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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctttttcccaattcagtaacttcattttgagacttctctattccaacttttgaattattattttcaagaaattaaaactcattccaaggggtgttcttagGTTCGCACCTTCAGAGGACACACTAATGAGAAGAACTTCGTGGGCCTCTCTGTAAACAGTGAATATATTTCTTGTGGCAGTGAAACAAACGACGTCTTCG

Basic information

species Vitis vinifera
transcript Vv12s0059g01420.t01
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv12s0059g01420.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: GRMZM2G104920_T02 (Zea mays), 3'ss of exon 9
ctttttcccaattcagtaacttcattttgagacttctctattccaacttttgaattattattttcaaga--aattaaaactcattccaaggggtgttcttagGTTCGCACCTTCAGAGGACACACTAATGAGAAGAACTTCGTGGGCCTCTCTGTAAACAGTGAATATATTTCTTGTGGCAGTGAAACAAACGACGTCTTCG
 | |       ||||  |  | |||    |   |    || | || ||    |  || | |||  | ||  | ||     | |   ||  | || || | |||| || || |||||||||||||  ||||| |||||||| || ||| | ||||| |||| |||||||||| ||||||| ||||| ||||| || || || |
-tctgatttggttcaaca-ttacatgcccaatttgaaatagtgcagctacgaacataatttttggatgaccattttgttataacaacattgtgttttttcagGTACGGACATTCAGAGGACACAAAAATGAAAAGAACTTTGTTGGCTTGTCTGTGAACAATGAATATATTGCTTGTGGAAGTGAGACAAATGAGGTTTTTG

upper sequence: Vv12s0059g01420.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: GRMZM2G126795_T02 (Zea mays), 3'ss of exon 13
-ctttttcccaattcagtaacttcattttgagacttctctattccaacttttgaattattattttcaagaaattaaaactcattccaaggggtgttcttagGTTCGCACCTTCAGAGGACACACTAATGAGAAGAACTTCGTGGGCCTCTCTGTAAACAGTGAATATATTTCTTGTGGCAGTGAAACAAACGACGTCTTCG
  |||    ||||     |    || ||||| |     |       |   |  | ||   ||   | |    ||| |||  |      ||  | ||   |||| || || |||||||| ||||  ||||| ||||||||||| ||  | ||||| |||| ||| |||||| ||||||| ||||||||||| || || || |
gatttggttcaatattacatgcccagtttgaaataatgcagcaatgaacatacattttggatgaccgatttgttataaca-acattgtggtttttttccagGTACGGACATTCAGAGGGCACAAAAATGAAAAGAACTTCGTTGGATTGTCTGTGAACAATGAGTATATTGCTTGTGGAAGTGAAACAAATGAGGTTTTTG

upper sequence: Vv12s0059g01420.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: GLYMA02G43540.2 (Glycine max), 3'ss of exon 11
---ctttttcccaattcagtaacttcattttgagacttctctattccaacttttgaattattattttcaagaaattaaaactcattccaa--ggggtgttcttagGTTCGCACCTTCAGAGGACACACTAATGAGAAGAACTTCGTGGGCCTCTCTGTAAACAGTGAATATATTTCTTGTGGCAGTGAAACAAACGACGTCTTCG
      | |   ||||   | |  | ||||||    ||||  | |  ||  ||  | ||| |||    || | |||    ||||||   |      |||    ||||||| || |||| ||| ||  | |||||||| ||||| || || ||  | |||| ||||||||||||| | ||||||||||||||||| || ||||| |
ttaaaatatttaaattggatcatattattttgtactttctaaaataaaatatt--atttaatata---aatatattttttctcattttcattcaaatgtgtacagGTTCGTACTTTCAAAGGCCATGCAAATGAGAAAAACTTTGTTGGTCTTACAGTAAGCAGTGAATATATTGCGTGTGGCAGTGAAACAAATGAAGTCTTTG

upper sequence: Vv12s0059g01420.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: GLYMA14G05430.1 (Glycine max), 3'ss of exon 11
ctttttcccaattcagtaacttcattttgagacttctctattccaacttttgaattattattttcaagaaattaaaactcattccaa--ggggtgttcttagGTTCGCACCTTCAGAGGACACACTAATGAGAAGAACTTCGTGGGCCTCTCTGTAAACAGTGAATATATTTCTTGTGGCAGTGAAACAAACGACGTCTTCG
   | |   |||| | ||  ||  |||||    ||||  | |  ||  | |    | | || |  |   ||||    ||||||   |      |||    ||||||| || |||| ||| ||  | |||||||| ||||| || |||||  | |||| ||||||||| ||| | ||||||||||||||||| || ||||| |
aaatatttaaattgattatatt--ttttgtactttctaaaataaaatatatattatgtaatatgaatataattttttctcattttcattcaaatgtgtacagGTTCGTACTTTCAAAGGCCATGCAAATGAGAAAAACTTTGTTGGCCTTACAGTAAGCAGTGAATACATTGCGTGTGGCAGTGAAACAAATGAAGTCTTTG

upper sequence: Vv12s0059g01420.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: AT2G32950.1 (Arabidopsis thaliana), 3'ss of exon 11
ctttttcccaattcagtaacttcattttgagacttctctattccaacttttgaattattattttcaagaaattaaaactcattccaaggggtgttcttagGTTCGCACCTTCAGAGGACACACTAATGAGAAGAACTTCGTGGGCCTCTCTGTAAACAGTGAATATATTTCTTGTGGCAGTGAAACAAACGACGTCTTCG
           ||   | ||| |        |  |  |   | ||       |   |   || ||  ||   |     ||| |   |      || | ||||||| || ||||||||||| ||||| ||||||||||| ||||| ||| | || ||||| || ||| |  | ||||| || || |||||||| || |  |
----------gttagattactgcccgagccaatcttgcagattcagtcaaaaagaaaaacttgtcttgactatgttgttcaattttac-----ttttcagGTTCGAACATTCAGAGGACATACTAACGAGAAGAACTTTGTGGGTCTCACAGTGAACAGCGAGTATCTCGCCTGTGGAAGCGAGACAAACGAAGTATATG

upper sequence: Vv12s0059g01420.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: PP1S37_28V6.1 (Physcomitrella patens), 3'ss of exon 11
ctttttcccaattcagtaacttcattttgagacttctctattccaacttttgaattattattttcaagaaattaaaactcattccaaggggtgttctt-----agGTTCGCACCTTCAGAGGACACACTAATGAGAAGAACTTCGTGGGCCTCTCTGTAAACAGTGAATATATTTCTTGTGGCAGTGAAACAAACGACGTCTTCG
||||||| | |||     |      |  | |||||| | |    |||  ||  |  | |    ||   |   |        |||  |||  |     |     |||| |  ||  |  |||||||||| ||||| ||||| || ||||| ||  ||||||| ||||| || ||  |||||||||||||||| | ||| || || |
ctttttcgcgatttgtgtagcgtgctaagtgacttcgcaa----aacacttagaaaagt-cgctcgctaccctgtcgtaatttctgaggtttacctctcctgcagGTACAAACGCTTGGAGGACACACCAATGAAAAGAATTTTGTGGGGCTTACTGTAAATAGTGACTACATCGCTTGTGGCAGTGAAACGAGCGAGGTTTTTG

upper sequence: Vv12s0059g01420.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: PP1S81_234V6.1 (Physcomitrella patens), 3'ss of exon 10
--------------------------------------------ctttttcccaatt--cagtaacttcattttgagacttctctattccaactt--ttgaattattattttcaagaaattaaaactcattccaaggggtgttctt-----agGTTCGCACCTTCAGAGGACACACTAATGAGAAGAACTTCGTGGGCCTCTCTGTAAACAGTGAATATATTTCTTGTGGCAGTGAAACAAACGACGTCTTCG
                                             || |||    ||   |  ||     | |  | | ||||    |  ||  |  ||   || || |  |   |     | | ||  |  || ||  | |         ||   || ||  | ||||||||||| |||||||||||||| ||||| ||  |||| |||||||||||| || |||| || |||||| | ||||| ||||| |
gtatgtcgggctgctctgatatgtgcctcaaccccgtacttttgattattcttgtttgttatcaagcatgtatgaaaatttctgatgtggaagatgattactttcttctgctttcggttccacacctggtgacatggtttttgtccgatgcagACCCGAACTCTGAGAGGACACACGAATGAGAAGAACTTTGTGGGACTGACTGTCAACAGTGAATATGTTGCTTGCGGTAGTGAATCGAACGAGGTCTTTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acttttgaattattattttcaagaaattaaaactcattccaaggggtgttcttagGTTCGCACCTTCAGAGGACACACTAATGAGAAGAACTTCGTGGGCCTCTCTGTAAACAGTGAATATATTTCTTGTGGCAGTGAAACAAACGACGTCTTCG
                                              tgttctt  CT-rich tract
       aattattattttcaag  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ctttttcccaattcagtaacttcattttgagacttctctattccaacttttgaattattattttcaagaaattaaaactcattccaaggggtgttcttagGTTCGCACCTTCAGAGGACACACTAATGAGAAGAACTTCGTGGGCCTCTCTGTAAACAGTGAATATATTTCTTGTGGCAGTGAAACAAACGACGTCTTCG

- - ttcccaa
- - - - - - - - - - - - - - - - - - - - -tccaact
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaattaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tcattcc