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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...taatctcaagttttcctggcttatcttgatttcctttctttctttctttctttctttttttttttttttttttttttgtggtgactgatatcattttaagAACGGACTTGGTTCCCGCTTATATGCGGTTACTTCGAGATAATGAGGCTGAAGTACGAATAGCAGCTGCTGGCAAAGTAACTAAATTCTGTCAGATCTTA

Basic information

species Vitis vinifera
transcript Vv01s0011g03280.t01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv01s0011g03280.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM2G122135_T01 (Zea mays), 3'ss of exon 5
------------------------------taatctcaagttttcctggct--tatcttgatttcctttctttctttctttctttctttttttttttttttttttttttgtggtgactgatatcattttaagAACGGACTTGGTTCCCGCTTATATGCGGTTACTTCGAGATAATGAGGCTGAAGTACGAATAGCAGCTGCTGGCAAAGTAACTAAATTCTGTCAGATCTTA
                              | ||  || | ||      |   |||||  ||||       |  | |    |  |    |||| |  |   ||   | | |    | || | |     | ||| | || ||||| || || ||| | ||  | ||||| ||||||||||||||||| |||||||| |||||||| ||||||||||| ||||| |  || |||
gtattatttgtgctagctgaattcaacctattattgcagggttgtaaaacatgtatctgaatttttgagtatcatgtaaacccataaccttttctaatggattaactgtatatcta-tgtttttgggattagAGCTGATTTGGTGCCTGCATATGTTCGTCTCCTTCGCGATAATGAGGCTGAAGTGCGAATAGCGGCTGCTGGAAAAGTAACTAAGTTCTGCCGCATATTA

upper sequence: Vv01s0011g03280.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM2G164352_T04 (Zea mays), 3'ss of exon 5
-----------------taatctcaagttttcctggc-------ttatct---tgatttcctttctttctttctttctttctttttttttttttttttttttttgtggtgactgatatcattttaagAACGGACTTGGTTCCCGCTTATATGCGGTTACTTCGAGATAATGAGGCTGAAGTACGAATAGCAGCTGCTGGCAAAGTAACTAAATTCTGTCAGATCTTA
                 | |  ||||  | |  | ||         || |   ||| ||| |   | || |     |        ||||    |   ||   |     |  ||| | |     | ||| | || ||||| || || ||| | ||  | ||||| ||||||||||||||||| || |||||||||||||| ||||||||||| || || |  || |||
gtattatttgtcctagctgaattcaacctattattgcagggaaaccatgtgtctgaattcttgagtatcatgtaaacccatagccttttcaaatggattaactgtaaatctctgcttttgggattagAGCTGATTTGGTGCCTGCCTATGTTCGCCTCCTTCGTGATAATGAGGCTGAAGTGCGGATAGCAGCTGCTGGAAAAGTAACTAAGTTTTGCCGCATATTA

upper sequence: Vv01s0011g03280.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM2G102858_T01 (Zea mays), 3'ss of exon 5
------------------taatctcaa----gttttcctggcttatcttgatttcctttctttctttc------tttctttctttttttttttttttttttttttgtggtgactgatatcattt-taagAACGG--ACTTGGTTCCCGCTTATATGCGGTTACTTCGAGATAATGAGGCTGAAGTACGAATAGCAGCTGCTGGCAAAGTAACTAAATTCTGTCAGATCTTA
                  | || | ||    | ||   || | ||  ||||||     | | |   |       ||  |     |  |    |   |  |||  | | | |||   |  | ||| ||| |  ||  |  ||||  | || ||| | ||  | ||  | || |||||||||||||| || || ||||||||||| ||||| || ||||||||  | || |||
gtgttcaatcttctttctttatgttaaaaatgattctttgacataaattgattattgctttatacatggaaagattaatcaacataatgccatgactcgtttactattgagaccattgccttttataatagGGGTGATCTGGTGTCAGCGTATGTTCGCCTTCTCTGTGACAATGAGGCTGAAGTGCGGATTGCAGCTGCTGGAAAAGTTACAAAATTCTGCAAAATATTA

upper sequence: Vv01s0011g03280.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA10G42250.1 (Glycine max), 3'ss of exon 5
taatctcaagttttcctggcttatc-ttgatttcctttctttctttctttctttctttttttttttttttttttttttgtggtgactgatatcattttaagAACGGACTTGGTTCCCGCTTATATGCGGTTACTTCGAGATAATGAGGCTGAAGTACGAATAGCAGCTGCTGGCAAAGTAACTAAATTCTGTCAGATCTTA
|||||    | |||      | ||  |   ||    ||  |     |   || |      |      | | ||| ||| |  | |||  | |  | | ||||||||| ||||| || |||||| ||||||| ||||||||||||||||||||||| || |||||||||||||| ||||| || || || || | ||| |||
taatcatgtgatttttgtattgattatctcttatgattactaaggcccaactctgaagcctaagcaatatatttatttttcttaactattgtt-tatgaagAACGGAATTGGTACCTGCTTATGTGCGGTTGCTTCGAGATAATGAGGCTGAAGTGCGCATAGCAGCTGCTGGAAAAGTGACCAAGTTTTGCCGGATTTTA

upper sequence: Vv01s0011g03280.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA20G24790.1 (Glycine max), 3'ss of exon 5
---taatctcaagttttcctggcttatcttgatttcctttctttctttctttctttctttttttttttttttttttttttgtggtgactgatatcattttaagAACGGACTTGGTTCCCGCTTATATGCGGTTACTTCGAGATAATGAGGCTGAAGTACGAATAGCAGCTGCTGGCAAAGTAACTAAATTCTGTCAGATCTTA
   | || | |  |||   | | ||||||    |   |  |          |||      |      | | ||| ||||| |  | |||  | |   | || ||||||| ||||| || |||||| ||||||| ||||| |||||||||||||||||||| |||||||||||||| ||||| || || || || | ||| |||
aaatcatgtgatttttgtattgattatctcttatgattaccaaggcccaactctgaagcctaagcaatatatttatttttct--taactattgtttgtgta-gAACGGAATTGGTACCTGCTTATGTGCGGTTGCTTCGTGATAATGAGGCTGAAGTACGCATAGCAGCTGCTGGAAAAGTGACCAAGTTTTGCCGGATTTTA

upper sequence: Vv01s0011g03280.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA02G10790.2 (Glycine max), 3'ss of exon 5
--taatctcaagttttcctggctta--tcttgatttcctttctttctttctttctttctttttttttttttttttttttttgtggtgactgatatcattttaagAACGGACTTGGTTCCCGCTTATATGCGGTTACTTCGAGATAATGAGGCTGAAGTACGAATAGCAGCTGCTGGCAAAGTAACTAAATTCTGTCAGATCTTA
  | || ||   || |  |  |  |  ||  ||||   | || |      ||   |  || | ||| ||    |||| |     || |||  |||  | | ||||||||| |||||||| || ||| ||||||| |||||||| ||||| ||||||||||| || ||||||||||| ||||| || || || || | ||| |||
attgatttcctcttatatttacgaaggtccagattcagtgtcctataaatttaactggttatgtttcttaagattttctc----gtcactattattttgtaaagAACGGAATTGGTTCCTGCCTATGTGCGGTTGCTTCGAGACAATGAAGCTGAAGTACGGATTGCAGCTGCTGGGAAAGTGACCAAGTTTTGCCGGATATTA

upper sequence: Vv01s0011g03280.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: AT3G25800.2 (Arabidopsis thaliana), 3'ss of exon 4
------------------------------------------------------taatctcaagttttcctggcttatcttgatttcctttctttctttctttctttctttttttttttttttttttttttgtggtgactgatat------cattttaagAACGGACTTGGTTCCCGCTTATATGCGGTTACTTCGAGATAATGAGGCTGAAGTACGAATAGCAGCTGCTGGCAAAGTAACTAAATTCTGTCAGATCTTA
                                                      |||| | | |||          ||    ||   |       |||       ||  |  |    |||  ||  | ||  |  |   |  | |       |||||||| |||||  |||| || || ||| ||||  ||||||| |||||||| ||||||||||| ||||||||||| || ||||| || || || |||| |||  ||
gtaagaacgttttgcataaacctaatgcagcatgttttaatacctttgatgggctaatttaatgttcaatatagaaatgcatatcatccaataggcttaaggaacttgatgatcccatttacttcctcttgatactatttactgtgtcttctattttaagGACGGAGCTGGTGCCTGCATATGTGCGCCTACTTCGTGATAATGAAGCTGAAGTACGCATAGCAGCTGCCGGAAAAGTTACAAAGTTTTGTCGGATTCTA

upper sequence: Vv01s0011g03280.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: AT1G13320.2 (Arabidopsis thaliana), 3'ss of exon 5
-----------------------------------------------------------------------------------taatctcaagttttcctggcttatcttgatttcctttctttctttctt-tctttctttttttttttttttttttttttgtggtgactgatat------cattttaagAACGGACTTGGTTCCCGCTTATATGCGGTTACTTCGAGATAATGAGGCTGAAGTACGAATAGCAGCTGCTGGCAAAGTAACTAAATTCTGTCAGATCTTA
                                                                                   | |  |||    |   |||  ||  | ||  ||| |  ||  |   |  ||||  |   ||| |||   |  |||||| |  |  || || |        | ||||| |||||  |||| || || |||   ||  ||||| | ||||||||||| ||||| || |||||||||||||| ||||| || || || ||||  || |||
gtaagcagtgatggttgaagttagttatggtttaatgtagtattgacctttagtatgcaattctatatcaaacaatagattactgacttcagaggtatttgg--tacttggaagtccatgtttgttgagtcatcttaataaatttctttgagtcgttttttatactttctcatgtgccttatgtattaagGACGGATCTGGTGCCTGCATATGCTCGTCTACTTTGTGATAATGAGGCAGAAGTTCGGATAGCAGCTGCTGGAAAAGTTACCAAGTTTTGTCGCATTTTA

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|71884601|gb|DT033656.1|DT033656
EST:     GCAGATCAATTATATGAGCTTTGTCATGCTGTAGGGCCTGAACCTACCAG                         AACGGACTTGGTTCCCGCTTATATGCGGTTACTTCGAGATAATGAGGCTGA
genomic: GCAGATCAATTATATGAGCTTTGTCATGCTGTAGGGCCTGAAGCTACCAGgtattaataa ... tcattttaagAACGGACTTGGTTCCCGCTTATATGCGGTTACTTCGAGATAATGAGGCTGA
EST: gi|71884162|gb|DT033217.1|DT033217
EST:     GCAGATCAATTATATGAGCTTTGTCATGCTGTAGGGCCTGAACCTACCAG                         AACGGACTTGGTTCCCGCTTATATGCGGTTACTTCGAGATAATGAGGCTGA
genomic: GCAGATCAATTATATGAGCTTTGTCATGCTGTAGGGCCTGAAGCTACCAGgtattaataa ... tcattttaagAACGGACTTGGTTCCCGCTTATATGCGGTTACTTCGAGATAATGAGGCTGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctttctttctttttttttttttttttttttttgtggtgactgatatcattttaagAACGGACTTGGTTCCCGCTTATATGCGGTTACTTCGAGATAATGAGGCTGAAGTACGAATAGCAGCTGCTGGCAAAGTAACTAAATTCTGTCAGATCTTA
                                     gactgat  putative branch site (score: 3)
                                             tcatttt  CT-rich tract
     tttctttttttttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
taatctcaagttttcctggcttatcttgatttcctttctttctttctttctttctttttttttttttttttttttttgtggtgactgatatcattttaagAACGGACTTGGTTCCCGCTTATATGCGGTTACTTCGAGATAATGAGGCTGAAGTACGAATAGCAGCTGCTGGCAAAGTAACTAAATTCTGTCAGATCTTA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAAG
- - - - - - ttcctgg
- - - - - - - - - - - - - - - -tcctttc