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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtaaaatattaaactacaaaatattttgattgcaatagtgaaccttgttcaagcatccacttgcctttgcccatgaatggattccacttacatttcaattgttttctagttatgatctaatctttttattcatgttgggcagGCTGTTGTTACAATGTTCAACTTCCAGCAATATCGCCACATTCAAGCACCAGGGTGGTCACTTGGATGGTCATGGGCCAAAAAGGAAGTAATCTGGAGTA

Basic information

species Vitis vinifera
transcript Vv17s0000g05070.t01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv17s0000g05070.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA04G32130.1 (Glycine max), 3'ss of exon 2
gtaagtaaaatattaaactacaaaatattttgattgcaatagtgaaccttgttcaagcatccacttgcctttgcccatgaatggattccacttacatttcaattgttttctagttatg-atctaatctttttattcatgttgggcagGCTGTTGTTACAATGTTCAACTTCCAGCAATATCGCCACATTCAAGCACCAGGGTGGTCACTTGGATGGTCATGGGCCAAAAAGGAAGTAATCTGGAGTA
                                             |  |  || |   || ||  || |  ||      | || |    |       ||    |||||  ||       |   || ||| ||       ||| |||||||||||| ||||||| |||||| || ||||||||||||||||| || || || |||||| | || ||| ||||||| ||||||||||| || ||||| |
---------------------------------------------atttcttttag--attcaaatgtcaatgaaatatattgtagcttatacgatcttttcctgtttcttaaaagcataatgaaccttcttgcatggcttgagcagGCTGTTGTGACAATGTACAACTTTCAACAATATCGCCACATTCAGGCCCCCGGATGGTCATTAGGGTGGACATGGGCTAAAAAGGAAGTGATTTGGAGCA

upper sequence: Vv17s0000g05070.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA06G22410.1 (Glycine max), 3'ss of exon 2
gtaagtaaaatattaaactacaaaatattttgattgcaatagtgaaccttgttcaagcatccacttgcctttgcccatgaatggattccacttacatttcaattgttttctagttatg-atctaatctttttattcatgttgggcagGCTGTTGTTACAATGTTCAACTTCCAGCAATATCGCCACATTCAAGCACCAGGGTGGTCACTTGGATGGTCATGGGCCAAAAAGGAAGTAATCTGGAGTA
                                                || ||  || || ||  ||||  ||      | ||         |    ||    |||||  ||   |   ||  || | | ||       ||| |||||||||||| ||||||| |||||| || ||||||||||||||||| || || || |||||| | || ||| ||||||| ||||||||||| || ||||  |
----------------------------------------------ttttcttttag-attcaaatgccaatgaaatatattgtggcttctatggtctttttctgtttcttaaaaacatattgaaccgtcttgcatggcttgagcagGCTGTTGTCACAATGTACAACTTTCAACAATATCGCCACATTCAGGCCCCCGGATGGTCATTAGGGTGGACATGGGCTAAAAAGGAAGTGATTTGGAACA

upper sequence: Vv17s0000g05070.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA02G35400.1 (Glycine max), 3'ss of exon 2
gtaagtaaaatattaaactacaaaatattttgattgcaatagtgaaccttgttcaagcatccacttgcctttgcccatgaatggattccacttacatttcaattgttttctagttatgatctaatctttttattcatgttgggcagGCTGTTGTTACAATGTTCAACTTCCAGCAATATCGCCACATTCAAGCACCAGGGTGGTCACTTGGATGGTCATGGGCCAAAAAGGAAGTAATCTGGAGTA
                                         ||  |  |   | | | | | | | ||| ||    |||||| |  |  | ||   |||||||  ||   || |||       |       ||| |   ||| ||||||||||||||||||| ||||||||| |||||||| || ||   ||  || ||||||||||| |||||| ||||||| || ||||| ||||| ||||| |
-----------------------------------------gtttatttaaatta-gtaacta-tagccatttaaaatgaattgcgtttatttgt-tttcaatcattagttatttagatgtctaagaaacaattgaa--tggacagGCTGTTGTTACAATGTACAACTTCCAACAATATCGTCATATCTCAGTGCCTGGGTGGTCACTAGGATGGACATGGGCAAAGAAGGAGGTAATATGGAGCA

upper sequence: Vv17s0000g05070.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA13G06660.1 (Glycine max), 3'ss of exon 2
gtaagtaaaatattaaactacaaaatattttgattgcaatagtgaaccttgttcaagcatccacttgcctttgcccatgaatggattccacttacatttcaattgttttctagttatgatctaatctttttattcatgttgggcagGCTGTTGTTACAATGTTCAACTTCCAGCAATATCGCCACATTCAAGCACCAGGGTGGTCACTTGGATGGTCATGGGCCAAAAAGGAAGTAATCTGGAGTA
                                         ||  |  |   | |   |     | ||  ||    |||||| || |  | ||   |||||||  ||   || |||       |       ||| |   ||| ||||||||||||||||||| ||||||||| |||||||| || ||   ||| || ||||||||| | |||||| ||||||| || ||||| ||||| ||||| |
-----------------------------------------gtttatttaaattagttacta--tagcaatttaaaatgaattgagtttatttgt-tttcaatcattagttatttagatgtctaagaaacaattgaa--tggacagGCTGTTGTTACAATGTACAACTTCCAACAATATCGTCATATCTCAGCGCCTGGGTGGTCATTAGGATGGACATGGGCAAAGAAGGAGGTAATATGGAGCA

upper sequence: Vv17s0000g05070.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA17G08830.1 (Glycine max), 3'ss of exon 1
gtaagtaaaatattaaactacaaaatattttgattgcaatagtgaaccttgttcaagcatccacttgcctttgcccatgaatggat-tccacttacatttcaattgttttctagttatgatctaatctttttattcatgttgggcagGCTGTTGTTACAATGTTCAACTTCCAGCAATATCGCCACATTCAAGCACCAGGGTGGTCACTTGGATGGTCATGGGCCAAAAAGGAAGTAATCTGGAGTA
                                          | |   ||   |||  | |   ||   ||||    | |||  || |   || |  | |    |||||  |    | |||  |||| |||  | | |||    ||||||||||||||||||| |||||| || || |||||||| ||||| || || || |||  ||| || ||| ||||||| |||||||||||||| |||| | 
-----------------------------------------tttaggttttaccaattacct--ttaaatttgtatgtaaataaatattagctcatgtcttccctgtttctttaaca-gattaaatcctttcttgcttgt---acagGCTGTTGTTACAATGTACAACTTTCAACAGTATCGCCATATTCAGGCTCCTGGATGGATACTAGGTTGGACATGGGCAAAAAAGGAAGTAATTTGGAATG

upper sequence: Vv17s0000g05070.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA19G04210.1 (Glycine max), 3'ss of exon 2
gtaagtaaaatattaaactacaaaatattttgattgcaatagtgaaccttgttcaagcatccacttgcctttgcccatgaatggattccacttacatttcaattgttttctagttatgatctaatctttttattcatgttgggcagGCTGTTGTTACAATGTTCAACTTCCAGCAATATCGCCACATTCAAGCACCAGGGTGGTCACTTGGATGGTCATGGGCCAAAAAGGAAGTAATCTGGAGTA
                                         ||| |  || |   ||   | |   ||| ||    || ||| || |  | ||   || ||||  ||   || ||     |  |     | ||| |   ||||||||||||||||||||||  |||||| || ||||||||||| ||    |  || |||||||| ||||||||| ||||||| || ||||| ||||| ||||| |
-----------------------------------------gtgtat-ttatattagtgactaga-gccatttaaaataaattgagtttatttttgtt-caatcattagttatttcgatgcctaagaaataattgaa--tgggcagGCTGTTGTTACAATGAACAACTTTCAACAATATCGCCATATCTCGGAGCCTGGGTGGTCGCTTGGATGGACATGGGCGAAGAAGGAGGTAATATGGAGCA

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|110365645|gb|EC928981.1|EC928981
EST:     ATATCACCATCAAGTGGGATGTAATGAGCTGGACTCCAGATGGTTATGTT                         GCTGTTGTTACAATGTTCAACTTCCAGCAATATCGCCACATTCAAGCACCA
genomic: ATATCACCATCAAGTGGGATGTAATGAGCTGGACTCCAGATGGTTATGTTgtaagtaaaa ... tgttgggcagGCTGTTGTTACAATGTTCAACTTCCAGCAATATCGCCACATTCAAGCACCA
EST: gi|110709853|gb|EE085677.1|EE085677
EST:     ATATCACCATCAAGTGGGATGTAATGAGCTGGACTCCAGATGGTTATGTT                         GCTGTTGTTACAATGTTCAACTTCCAGCAATATCGCCACATTCAAGCACCA
genomic: ATATCACCATCAAGTGGGATGTAATGAGCTGGACTCCAGATGGTTATGTTgtaagtaaaa ... tgttgggcagGCTGTTGTTACAATGTTCAACTTCCAGCAATATCGCCACATTCAAGCACCA
EST: gi|110711294|gb|EE087628.1|EE087628
EST:     ATATCACCATCAAGTGGGATGTAATGAGCTGGACTCCAGATGGTTATGTT                         GCTGTTGTTACAATGTTCAACTTCCAGCAATATCGCCACATTCAAGCACCA
genomic: ATATCACCATCAAGTGGGATGTAATGAGCTGGACTCCAGATGGTTATGTTgtaagtaaaa ... tgttgggcagGCTGTTGTTACAATGTTCAACTTCCAGCAATATCGCCACATTCAAGCACCA
EST: gi|110719674|gb|EE095008.1|EE095008
EST:     ATGTAATGAGCTGGACTCCAGATGGTTATGTT                         GCTGTTGTTACAATGTTCAACTTCCAGCAATATCGCCACATTCAAGCACCA
genomic: ATGTAATGAGCTGGACTCCAGATGGTTATGTTgtaagtaaaa ... tgttgggcagGCTGTTGTTACAATGTTCAACTTCCAGCAATATCGCCACATTCAAGCACCA
EST: gi|110709374|gb|EE084778.1|EE084778
EST:     ATATCACCATCAAGTGGGATGTAATGAGCTGGACTCCAGATGGTTATGTT                         GCTGTTGTTACAATGTTCAACTTCCAGCAATATCGCCACATTCAAGCACCA
genomic: ATATCACCATCAAGTGGGATGTAATGAGCTGGACTCCAGATGGTTATGTTgtaagtaaaa ... tgttgggcagGCTGTTGTTACAATGTTCAACTTCCAGCAATATCGCCACATTCAAGCACCA
EST: gi|33407966|gb|CF213593.1|CF213593
EST:     ATATCACCATCAAGTGGGATGTAATGAGCTGGACTCCAGATGGTTATGTT                         GCTGTTGTTACAATGTTCAACTTCCAGCAATATCGCCACATTCAAGCACCA
genomic: ATATCACCATCAAGTGGGATGTAATGAGCTGGACTCCAGATGGTTATGTTgtaagtaaaa ... tgttgggcagGCTGTTGTTACAATGTTCAACTTCCAGCAATATCGCCACATTCAAGCACCA
EST: gi|110713068|gb|EE088664.1|EE088664
EST:     ATATCACCATCAAGTGGGATGTAATGAGCTGGACTCCAGATGGTTATGTT                         GCTGTTGTTACAATGTTCAACTTCCAGCAATATCGCCACATTCAAGCACCA
genomic: ATATCACCATCAAGTGGGATGTAATGAGCTGGACTCCAGATGGTTATGTTgtaagtaaaa ... tgttgggcagGCTGTTGTTACAATGTTCAACTTCCAGCAATATCGCCACATTCAAGCACCA
EST: gi|110712428|gb|EE090037.1|EE090037
EST:     ATATCACCATCAAGTGGGATGTAATGAGCTGGACTCCAGATGGTTATGTT                         GCTGTTGTTACAATGTTCAACTTCCAGCAATATCGCCACATTCAAGCACCA
genomic: ATATCACCATCAAGTGGGATGTAATGAGCTGGACTCCAGATGGTTATGTTgtaagtaaaa ... tgttgggcagGCTGTTGTTACAATGTTCAACTTCCAGCAATATCGCCACATTCAAGCACCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttacatttcaattgttttctagttatgatctaatctttttattcatgttgggcagGCTGTTGTTACAATGTTCAACTTCCAGCAATATCGCCACATTCAAGCACCAGGGTGGTCACTTGGATGGTCATGGGCCAAAAAGGAAGTAATCTGGAGTA
                      ttatgatctaatcttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtaaaatattaaactacaaaatattttgattgcaatagtgaaccttgttcaagcatccacttgcctttgcccatgaatggattccacttacatttcaattgttttctagttatgatctaatctttttattcatgttgggcagGCTGTTGTTACAATGTTCAACTTCCAGCAATATCGCCACATTCAAGCACCAGGGTGGTCACTTGGATGGTCATGGGCCAAAAAGGAAGTAATCTGGAGTA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA