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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtgggtgatctaaatttcactaatgtgctttcaagccctccctattatcaccatgctgttctatcagttcatcaatttcttttactttcctaaattgcagATAGAACCCAATTCTCAAACTCGGCTTTTGGATGCTACTATGGACATGGAAGGAGTTCTATTGGCTGGAGTTCCAGGAGCAGGTGGATTTGATGCAATTT

Basic information

species Vitis vinifera
transcript Vv02s0012g02530.t01
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv02s0012g02530.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: LOC_Os03g14830.1 (Oryza sativa), 3'ss of exon 9
------------------------------------------------------------------gtgggtgatctaaatttcacta-atgtgctttcaagccctccctattatcaccatgctgttctatcagtt-catcaatttcttttactttcctaaatt-gcagATAGAACCCAATTCTCAAACTCGGCTTTTGGATGCTACTATGGACATGGAAGGAGTTCTATTGGCTGGAGTTCCAGGAGCAGGTGGATTTGATGCAATTT
                                                                  |||| ||   ||  |    ||| |     | |  |||  |   | |    |  |||  |   |   |||   ||  |  | | |   | |||| | || |||||| || ||  | || |||||||  ||| ||||||| |||||| | ||||| || |||||| | ||||||||||| || || ||||| ||||||||| |||
gtaagacttagttccttttaatgaaattatggatgttgaagataacatgatcgattcttctacatggtggctggcatagttacatctagacaaattgtttagctattaatttgtagataatggggacattatagtaatatacacctgtctcgttgtcctcattttgcagATTGAGCCAGAATCACAAACTCAACTTCTGGATGCCACTATGAATATGGAGGGTGTTCTACTAGCTGGAGTTCCTGGGGCCGGTGGCTTTGATGCAGTTT

upper sequence: Vv02s0012g02530.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GLYMA04G41570.1 (Glycine max), 3'ss of exon 9
--gtgggtgatctaaatttcac-taatgtgctttcaagccctccctattatcaccatgctgttctatcagttcatcaatttcttttactttcctaaattgcagATAGAACCCAATTCTCAAACTCGGCTTTTGGATGCTACTATGGACATGGAAGGAGTTCTATTGGCTGGAGTTCCAGGAGCAGGTGGATTTGATGCAATTT
   |   |||  |  | |  |  |  |||  |   ||  | |   | | |           ||  |  | |||  |||| |        |||     || ||||| |||||  |  | ||||| |  ||||| |||||||| ||| || ||||||||||  | ||||||||||||||||| ||||| |||||||||||| | |
tctttattgaaatgtactcgaggttttgtaatagaaactcatttttctgaaggattcatcatttaaaaaattcgacaatatac---gacttcaatgtttacagATTGAACCAGAACCACAAACACAACTTTTAGATGCTACAATGAACTTGGAAGGAGTATTGTTGGCTGGAGTTCCAGGGGCAGGAGGATTTGATGCAGTCT

upper sequence: Vv02s0012g02530.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GLYMA06G13260.1 (Glycine max), 3'ss of exon 9
---gtgggtgatctaaatttcactaatgtgctttcaagccctccctattatcaccatgctgttctatcagttcatcaatttcttttactttcctaaattgcagATAGAACCCAATTCTCAAACTCGGCTTTTGGATGCTACTATGGACATGGAAGGAGTTCTATTGGCTGGAGTTCCAGGAGCAGGTGGATTTGATGCAATTT
       |  || ||        |  |||  |   ||  | |   | | ||          ||  |  | ||   |||||| |   ||||   |  ||  ||||| |||||  | || ||||| |  ||||| ||||||||  || || ||||||||||  | ||||||||||| ||||| ||||| |||||||||||| | |
ataaattgaaatgtagtcagaggttttgtattagaaactcgtttatctgatggattcatcatttaaaaaatttgacaatttatg--acttcaatgtat-acagATTGAACCAGAATCACAAACACAACTTTTAGATGCTACAGTGAACTTGGAAGGAGTATTGTTGGCTGGAGTGCCAGGGGCAGGAGGATTTGATGCAGTCT

upper sequence: Vv02s0012g02530.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: AT1G31910.1 (Arabidopsis thaliana), 3'ss of exon 11
------------------------------------------------------------------------------------------------gtgggtgatctaaatttcac---taatgtgc---tttcaagccctccctattatcaccatgctg-ttctatcagttcatcaatttcttttactttcctaaattgcagATAGAACCCAATTCTCAAACTCGGCTTTTGGATGCTACTATGGACATGGAAGGAGTTCTATTGGCTGGAGTTCCAGGAGCAGGTGGATTTGATGCAATTT
                                                                                                 ||    |||| ||   ||    | || | |   || ||     |||  |||   | ||   ||  |  ||||  | ||  |  ||             ||||||||||||| ||  | ||||||||||  ||||||||| |||| |||      |||||||||||| | ||||| ||||| ||||| |||||||||||||| || |
gtaagtgattttgttctgttttgatagttgcttcagatctcaacggaccatttgtgcatgattacttagtgctgttgcataataatactcgtctggctgtagaatcttaacagcatacatgatatacgggttccacaaattccgcatttagaacaaattgacttcatca--taattgacctcgagggaccatg-gaattgcagATAGAGCCTGAATCTCAAACTCAACTTTTGGATTCTACAATGAGTGCTGAAGGAGTTCTACTTGCTGGTGTTCCTGGAGCTGGTGGATTTGATGCCATAT

upper sequence: Vv02s0012g02530.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: PP1S77_144V6.1 (Physcomitrella patens), 3'ss of exon 9
gtgggtgatctaaatttcactaatgtgct-ttcaagccctccctattatcaccatgct---gttctatcagttcatcaatttcttttactttcctaaattgcagATAGAACCCAATTCTCAAACTCGGCTTTTGGATGCTACTATGGACATGGAAGGAGTTCTATTGGCTGGAGTTCCAGGAGCAGGTGGATTTGATGCAATTT
   | ||    ||  |    | |||| || || |  |  ||   |||   |  ||| |   | |     |  | ||  | || ||     ||   ||  ||||||| ||||||   ||||||||    ||  | ||||| || ||||| ||||| ||||| ||||||||||||||||| || || ||||| || |||||  | |
--agctggg--aagctcttttgatgtactatttattcgttcaagatttagaaaatgattaggctacggaaagttatgtaatttttggcaattgtaaacctgcagATCGAACCCCCGTCTCAAACAGCTCTGCTAGATGCAACCATGGAGATGGACGGAGTACTATTGGCTGGAGTTCCCGGTGCGGGTGGTTTCGATGCCGTCT

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|110428074|gb|EC994535.1|EC994535
EST:     TTAGGATCAGAAGTAATATGCGCCAGATGGGTGAGGCTGCAGGCATCCCG                         ATAGAACCTGATTCTCAAACTCGGCTTTTGGATGCTACTATGGACATGGAA
genomic: TTAGGATCAGAAGTAATATGCGCCAGATGGGTGAGGCTGCAGGCATCCCGgtaggtcttt ... taaattgcagATAGAACCCAATTCTCAAACTCGGCTTTTGGATGCTACTATGGACATGGAA
EST: gi|30330294|gb|CD013556.1|CD013556
EST:     TTAGGATCAGAAGTAATATGCGCCAGATGGGTGAGGCTGCAGGCATCCCG                         ATAGAACCCGATTCTCAAACTCGGCTTTTGGATGCTACTATGGACATGGAA
genomic: TTAGGATCAGAAGTAATATGCGCCAGATGGGTGAGGCTGCAGGCATCCCGgtaggtcttt ... taaattgcagATAGAACCCAATTCTCAAACTCGGCTTTTGGATGCTACTATGGACATGGAA
EST: gi|77588902|gb|DV223694.1|DV223694
EST:     TTAGGATCAGAAGTAATATGCGCCAGATGGGTGAGGCTGCAGGCATCCCG                         ATAGAACCTGATTCTCAAACTCGGCTTTTGGATGCTACTATGGACATGGAA
genomic: TTAGGATCAGAAGTAATATGCGCCAGATGGGTGAGGCTGCAGGCATCCCGgtaggtcttt ... taaattgcagATAGAACCCAATTCTCAAACTCGGCTTTTGGATGCTACTATGGACATGGAA
EST: gi|30254524|gb|CB971269.1|CB971269
EST:     TTAGGATCAGAAGTAATATGCGCCAGATGGGTGAGGCTGCAGGCATCCCG                         ATAGAACCTGATTCTCAAACTCGGCTTTTGGATGCTACTATGGACATGGAA
genomic: TTAGGATCAGAAGTAATATGCGCCAGATGGGTGAGGCTGCAGGCATCCCGgtaggtcttt ... taaattgcagATAGAACCCAATTCTCAAACTCGGCTTTTGGATGCTACTATGGACATGGAA
EST: gi|30254602|gb|CB971347.1|CB971347
EST:     TTAGGATCAGAAGTAATATGCGCCAGATGGGTGAGGCTGCAGGCATCCCG                         ATAGAACCTGATTCTCAAACTCGGCTTTTGGATGCTACTATGGACATGGAA
genomic: TTAGGATCAGAAGTAATATGCGCCAGATGGGTGAGGCTGCAGGCATCCCGgtaggtcttt ... taaattgcagATAGAACCCAATTCTCAAACTCGGCTTTTGGATGCTACTATGGACATGGAA
EST: gi|71888427|gb|DT037482.1|DT037482
EST:     TTAGGATCAGAAGTAATATGCGCCAGATGGGTGAGGCTGCAGGCATCCCG                         ATAGAACCTGATTCTCAAACTCGGCTTTTGGATGCTACTATGGACATGGAA
genomic: TTAGGATCAGAAGTAATATGCGCCAGATGGGTGAGGCTGCAGGCATCCCGgtaggtcttt ... taaattgcagATAGAACCCAATTCTCAAACTCGGCTTTTGGATGCTACTATGGACATGGAA
EST: gi|30329683|gb|CD012945.1|CD012945
EST:     TTAGGATCAGAAGTAATATGCGCCAGATGGGTGAGGCTGCAGGCATCCCG                         ATAGAACCCGATTCTCAAACTCGGCTTTTGGATGCTACTATGGACATGGAA
genomic: TTAGGATCAGAAGTAATATGCGCCAGATGGGTGAGGCTGCAGGCATCCCGgtaggtcttt ... taaattgcagATAGAACCCAATTCTCAAACTCGGCTTTTGGATGCTACTATGGACATGGAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatcaccatgctgttctatcagttcatcaatttcttttactttcctaaattgcagATAGAACCCAATTCTCAAACTCGGCTTTTGGATGCTACTATGGACATGGAAGGAGTTCTATTGGCTGGAGTTCCAGGAGCAGGTGGATTTGATGCAATTT
                                          tcctaaa  putative branch site (score: 2)
                              tttcttttactttcct  CT-rich tract
                            aatttcttttacttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgggtgatctaaatttcactaatgtgctttcaagccctccctattatcaccatgctgttctatcagttcatcaatttcttttactttcctaaattgcagATAGAACCCAATTCTCAAACTCGGCTTTTGGATGCTACTATGGACATGGAAGGAGTTCTATTGGCTGGAGTTCCAGGAGCAGGTGGATTTGATGCAATTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGTGGA
gtgggtg
- - - - - - - - - - - - -tgctttc
- - - - - - - - - - - - - - - - - -ccctccc
- - - - - - - - - - - - - - - - - - - - - - - - - ccatgct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tcatcaa