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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gctcttgatattactgttatgggcatgctctcattctactggatctttgtaacacaattggaagaagaactccacactgattggtttaaactttctccagGTATTCGGGGTATTATTTGAAGCTCAGTATTTTCAGAATGTCATGCGTGTGGGTTTCCGGGTTAGATCAACTTTG

Basic information

species Vitis vinifera
transcript Vv10s0003g04390.t01
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv10s0003g04390.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GRMZM2G084181_T01 (Zea mays), 3'ss of exon 9
gctcttgatattactgttatgggcatgctct-cattctactggatctttgt---aacacaattggaagaagaactcca-cactgattggtttaaactttctccagGTATTCGGGGTATTATTTGAAGCTCAGTATTTTCAGAATGTCATGCGTGTGGGTTTCCGGGTTAGATCAACTTTG
  | | | |  |  ||||    ||||||| | ||    | | | |  ||||       || ||| || |  || |  |  ||| |    | |   | || || ||  | | |||||  |   ||| || ||||| |||||||| |||||||||||||||||| || | || || || |||
-gtatgggtcattttgtttcctgcatgctgtgcaccacatttgtttcttgtttcggtgcagttgaaacagcaattatagtacttacgtctcttctcattttc-agTCACTTGGGGTTCTTGCTGAGGCACAGTACTTTCAGAACGTCATGCGTGTGGGTTTCAGGTTGAGGTCCACATTG

upper sequence: Vv10s0003g04390.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GLYMA13G29180.1 (Glycine max), 3'ss of exon 9
gctcttg-atattactgttatgggcatgctctcattctactggatctttgtaacacaattggaagaag-aactccacactgattggtttaaactttctcc----agGTATTCGGGGTATTATTTGAAGCTCAGTATTTTCAGAATGTCATGCGTGTGGGTTTCCGGGTTAGATCAACTTTG
  | ||| | ||||   |  | |      |  ||| | | |     ||| ||||    ||| |||     |||    |        | | || ||  |      |||| || ||||| |||| ||||||||| ||||||||||||||||||||||| |||| |||| | |||||||| |||
-tttttgtaaattaggctgcttgatggaattacatgcaagtaa---tttataacct--ttgcaagttttgacttattaagagcctatctgaatttgtttttgatagGTCTTTGGGGTGTTATGTGAAGCTCAATATTTTCAGAATGTCATGCGTGTTGGTTACCGGTTAAGATCAACATTG

upper sequence: Vv10s0003g04390.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GLYMA15G09900.1 (Glycine max), 3'ss of exon 9
-----gctcttgatattactgttatgggcatgctctcattctactggatctttgtaacacaattggaagaagaactccacactgattggtttaaactttctccagGTATTCGGGGTATTATTTGAAGCTCAGTATTTTCAGAATGTCATGCGTGTGGGTTTCCGGGTTAGATCAACTTTG
     | | || |||        ||    ||  | |  |  |  |  ||     | |      |||      |     |  ||   ||  ||   ||||    |||| || ||||| |||| ||||||||| ||||||||||||||||||||||| |||| |||| | |||||||| |||
tacaagtttttaataa----acaataaagatttttttttgtttgtaaattaggctgatctctatggtcacttattaagagcctatctgaatttgtctttgat-agGTCTTTGGGGTGTTATGTGAAGCTCAATATTTTCAGAATGTCATGCGTGTTGGTTACCGGTTAAGATCAACATTG

upper sequence: Vv10s0003g04390.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: AT1G30400.1 (Arabidopsis thaliana), 3'ss of exon 10
gctcttgatattactgt-tatgggcatgctctcattctac-tggatctttgtaacacaattggaagaagaactccac-actgattggtttaaacttt-----ctccagGTATTCGGGGTATTATTTGAAGCTCAGTATTTTCAGAATGTCATGCGTGTGGGTTTCCGGGTTAGATCAACTTTG
       |||    ||  | | |  | | | |  ||  |  | | ||   || ||||  |||    | | |||||   |  | ||| | |  |  ||      | |||||||| ||||| |||| ||||||||||||||| || ||||| |||||||| |||| |||| |||| ||  |  ||
------aatacatttgcatgttgaaaaggttttgtttaatgtaggtcaaggtgacac--ttgaccaatggactccttgatcgcttgatgttgatgttgacattttcagGTATTGGGGGTTTTATGTGAAGCTCAGTATTTCCAAAATGTGATGCGTGTTGGTTACCGGCTTAGGTCTGCACTG

upper sequence: Vv10s0003g04390.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: AT2G34660.1 (Arabidopsis thaliana), 3'ss of exon 9
gctcttgatattactgttatgggcatgctctcattcta-ctggatctttgtaacacaattggaagaagaactccac-----actgat-tggtttaaactttctccagGTATTCGGGGTATTATTTGAAGCTCAGTATTTTCAGAATGTCATGCGTGTGGGTTTCCGGGTTAGATCAACTTTG
     |  |    ||||||  |  | | ||| | | || || |      || | ||  |      |  |||||  |     |||||| | | | | |   | || |||| ||||||||  ||| ||||||||| ||||| ||||||||||||||||| |||| |||  | |||||  || ||
-----ttttgcgtctgtta--gataggttctgactttatctagtgtagggtgatactttaaagctacaaactcatcgagtgactgatgttgatgacaacgtttctagGTGTTCGGGGTGCTATGTGAAGCTCAATATTTCCAGAATGTCATGCGTGTTGGTTACCGACTGAGATCTGCTCTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttgtaacacaattggaagaagaactccacactgattggtttaaactttctccagGTATTCGGGGTATTATTTGAAGCTCAGTATTTTCAGAATGTCATGCGTGTGGGTTTCCGGGTTAGATCAACTTTG
                                             ctttctcc  CT-rich tract
                                       tttaaacttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gctcttgatattactgttatgggcatgctctcattctactggatctttgtaacacaattggaagaagaactccacactgattggtttaaactttctccagGTATTCGGGGTATTATTTGAAGCTCAGTATTTTCAGAATGTCATGCGTGTGGGTTTCCGGGTTAGATCAACTTTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGATCA
gctcttg
- - - - - - - - ttatggg
- - - - - - - - - - - -catgctc
- - - - - - - - - - - - - - - - - tctactg
- - - - - - - - - - - - - - - - - - - - - - - - - aacacaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ggaagaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctccaca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgattgg