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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttggtttcttttcttttcttttcttttcttttctttttttttttcttttttttttttgcctcagatttattttatcaactaaattgcaattaccaataaagttgttaatgtcaatagGATTGGATGAGATTCAGTGTTGCATTTTGGCACACATTCCGTGGAACCGGAGGTGATCCATTTGGTGCACCTACAAAGTTTTGGCCATGGGAAGATGGTA

Basic information

species Vitis vinifera
transcript Vv11s0052g01710.t01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv11s0052g01710.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: LOC_Os07g47290.1 (Oryza sativa), 3'ss of exon 4
gttggtttcttttcttttcttttcttttcttttctttttttttttcttttttttttttgcctcagatttattttatcaactaaat-tgcaattaccaataaagttgttaatgtcaatagGATTGGATGAGATTCAGTGTTGCATTTTGGCACACATTCCGTGGAACCGGAGGTGATCCATTTGGTGCACCTACAAAGTTTTGGCCATGGGAAGATGGTA
                |    ||  |   || | | || ||       |  |||| || |||    |||   | ||  | || || ||   ||   | |  |  || |   ||   |||||||||||| | ||||| || || |||||||| || |||||||| || ||||| ||||| |||||||| |||||||||| |||||| ||||| ||||| |
---------------gtagggtttatgaattatgtcttgttgaacagatccttttattccct----tttgcgtcatggaatacatctgagttttgtattttatctgcttgcgtt--tagGATTGGATGCGGTTCAGCGTGGCCTTTTGGCATACGTTCCGTGGTACTGGAGGAGATCCTTTTGGTGCCCCTACAAAGTCTTGGCCTTGGGAGGATGGCA

upper sequence: Vv11s0052g01710.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GRMZM2G081682_T02 (Zea mays), 3'ss of exon 4
gttggtttcttttcttttcttttcttttcttttctttttttttttcttttttttttttgcctcagatttattttatcaactaaattgcaattaccaataaagttgttaatgtcaatagGATTGGATGAGATTCAGTGTTGCATTTTGGCACACATTCCGTGGAACCGGAGGTGATCCATTTGGTGCACCTACAAAGTTTTGGCCATGGGAAGATGGTA
    || ||  |   |   |   | | |  |   |   | |    | | ||||    |  ||  ||  ||     |||||    |||||  ||    ||   ||| |  ||  | |||||||||||| | |||||||||||||| |||||||| |||||||| || || | |||||| || ||||| |||||||||  |||||| ||||| || || |
----gtatcgatcagtgaatccccatctgctgcttcactataccccctcttttacactcactgtgaagtac---gtcaaccct-ttgcatctatgcttat--ttgctt-tgctattagGATTGGATGCGCTTCAGTGTTGCATTCTGGCACACGTTCCGTGGTACTGGCGCTGATCCTTTCGGTGCTCCTACAAAGACTTGGCCTTGGGAGGACGGCA

upper sequence: Vv11s0052g01710.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GRMZM2G005493_T01 (Zea mays), 3'ss of exon 4
------------gttggtttcttttcttttcttttcttttcttttctttttttttttcttttttttttttgcctcagatttattttatcaactaaattgcaattaccaataaag-ttgttaat---gtcaatagGATTGGATGAGATTCAGTGTTGCATTTTGGCACACATTCCGTGGAACCGGAGGTGATCCATTTGGTGCACCTACAAAGTTTTGGCCATGGGAAGATGGTA
            ||      | | |  |  ||||  ||   |||   | |      ||||||    | |      | |    ||  |     ||   || | | | || | | | || ||  |   |  | ||||| |||||| | ||||||||||| || |||||||| |||||||| || || | |||||| |||||||| ||||||||| ||||||| ||||| || || |
gtatgatcagtagtgaaccccatctgctggctttgtttagttttcactgtaccccctcttttacactgtaaaggtaaaacctttgcacgctgtaggatgaagtcaacatttatgcttatttgttctgctactagGACTGGATGCGCTTCAGTGTTGCGTTCTGGCACACGTTCCGTGGTACTGGTGCTGATCCTTTTGGTGCGCCTACAAAGGTTTGGCCTTGGGAGGACGGCA

upper sequence: Vv11s0052g01710.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: AC190975.3_FGT004 (Zea mays), 3'ss of exon 1
gttggtttcttttcttttcttttcttttcttttctttttttttttcttttttttttttgcctcagatttattttatcaactaaattgcaattaccaataaagttgttaatgtcaatagGATTGGATGAGATTCAGTGTTGCATTTTGGCACACATTCCGTGGAACCGGAGGTGATCCATTTGGTGCACCTACAAAGTTTTGGCCATGGGAAGATGGTA
         | |   |   |   |     | | ||  ||   | |      | |||   |      |  | |  ||||||    |||||  ||    ||   ||| |  ||  | ||||||||||||   ||||||||||| || |||||||| ||| |||| || ||   |||||| |||||||| |||||||||  |||||| ||||| ||||| |
--------gtatcaatcagtgaacccccatctgctgcttcactataccccctctttacactcactgtgaagtacatcaaccct-ttgcatctatgcttat--ttgctt-tgctattagGATTGGATGCACTTCAGTGTTGCCTTCTGGCACACGTTCTGTGGTACTGGCACTGATCCTTTTGGTGCTCCTACAAAGACTTGGCCTTGGGAGGATGGCA

upper sequence: Vv11s0052g01710.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GRMZM2G313536_T01 (Zea mays), 3'ss of exon 3
gttggtttcttttcttttcttttcttttcttttctttttttttttcttttttttttttgcctcagatttattttatcaactaaattgcaattaccaataaagttgttaatgtcaatagGATTGGATGAGATTCAGTGTTGCATTTTGGCACACATTCCGTGGAACCGGAGGTGATCCATTTGGTGCACCTACAAAGTTTTGGCCATGGGAAGATGGTA
              | |  |   |     | | |   ||   | |      | |||   |      |  | |  ||||||    |||||  ||    ||   ||| |  ||  | |||||||||||| | ||||||||||| || |||||||| ||| |||| ||  | | |||||| || ||||| ||||||| |  |||||| ||||| ||||| |
--------------tctggtgaacccccatctgccgcttcactataccccctctttacactcactgtgaagtacatcaaccct-ttgcatctatgcttat--ttgctt-tgctattagGATTGGATGCGCTTCAGTGTTGCCTTCTGGCACACGTTCTGTGGTACTAGCGCTGATCCTTTCGGTGCTCCTACAATGACTTGGCCTTGGGAGGATGGCA

upper sequence: Vv11s0052g01710.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA17G07380.1 (Glycine max), 3'ss of exon 4
gttggtttcttttcttttcttttcttttcttttctttttttttttcttttttttttttgcctcag-atttattt-tatcaactaaattgcaattaccaataaagttgt-taatgtcaatagGATTGGATGAGATTCAGTGTTGCATTTTGGCACACATTCCGTGGAACCGGAGGTGATCCATTTGGTGCACCTACAAAGTTTTGGCCATGGGAAGATGGTA
               ||  ||||| ||| | |||       || ||  |||| | | | | |||  ||  |     | | | |   ||   | |   | | |   | | ||||  |   |||||||| | ||||| ||||||||||||||||| |||||||||||||| || | ||| ||||||||||||||||| || |  |||| ||||||||||||||
--------------gttggttttcatttatattccaagaagttgtcagttttatctatacttcatcatccaccaacacccattggcttttgacttgaatttattctatataatacctgcagGATTGGTTAAGATTTAGTGTTGCATTTTGGCATACATTCCGTGGAACAGGTGCTGACCCATTTGGTGCACCTACCAAATACTGGCTATGGGAAGATGGTA

upper sequence: Vv11s0052g01710.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: AT5G57655.1 (Arabidopsis thaliana), 3'ss of exon 3
gttggtttcttttcttttcttttcttttcttttctttttttttttcttttttttttttgcctcagatttattttatcaactaaattgcaattaccaataaagttgttaatgtcaatagGATTGGATGAGATTCAGTGTTGCATTTTGGCACACATTCCGTGGAACCGGAGGTGATCCATTTGGTGCACCTACAAAGTTTTGGCCATGGGAAGATGGTA
  |  |||  |||  ||  || | |||||||       |||||   || | ||||| ||  |  ||   |   | |    |   |     ||  |  | || || || |     | |||||||| | |||||||||||||| |||||||| || |||||||| || ||||||||||||||||||||  |||| |||| |||||| |||||||||||||
-gtacttttattttcttgtttgtattttcttgcaacaatttttgagttatgtttttatggatttgaagaaacgtgtgggatgtttgtttgttgtcc-tgaattttttga-----acagGATTGGTTTAGATTCAGTGTTGCGTTTTGGCATACTTTCCGTGGGACTGGAGGTGATCCATTTGGTGCTGCTACTAAGTATTGGCCTTGGGAAGATGGTA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agatttattttatcaactaaattgcaattaccaataaagttgttaatgtcaatagGATTGGATGAGATTCAGTGTTGCATTTTGGCACACATTCCGTGGAACCGGAGGTGATCCATTTGGTGCACCTACAAAGTTTTGGCCATGGGAAGATGGTA
     tattttatcaactaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttggtttcttttcttttcttttcttttcttttctttttttttttcttttttttttttgcctcagatttattttatcaactaaattgcaattaccaataaagttgttaatgtcaatagGATTGGATGAGATTCAGTGTTGCATTTTGGCACACATTCCGTGGAACCGGAGGTGATCCATTTGGTGCACCTACAAAGTTTTGGCCATGGGAAGATGGTA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG