattgtattggttgctgtggatgttgacttatgtta--ttctacttgattttgttggctttgtcagTTTGTTAGTGAGTTGGCTCGAGTTGTAGCCCCAGGTGGCACAATAATACTTGTAACATGGTGCCATAGGGATCTCTCCCCTTCTGAAGAATCCTTAAAGC
                                                       |  |   ||   | |  |   ||||| || |   ||   |   |  |||         | || |  || |   || |  |||  ||| |||| ||      | |      |||||||| | || || ||||| || | ||| ||||||||||| |||||| | |||||||||||||| ||||||||   ||||  |||| ||||| ||   |
------------------------------------------------------ttaagtaattaccttacagttgaaatatctctttctatgatctgtactat-------actactattaatctcacctcagcttaatttccacttaatgcaaccgac------agTTTGTTGGAGAATTAGCTCGGGTAGCAGCACCAGGTGGCACCATAATAATAGTAACATGGTGCCACAGGGATCTTGGCCCTGATGAACAATCCCTACTTC

upper sequence: Vv16s0039g01410.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA12G01690.1 (Glycine max), 3'ss of exon 3
gtggattcttctcactttcactctcacactttgtattttgatcatattacattccttggattttgattcattgaacaaatacctatgcttaattttcatgttattgtattggttgctgtggatgttgacttatgttattctacttgattttgttggctttgtcagTTTGTTAGTGAGTTGGCTCGAGTTGTAGCCCCAGGTGGCACAATAATACTTGTAACATGGTGCCATAGGGATCTCTCCCCTTCTGAAGAATCCTTAAAGC
                                                        |  | | || || | |      ||  || |   || |||  | | | |  | |    |  |  |  |   |  | |    |    || ||    || || |      |||||||| | ||||| ||||| || | ||| ||||||| ||| |||||| | |||||||||||||| ||||||||   ||||   ||| |||||||| | |
-------------------------------------------------------ctcaagtgtggtttact---ttgatgtctctttctattttgtacgctttaatctcatctcatcagtttcccgcttcacac-acaacacgtgcaactgatgac------agTTTGTTGGAGAGTTAGCTCGGGTAGCAGCACCAGGTGCCACTATAATAATAGTAACATGGTGCCACAGGGATCTTGGCCCTGACGAACAATCCTTACATC
















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|351051597|gb|FQ450149.1|FQ450149
EST:     ATCTGGTTTGGTCCATGGAGAGTGGAGAACACATGCCTGACNNNNNNNNG                         TTTGTTAGTGAGTTGGCTCGAGTTGTAGCCCCAGGTGGCACAATAATACTT
genomic: ATCTGGTTTGGTCCATGGAGAGTGGAGAACACATGCCTGACAAAAAAAAGgtggattctt ... gctttgtcagTTTGTTAGTGAGTTGGCTCGAGTTGTAGCCCCAGGTGGCACAATAATACTT
EST: gi|32249778|gb|CD715597.1|CD715597
EST:     ATCTGGTTTGGTCCATGGAGAGTGGAGAACACATGCCTGACNNNNNNNNG                         TTTGTTAGTGAGTTGGCTCGAGTTGTAGCCCCAGGTGGCACAATAATACTT
genomic: ATCTGGTTTGGTCCATGGAGAGTGGAGAACACATGCCTGACAAAAAAAAGgtggattctt ... gctttgtcagTTTGTTAGTGAGTTGGCTCGAGTTGTAGCCCCAGGTGGCACAATAATACTT
EST: gi|110360881|gb|EC924323.1|EC924323
EST:     ATCTGGTTTGGTCCATGGAGAGTGGAGAACACATGCCTGACNNNNNNNNG                         TTTGTTAGTGAGTTGGCTCGAGTTGCAGCCCCAGGTGGCACAATAATACTT
genomic: ATCTGGTTTGGTCCATGGAGAGTGGAGAACACATGCCTGACAAAAAAAAGgtggattctt ... gctttgtcagTTTGTTAGTGAGTTGGCTCGAGTTGTAGCCCCAGGTGGCACAATAATACTT
EST: gi|34547143|gb|CF515375.1|CF515375
EST:     ATCTGGTTTGGTCCATGGAGAGTGGAGAACACATGCCTGACNNNNNNNNG                         TTTGTTAGTGAGTTGGCTCGAGTTGCAGCCCCAGGTGGCACAATAATACTT
genomic: ATCTGGTTTGGTCCATGGAGAGTGGAGAACACATGCCTGACAAAAAAAAGgtggattctt ... gctttgtcagTTTGTTAGTGAGTTGGCTCGAGTTGTAGCCCCAGGTGGCACAATAATACTT
EST: gi|28960633|gb|CB340324.1|CB340324
EST:     ATCTGGTTTGGTCCATGGAGAGTGGAGAACACATGCCTGACNNNNNNN-G                         TTTGTTAGTGAGTTGGCTCGAGTTGCAGCCCCAGGTGGCACAATAATACTT
genomic: ATCTGGTTTGGTCCATGGAGAGTGGAGAACACATGCCTGACAAAAAAAAGgtggattctt ... gctttgtcagTTTGTTAGTGAGTTGGCTCGAGTTGTAGCCCCAGGTGGCACAATAATACTT
EST: gi|32271736|gb|CD720895.1|CD720895
EST:     ATCTGGTTTGGTCCATGGAGAGTGGAGAACACATGCCTGACNNNNNNNNG                         TTTGTTAGTGAGTTGGCTCGAGTTGTAGCCCCAGGTGGCACAATAATACTT
genomic: ATCTGGTTTGGTCCATGGAGAGTGGAGAACACATGCCTGACAAAAAAAAGgtggattctt ... gctttgtcagTTTGTTAGTGAGTTGGCTCGAGTTGTAGCCCCAGGTGGCACAATAATACTT
EST: gi|351032554|gb|FQ458919.1|FQ458919
EST:     ATCTGGTTTGGTCCATGGAGAGTGGAGAACACATGCCTGACNNNNNNNNG                         TTTGTTAGTGAGTTGGCTCGAGTTGTAGCCCCAGGTGGCACAATAATACTT
genomic: ATCTGGTTTGGTCCATGGAGAGTGGAGAACACATGCCTGACAAAAAAAAGgtggattctt ... gctttgtcagTTTGTTAGTGAGTTGGCTCGAGTTGTAGCCCCAGGTGGCACAATAATACTT
EST: gi|32247466|gb|CD713285.1|CD713285
EST:     ATCTGGTTTGGTCCATGGAGAGTGGAGAACACATGCCTGACNNNNNNNNG                         TTTGTTAGTGAGTTGGCTCGAGTTGTAGCCCCAGGTGGCACAATAATACTT
genomic: ATCTGGTTTGGTCCATGGAGAGTGGAGAACACATGCCTGACAAAAAAAAGgtggattctt ... gctttgtcagTTTGTTAGTGAGTTGGCTCGAGTTGTAGCCCCAGGTGGCACAATAATACTT
EST: gi|32270284|gb|CD719443.1|CD719443
EST:     GGTTTGGTCCATGGAGAGTGGAGAACACATGCCTGACNNNNNNNNG                         TTTGTTAGTGAGTTGGCTCGAGTTGTAGCCCCAGGTGGCACAATAATACTT
genomic: GGTTTGGTCCATGGAGAGTGGAGAACACATGCCTGACAAAAAAAAGgtggattctt ... gctttgtcagTTTGTTAGTGAGTTGGCTCGAGTTGTAGCCCCAGGTGGCACAATAATACTT
EST: gi|352790125|gb|FQ481324.1|FQ481324
EST:     ATCTGGTTTGGTCCATGGAGAGTGGAGAACACATGCCTGACNNNNNNNNG                         TTTGTTAGTGAGTTGGCTCGAGTTGTAGCCCCAGGTGGCACAATAATACTT
genomic: ATCTGGTTTGGTCCATGGAGAGTGGAGAACACATGCCTGACAAAAAAAAGgtggattctt ... gctttgtcagTTTGTTAGTGAGTTGGCTCGAGTTGTAGCCCCAGGTGGCACAATAATACTT
EST: gi|351033929|gb|FQ462984.1|FQ462984
EST:     ATCTGGTTTGGTCCATGGAGAGTGGAGAACACATGCCTGACNNNNNNNNG                         TTTGTTAGTGAGTTGGCTCGAGTTGTAGC
genomic: ATCTGGTTTGGTCCATGGAGAGTGGAGAACACATGCCTGACAAAAAAAAGgtggattctt ... gctttgtcagTTTGTTAGTGAGTTGGCTCGAGTTGTAGC
EST: gi|110425522|gb|EC991909.1|EC991909
EST:     ATCTGGTTTGGTCCATGGAGAGTGGAGAACACATGCCTGACNNNNNNNNG                         TTTGTTAGTGAGTTGGCTCGAGTTGCAGCCCCAGGTGGCACAATAATACTT
genomic: ATCTGGTTTGGTCCATGGAGAGTGGAGAACACATGCCTGACAAAAAAAAGgtggattctt ... gctttgtcagTTTGTTAGTGAGTTGGCTCGAGTTGTAGCCCCAGGTGGCACAATAATACTT
EST: gi|351037069|gb|FQ465061.1|FQ465061
EST:     ATCTGGTTTGGTCCATGGAGAGTGGAGAACACATGCCTGACNNNNNNNNG                         TTTGTTAGTGAGTTGGCTCGAGTTGTAGCCCCAGGTGGCACAATAATACTT
genomic: ATCTGGTTTGGTCCATGGAGAGTGGAGAACACATGCCTGACAAAAAAAAGgtggattctt ... gctttgtcagTTTGTTAGTGAGTTGGCTCGAGTTGTAGCCCCAGGTGGCACAATAATACTT
EST: gi|351037494|gb|FQ460693.1|FQ460693
EST:     ATCTGGTTTGGTCCATGGAGAGTGGAGAACACATGCCTGACNNNNNNNNG                         TTTGTTAGTGAGTTGGCTCGAGTTGTAGCCCCAGGTGGCACAATAATACTT
genomic: ATCTGGTTTGGTCCATGGAGAGTGGAGAACACATGCCTGACAAAAAAAAGgtggattctt ... gctttgtcagTTTGTTAGTGAGTTGGCTCGAGTTGTAGCCCCAGGTGGCACAATAATACTT
EST: gi|32248194|gb|CD714013.1|CD714013
EST:     ATCTGGTTTGGTCCATGGAGAGTGGAGAACACATGCCTGACNNNNNNNNG                         TTTGTTAGTGAGTTGGCTCGAGTTGTAGCCCCAGGTGGCACAATAATACTT
genomic: ATCTGGTTTGGTCCATGGAGAGTGGAGAACACATGCCTGACAAAAAAAAGgtggattctt ... gctttgtcagTTTGTTAGTGAGTTGGCTCGAGTTGTAGCCCCAGGTGGCACAATAATACTT
EST: gi|32247586|gb|CD713405.1|CD713405
EST:     ATCTGGTTTGGTCCATGGAGAGTGGAGAACACATGCCTGACNNNNNNNNG                         TTTGTTAGTGAGTTGGCTCGAGTTGTAGCCCCAGGTGGCACAATAATACTT
genomic: ATCTGGTTTGGTCCATGGAGAGTGGAGAACACATGCCTGACAAAAAAAAGgtggattctt ... gctttgtcagTTTGTTAGTGAGTTGGCTCGAGTTGTAGCCCCAGGTGGCACAATAATACTT
EST: gi|110421515|gb|EC987813.1|EC987813
EST:     ATCTGGTTTGGTCCATGGAGAGTGGAGAACACATGCCTGACNNNNNNNNG                         TTTGTTAGTGAGTTGGCTCGAGTTGCAGCCCCAGGTGGCACAATAATACTT
genomic: ATCTGGTTTGGTCCATGGAGAGTGGAGAACACATGCCTGACAAAAAAAAGgtggattctt ... gctttgtcagTTTGTTAGTGAGTTGGCTCGAGTTGTAGCCCCAGGTGGCACAATAATACTT
EST: gi|110376167|gb|EC941211.1|EC941211
EST:     ATCTGGTTTGGTCCATGGAGAGTGGAGAACACATGCCTGACNNNNNNNNG                         TTTGTTAGTGAGTTGGCTCGAGTTGCAGCCCCAGGTGGCACAATAATACTT
genomic: ATCTGGTTTGGTCCATGGAGAGTGGAGAACACATGCCTGACAAAAAAAAGgtggattctt ... gctttgtcagTTTGTTAGTGAGTTGGCTCGAGTTGTAGCCCCAGGTGGCACAATAATACTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggttgctgtggatgttgacttatgttattctacttgattttgttggctttgtcagTTTGTTAGTGAGTTGGCTCGAGTTGTAGCCCCAGGTGGCACAATAATACTTGTAACATGGTGCCATAGGGATCTCTCCCCTTCTGAAGAATCCTTAAAGC
                                              ctttgtc  CT-rich tract
                   ttatgttatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtggattcttctcactttcactctcacactttgtattttgatcatattacattccttggattttgattcattgaacaaatacctatgcttaattttcatgttattgtattggttgctgtggatgttgacttatgttattctacttgattttgttggctttgtcagTTTGTTAGTGAGTTGGCTCGAGTTGTAGCCCCAGGTGGCACAATAATACTTGTAACATGGTGCCATAGGGATCTCTCCCCTTCTGAAGAATCCTTAAAGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA