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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctatacctcaggattttatggtttggtttgagtcaaacataatggtttcactttctcattccatatcagattattaacgtttcttctctctttaccctagGAATTTTTGAAGGAAGAACCATATACAGCTGAAGAAATTGAGAAAATCATTGAGGAAAGTCTGCCATCAGTCTTTGGCAATTCGCCAACCTCTTTGGATG

Basic information

species Vitis vinifera
transcript Vv05s0077g00690.t01
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv05s0077g00690.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: GLYMA08G47350.1 (Glycine max), 3'ss of exon 7
-------------------------------------------------------------------------------ctatacctcaggattt-tatggtttggtttgagtcaaacataatggtttcacttt-ctcattccatatcagattattaacgtttcttctctctttaccctagGAATTTTTGAAGGAAGAACCATATACAGCTGAAGAAATTGAGAAAATCATTGAGGAAAGTCTGCCATCAGTCTTTGGCAATTCGCCAACCTCTTTGGATG
                                                                                 |||| || ||| ||  |   ||| || ||  | |  || | |  |   | | |  ||  ||  |||   | ||  ||    ||| || | | |||   ||||||||||||||||||||||||| ||||||||||||||||||||||| ||||| ||||  ||  | ||| | ||| |||||   || |  | |||| |||
gtaactttaccttgtattatcccattattgctttatctttttaaatttctaaatcttgtccttgtgaatacacgaagagtgatacttctggagttacagaattttgtgtgttttattcagattcatgatattgtattccctctgtattttaataaaaaaaagtctcctttttctac---agGAATTTTTGAAGGAAGAACCATACACAGCTGAAGAAATTGAGAAAATTATTGATGAAAACCTCACCTCAATTTTTAGCAATAATCCTATTTATTTGAATG

upper sequence: Vv05s0077g00690.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: GLYMA17G03990.1 (Glycine max), 3'ss of exon 8
-------------------------------------------------------------------ctatacctcaggatttta--tggtttggtttgagtcaaacat-aatggtttcactttctcattccatatcagattattaacgtttct--------tctctctttaccctagGAATTTTTGAAGGAAGAACCATATACAGCTGAAGAAATTGAGAAAATCATTGAGGAAAGTCTGCCATCAGTCTTTGGCAATTCGCCAACCTCTTTGGATG
                                                                     | | |     |||| |  || | ||| ||   |  ||| | |||  | ||   |  |  |   ||   | |   || ||     |        | ||  |||     |||||| ||||||||||||||||||||||||||||||||||||   | | |  | |||||  ||| | ||| | ||   ||||    || | | ||| || |
gtaattgtacctcgtatgatgtcatccttagaattagccttgtgtgacactatctttttatttgtattgagaacatttcatttcaattgatatggatttctttgaactttaatattctcttgtgtttgtaaaattctaaaacctttaccccgttataaaaactttccttttggtacagGAATATTTGAAGGAAGAACCATATACAGCTGAAGAAATTGAAGCAGTTACAGGGGAAAAGCTGACTTCATTTTTGAACAATAATGCAGCTTATTTAGAAG

upper sequence: Vv05s0077g00690.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: GLYMA07G36610.1 (Glycine max), 3'ss of exon 8
-----------------------------------------------------------------------------ctatacc--tcaggattttatggtttg-gtttgagtcaaacataatggtt-tcactttctcattccatatcagattattaacgtttcttctctctttaccctagGAATTTTTGAAGGAAGAACCATATACAGCTGAAGAAATTGAGAAAATCATTGAGGAAAGTCTGCCATCAGTCTTTGGCAATTCGCCAACCTCTTTGGATG
                                                                               ||  |  |||  ||    |  ||||  ||| |||      |  || || | |  ||||||  || |  |   |||| ||   ||    ||  |||     |||||| ||||||||||||||||||||||||||||||||||||   | | |  | |||||  ||| | ||| | ||   ||||    || | | ||| || |
gtaattgtacctggtatgatgtcatccttagaattagccttgcctgacactatctttttatttttattgagaacatttcatttcaatcaatatggatttctttgcattttagtattctcttgtgtttgtaaaattctcaaacctttacctgttataaaaactt----tccttttggtacagGAATATTTGAAGGAAGAACCATATACAGCTGAAGAAATTGAAGCAGTTACAGGGGAAAAGCTGACTTCATTTTTGAACAATAATGCAGCTTATTTAGAAG

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|37184342|gb|CF603696.1|CF603696
EST:     TATCATTTGCAAGTGATCATGGCTCTTCCAATCCTGTCGTAGCTGTCAAG                         GAATTTTTGAAGGAAGAACCATATACAGCTGAAGAAATTGAGAAAATCATT
genomic: TATCATTTGCAAGTGATCATGGCTCTTCCGATCCTGTCGTAGCTGTCAAGgtatttaaga ... tttaccctagGAATTTTTGAAGGAAGAACCATATACAGCTGAAGAAATTGAGAAAATCATT
EST: gi|110720147|gb|EE095816.1|EE095816
EST:     TATCATTTGCAAGTGATCATGGCTCTTCCGATCCTGTCGTAGCTGTCAAG                         GAATTTTTGAAGGAAGA-CCATATACAGCTGAAGAAATTGAGAAAATCATT
genomic: TATCATTTGCAAGTGATCATGGCTCTTCCGATCCTGTCGTAGCTGTCAAGgtatttaaga ... tttaccctagGAATTTTTGAAGGAAGAACCATATACAGCTGAAGAAATTGAGAAAATCATT
EST: gi|30299412|gb|CB976206.1|CB976206
EST:     TATCATTTGCAAGTGATCATGGCTCTTCCGATCCTGTCGTAGCTGTCAAG                         GAATTTTTGAAGGAAGAACCATATACAGCTGAAGAAATTGAGAAAATCATT
genomic: TATCATTTGCAAGTGATCATGGCTCTTCCGATCCTGTCGTAGCTGTCAAGgtatttaaga ... tttaccctagGAATTTTTGAAGGAAGAACCATATACAGCTGAAGAAATTGAGAAAATCATT
EST: gi|27583346|gb|CB006041.1|CB006041
EST:     TATCATTTGCAAGTGATCATGGCTCTTCCGATCCTGTCGTAGCTGTCAAG                         GAATTTTTGAAGGAAGAACCATATACAGCTGAAGAAATTGAGAAAATCATT
genomic: TATCATTTGCAAGTGATCATGGCTCTTCCGATCCTGTCGTAGCTGTCAAGgtatttaaga ... tttaccctagGAATTTTTGAAGGAAGAACCATATACAGCTGAAGAAATTGAGAAAATCATT
EST: gi|33406611|gb|CF212238.1|CF212238
EST:     TATCATTTGCAAGTGATCATGGCTCTTCCGATCCTGTCGTAGCTGTCAAG                         GAATTTTTGAAGGAAGAACCATATACAGCTGAAGAAATTGAGAAAATCATT
genomic: TATCATTTGCAAGTGATCATGGCTCTTCCGATCCTGTCGTAGCTGTCAAGgtatttaaga ... tttaccctagGAATTTTTGAAGGAAGAACCATATACAGCTGAAGAAATTGAGAAAATCATT
EST: gi|33407058|gb|CF212685.1|CF212685
EST:     TATCATTTGCAAGTGATCATGGCTCTTCCGATCCTGTCGTAGCTGTCAAG                         GAATTTTTGAAGGAAGAACCATATACAGCTGAAGAAATTGAGAAAATCATT
genomic: TATCATTTGCAAGTGATCATGGCTCTTCCGATCCTGTCGTAGCTGTCAAGgtatttaaga ... tttaccctagGAATTTTTGAAGGAAGAACCATATACAGCTGAAGAAATTGAGAAAATCATT
EST: gi|110392261|gb|EC957554.1|EC957554
EST:     TATCATTTGCAAGTGATCATGGCTCTTCCGATCCTGTCGTAGCTGTCAAG                         GAATTTTTGAAGGAAGAACCATATACAGCTGAAGAAATTGAGAAAATCATT
genomic: TATCATTTGCAAGTGATCATGGCTCTTCCGATCCTGTCGTAGCTGTCAAGgtatttaaga ... tttaccctagGAATTTTTGAAGGAAGAACCATATACAGCTGAAGAAATTGAGAAAATCATT
EST: gi|27585689|gb|CB008384.1|CB008384
EST:     TATCATTTGCAAGTGATCATGGCTCTTCCGATCCTGTCGTAGCTGTCAAG                         GAATTTTTGAAGGAAGAACCATATACAGCTGAAGAAATTGAGAAAATCATT
genomic: TATCATTTGCAAGTGATCATGGCTCTTCCGATCCTGTCGTAGCTGTCAAGgtatttaaga ... tttaccctagGAATTTTTGAAGGAAGAACCATATACAGCTGAAGAAATTGAGAAAATCATT
EST: gi|27585107|gb|CB007802.1|CB007802
EST:     ATCATTTGCAAGTGATCATGGCTCTTCCGATCCTGTCGTAGCTGTCAAG                         GAATTTTTGAAGGAAGAACCATATACAGCTGAAGAAATTGAGAAAATCATT
genomic: ATCATTTGCAAGTGATCATGGCTCTTCCGATCCTGTCGTAGCTGTCAAGgtatttaaga ... tttaccctagGAATTTTTGAAGGAAGAACCATATACAGCTGAAGAAATTGAGAAAATCATT
EST: gi|110719299|gb|EE097116.1|EE097116
EST:     TATCATTTGCAAGTGATCATGGCTCTTCCAATCCTGTCGTAGCTGTCAAG                         GAATTTTTGAAGGAAGAACCATATACAGCTGAAGAAATTGAGAAAATCATT
genomic: TATCATTTGCAAGTGATCATGGCTCTTCCGATCCTGTCGTAGCTGTCAAGgtatttaaga ... tttaccctagGAATTTTTGAAGGAAGAACCATATACAGCTGAAGAAATTGAGAAAATCATT
EST: gi|30299334|gb|CB976128.1|CB976128
EST:     TATCATTTGCAAGTGATCATGGCTCTTCCGATCCTGTCGTAGCTGTCAAG                         GAATTTTTGAAGGAAGAACCATATACAGCTGAAGAAATTGAGAAAATCATT
genomic: TATCATTTGCAAGTGATCATGGCTCTTCCGATCCTGTCGTAGCTGTCAAGgtatttaaga ... tttaccctagGAATTTTTGAAGGAAGAACCATATACAGCTGAAGAAATTGAGAAAATCATT
EST: gi|33406531|gb|CF212158.1|CF212158
EST:     TCCGATCCTGTCGTAGCTGTCAAG                         GAATTTTTGAAGGAAGAACCATATACAGCTGAAGAAATTGAGAAAATCATT
genomic: TCCGATCCTGTCGTAGCTGTCAAGgtatttaaga ... tttaccctagGAATTTTTGAAGGAAGAACCATATACAGCTGAAGAAATTGAGAAAATCATT
EST: gi|294964251|gb|GW838054.1|GW838054
EST:     TATCATTTGCAAGTGATCATGGCTCTTCCGATCCCGTCGTAGCTGTCAAG                         GAATTTTTGAAGGAAGAACCATATACAGCTGAAGAAATTGAGAAAATCATT
genomic: TATCATTTGCAAGTGATCATGGCTCTTCCGATCCTGTCGTAGCTGTCAAGgtatttaaga ... tttaccctagGAATTTTTGAAGGAAGAACCATATACAGCTGAAGAAATTGAGAAAATCATT
EST: gi|110732746|gb|EE108300.1|EE108300
EST:     TATCATTTGCAAGTGATCATGGCTCTTCCAATCCTGTCGTAGCTGTCAAG                         GAATTTTTGAAGGAAGAACCATATACAGCTGAAGAAATTGAGAAAATCATT
genomic: TATCATTTGCAAGTGATCATGGCTCTTCCGATCCTGTCGTAGCTGTCAAGgtatttaaga ... tttaccctagGAATTTTTGAAGGAAGAACCATATACAGCTGAAGAAATTGAGAAAATCATT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttcactttctcattccatatcagattattaacgtttcttctctctttaccctagGAATTTTTGAAGGAAGAACCATATACAGCTGAAGAAATTGAGAAAATCATTGAGGAAAGTCTGCCATCAGTCTTTGGCAATTCGCCAACCTCTTTGGATG
                          tattaac  putative branch site (score: 1)
                                cgtttcttctctcttt  CT-rich tract
                 atatcagattattaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ctatacctcaggattttatggtttggtttgagtcaaacataatggtttcactttctcattccatatcagattattaacgtttcttctctctttaccctagGAATTTTTGAAGGAAGAACCATATACAGCTGAAGAAATTGAGAAAATCATTGAGGAAAGTCTGCCATCAGTCTTTGGCAATTCGCCAACCTCTTTGGATG

- -tacctca
- - - - - - - - - -ggtttgg
- - - - - - - - - - - - - - - - -caaacat