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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...taatgatttccttaggtagcaacttaaacggatttactgaaatatttccgtagtctttctacacaagtttgacagaaaatttcaatgtggttgaatgtagCTTGCTGGAAAAAATTCTCATCATATTATTGAGGCAACTTTCAAGGCTTTCGCTAAAGCTCTTCGACAAGCTGTGGAATATGACCCACGCCGTCATGGCA

Basic information

species Vitis vinifera
transcript Vv05s0020g03430.t01
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv05s0020g03430.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: LOC_Os04g52710.1 (Oryza sativa), 3'ss of exon 6
------------------------------------------------------------------------------taatgatttccttaggtagcaacttaaacggatttactgaaatatttccg--tagtctttcta-----cacaagtttgacagaaaa------tttcaatgtggttgaatgtagCTTGCTGGAAAAAATTCTCATCATATTATTGAGGCAACTTTCAAGGCTTTCGCTAAAGCTCTTCGACAAGCTGTGGAATATGACCCACGCCGTCATGGCA
                                                                               |||    ||| ||| |    |    |    || |  ||   |   |||   ||  |   |||      ||   | | | |    |       ||   | || |   ||| |||||||||||||||| || || ||||||||||||||||||||||| || || |||| ||| |||||||||||    |||||||||   ||||| |  ||||
gtacatattgctttgcttcagatcaaatttccatccagtgttggatcattattacaagagtgctgtttggcactgaataaattgcatccctagttgaacataagagtcaatct-ttgcttttcctccagttaagcgagctaagaagtacgtatatcatacctgagcctgccttttctttgctcttatgaagCTTGCTGGAAAAAACTCACACCATATTATTGAGGCAACTTTCAAAGCATTTGCTAGAGCCCTTCGACAAGCAACAGAATATGACTTGCGCCGACGCGGCA

upper sequence: Vv05s0020g03430.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: LOC_Os04g52710.2 (Oryza sativa), 3'ss of exon 6
---------------------------taatgattt--ccttaggtagcaacttaaacggatttact--gaaatatttccgtagtctttctacacaagtttgacagaaaatttcaa--tgtggttgaatgtagCTTGCTGGAAAAAATTCTCATCATATTATTGAGGCAAC--TTTCAAGGCTTTCGCTAAAGCTCTTCGACAAGCTGTGGAATATGACCCACGCCGTCATGGCA--
                           |    ||      || | |    | |  ||  |   |  |  | | |   |   | |  |  |||    |   | | ||  ||| |     | |  |  | |  |||  |||   ||  |     ||||||    |||| |  |  ||||   ||| |   | |||||    |  ||       ||      |||     |   ||||  
gtacatattgctttgcttcagatcaaatttccatccagtgttggatcattattacaagagtgctgtttggcactgaataaattgcatccctagttgaacataagagtcaatctttgcttttcctccagTTAAGCGAGCTAAGAAGTACGTATATCATACC--TGAGCCTGCCTTTTCTTTGCTCTTA-TGAAGCTTGCTGGAAAA------AACTCACACCATATTATTGAGGCAAC

upper sequence: Vv05s0020g03430.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA20G28420.2 (Glycine max), 3'ss of exon 6
taatgatttccttaggtagcaacttaaacggatttactgaaatatttccgtagtctttctacacaag---tttgacagaaaat---ttcaatgtggttgaatgtagCTTGCTGGAAAAAATTCTCATCATATTATTGAGGCAACTTTCAAGGCTTTCGCTAAAGCTCTTCGACAAGCTGTGGAATATGACCCACGCCGTCATGGCA
       |     |  | |   ||||  |   |||   |  |   ||   || ||    |    ||    ||| |||||| ||   | || |     |||    |||||||||| ||||||||||||||||||||||||||||| ||||| ||||| |||   ||||||||||||||    || ||||| ||||| || | ||| |
------atcatccaacttgaggcttatgcttttttctagttaatgttttatattccaattttgaaaaccttttaacagaatatacatgcattccctctgagcacagCTTGCTGGGAAAAATTCTCATCATATTATTGAGGCAACCTTCAAAGCTTTTGCTCGGGCTCTTCGACAAGCAACAGAGTATGATCCACGTCGCCGTGGAA

upper sequence: Vv05s0020g03430.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA20G28420.1 (Glycine max), 3'ss of exon 6
taatgatttccttaggtagcaacttaaacggatttactgaaatatttccgtagtc---tttctacacaagtttgacagaaaat---ttcaatgtggttgaatgtagCTTGCTGGAAAAAATTCTCATCATATTATTGAGGCAACTTTCAAGGCTTTCGCTAAAGCTCTTCGACAAGCTGTGGAATATGACCCACGCCGTCATGGCA
 | |   |     |  | |   ||||  |   |||   |  |   ||   || ||   |||  | |    ||| |||||| ||   | || |     |||    |||||||||| ||||||||||||||||||||||||||||| ||||| ||||| |||   ||||||||||||||    || ||||| ||||| || |      
-actacatcatccaacttgaggcttatgcttttttctagttaatgttttatattccaattttgaaaaccttttaacagaatatacatgcattccctctgagCACAGCTTGCTGGGAAAAATTCTCATCATATTATTGAGGCAACCTTCAAAGCTTTTGCTCGGGCTCTTCGACAAGCAACAGAGTATGATCCACGTCGCCG-----

upper sequence: Vv05s0020g03430.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA02G13140.1 (Glycine max), 3'ss of exon 5
-----taatgatttccttaggtagcaacttaaacggatttactgaaatattt--ccgtagtctttctacacaagtttgacagaaaattt--caatgtg-gttgaatgtagCTTGCTGGAAAAAATTCTCATCATATTATTGAGGCAACTTTCAAGGCTTTCGCTAAAGCTCTTCGACAAGCTGTGGAATATGACCCACGCCGTCATGGCA
     || |   ||| | | | |   ||  |    |||| |||  |  ||    |   ||||||| ||  | | |||   | |   |||  ||   |   | ||    ||||||||| |||||||||||||| |||||||||||| |      |  | |||   |||||| ||                                     
attgttactacgttcttcatgcattgacacat---gattgactacataatccaacttaagtctttatatcccaattttgaaaaccttttaacagaatatatagAGCACAGCTTGCTGAAAAAAATTCTCATCGTATTATTGAGGCCAGGC---AAACATTC---AAAGCTTTT-------------------------------------

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|349810627|gb|FQ402870.1|FQ402870
EST:     TTTTCCAGTCTTTGGTGAATACTTCANGCATGACACTTCACATTCGACAG                         CTTGCTGGAAAAAATTCTCATCATATTATTGAGGCAACTTTCAAGGCTTTC
genomic: TTTTCCAGTCTTTGGTGAATACTTCAGGCATGACACTTCACATTCGACAGgtataatgag ... ttgaatgtagCTTGCTGGAAAAAATTCTCATCATATTATTGAGGCAACTTTCAAGGCTTTC
EST: gi|110385086|gb|EC949578.1|EC949578
EST:     TTTTCCAGTCTTTGGTAAATACTTCAGGCATGACACTTCACATTCGACAG                         CTTGCTGGAAAAAATTCTCATCATATTATTGAGGCAACTTTCAAGGCTTTC
genomic: TTTTCCAGTCTTTGGTGAATACTTCAGGCATGACACTTCACATTCGACAGgtataatgag ... ttgaatgtagCTTGCTGGAAAAAATTCTCATCATATTATTGAGGCAACTTTCAAGGCTTTC
EST: gi|110373814|gb|EC938184.1|EC938184
EST:     TTTTCCAGTCTTTGGTAAATACTTCAGGCATGACACTTCACATTCGACAG                         CTTGCTGGAAAAAATTCTCATCATATTATTGAGGCAACTTTCAAGGCTTTC
genomic: TTTTCCAGTCTTTGGTGAATACTTCAGGCATGACACTTCACATTCGACAGgtataatgag ... ttgaatgtagCTTGCTGGAAAAAATTCTCATCATATTATTGAGGCAACTTTCAAGGCTTTC
EST: gi|110695035|gb|EE072588.1|EE072588
EST:     TTTTCCAGTCTTTGGTAAATACTTCAGGCATGACACTTCACATTCGACAG                         CTTGCTGGAAAAAATTCTCATCATATTATTGAGGCAACTTTCAAGGCTTTC
genomic: TTTTCCAGTCTTTGGTGAATACTTCAGGCATGACACTTCACATTCGACAGgtataatgag ... ttgaatgtagCTTGCTGGAAAAAATTCTCATCATATTATTGAGGCAACTTTCAAGGCTTTC
EST: gi|45771814|gb|CN007666.1|CN007666
EST:     TTTTCCAGTCTTTGGTAAATACTTCAGGCATGACACTTCGCATTCGACAG                         CTTGCTGGAAAAAATTCTCATCATATTATTGAGGCAACTTTCAAGGCTTTC
genomic: TTTTCCAGTCTTTGGTGAATACTTCAGGCATGACACTTCACATTCGACAGgtataatgag ... ttgaatgtagCTTGCTGGAAAAAATTCTCATCATATTATTGAGGCAACTTTCAAGGCTTTC
EST: gi|30303843|gb|CB980637.1|CB980637
EST:     TTTTCCAGTCTTTGGTAAATACTTCAGGCATGACACTTCACATTCGACAG                         CTTGCTGGAAAAAATTTTCATCATATTATTGAGGCAACTTTCAAGGCTTTC
genomic: TTTTCCAGTCTTTGGTGAATACTTCAGGCATGACACTTCACATTCGACAGgtataatgag ... ttgaatgtagCTTGCTGGAAAAAATTCTCATCATATTATTGAGGCAACTTTCAAGGCTTTC
EST: gi|30303775|gb|CB980569.1|CB980569
EST:     TTTTCCAGTCTTTGGTAAATACTTCAGGCATGACACTTCACATTCGACAG                         CTTGCTGGAAAAAATTCTCATCATATTAT
genomic: TTTTCCAGTCTTTGGTGAATACTTCAGGCATGACACTTCACATTCGACAGgtataatgag ... ttgaatgtagCTTGCTGGAAAAAATTCTCATCATATTAT
EST: gi|161721145|gb|FC070387.1|FC070387
EST:     TTTTCCAGTCTTTGGTAAATACTTCAGGCATGACACTTCACATTCGACAG                         CTTGCTGGAAAAA-TTCTCA
genomic: TTTTCCAGTCTTTGGTGAATACTTCAGGCATGACACTTCACATTCGACAGgtataatgag ... ttgaatgtagCTTGCTGGAAAAAATTCTCA
EST: gi|110386630|gb|EC951244.1|EC951244
EST:     TTTTCCAGTCTTTGGTAAATACTTCAGGCATGACACTTCACATTCGACAG                         CTTGCTGGAAAAAATTCTCATCATATTATTGAGGCAACTTTCAAGGCTTTC
genomic: TTTTCCAGTCTTTGGTGAATACTTCAGGCATGACACTTCACATTCGACAGgtataatgag ... ttgaatgtagCTTGCTGGAAAAAATTCTCATCATATTATTGAGGCAACTTTCAAGGCTTTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttccgtagtctttctacacaagtttgacagaaaatttcaatgtggttgaatgtagCTTGCTGGAAAAAATTCTCATCATATTATTGAGGCAACTTTCAAGGCTTTCGCTAAAGCTCTTCGACAAGCTGTGGAATATGACCCACGCCGTCATGGCA
                     gtttgac  putative branch site (score: 4)
                              aaaatttcaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
taatgatttccttaggtagcaacttaaacggatttactgaaatatttccgtagtctttctacacaagtttgacagaaaatttcaatgtggttgaatgtagCTTGCTGGAAAAAATTCTCATCATATTATTGAGGCAACTTTCAAGGCTTTCGCTAAAGCTCTTCGACAAGCTGTGGAATATGACCCACGCCGTCATGGCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - -aaacgga
- - - - - - - - - - - - - - - - - - -tgaaata
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -agaaaat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - caatgtg