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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgtggagtctactggcacccttctttttctatctccttgcttttgtttgtatatttctgggtgaagaaagagaattcttacaaataattttttcttctagGTACTTGACCATTCAGTTTGTTCGTTTTTTCTGGAAAAGGGAGTCGAATCAGAAGGCAAAGATTTTGCGG

Basic information

species Vitis vinifera
transcript Vv09s0002g02500.t01
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv09s0002g02500.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: LOC_Os01g36930.1 (Oryza sativa), 3'ss of exon 11
tgtggagtctactggcacccttctttttctatctccttgcttttgtttgtatatttctgggtgaagaaagagaattcttacaaataattttttcttctagGTACTTGACCATTCAGTTTGTTCGTTTTTTCTGGAAAAGGGAGTCGAATCAGAAGGCAAAGATTTTGCGG
                 |       |   ||| | |||| || | ||      | | |   | |  ||  | || | |  |||     || |   |  |||||||||||  | |||||||||||||| || ||||||||||| || || ||||||||||||||||| |||
----------------gcaagaacctaaatattttcttgattatattatctcttattttattcagaaattataagtatgccaa-----ttctgtgttcagGTACTTGACTGTGCAGTTTGTTCGTTTCTTTTGGAAAAGGGAATCAAACCAGAAGGCAAAGATTTTACGG

upper sequence: Vv09s0002g02500.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: GRMZM2G017086_T03 (Zea mays), 3'ss of exon 11
tgtggagtctactggcacccttctttttctatctccttgcttttgtttgtatatttctgggtgaagaaagagaattcttacaaataattttttcttctagGTACTTGACCATTCAGTTTGTTCGTTTTTTCTGGAAAAGGGAGTCGAATCAGAAGGCAAAGATTTTGCGG
                        |    ||  || |||| |||   | | |  |  |   |  || || | || |      |||| ||  ||| | ||||||||||||  | ||||| ||||| || || ||||||||||| || || || |||||||||||||| || 
-------------------gcaagtacattaaatctttgcatttcact-tgtcctcgttaatacagcaaaaaaagt------aata-ttccttcctttagGTACTTGACTGTGCAGTTCGTTCGCTTCTTTTGGAAAAGGGAATCAAACCAAAAGGCAAAGATTTTACGA

upper sequence: Vv09s0002g02500.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: GRMZM2G028733_T02 (Zea mays), 3'ss of exon 12
tgtggagtctactggcacccttctttt--tctatctccttgcttttgtttgtatatttctgggtgaagaaagagaattcttacaaataattttttcttctagGTACTTGACCATTCAGTTTGTTCGTTTTTTCTGGAAAAGGGAGTCGAATCAGAAGGCAAAGATTTTGCGG
 ||  |||| | |    |  | | |||    | | |||| | || |    || |  |  |   |  ||||| | |||    ||| |  | |  ||| | ||||||||||||  | ||||| |||||||| || ||||||||||| || || || ||||| |||||||| || 
-gta-agtccattaaatctttgcatttcacttgtgtcctcgtttataca-gtgtcctcatttatacagaaaaaaaat----acataatactccttcctttagGTACTTGACTGTGCAGTTCGTTCGTTTCTTTTGGAAAAGGGAATCAAACCAAAAGGCGAAGATTTTACGA

upper sequence: Vv09s0002g02500.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: GLYMA07G01480.1 (Glycine max), 3'ss of exon 11
tgtggagtctactggcacccttcttt-ttctatctccttgcttttgtttgtatatttctgggtgaagaaagaga-attcttacaaataattttttcttctagGTACTTGACCATTCAGTTTGTTCGTTTTTTCTGGAAAAGGGAGTCGAATCAGAAGGCAAAGATTTTGCGG
  | |    |  ||  |      ||  || | |||   |  | || ||| |   ||  |   ||     || ||  |  ||   ||   |||  | ||| |||||||||||  |||||||||| ||||| || ||||| ||||| || || |||||||| ||||||||||||
--ttgtaattgttgagatgaagattggttgtttctttgttgtgttatttcttccttggtaattgctatgagtgatgtgattttcaaccttttcctgttcaagGTACTTGACTGTTCAGTTTGTCCGTTTCTTTTGGAAGAGGGAATCCAACCAGAAGGCTAAGATTTTGCGG

upper sequence: Vv09s0002g02500.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: GLYMA08G20900.1 (Glycine max), 3'ss of exon 11
tgtggagtctactggcacccttctttttctatctccttgcttttgtttgtatatttctgggtgaagaaagaga-attcttacaaataattttttcttctagGTACTTGACCATTCAGTTTGTTCGTTTTTTCTGGAAAAGGGAGTCGAATCAGAAGGCAAAGATTTTGCGG
  || | |      |      | |  || | |||   |  | || ||| |   ||  |   ||     || || ||  ||   ||   |||  | ||| |||||||||||  |||||||||| ||||| || ||||| ||||| || || || ||||| ||||||||||||
-ttgtaattgttcagatgaagtttggttgtttctttgttgtgttatttcttccttggtaattgctatgagtgatatgattttcaaccttttccttttcaagGTACTTGACTGTTCAGTTTGTCCGTTTCTTTTGGAAGAGGGAATCCAACCAAAAGGCTAAGATTTTGCGG

upper sequence: Vv09s0002g02500.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: AT1G51710.2 (Arabidopsis thaliana), 3'ss of exon 8
-------------------------------------------------------------------------------tgtggagtctactggcacccttctttttctatctccttgcttttgt-----ttgtatatttctgggtgaagaaagagaattcttacaaataattttt-tcttctagGTACTTGACCATTCAGTTTGTTCGTTTTTTCTGGAAAAGGGAGTCGAATCAGAAGGCAAAGATTTTGCGG
                                                                               |   |  |  ||  |      |  |||   | ||   |  | | ||     || ||   || |         | ||   ||||| |   || |  |  ||||  |||||||||||  ||||||| || || ||||||||||||||||||   |||||||| ||||||||  |  ||
gtgatcagtctctgcttattgtttgcgacttttatttcacctctcagttttctgtaaccctcttgtggcatgcttcatattcagcatgcaccagagaatgtactttgtcaacttactaatgtagtgcaacttctaaccttttaccactgacacgaagtttctttctcttattactgatcttgaagGTACTTGACTGTTCAGTTCGTGCGGTTTTTCTGGAAAAGGGAGAGTAATCAGAAAGCAAAGATCCTCAGG

upper sequence: Vv09s0002g02500.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: EFJ09332 (Selaginella moellendorffii), 3'ss of exon 10
tgtggagtctactggcacccttctttttctatctccttgcttttgtttgtatatttctgggtgaagaaagagaattcttacaaataattttttcttctagGTACTTGACCATTCAGTTTGTTCGTTTTTTCTGGAAAAGGGAGTCGAATCAGAAGGCAAAGATTTTGCGG
                                                ||   |||   | |  |  ||  |   ||| |     | | |||| ||| || ||||||||  | |||||||||||||| ||||||||| ||||  |||| ||||| |||||||| ||| ||
------------------------------------------------gtgggttttatgatttatcaattg--ctctaatgtgcactgttttgttc-agatacTTGACTGTGCAGTTTGTTCGTTTCTTCTGGAAACGGGAAACGAAACAGAAAGCAAAGATCTTGAGG

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|30296415|gb|CB973209.1|CB973209
EST:     GGGCGTAGTGCAATTTATGTGAAAGAGTCACGTATCAATGGCTTGCCAAG                         GTACTTGACCATTCAGTTTGTTCGTTTTTTCTGGAAAAGGGAGTCGAATCA
genomic: GGGCGTAGTGCAATTTATGTGAAAGAGTCACGTATCAATGGCTTGCCAAGgtaacacctg ... tttcttctagGTACTTGACCATTCAGTTTGTTCGTTTTTTCTGGAAAAGGGAGTCGAATCA
EST: gi|110422111|gb|EC988423.1|EC988423
EST:     GGGCGTAGTGCAATTTATGTGAAAGAGTCACGTATCAATGGCTTGCCAAG                         GTACTTGACCATTCAGTTTGTTCGTTTTTTCTGGAAAAGGGAGTCGAATCA
genomic: GGGCGTAGTGCAATTTATGTGAAAGAGTCACGTATCAATGGCTTGCCAAGgtaacacctg ... tttcttctagGTACTTGACCATTCAGTTTGTTCGTTTTTTCTGGAAAAGGGAGTCGAATCA
EST: gi|33405442|gb|CF211069.1|CF211069
EST:     GGGCGTAGTGCAATTTATGTGAAAGAGTCACGTATCAATGGCTTGCCAAG                         GTACTTGACCATCCAGTTTGTTCGTTTTTTCTGGAAAAGGGAGTCGAATCA
genomic: GGGCGTAGTGCAATTTATGTGAAAGAGTCACGTATCAATGGCTTGCCAAGgtaacacctg ... tttcttctagGTACTTGACCATTCAGTTTGTTCGTTTTTTCTGGAAAAGGGAGTCGAATCA
EST: gi|22012121|gb|BQ797155.1|BQ797155
EST:     GGGCGTAGTGCAATTTATGTGAAAGAGTCACGTATCAATGGCTTGCCAAG                         GTACTTGACCATTCAGTTTGTTCGTTTTTTCTGGAAAAGGGAGTCGAATCA
genomic: GGGCGTAGTGCAATTTATGTGAAAGAGTCACGTATCAATGGCTTGCCAAGgtaacacctg ... tttcttctagGTACTTGACCATTCAGTTTGTTCGTTTTTTCTGGAAAAGGGAGTCGAATCA
EST: gi|110428084|gb|EC994545.1|EC994545
EST:     GGGCGTAGTGCAATTTATGTGAAAGAGTCACGTATCAATGGCTTGCCAAG                         GTACTTGACCATTCAGTTTGTTCGTTTTTTCTGGAAAAGGGAGTCGAATCA
genomic: GGGCGTAGTGCAATTTATGTGAAAGAGTCACGTATCAATGGCTTGCCAAGgtaacacctg ... tttcttctagGTACTTGACCATTCAGTTTGTTCGTTTTTTCTGGAAAAGGGAGTCGAATCA
EST: gi|22009862|gb|BQ794896.1|BQ794896
EST:     GGGCGTAGTGCAATTTATGTGAAAGAGTCACGTATCAATGGCTTGCCAAG                         GTACTTGACCATTCAGTTTGTTCG-TTTTTCTGGAAAAGGGAGTCGAATCA
genomic: GGGCGTAGTGCAATTTATGTGAAAGAGTCACGTATCAATGGCTTGCCAAGgtaacacctg ... tttcttctagGTACTTGACCATTCAGTTTGTTCGTTTTTTCTGGAAAAGGGAGTCGAATCA
EST: gi|33404796|gb|CF210423.1|CF210423
EST:     GGGCGTAGTGCAATTTATGTGAAAGAGTCACGTATCAATGGCTTGCCAAG                         GTACTTGACCATTCAGTTTGTTCGTTTTTTCTGGAAAAGGGAGTCGAATCA
genomic: GGGCGTAGTGCAATTTATGTGAAAGAGTCACGTATCAATGGCTTGCCAAGgtaacacctg ... tttcttctagGTACTTGACCATTCAGTTTGTTCGTTTTTTCTGGAAAAGGGAGTCGAATCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttgtatatttctgggtgaagaaagagaattcttacaaataattttttcttctagGTACTTGACCATTCAGTTTGTTCGTTTTTTCTGGAAAAGGGAGTCGAATCAGAAGGCAAAGATTTTGCGG
                             ttcttac  putative branch site (score: 2)
                                       taattttttcttct  putative PPT
                     aaagagaattcttaca  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgtggagtctactggcacccttctttttctatctccttgcttttgtttgtatatttctgggtgaagaaagagaattcttacaaataattttttcttctagGTACTTGACCATTCAGTTTGTTCGTTTTTTCTGGAAAAGGGAGTCGAATCAGAAGGCAAAGATTTTGCGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAAG
- - - -tctactg
- - - - - - - - -cccttct
- - - - - - - - - - - - - - - - -tccttgc
- - - - - - - - - - - - - - - - - - - - - - - - - - -tttctgg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gaagaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - caaataa