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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gattctgatgctattaaaattttgcttattgcttgatttcatggttacgtcaacatatagttatttcccactttgttgttcttgttgcttgtgcatctagGCTATGATGAAAGATCAGTTTGCAAACTATGTTGTACAAAAGGTGCTGGAGACTTGTGATGACCAGCAGCGTGAGCTGATCTTGTCCCGAATTAAGGTTC

Basic information

species Vitis vinifera
transcript Vv06s0004g05100.t01
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv06s0004g05100.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: LOC_Os01g62650.1 (Oryza sativa), 3'ss of exon 8
------gattctgatgctattaaaattttgcttattgcttgatttcatggttacgtcaacatatagttatttcccactttgttgttcttgttgcttgtgcatctagGCTATGATGAAAGATCAGTTTGCAAACTATGTTGTACAAAAGGTGCTGGAGACTTGTGATGACCAGCAGCGTGAGCTGATCTTGTCCCGAATTAAGGTTC
      |     | |||  | || ||| || |   |   || |||  || ||  ||     | | ||| ||       || || || |      |    | |  |||| |||||||| ||||||||||  |||||||||||||| || || ||||||||||||||||| |||||||||||| ||||| |||| ||| | |||||||
ccccccggaaaagttgcattcaacattctgatctct--ctgtttttttgtttttgtttttgttttgttttt----gtgttttttttttgaaaaataacacttgcagGCCATGATGAAGGATCAGTTTGGTAACTATGTTGTACAGAAAGTACTGGAGACTTGTGATGATCAGCAGCGTGAGTTGATCCTGTCACGAGTAAAGGTTC

upper sequence: Vv06s0004g05100.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GLYMA11G14530.1 (Glycine max), 3'ss of exon 8
-gattctgatgctattaaaattttgcttattgcttgatttcatggttacgtcaacatatagttatttcccactttgttgt-tcttgttgcttgtgcatctagGCTATGATGAAAGATCAGTTTGCAAACTATGTTGTACAAAAGGTGCTGGAGACTTGTGATGACCAGCAGCGTGAGCTGATCTTGTCCCGAATTAAGGTTC
  |  |||     | || |  || | || |  |||| |   |  |  || ||    |       |||  ||   || ||  ||   ||  |  |  ||  |||| |||||||||||||| |||||||| ||||||||||||||||||||||| ||||||||||| || || |||||||||||  ||| | ||||||||||||
acaacctgtaa--aatagatcttggtttgtcacttgttcaaagaggcacttccttcttccccagttttgcaaaatgatgaatcagatttttcttatatacagGCAATGATGAAAGATCAATTTGCAAATTATGTTGTACAAAAGGTGCTGGAAACTTGTGATGATCAACAACGTGAGCTGATTCTGTACAGAATTAAGGTTC

upper sequence: Vv06s0004g05100.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GLYMA12G06450.1 (Glycine max), 3'ss of exon 8
-gattctgatgctattaaaattttgcttattgcttgatttcatggttacgtcaacatatagttatttcccactttgttgttcttgttgcttgtgcatctagGCTATGATGAAAGATCAGTTTGCAAACTATGTTGTACAAAAGGTGCTGGAGACTTGTGATGACCAGCAGCGTGAGCTGATCTTGTCCCGAATTAAGGTTC
  |  |||     | || |  || | ||    |||| ||  |  |     ||            |||| |    || |      | | | | |  ||  |||| |||||||||||||| |||||||| || |||||||||||||||||||| ||||||||||| || ||||| ||||||||  | ||||||||||||||||
acaacctgtaaaaaatagatcttggtttgccacttgtttaaagaggcttttccctcctccccagtttctcgaaatgataaatcagattcct-tatatacagGCGATGATGAAAGATCAATTTGCAAATTACGTTGTACAAAAGGTGCTGGAAACTTGTGATGATCAACAGCGCGAGCTGATTCTTTCCCGAATTAAGGTTC

upper sequence: Vv06s0004g05100.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GLYMA11G14550.1 (Glycine max), 3'ss of exon 10
gattctgatgctattaaaattttgcttattgcttgatttcatggttacgtcaacatatagttatttcccac---tttgttgttcttgttgcttgtgcatctagGCTATGATGAAAGATCAGTTTGCAAACTATGTTGTACAAAAGGTGCTGGAGACTTGTGATGACCAGCAGCGTGAGCTGATCTTGTCCCGAATTAAGGTTC
        ||     ||   |||  |||   |       ||          || | ||  |   ||  |||    |  |   ||   || ||| |  ||  |||| |||||||||||||| |||||||| || |||||||||||||||||||| ||||||||||| || || |||||||||||  | ||||||||||||||||
---gtcagtgtggcgaatgctttagttaactcccagaaccacaacctgtaaaatagatcttggcttgtcacaaaatgataaatcagattccttttatatgcagGCGATGATGAAAGATCAATTTGCAAATTACGTTGTACAAAAGGTGCTGGAAACTTGTGATGATCAACAACGTGAGCTGATTCTTTCCCGAATTAAGGTTC

upper sequence: Vv06s0004g05100.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GLYMA11G14500.1 (Glycine max), 3'ss of exon 9
gattctgatgctattaaaattttgcttattgcttgatttcatggttacgtcaacatatagttatttcccac---tttgttgttcttgttgcttgtgcatctagGCTATGATGAAAGATCAGTTTGCAAACTATGTTGTACAAAAGGTGCTGGAGACTTGTGATGACCAGCAGCGTGAGCTGATCTTGTCCCGAATTAAGGTTC
        ||     ||   |||  |||   |       ||          || | ||  |  |||  |||    |  |   ||   || ||| |  ||  |||| |||||||||||||| |||||||| || |||||||||||||||||||| ||||||||||| || || |||||||||||  | ||||||||||||||||
---gtcagtgtggcgaatgctttagttaactcccagaaccacaacctgtaaaatagatcttggtttgtcacaaaatgataaatcagattccttttatatgcagGCGATGATGAAAGATCAATTTGCAAATTACGTTGTACAAAAGGTGCTGGAAACTTGTGATGATCAACAACGTGAGCTGATTCTTTCCCGAATTAAGGTTC

upper sequence: Vv06s0004g05100.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GLYMA15G04060.2 (Glycine max), 3'ss of exon 9
gattctgatgctattaaaattttgcttattgcttgatttcatggttacgtcaacatata-gttatttcccactttgttgttcttgttgcttgtgcatctagGCTATGATGAAAGATCAGTTTGCAAACTATGTTGTACAAAAGGTGCTGGAGACTTGTGATGACCAGCAGCGTGAGCTGATCTTGTCCCGAATTAAGGTTC
   |||  |  ||  ||| | |     |   |||||    || | ||     ||  ||   ||  |||  |   | |   ||||||| ||  |  ||  |||| |||||||||||||| || || ||||||||||||||||||||||||||||||||||||||||| ||||| ||||| ||  | || |||||||| ||||
tgctctagttataccaaactctcagc-acatcttgacaaaattgatagtaggactcattcattccttcttatgatatatatcttgttcctcttatatgcagGCAATGATGAAAGATCAATTCGCCAACTATGTTGTACAAAAGGTGCTGGAGACTTGTGATGACCAACAGCGAGAGCTAATTCTTTCACGAATTAAAGTTC

upper sequence: Vv06s0004g05100.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GLYMA12G06430.1 (Glycine max), 3'ss of exon 7
-gattctgatgctattaaaattttgcttattgcttgatttcatggttacgtcaacatatagttatttcccactttg-ttgttcttgttgcttgtgcatctagGCTATGATGAAAGATCAGTTTGCAAACTATGTTGTACAAAAGGTGCTGGAGACTTGTGATGACCAGCAGCGTGAGCTGATCTTGTCCCGAATTAAGGTTC
     |||     | || |  || | ||    |||| |   |  ||  | ||    |       |||  ||   || |   ||   || ||| |  ||  |||| |||||||||||||| |||||||| || |||||||||||||||||||| ||||||||||| || || || ||||||||  | | ||||||||||||||
acgacctgtaa--aatagatcttggtttgccacttgttcaaagagtcccttccctcttccccagttttgcaaaatgataaatcagattccttttatatacagGCGATGATGAAAGATCAATTTGCAAATTACGTTGTACAAAAGGTGCTGGAAACTTGTGATGATCAACAACGCGAGCTGATTCTTTACCGAATTAAGGTTC

upper sequence: Vv06s0004g05100.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: PP1S35_216V6.1 (Physcomitrella patens), 3'ss of exon 9
gattctgatgctattaaaattttgcttattgcttgatttcatggttacgtcaacatatagttatttcccactttgttgttct--tgtt-gcttgtgc-atctagGCTATGATGAAAGATCAGTTTGCAAACTATGTTGTACAAAAGGTGCTGGAGACTTGTGATGACCAGCAGCGTGAGCTGATCTTGTCCCGAATTAAGGTTC
|  | ||   || |  |      ||| |||   || | |  ||  | | ||||  | |      |   |   |   |   ||  |||| | |  ||  ||  |||| ||||||||||| |||||||||||||| || || || |||||| |||| || ||||||||    || || |||||| |  ||   || |||  |||||
ggatttgtacctgtggaggaa--gctgatt-tgtgttatggtgaatgcctcaat-tgtttccggtatgcgtatgagtagcctgatgttcggtgatgtgatgcagGCAATGATGAAAGACCAGTTTGCAAACTACGTGGTCCAGAAGGTGTTGGAAACCTGTGATGAATCTCAACGCGAGCTGTTGCTGGGTCGTATTCGGGTTC

upper sequence: Vv06s0004g05100.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: EFJ35801 (Selaginella moellendorffii), 3'ss of exon 5
gattctgatgctattaaaattttgcttattgcttgatttcatggttacgtcaacatatagttatttcccactttgttgttcttgttgcttgtgcatctagGCTATGATGAAAGATCAGTTTGCAAACTATGTTGTACAAAAGGTGCTGGAGACTTGTGATGACCAGCAGCGTGAGCTGATCTTGTCCCGAATTAAGGTTC
                                 | |    |||   ||  ||| | | ||||  || |   ||  |    || |   |   | ||   |||| |||||||| || |||||||||||||| || || ||||||||  ||||||||||   ||||||||| || ||| || || ||   || || || || |
--------------------------------gtaaagagatga--acagcaagagagagtt--tttcgttttgctcacgctcggctccactccacgcagGCGATGATGAAGGACCAGTTTGCAAACTACGTGGTGCAAAAGGTTTTGGAGACTTGCAGTGACCAGCAACGAGAGATGCTCCTGGGTCGTATCAAAGTCC

upper sequence: Vv06s0004g05100.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: EFJ36402 (Selaginella moellendorffii), 3'ss of exon 6
gattctgatgctattaaaattttgcttattgcttgatttcatggttacgtcaacatatagttatttcccactttgttgttcttgttgcttgtgcatctagGCTATGATGAAAGATCAGTTTGCAAACTATGTTGTACAAAAGGTGCTGGAGACTTGTGATGACCAGCAGCGTGAGCTGATCTTGTCCCGAATTAAGGTTC
                                 | |    |||   ||  ||| | | |||| ||| |   ||  |    || |   |   | ||   |||| |||||||| || |||||||||||||| || || ||||||||  ||||||||||   ||||||||| || ||| || || ||   || || || || |
--------------------------------gtaaagagatga--acagcaaaagagagtttttttcgttttgctcacgctcggctccactccacgcagGCGATGATGAAGGACCAGTTTGCAAACTACGTGGTGCAAAAGGTTTTGGAGACTTGCAGTGACCAGCAACGAGAGATGCTCCTGGGTCGTATCAAAGTCC

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|32458085|gb|CD799259.1|CD799259
EST:     GGTGAATGAGATGCTTGGCACTACTGATGAGAATGAGCCTCTCTTCAG                         GCTATGATGAAAGATCAGTTTGCAAACTATGTTGTACAAAAGGTGCTGGA
genomic: GGTGAATGAGATGCTTGGCACTACTGATGAGAATGAG-C-CTCTTCAGgtttggccaa ... gtgcatctagGCTATGATGAAAGATCAGTTTGCAAACTATGTTGTACAAAAGGTGCTGGA






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tacgtcaacatatagttatttcccactttgttgttcttgttgcttgtgcatctagGCTATGATGAAAGATCAGTTTGCAAACTATGTTGTACAAAAGGTGCTGGAGACTTGTGATGACCAGCAGCGTGAGCTGATCTTGTCCCGAATTAAGGTTC
      aacatatagttattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gattctgatgctattaaaattttgcttattgcttgatttcatggttacgtcaacatatagttatttcccactttgttgttcttgttgcttgtgcatctagGCTATGATGAAAGATCAGTTTGCAAACTATGTTGTACAAAAGGTGCTGGAGACTTGTGATGACCAGCAGCGTGAGCTGATCTTGTCCCGAATTAAGGTTC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
- - -tgatgct
- - - - - - attaaaa
- - - - - - - - - - - - - - -tgcttga
- - - - - - - - - - - - - - - - - - -ttcatgg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgttgct