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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gagggtttatttcatggttagtgataggttctttttcttcaattcaccagtttttaataccattctctgctgtctaactctctttttctttctttaacagTGAGACTGTCAAATTTGGTCATGTTACCTTTTTCTGGAATGGAAATCGCTCAGGGTATTTTGATCCAAGTATGGAGGAATATGTAGAAATTCCCAGTGAT

Basic information

species Vitis vinifera
transcript Vv08s0056g00200.t01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv08s0056g00200.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GRMZM2G003385_T02 (Zea mays), 3'ss of exon 6
gagggtttatttcatggttagtgataggttctttttcttcaattcaccagtttttaataccattctctgctgtctaactctctttttctttctttaacagTGAGACTGTCAAATTTGGTCATGTTACCTTTTTCTGGAATGGAAATCGCTCAGGGTATTTTGATCCAAGTATGGAGGAATATGTAGAAATTCCCAGTGAT
||  |  |  || |||  |  |  | |    |       || |||  || |||||  |   ||| |    | |    |    ||  | | | | | |||||||||| || |||||||| ||||| || |||||||||||||| || ||||| || || ||||||  || || ||| || ||||||||| |||| ||||| 
gattgactcattgatgtatcatccttgtgcttgcaatggcatttcttcattttttcttcttatttttacttatgctgcaacattgatttgtgtgtgacagTGAGACAGTGAAATTTGGCCATGTCACATTTTTCTGGAATGGTAACCGCTCGGGATACTTTGATGAAACTAAGGAAGAGTATGTAGAAGTTCCTAGTGAC

upper sequence: Vv08s0056g00200.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GRMZM5G833389_T02 (Zea mays), 3'ss of exon 6
gagggtttatttcatggttagtgataggttctttttcttcaattcaccagtttttaataccattctctgct-gtctaactctctttttctttctttaacagTGAGACTGTCAAATTTGGTCATGTTACCTTTTTCTGGAATGGAAATCGCTCAGGGTATTTTGATCCAAGTATGGAGGAATATGTAGAAATTCCCAGTGAT
      || | ||||  || ||| | |   | |  ||| || ||  ||   | |   |  |  ||||| ||  |  | |    || || | | | | |||||||||| || |||||||| ||||| || ||||||||||| || || || || || || |||||| ||| || |||||| ||||||||| | || ||||| 
tcattgttgtatcatcctt-gtgcttgcaacatgatctacattttcccttctctctctctctctctctacttatgcagcaacattgttttgtgtgtgacagTGAGACAGTTAAATTTGGCCATGTCACATTTTTCTGGAACGGTAACCGTTCGGGATACTTTGATGCAACTAAGGAGGAGTATGTAGAAGTACCTAGTGAC

upper sequence: Vv08s0056g00200.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA09G40690.1 (Glycine max), 3'ss of exon 5
gagggtttatttcatggttagtgataggttctttttcttcaattcaccagtttttaataccattctctgctgtctaactctctttttctttctttaacagTGAGACTGTCAAATTTGGTCATGTTACCTTTTTCTGGAATGGAAATCGCTCAGGGTATTTTGATCCAAGTATGGAGGAATATGTAGAAATTCCCAGTGAT
   |    ||||  |      | | |  |  |  || |  | | |     | || |||      |      |||           ||  ||  | |||||||||||||| ||||||||||| || || || |||||||||||||| ||||| ||||||||| || ||    ||||||| ||||| |||||||||||||| 
tttgcaacattttgtttaccttaagaactcttcattatctagtacttatctgttaaatgatggccatcatagtcacttgtatgaatttctttgtcaacagTGAGACTGTTAAATTTGGTCACGTCACATTCTTCTGGAATGGAAACCGCTCTGGGTATTTTAATTCAGAATTGGAGGAGTATGTGGAAATTCCCAGTGAC

upper sequence: Vv08s0056g00200.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: AT1G09780.1 (Arabidopsis thaliana), 3'ss of exon 3
---------------------------------------------------------------------gagggtttatttcatggttagtgataggttctttttcttcaattcaccagtttttaataccattctctgctgtctaactctctttttctttctttaacagTGAGACTGTCAAATTTGGTCATGTTACCTTTTTCTGGAATGGAAATCGCTCAGGGTATTTTGATCCAAGTATGGAGGAATATGTAGAAATTCCCAGTGAT
                                                                     |   | | |||  | |||   |  || | | |   | ||     ||  ||| | | |  |            | ||  |   | | | |  ||  ||||||||||| ||||| ||||| ||||| ||||| ||||||||||||||||| || || |||||  |    |   ||||||| ||||| ||||| || ||||| 
gtatttcaacttctgtccttttctcactttgagtaatggttatatgctttgtttagtatagttccagttgcttgctcattata-ggtctatactatgctttgcatttttg--ccaatagtgtatcacgcttgaactgatcatatatattaatgtatgtgactgaaacagTGAGACCGTCAAGTTTGGGCATGTCACCTTCTTCTGGAATGGAAATCGATCTGGATATTTCAACGAGAAATTGGAGGAGTATGTTGAAATCCCAAGTGAC

upper sequence: Vv08s0056g00200.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: AT3G08590.2 (Arabidopsis thaliana), 3'ss of exon 4
gagggtttatttcatggttagtgataggttctttttcttcaattcaccagtttttaataccattctctgctgtctaactct-----ctttttctttctttaacagTGAGACTGTCAAATTTGGTCATGTTACCTTTTTCTGGAATGGAAATCGCTCAGGGTATTTTGATCCAAGTATGGAGGAATATGTAGAAATTCCCAGTGAT
       | |||| || | ||   ||     ||  |  | | || ||   |  | |||   |||||| ||| |  | || |      ||| | |  ||  |||||||||||||| || ||||| ||||| ||||| ||||||||||| || ||||| || |||||  ||  ||   | || || || || || ||||| ||||||
--ctcactttttcttgatgag-attataccgttgatggttagtt-acatataatgaatga-attctcagctattaacctattaaaattttatttcactgaaacagTGAGACTGTGAAGTTTGGCCATGTAACCTTCTTCTGGAATGGCAACCGCTCTGGATATTTCAATGAAAAGTTAGAAGAGTACGTTGAGATTCCAAGTGAT

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|30251274|gb|CB969007.1|CB969007
EST:     ACATCTGGTGAATATTTAGTGCACAATGGTGTTCGTACTTTTGCTTGCAG                         TGAGACTGTCAAATTTGGTCATGTTACCTTTTTCTGGAATGGAAATCGCTC
genomic: ACATCTGGTGAATATTTAGTGCACAATGGTGTTCGTACTTTTGCTTGCAGgtaaggtggc ... tctttaacagTGAGACTGTCAAATTTGGTCATGTTACCTTTTTCTGGAATGGAAATCGCTC
EST: gi|110361200|gb|EC924656.1|EC924656
EST:     TTTGCTTGCAG                         TGAGACTGTCAAATTTGGTCATGTTACCTTTTTCTGGAATGGAAATCGCTC
genomic: TTTGCTTGCAGgtaaggtggc ... tctttaacagTGAGACTGTCAAATTTGGTCATGTTACCTTTTTCTGGAATGGAAATCGCTC
EST: gi|110720573|gb|EE096613.1|EE096613
EST:     ACATCTGGTGAATATTTAGTGCACAATGGTGTTCGTACTTTTGCTTGCAG                         TGAGACTGTCAAATTTGGTCATGTTACCTTTTTCTGGAATGGAAATCGCTC
genomic: ACATCTGGTGAATATTTAGTGCACAATGGTGTTCGTACTTTTGCTTGCAGgtaaggtggc ... tctttaacagTGAGACTGTCAAATTTGGTCATGTTACCTTTTTCTGGAATGGAAATCGCTC
EST: gi|30252044|gb|CB968683.1|CB968683
EST:     ACATCTGGTGAATATTTAGTGCACAATGGTGTTCGTACTTTTGCTTGCAG                         TGAGACTGTCAAATTTGGTCATGTTACCTTTTTCTGGAATGGAAATCGCTC
genomic: ACATCTGGTGAATATTTAGTGCACAATGGTGTTCGTACTTTTGCTTGCAGgtaaggtggc ... tctttaacagTGAGACTGTCAAATTTGGTCATGTTACCTTTTTCTGGAATGGAAATCGCTC
EST: gi|110366484|gb|EC930392.1|EC930392
EST:     TAGTGCACAATGGTGTTCGTACTTTTGCTTGCAG                         TGAGACTGTCAAATTTGGTCATGTTACCTTTTTCTGGAATGGAAATCGCTC
genomic: TAGTGCACAATGGTGTTCGTACTTTTGCTTGCAGgtaaggtggc ... tctttaacagTGAGACTGTCAAATTTGGTCATGTTACCTTTTTCTGGAATGGAAATCGCTC
EST: gi|30301264|gb|CB978058.1|CB978058
EST:     TGGTGTTCGTACTTTTGCTTGCAG                         TGAGACTGTCAAATTTGGTCATGTTACCTTTTTCTGGAATGGAAATCGCTC
genomic: TGGTGTTCGTACTTTTGCTTGCAGgtaaggtggc ... tctttaacagTGAGACTGTCAAATTTGGTCATGTTACCTTTTTCTGGAATGGAAATCGCTC
EST: gi|110719729|gb|EE095112.1|EE095112
EST:     ATATCTGGTGAATATTTAGTGCACAATGGTGTTCGTACTTTTGCTTGCAG                         TGAGACTGTCAAATTTGGTCATGTTACCTTTTTCTGGAATGGAAATCGCTC
genomic: ACATCTGGTGAATATTTAGTGCACAATGGTGTTCGTACTTTTGCTTGCAGgtaaggtggc ... tctttaacagTGAGACTGTCAAATTTGGTCATGTTACCTTTTTCTGGAATGGAAATCGCTC
EST: gi|33406588|gb|CF212215.1|CF212215
EST:     ACATCTGGTGAATATTTAGTGCACAATGGTGTTCGTACTTTTGCTTGCAG                         TGAGACTGTCAAATTTGGTCATGTTACCTTTTTCTGGAATGGAAATCGCTC
genomic: ACATCTGGTGAATATTTAGTGCACAATGGTGTTCGTACTTTTGCTTGCAGgtaaggtggc ... tctttaacagTGAGACTGTCAAATTTGGTCATGTTACCTTTTTCTGGAATGGAAATCGCTC
EST: gi|161712531|gb|FC061836.1|FC061836
EST:     ACATCTGGTGAATATTTAGTGCACAATGGTGTTCGTACTTTTGCTTGCAG                         TGAGACTGTCAAATTTGGTCATGTTACCTTTTTCTGGAATGGAAATCGCTC
genomic: ACATCTGGTGAATATTTAGTGCACAATGGTGTTCGTACTTTTGCTTGCAGgtaaggtggc ... tctttaacagTGAGACTGTCAAATTTGGTCATGTTACCTTTTTCTGGAATGGAAATCGCTC
EST: gi|110724634|gb|EE100633.1|EE100633
EST:     ACATCTGGTGAATATTTAGTGCACAATGGTGTTCGTACTTTTGCTTGCAG                         TGAGACTGTCAAATTTGGTCATGTTACCTTTTTCTGGAATGGAAATCGCTC
genomic: ACATCTGGTGAATATTTAGTGCACAATGGTGTTCGTACTTTTGCTTGCAGgtaaggtggc ... tctttaacagTGAGACTGTCAAATTTGGTCATGTTACCTTTTTCTGGAATGGAAATCGCTC
EST: gi|161721567|gb|FC070103.1|FC070103
EST:     ACATCTGGTGAATATTTAGTGCACAATGGTGTTCGTACTTTTGCTTGCAG                         TGAGACTGTCAAATTTGGTCATGTTACCTTTTTCTGGAATGGAAATCGCTC
genomic: ACATCTGGTGAATATTTAGTGCACAATGGTGTTCGTACTTTTGCTTGCAGgtaaggtggc ... tctttaacagTGAGACTGTCAAATTTGGTCATGTTACCTTTTTCTGGAATGGAAATCGCTC
EST: gi|110690736|gb|EE068154.1|EE068154
EST:     ACATCTGGTGAATATTTAGTGCACAATGGTGTTCGTACTTTTGCTTGCAG                         TGAGACTGTCAAATTTGGTCATGTTACCTTTTTCTGGAATGGAAATCGCTC
genomic: ACATCTGGTGAATATTTAGTGCACAATGGTGTTCGTACTTTTGCTTGCAGgtaaggtggc ... tctttaacagTGAGACTGTCAAATTTGGTCATGTTACCTTTTTCTGGAATGGAAATCGCTC
EST: gi|33403584|gb|CF209211.1|CF209211
EST:     ACATCTGGTGAATATTTAGTGCACAATGGTGTTCGTACTTTTGCTTGCAG                         TGAGACTGTCAAATTTGGTCATGTTACCTTTTTCTGGAATGGAAATCGCTC
genomic: ACATCTGGTGAATATTTAGTGCACAATGGTGTTCGTACTTTTGCTTGCAGgtaaggtggc ... tctttaacagTGAGACTGTCAAATTTGGTCATGTTACCTTTTTCTGGAATGGAAATCGCTC
EST: gi|110357218|gb|EC920600.1|EC920600
EST:     ACATCTGGTGAATATTTAGTGCACAATGGTGTTCGTACTTTTGCTTGCAG                         TGAGACTGTCAAATTTGGTCATGTTACCTTTTTCTGGAATGGAAATCGCTC
genomic: ACATCTGGTGAATATTTAGTGCACAATGGTGTTCGTACTTTTGCTTGCAGgtaaggtggc ... tctttaacagTGAGACTGTCAAATTTGGTCATGTTACCTTTTTCTGGAATGGAAATCGCTC
EST: gi|110361556|gb|EC925038.1|EC925038
EST:     ACATCTGGTGAATATTTAGTGCACAATGGTGTTCGTACTTTTGCTTGCAG                         TGAGACTGTCAAATTTGGTCATGTTACCTTTTTCTGGAATGGAAATCGCTC
genomic: ACATCTGGTGAATATTTAGTGCACAATGGTGTTCGTACTTTTGCTTGCAGgtaaggtggc ... tctttaacagTGAGACTGTCAAATTTGGTCATGTTACCTTTTTCTGGAATGGAAATCGCTC
EST: gi|110709676|gb|EE085346.1|EE085346
EST:     ACATCTGGTGAATATTTAGTGCACAATGGTGTTCGTACTTTTGCTTGCAG                         TGAGACTGTCAAATTTGGTCATGTTACCTTTTTCTGGAATGGAAATCGCTC
genomic: ACATCTGGTGAATATTTAGTGCACAATGGTGTTCGTACTTTTGCTTGCAGgtaaggtggc ... tctttaacagTGAGACTGTCAAATTTGGTCATGTTACCTTTTTCTGGAATGGAAATCGCTC
EST: gi|29783243|gb|CB349288.2|CB349288
EST:     ATTTAGTGCACAATGGTGTTCGTACTTTTGCTTGCAG                         TGAGACTGTCAAATTTGGTCATGTTACCTTTTTCTGGAATGGAAATCGCTC
genomic: ATTTAGTGCACAATGGTGTTCGTACTTTTGCTTGCAGgtaaggtggc ... tctttaacagTGAGACTGTCAAATTTGGTCATGTTACCTTTTTCTGGAATGGAAATCGCTC
EST: gi|30301324|gb|CB978118.1|CB978118
EST:     ACATCTGGTGAATATTTAGTGCACAATGGTGTTCGTACTTTTGCTTGCAG                         TGAGACTGTCAAATTTGGTCATGTTACCTTTTTCTGGAATGGAAATCGCTC
genomic: ACATCTGGTGAATATTTAGTGCACAATGGTGTTCGTACTTTTGCTTGCAGgtaaggtggc ... tctttaacagTGAGACTGTCAAATTTGGTCATGTTACCTTTTTCTGGAATGGAAATCGCTC
EST: gi|30251262|gb|CB968995.1|CB968995
EST:     ACATCTGGTGAATATTTAGTGCACAATGGTGTTCGTACTTTTGCTTGCAG                         TGAGACTGTCAAATTTGGTCATGTTACCTTTTTCTGGAATGGAAATCGCTC
genomic: ACATCTGGTGAATATTTAGTGCACAATGGTGTTCGTACTTTTGCTTGCAGgtaaggtggc ... tctttaacagTGAGACTGTCAAATTTGGTCATGTTACCTTTTTCTGGAATGGAAATCGCTC
EST: gi|110717711|gb|EE093807.1|EE093807
EST:     GCACAATGGTGTTCGTACTTTTGCTTGCAG                         TGAGACTGTCAAATTTGGTCATGTTACCTTTTTCTGGAATGGAAATCGCTC
genomic: GCACAATGGTGTTCGTACTTTTGCTTGCAGgtaaggtggc ... tctttaacagTGAGACTGTCAAATTTGGTCATGTTACCTTTTTCTGGAATGGAAATCGCTC
EST: gi|33409359|gb|CF214986.1|CF214986
EST:     ACATCTGGTGAATATTTAGTGCACAATGGTGTTCGTACTTTTGCTTGCAG                         TGAGACTGTCAAATTTGGTCATGTTACCTTTTTCTGGAATGGAAATCGCTC
genomic: ACATCTGGTGAATATTTAGTGCACAATGGTGTTCGTACTTTTGCTTGCAGgtaaggtggc ... tctttaacagTGAGACTGTCAAATTTGGTCATGTTACCTTTTTCTGGAATGGAAATCGCTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

accagtttttaataccattctctgctgtctaactctctttttctttctttaacagTGAGACTGTCAAATTTGGTCATGTTACCTTTTTCTGGAATGGAAATCGCTCAGGGTATTTTGATCCAAGTATGGAGGAATATGTAGAAATTCCCAGTGAT
                          gtctaac  putative branch site (score: 2)
              ccattctctgctgtct  CT-rich tract
                                     tttttctttctttaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gagggtttatttcatggttagtgataggttctttttcttcaattcaccagtttttaataccattctctgctgtctaactctctttttctttctttaacagTGAGACTGTCAAATTTGGTCATGTTACCTTTTTCTGGAATGGAAATCGCTCAGGGTATTTTGATCCAAGTATGGAGGAATATGTAGAAATTCCCAGTGAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - ttcatgg
- - - - - - - - - - - - - - - - - - - - - ttcacca
- - - - - - - - - - - - - - - - - - - - - - - - - - - -aatacca