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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atgtaatgtgcttatgtcgaatcccttctatgacagtgctgcactatgcctatggaacgtctctcttttgcagtttggttgctaactttgtttactgcagGCGTTCCAACCGACAAGGAAACACACTTGACTGGAATTTATGATCTGGTTGCTGTGTTGACCCACAAGGGCAGGAGTGCTGATTCAGGGCATTATGTTGC

Basic information

species Vitis vinifera
transcript Vv09s0002g02500.t01
intron # 15
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 15
lower sequence: GLYMA08G20900.1 (Glycine max), 3'ss of exon 15
atgtaatgtgcttatgtcgaatcccttctatgacagtgctgcactatgcctatggaacgtctctcttttgcagtttggttgctaactttgtttactgcagGCGTTC-CAACCGACAAGGAAACACACTTGACTGGAATTTATGATCTGGTTGCTGTGTTGACCCACAAGGGCAGGAGTGCTGATTCAGGGCATTATGTTGC---------
  ||||    ||        || ||| ||    || |  |  | | |   | | |    | | | || | || |  | || ||   |||   | |       ||    |   || |||||||||||  ||||||||||||||||| |||||||||| || |||||||||||||| |||||||||||||| ||||||||||          
--gtaaaaacctgcaacattatgcctact----catttatttattttattttttgtttttttgttttct-caatccgctttctgctttttactccattctctgtctatagGTGAAAAGGAAACACAGATGACTGGAATTTATGATTTGGTTGCTGTATTAACCCACAAGGGCAGAAGTGCTGATTCAGGACATTATGTTGGTTGGGTCAA

upper sequence: Vv09s0002g02500.t01 (Vitis vinifera), 3'ss of exon 15
lower sequence: GLYMA07G01480.1 (Glycine max), 3'ss of exon 15
atgtaatgtgcttatgtcgaatcccttctatgacagtgctgcac-tatgcctatggaacgtctctcttttg-cagtttggttgctaactttgtttactgcagGCGT-TCCAACCGACAAGGAAACACACTTGACTGGAATTTATGATCTGGTTGCTGTGTTGACCCACAAGGGCAGGAGTGCTGATTCAGGGCATTATGTTGC---------
               ||  || ||  |  |  |   |||| | | |||   | |     || | | ||||  || |    || ||   |||   | |       || |  |   || |||||||||||  ||||||||||||||||| |||||||||| || ||||||||||| || |||||||||||||| ||||||||||          
---------------gtaaaaacc--tgcaacattatgctactcatatttatttattttgtttttgttttctcaatccactttctgctttttactccattctctgtctatagGTGAAAAGGAAACACAGATGACTGGAATTTATGATTTGGTTGCTGTATTAACCCACAAGGGTAGAAGTGCTGATTCAGGACATTATGTTGGTTGGGTCAA

upper sequence: Vv09s0002g02500.t01 (Vitis vinifera), 3'ss of exon 15
lower sequence: AT1G51710.1 (Arabidopsis thaliana), 3'ss of exon 14
------------------------------------------------------------------------------------atgtaatgtgcttatgtcgaatcccttctatgacagtgctgcactatgcctatgga-acgtctctcttttgcagtttggttgctaactttgtttactgcagGCGTTCCAACCGACAAGGAAACACACTTGACTGGAATTTATGATCTGGTTGCTGTGTTGACCCACAAGGGCAGGAGTGCTGATTCAGGGCATTATGTTGC
                                                                                    ||    |||   | | | ||   | ||  |   || |   | ||  || |   |   |  | |      |  | ||  |||    | |     |  |  |||   | |  | || |||||||| ||| |||||||||| |||||  |||| ||||||||||||||||||||||||||||| || || || |||||||||||
gtacattatctaagacccccttttcaacatttttcttttctggcttggaaagagcggtaattggtttgtgtaaatactttgatgattgtttgtctatctatagatctcatttcaaagcaatcaagaaccttgtcagagcctaattgtgaggaatctaattctgttatataatggaactttt-tagGTACTTCTTCTGAGAAGGAAACTCACATGACTGGAATCTATGACTTGGTCGCTGTGTTGACCCACAAGGGCAGGAGTGCAGACTCTGGTCATTATGTTGC

upper sequence: Vv09s0002g02500.t01 (Vitis vinifera), 3'ss of exon 15
lower sequence: AT3G21280.1 (Arabidopsis thaliana), 3'ss of exon 14
atgtaatgtgcttatgtcgaatcccttctatgacagtgctgcactatgcctatggaacgtctctcttttgcagtttggttgctaactttgt------ttactgcagGCGTTC-CAACCGACAAGGAAACACACTTGACTGGAATTTATGATCTGGTTGCTGTGTTGACCCACAAGGGCAGGAGTGCTGATTCAGGGCATTATGTTGC------------
              || | ||    |||  |||  ||  |  |    ||| |||||   | | |||    || |||   |  | | ||| |      ||||| ||| | ||  |||| |         | ||| |||| ||||||||||| |||||  | |||||||||||||| ||||| || || || || ||||||||||||||            
--------------tggctaacagattcgttgat-gtctttta----gcccatggagtctttttctcgatcaattttagtatttagtttctatatccttactccagacctttgcaacagGTGCTTCGCCTCACATGACCGGAATTTATGACCTGGTATCGGTGTTGACCCACAAAGGCAGAAGCGCAGACTCTGGGCATTATGTTGCATGGGTCAAGCA

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:     GGATCGTCAAATAGAAGCGGTGAATCATCTTTAGCTACATCTGATGAAG                         GCGTTCCAACCGACAAGGAAACACACTTGACTGGAATTTATGATCTGGTTG
genomic: GGATCGTCAAATAGAAGCGGTGAATCATCTTTAGCTACATCTGATGAAGgtaaaaaaat ... tttactgcagGCGTTCCAACCGACAAGGAAACACACTTGACTGGAATTTATGATCTGGTTG
EST: gi|33404879|gb|CF210506.1|CF210506
EST:     GGATCATCAAATAGAAGCGGTGAATCATCTTTAGCTACATCTGATGAAG                         GCGTTCCAACCGACAAGGAAACACACTTGACTGGAATTTATGATCTGGTTG
genomic: GGATCGTCAAATAGAAGCGGTGAATCATCTTTAGCTACATCTGATGAAGgtaaaaaaat ... tttactgcagGCGTTCCAACCGACAAGGAAACACACTTGACTGGAATTTATGATCTGGTTG
EST: gi|110422111|gb|EC988423.1|EC988423
EST:     GGATCGTCAAATAGAAGCGGTGAATCATCTTTAGCTACATCTGATGAAG                         GCGTTCCAACCAACAAGGAAACACACTTGACTGGAATTTATGATCTGGTTG
genomic: GGATCGTCAAATAGAAGCGGTGAATCATCTTTAGCTACATCTGATGAAGgtaaaaaaat ... tttactgcagGCGTTCCAACCGACAAGGAAACACACTTGACTGGAATTTATGATCTGGTTG
EST: gi|33405442|gb|CF211069.1|CF211069
EST:     GGATCGTCAAATAGAAGCGGTGAATCATCTTTAGCTACATCTGATGAAG                         GCGTTCCAACCGACAAGGAAACACACTTGACTGGAATTTATGATCTGGTTG
genomic: GGATCGTCAAATAGAAGCGGTGAATCATCTTTAGCTACATCTGATGAAGgtaaaaaaat ... tttactgcagGCGTTCCAACCGACAAGGAAACACACTTGACTGGAATTTATGATCTGGTTG
EST: gi|110701778|gb|EE079734.1|EE079734
EST:     GGATCGTCAAATAGAAGCGGTGAATCATCTTTAGCTACATCTGATGAAG                         GCGTTCCAACCGACAAGGAAACACACTTGACTGGAATTTATGATCTGGTTG
genomic: GGATCGTCAAATAGAAGCGGTGAATCATCTTTAGCTACATCTGATGAAGgtaaaaaaat ... tttactgcagGCGTTCCAACCGACAAGGAAACACACTTGACTGGAATTTATGATCTGGTTG
EST: gi|22008798|gb|BQ793832.1|BQ793832
EST:     GGATCATCAAATAGAAGCGGTGAATCATCTTTAGCTACATCTGATGAAG                         GCGTTCCAACCGACAAGGAAACACACTTGACTGGAATTTATGATCTGGTTG
genomic: GGATCGTCAAATAGAAGCGGTGAATCATCTTTAGCTACATCTGATGAAGgtaaaaaaat ... tttactgcagGCGTTCCAACCGACAAGGAAACACACTTGACTGGAATTTATGATCTGGTTG
EST: gi|83275868|gb|DV939876.1|DV939876
EST:     GGATCATCAAATAGAAGCGGTGAATCATCTTTAGCTACATCTGATGAAG                         GCGTTCCAACCGACAAGGAAACACACTTGACTGGAATTTATGATCTGGTTG
genomic: GGATCGTCAAATAGAAGCGGTGAATCATCTTTAGCTACATCTGATGAAGgtaaaaaaat ... tttactgcagGCGTTCCAACCGACAAGGAAACACACTTGACTGGAATTTATGATCTGGTTG
EST: gi|22009589|gb|BQ794623.1|BQ794623
EST:     GGATCATCAAATAGAAGCGGTGAATCATCTTTAGCTACATCTGATGAAG                         GCGTTCCAACCGACAAGGAAACACACTTGACTGGAATTTATGATCTGGTTG
genomic: GGATCGTCAAATAGAAGCGGTGAATCATCTTTAGCTACATCTGATGAAGgtaaaaaaat ... tttactgcagGCGTTCCAACCGACAAGGAAACACACTTGACTGGAATTTATGATCTGGTTG
EST: gi|22012121|gb|BQ797155.1|BQ797155
EST:     GGATCATCAAATAGAAGCGGTGAATCATCTTTAGCTACATCTGATGAAG                         GCGTTCCAACCGACAAGGAAACACACTTGACTGGAATTTATGATCTGGTTG
genomic: GGATCGTCAAATAGAAGCGGTGAATCATCTTTAGCTACATCTGATGAAGgtaaaaaaat ... tttactgcagGCGTTCCAACCGACAAGGAAACACACTTGACTGGAATTTATGATCTGGTTG
EST: gi|110428084|gb|EC994545.1|EC994545
EST:     GGATCGTCAAATAGAAGCGGTGAATCATCTTTAGCTACATCTGATGAAG                         GCGTTCCAACCGACAAGGAAACACACTTGACTGGAATTTATGATCTGGTTG
genomic: GGATCGTCAAATAGAAGCGGTGAATCATCTTTAGCTACATCTGATGAAGgtaaaaaaat ... tttactgcagGCGTTCCAACCGACAAGGAAACACACTTGACTGGAATTTATGATCTGGTTG
EST: gi|22009862|gb|BQ794896.1|BQ794896
EST:     GGATCATCAAATAGAAGCGGTGAATCATCTTTAGCTACATCTGATGAAG                         GCGTTCCAACCGACAAGGAAACACACTTGACTGGAATTTATGATCTGGTTG
genomic: GGATCGTCAAATAGAAGCGGTGAATCATCTTTAGCTACATCTGATGAAGgtaaaaaaat ... tttactgcagGCGTTCCAACCGACAAGGAAACACACTTGACTGGAATTTATGATCTGGTTG
EST: gi|83275368|gb|DV939376.1|DV939376
EST:     GGATCGTCAAATAGAAGCGGTGAATCATCTTTAGCTACATCTGATGAAG                         GCGTTCCAACCGACAAGGAAACACACTTGACTGGAATTTATGATCTGGTTG
genomic: GGATCGTCAAATAGAAGCGGTGAATCATCTTTAGCTACATCTGATGAAGgtaaaaaaat ... tttactgcagGCGTTCCAACCGACAAGGAAACACACTTGACTGGAATTTATGATCTGGTTG
EST: gi|22010204|gb|BQ795238.1|BQ795238
EST:     GGATCATCAAATAGAAGCGGTGAATCATCTTTAGCTACATCTGATGAAG                         GCGTTCCAACCGACAAGGAAACACACTTGACTGGAATTTATGATCTGGTTG
genomic: GGATCGTCAAATAGAAGCGGTGAATCATCTTTAGCTACATCTGATGAAGgtaaaaaaat ... tttactgcagGCGTTCCAACCGACAAGGAAACACACTTGACTGGAATTTATGATCTGGTTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atgcctatggaacgtctctcttttgcagtttggttgctaactttgtttactgcagGCGTTCCAACCGACAAGGAAACACACTTGACTGGAATTTATGATCTGGTTGCTGTGTTGACCCACAAGGGCAGGAGTGCTGATTCAGGGCATTATGTTGC
                                  tgctaac  putative branch site (score: 1)
                                        ctttgttt  CT-rich tract
                                         tttgttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atgtaatgtgcttatgtcgaatcccttctatgacagtgctgcactatgcctatggaacgtctctcttttgcagtttggttgctaactttgtttactgcagGCGTTCCAACCGACAAGGAAACACACTTGACTGGAATTTATGATCTGGTTGCTGTGTTGACCCACAAGGGCAGGAGTGCTGATTCAGGGCATTATGTTGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGAT
- - - - -gcttatg
- - - - - - - - - - - cccttct
- - - - - - - - - - - - - - - - - - tgctgca
- - - - - - - - - - - - - - - - - - - - - -ctatgcc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tggttgc