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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tctttatgaaaacgttttgaactttcttatttaattgtttcattattgtgttaccattaccgatgaaattttctgattggacttattatctttgattaagGTCGGCAATCTTTCCTAAACACTTCAAAGTGGATTGAAGAGGTTCGCACTGAGAGAGGTAGTGATGTTATTATCGTCCTTGTTGGAAACAAGACTGACCT

Basic information

species Vitis vinifera
transcript Vv02s0012g00710.t01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv02s0012g00710.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: LOC_Os07g31370.1 (Oryza sativa), 3'ss of exon 3
tctttatgaaaacgttttgaactttcttatttaattgtttcattattgtgtta-ccattaccgatgaaa----ttttctgattggacttattatctttgattaagGTCGGCAATCTTTCCTAAACACTTCAAAGTGGATTGAAGAGGTTCGCACTGAGAGAGGTAGTGATGTTATTATCGTCCTTGTTGGAAACAAGACTGACCT
     ||||       | | | | || | |||||||  ||    ||| |   | |  || || ||         ||| |  ||  | || || |   || |  |||  | || |||||||||||||||||||| ||||| || || ||| | |||||||| || ||||||||||| || || || ||||| ||||| ||||| ||
-----atgatttttaatagcaatgtcatttttaattcgttttgcattataaaagctctttcctatcctgcctcctttttccttaaatttgttttacatgctgtagGCAGACAGTCTTTCCTAAACACTTCAAAATGGATAGAGGAAGTTAGAACTGAGAGGGGCAGTGATGTTATCATTGTGCTGGTTGGGAACAAAACTGATCT

upper sequence: Vv02s0012g00710.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GRMZM2G075719_T02 (Zea mays), 3'ss of exon 3
------------------------------------------------------------------tctttatgaa-aacgttttgaactttcttatttaattgtttcattattgtgttaccattaccgatgaaattttctgattggacttattatctt--tgattaagGTCGGCAATCTTTCCTAAACACTTCAAAGTGGATTGAAGAGGTTCGCACTGAGAGAGGTAGTGATGTTATTATCGTCCTTGTTGGAAACAAGACTGACCT
                                                                  |    || |  | |       |||      ||| ||  ||| |  |||  |  ||    |    |   ||||| |  ||    |||||   ||  || |  |||  |||| |||||| |||| || || |||||||| || || |||||||||||||| || ||||||||||| || || |||||||| ||||| ||||||||
gtaatctctctctgtctctctcgcacacacaaacacacattctttaggaaaaaaaatggtatcagatgcacatcagtagcaacaatgactaggaagttttatcttttaaggattaagg-acataaatttttactattttattcttacctttatttgtttcatgttgtagGCAGGCAGTCTTTCTTAAATACATCCAAGTGGATAGATGAAGTTCGCACTGAGAGGGGCAGTGATGTTATCATTGTGCTTGTTGGGAACAAAACTGACCT

upper sequence: Vv02s0012g00710.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GRMZM2G169694_T01 (Zea mays), 3'ss of exon 3
-----------------------------------------------------------tctttatgaaaacgttttg-aactt-tcttatttaattgtttcattattgtgttaccattaccgatgaaattttctgattggacttattatctttgattaagGTCGGCAATCTTTCCTAAACACTTCAAAGTGGATTGAAGAGGTTCGCACTGAGAGAGGTAGTGATGTTATTATCGTCCTTGTTGGAAACAAGACTGACCT
                                                              | |  | || |  | | ||||| | |  |||||  |||| |   ||     ||    ||   |   ||||| |  ||    || |  |   || |  |||  |||| || ||| |||| || || |||||||| || || |||||||||||||| || ||||||||||| || || |||||||| ||||| ||||||||
gtaatctccctctctcatacacacacattctatagaaatagttgttgtcagacgcacatcagtaacaacaatgactaggaacttatatcttttaaaggtttaagcctttaaggacataaacttttactattttgttcttacctttttgtttcatgttgtagGCAGGCAGTCCTTCTTAAATACATCTAAGTGGATAGAGGAAGTTCGCACTGAGAGGGGCAGTGATGTTATCATTGTGCTTGTTGGGAACAAAACTGACCT

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|351046568|gb|FQ453184.1|FQ453184
EST:     GAGCTACATTAGGGATTCATCTGTTGCAGTCATTGTATATGATGTTGCAA                         GTCGGCAATCTTTCCTAAACACTTCAAAGTGGATTGAAGAGGTTCGCACTG
genomic: GAGCTACATTAGGGATTCATCTGTTGCAGTCATTGTATATGATGTTGCAAgtatgaaatc ... tttgattaagGTCGGCAATCTTTCCTAAACACTTCAAAGTGGATTGAAGAGGTTCGCACTG
EST: gi|294966167|gb|GW839390.1|GW839390
EST:     GAGCTACATTAGGGATTCATCTGTTGCAGTCATTGTATATGATGTTGCAA                         GTCGGCAATCTTTCCTAAACACTTCAAAGTGGATTGAAGAGGTTCGCACTG
genomic: GAGCTACATTAGGGATTCATCTGTTGCAGTCATTGTATATGATGTTGCAAgtatgaaatc ... tttgattaagGTCGGCAATCTTTCCTAAACACTTCAAAGTGGATTGAAGAGGTTCGCACTG
EST: gi|351042357|gb|FQ442824.1|FQ442824
EST:     GAGCTACATTAGGGATTCATCTGTTGCAGTCATTGTATATGATGTTGCAA                         GTCGGCAATCTTTCCTAAACACTTCAAAGTGGATTGAAGAGGTTCGCACTG
genomic: GAGCTACATTAGGGATTCATCTGTTGCAGTCATTGTATATGATGTTGCAAgtatgaaatc ... tttgattaagGTCGGCAATCTTTCCTAAACACTTCAAAGTGGATTGAAGAGGTTCGCACTG
EST: gi|110686975|gb|EE063981.1|EE063981
EST:     GAGCTACATTAGGGATTCATCTGTTGCAGTCATTGTATATGATGTTGCAA                         GTCGGCAATCTTTCCTAAACACTTCAAAGTGGATTGAAGAGGTTCGCACTG
genomic: GAGCTACATTAGGGATTCATCTGTTGCAGTCATTGTATATGATGTTGCAAgtatgaaatc ... tttgattaagGTCGGCAATCTTTCCTAAACACTTCAAAGTGGATTGAAGAGGTTCGCACTG
EST: gi|110723851|gb|EE099164.1|EE099164
EST:     AAGCTACATTAGGGATTCATCTGTTGCAGTCATTGTATATGATGTTGCAA                         GTCGGCAATCTTTCCTAAACACTTCAAAGTGGATTGAAGAGGTTCGCACTG
genomic: GAGCTACATTAGGGATTCATCTGTTGCAGTCATTGTATATGATGTTGCAAgtatgaaatc ... tttgattaagGTCGGCAATCTTTCCTAAACACTTCAAAGTGGATTGAAGAGGTTCGCACTG
EST: gi|351032522|gb|FQ458887.1|FQ458887
EST:     GAGCTACATTAGGGATCCATCTGTTGCAGTCATTGTATATGATGTTGCAA                         GTCGGCAATCTTTCCTAAACACTTCAAAGTGGATTGAAGAGGTTCGCACTG
genomic: GAGCTACATTAGGGATTCATCTGTTGCAGTCATTGTATATGATGTTGCAAgtatgaaatc ... tttgattaagGTCGGCAATCTTTCCTAAACACTTCAAAGTGGATTGAAGAGGTTCGCACTG
EST: gi|351056494|gb|FQ455146.1|FQ455146
EST:     GAGCTACATTAGGGATTCATCTGTTGCAGTCATTGTATATGATGTTGCAA                         GTCGGCAATCTTTCCTAAACACTTCAAAGTGGATTGAAGAGGTTCGCACTG
genomic: GAGCTACATTAGGGATTCATCTGTTGCAGTCATTGTATATGATGTTGCAAgtatgaaatc ... tttgattaagGTCGGCAATCTTTCCTAAACACTTCAAAGTGGATTGAAGAGGTTCGCACTG
EST: gi|351015547|gb|FQ447376.1|FQ447376
EST:     GAGCTACATTAGGGATTCATCTGTTGCAGTCATTGTATATGATGTTGCAA                         GTCGGCAATCTTTCCTAAACACTTCAAAGTGGATTGAAGAGGTTCGCACTG
genomic: GAGCTACATTAGGGATTCATCTGTTGCAGTCATTGTATATGATGTTGCAAgtatgaaatc ... tttgattaagGTCGGCAATCTTTCCTAAACACTTCAAAGTGGATTGAAGAGGTTCGCACTG
EST: gi|110731534|gb|EE106031.1|EE106031
EST:     GAGCTACATTAGGGATTCATCTGTTGCAGTCATTGTATATGATGTTGCAA                         GTCGGCAATCTTTCCTAAACACTTCAAAGTGGATTGAAGAGGTTCGCACTG
genomic: GAGCTACATTAGGGATTCATCTGTTGCAGTCATTGTATATGATGTTGCAAgtatgaaatc ... tttgattaagGTCGGCAATCTTTCCTAAACACTTCAAAGTGGATTGAAGAGGTTCGCACTG
EST: gi|351053354|gb|FQ455690.1|FQ455690
EST:     GAGCTACATTAGGGATTCATCTGTTGCAGTCATTGTATGTGATGTTGCAA                         GTCGGCAATCTTTCCTAAACACTTCAAAGTGGATTGAAGAGGTTCGCACTG
genomic: GAGCTACATTAGGGATTCATCTGTTGCAGTCATTGTATATGATGTTGCAAgtatgaaatc ... tttgattaagGTCGGCAATCTTTCCTAAACACTTCAAAGTGGATTGAAGAGGTTCGCACTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgtgttaccattaccgatgaaattttctgattggacttattatctttgattaagGTCGGCAATCTTTCCTAAACACTTCAAAGTGGATTGAAGAGGTTCGCACTGAGAGAGGTAGTGATGTTATTATCGTCCTTGTTGGAAACAAGACTGACCT
                                        ttatcttt  CT-rich tract
                                     ttattatctttgatta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tctttatgaaaacgttttgaactttcttatttaattgtttcattattgtgttaccattaccgatgaaattttctgattggacttattatctttgattaagGTCGGCAATCTTTCCTAAACACTTCAAAGTGGATTGAAGAGGTTCGCACTGAGAGAGGTAGTGATGTTATTATCGTCCTTGTTGGAAACAAGACTGACCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG
- - -atgaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - -ccattac