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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgttgaaactgaaatggcataatgtccatatcatataatgatgaatttgttcttaactcaagggttccttatagGAGGAAAGCACCACCGGTTCAAAAGGGGCTATAAAAATGTCATTGATGAAGCTATTCGCTTG

Basic information

species Vitis vinifera
transcript Vv13s0019g04370.t01
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv13s0019g04370.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: GLYMA20G32030.1 (Glycine max), 3'ss of exon 11
---------------------------------------------------------------gtatgttg-aaactgaaatggcat-------aatgtccatatcatataatgatgaatttgttcttaactca-----agggttccttatagGAGGAAAGCACCACCGGTTCAAAAGGGGCTATAAAAATGTCATTGATGAAGCTATTCGCTTG
                                                               ||    || ||||| ||||  | |       | |||  ||  | |  ||||| ||   || |  |||||       |  |||  |   ||| || |  ||||| ||||||||||| ||||| |||||||| ||||||||||||||||| |||
gtatggaggaatctaaactggcatgatctttagtctacccttctcacctttttttctttaagagttcactgtaaactaaaatcccttttattgaattgtaaattacttgaaatga-gatagtgctaataacttgccaatactgtttgtctcagGTGGCAGACACCATCGGTTCAAAAGAGGCTACAAAAATGTGATTGATGAAGCTATTCGTTTG

upper sequence: Vv13s0019g04370.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: GLYMA10G35490.2 (Glycine max), 3'ss of exon 11
----------------------------------------------------------------------------------------gtatgttgaaactgaaatggcataatgtccatatcatataatgatgaatttgttcttaactcaagggttccttatagGAGGAAAGCACCACCGGTTCAAAAGGGGCTATAAAAATGTCATTGATGAAGCTATTCGCTTG
                                                                                         | | |||||  ||||  |  |   | |  | || | ||| || | |     | || |  | |   ||      |||| ||||  ||||| ||||||||||| || || |||||||| ||||||||||||||||| |||
gtatggaggaatctaaactggcatgatctttagtctacccttctcaccttctttctttaagagttcactgtaaactaaaatcccttgcttttattgaatttgaatggaaaatttcttgaaatgagatagtgttaataacttgctaatgttatatgtct----tagGTGGAAGACACCATCGGTTCAAAAGAGGTTACAAAAATGTGATTGATGAAGCTATTCGTTTG

upper sequence: Vv13s0019g04370.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: AT5G17530.3 (Arabidopsis thaliana), 3'ss of exon 12
gtatgttgaaactgaaatggcataatgtccatatcatataatgatgaatttgttcttaactcaagggttccttatagGAGGAAAGCACCACCGGTTCAAAAGGGGCTATAAAAATGTCATTGATGAAGCTATTCGCTTG
||  |   | | |  |    |||  |||  || |  | |     ||| ||| |   | || ||  |  |  || |||| |||||||| ||| |||||||||| || || || ||||||||||| |||||||||||||||
gttagccaacaatttaccaccatgttgttaattttctctg----tgactttttcactgaccca--gacttattttagGCGGAAAGCATCACAGGTTCAAAAGAGGTTACAAGAATGTCATTGACGAAGCTATTCGCTTG

upper sequence: Vv13s0019g04370.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: EFJ15375 (Selaginella moellendorffii), 3'ss of exon 10
gtatgttgaaactgaaatggcataatgtccatatcatataatgatgaatttgttcttaactcaagggttccttatagGAGGAAAGCACCACCGGTTCAAAAGGGGCTATAAAAATGTCATTGATGAAGCTATTCGCTTG
                      |  ||  || || ||  || | ||   |||    |   ||  |      ||| ||| |||||||| ||||||||||| || || || |||||||| ||||||||||  || ||||||
-----------------gtatgttttgatcaaat-atgcaacggtgtgattgaatct--ttcctgttccttttacagGGGGAAAGCATCACCGGTTCAAGAGAGGATACAAAAATGTGATTGATGAAGGCATACGCTTG

upper sequence: Vv13s0019g04370.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: EFJ24972 (Selaginella moellendorffii), 3'ss of exon 10
gtatgttgaaactgaaatggcataatgtccatatcatataatgatgaatttgttcttaactcaagggttccttatagGAGGAAAGCACCACCGGTTCAAAAGGGGCTATAAAAATGTCATTGATGAAGCTATTCGCTTG
                      || ||  || || ||  || | ||   |||    |   ||  |      ||| ||| |||||||| ||||||||||| || || || |||||||| ||||||||||  || ||||||
-----------------gtatgtattgatcaaat-atgcaacggtgtgattgaatctg--tcctgttccttttacagGGGGAAAGCATCACCGGTTCAAGAGAGGATACAAAAATGTGATTGATGAAGGCATACGCTTG

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|30128717|gb|CB914056.1|CB914056
EST:     AGATAGTGTAACTTCAGATGGCCTGACTACATTCATTGAAAAGAAACTTG                         GAGGAAAGCACCGCCGGTTCAAAAGGGGCTATAAAAATGTCATTGATGAAG
genomic: GGATAGTGTAACTTCAGATGGCCTGACTACATTCATTGAAAAGAAACTTGgtatgttgaa ... ttccttatagGAGGAAAGCACCACCGGTTCAAAAGGGGCTATAAAAATGTCATTGATGAAG
EST: gi|30137604|gb|CB922942.1|CB922942
EST:     AGATAGTGTAACTTCAGATGGCCTGACTACATTCATTGAAAAGAAACTTG                         GAGGAAAGCACCGCCGGTTCAAAAGGGGCTATAAAAATGTCATTGATGAAG
genomic: GGATAGTGTAACTTCAGATGGCCTGACTACATTCATTGAAAAGAAACTTGgtatgttgaa ... ttccttatagGAGGAAAGCACCACCGGTTCAAAAGGGGCTATAAAAATGTCATTGATGAAG
EST: gi|30128985|gb|CB914324.1|CB914324
EST:     AGATAGTGTAACTTCAGATGGCCTGACTACATTCATTGAAAAGAAACTTG                         GAGGAAAGCACCGCCGGTTCAAAAGGGGCTATAAAAATGTCATTGATGAAG
genomic: GGATAGTGTAACTTCAGATGGCCTGACTACATTCATTGAAAAGAAACTTGgtatgttgaa ... ttccttatagGAGGAAAGCACCACCGGTTCAAAAGGGGCTATAAAAATGTCATTGATGAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taatgtccatatcatataatgatgaatttgttcttaactcaagggttccttatagGAGGAAAGCACCACCGGTTCAAAAGGGGCTATAAAAATGTCATTGATGAAGCTATTCGCTTG
                               tcttaac  putative branch site (score: 2)
                                             ttccttat  putative PPT
        atatcatataatgatg  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgttgaaactgaaatggcataatgtccatatcatataatgatgaatttgttcttaactcaagggttccttatagGAGGAAAGCACCACCGGTTCAAAAGGGGCTATAAAAATGTCATTGATGAAGCTATTCGCTTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC