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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttggtaccacctacctacccttctacattttctctcaaacacccacacaatccattaatttatagccattttttttaacatacaaacagAAAAAGCAAAGATGGGAGAGAAGGAGTGGTACTTCTTCAGCCTCCGCGATCGGAAGTATCCAACTGGCCTCCGAACCAACCGGGCCACAGAAGCTGGCTA

Basic information

species Vitis vinifera
transcript Vv19s0014g02200.t01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv19s0014g02200.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GRMZM2G393433_T02 (Zea mays), 3'ss of exon 1
gttggtaccacctacctaccct-tctacattttctctcaaacacccacacaatccattaatttatagccattttttttaac---atacaaacagAAAAAGCAAAGATGGGAGAGAAGGAGTGGTACTTCTTCAGCCTCCGCGATCGGAAGTATCCAACTGGCCTCCGAACCAACCGGGCCACAGAAGCTGGCTA
         |   | || |  |   | |||   |   | | |      | |  |  | |  || | |  || |  | | |    ||   | |||| || || |||||||| ||||||||||||||||||| |||||||||||| || ||||| || || ||||| || |||||||| ||||| |  || |||||
------gtgagtgagctgctttgcttgcatcgaccacccaccgattgaatagacattaagcttgtcgtgatgtgatgtgatctgatctgatcagACAAGGCGAAGATGGGGGAGAAGGAGTGGTACTTCTACAGCCTCCGCGACCGCAAGTACCCGACGGGCCTGCGCACCAACCGCGCCACGGTGGCCGGCTA

upper sequence: Vv19s0014g02200.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GRMZM2G139700_T01 (Zea mays), 3'ss of exon 1
----gttggt--accacctacctacccttctacattttctctca-aacacccacacaatccattaatttatagccattttttttaacat-acaaacagAAAAAGCAAAGATGGGAGAGAAGGAGTGGTACTTCTTCAGCCTCCGCGATCGGAAGTATCCAACTGGCCTCCGAACCAACCGGGCCACAGAAGCTGGCTA
    ||  ||        ||| ||  | |  | | | || ||    |   ||  ||    ||      |||    ||  |  | |  || |  | |||| || || |||||||| ||||||||||||||||||| | |||||||||| || ||||| || || ||||| || |||||||| ||||| |  || |||||
gtgagtgagtgagtgggttacatatacgtacatactctcgctggtgatgaccgtaccgatcacccgactatgatgatgatgatgatgatgatgagcagACAAGGCGAAGATGGGGGAGAAGGAGTGGTACTTCTACTGCCTCCGCGACCGCAAGTACCCGACGGGCCTGCGCACCAACCGCGCCACGGCGGCCGGCTA

upper sequence: Vv19s0014g02200.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA13G34950.1 (Glycine max), 3'ss of exon 1
-----------------------------------------------------gttggtaccacctacctacccttctacattt-tctctcaaaca--cccacacaatccattaatttatagccatttt--ttttaacatacaaacagAAAAAGCAAAGATGGGAGAGAAGGAGTGGTACTTCTTCAGCCTCCGCGATCGGAAGTATCCAACTGGCCTCCGAACCAACCGGGCCACAGAAGCTGGCTA
                                                      ||  ||   | | | |  | | ||| | |  |    |||| |       |   ||||   |    || || || |  || |    |     |||| ||||| |||||||||||||| |||||||||||||||||| | || ||  ||||||| ||||||||  |  |||||||  |||| || |||||||| ||
gtaaaattaagcactttcaacgccctttctttttttctttcttatctttggctattaatatttctttcattacttgctatagtggtagtacaaagaagtttggattttccacctaac-gtaacctttgtggttgtttgtttttggcagAGAAAGCTAAGATGGGAGAGAAAGAGTGGTACTTCTTCAGCTTACGTGACAGGAAGTACCCAACTGGGTTAAGAACCAATAGGGCTACTGAAGCTGGTTA

upper sequence: Vv19s0014g02200.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA06G35660.1 (Glycine max), 3'ss of exon 1
------------gttggtaccacctacctacccttctacattttctctcaaacacccacacaatccattaatttatagccattttttttaacatacaaacagAAAAAGCAAAGATGGGAGAGAAGGAGTGGTACTTCTTCAGCCTCCGCGATCGGAAGTATCCAACTGGCCTCCGAACCAACCGGGCCACAGAAGCTGGCTA
             || |||  |    | |     |  | | ||   |   ||||     |      | |   ||||   | | || ||| | ||     |||| |||||||||||||| |||||||| ||||||||||  ||||| || || || ||||| ||||||||  | || |||||  ||||||| |||||||| ||
taataactttctcttcgtaagataatcattgtggtggagaattatgccagaacattgttattgctaactttgttatttgc-tattgtttcatatgtgg-cagAGAAAGCAAAGATGGGTGAGAAGGAATGGTACTTCTATAGCCTTCGTGACCGAAAGTACCCAACTGGATTACGCACCAATAGGGCCACCGAAGCTGGTTA

upper sequence: Vv19s0014g02200.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA12G35530.1 (Glycine max), 3'ss of exon 1
-----------------gttggtaccacctacctacccttctacattttctctcaaacacccacacaatc-cattaa------tttatag---ccattttttttaacataca-----aacagAAAAAGCAAAGATGGGAGAGAAGGAGTGGTACTTCTTCAGCCTCCGCGATCGGAAGTATCCAACTGGCCTCCGAACCAACCGGGCCACAGAAGCTGGCTA
                   |         |   || |  |  | ||||||  |||         | | |  || |||      |||  |    |||  |    |||| |          |||| ||||| |||||||||||||| |||||||||||||||||| | || ||  | ||||| ||||||||  |  |||||||  |||| || |||||||| ||
gtaaaaacacttaacaccctttctttctttctttagctattaatattttcattcatggctttctatagtggcagtaaaaagagtttggactttccacctcacctaacctttgtttttggcagAGAAAGCTAAGATGGGAGAGAAAGAGTGGTACTTCTTCAGCTTACGTGACAGAAAGTACCCAACTGGGTTAAGAACCAATAGGGCTACTGAAGCTGGGTA

upper sequence: Vv19s0014g02200.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA12G26190.1 (Glycine max), 3'ss of exon 1
-------------------------------------------------------------------------gttggtaccacctacctacccttcta--cattttctctcaaacaccca---cacaatccattaatttatagccat-tttttttaacatacaaacagAAAAAGCAAAGATGGGAGAGAAGGAGTGGTACTTCTTCAGCCTCCGCGATCGGAAGTATCCAACTGGCCTCCGAACCAACCGGGCCACAGAAGCTGGCTA
                                                                         |    || | |  || ||      ||  |||  |       | |   |   || ||     |||||| || |  | || |  |  |||     |||| |||||||||||||| |||||||| ||||||||||  ||||| || || || ||||| ||||||||  | || || ||  | ||||| |||||||| ||
gtaactaattacaacaacaaaaccaaaaccctcatcgactaattttaagactaaaacaatgtatatatatgtagaaaataactctcacttagtaaaataatcatcatggggttgagaattaggccaaaactttgtaatttctaactttgttatcgtttcatgtgg-cagAGAAAGCAAAGATGGGTGAGAAGGAATGGTACTTCTATAGCCTTCGTGACCGAAAGTACCCAACTGGGTTACGCACAAATAGAGCCACTGAAGCTGGTTA

upper sequence: Vv19s0014g02200.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: AT5G53950.1 (Arabidopsis thaliana), 3'ss of exon 1
gttggtaccacctacctacccttctacattttctctcaaacacccacacaatccattaatttatagccattttttttaacatacaaacagAAAAAGCAAAGATGGGAGAGAAGGAGTGGTACTTCTTCAGCCTCCGCGATCGGAAGTATCCAACTGGCCTCCGAACCAACCGGGCCACAGAAGCTGGCTA
         |   |  |||    |||  ||   | |  |   |      |||  |    | |  |  | ||  | | ||  |  |   ||  | ||| |||||||||||||| || ||||||||||| |||||||| || ||||||||||| || || ||  |||| ||| | || || || ||||| ||
-------gtaagaaaatacaaaactaacttacttgt--agttcttttgtaattaaggtttctgaaatctttactctcaatgt-tacttagGGAGAGCTAAGATGGGAGAGAAAGAATGGTACTTCTTTAGCCTCCGTGACCGGAAGTATCCGACGGGACTGAGAACTAACAGAGCAACTGAGGCTGGTTA

upper sequence: Vv19s0014g02200.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: AT3G15170.1 (Arabidopsis thaliana), 3'ss of exon 1
-------------gttggtaccacctacctacccttctacattttctctcaaacacccacacaatccattaatttatagccattttttttaacatacaaacagAAAAAGCAAAGATGGGAGAGAAGGAGTGGTACTTCTTCAGCCTCCGCGATCGGAAGTATCCAACTGGCCTCCGAACCAACCGGGCCACAGAAGCTGGCTA
              ||   |  |   |||   |||| | |  ||   || |||||    |    |   |   ||| || |  |   || || |||   | |||| ||||| || ||||| ||||||||||||||||||||||  ||  | || || || || ||||| || ||  |||| ||| | || ||||||||||| ||
ctttatatcaacccttcacatgagtgaccagtccttgttcggtt---ctaaaacagagtcctccttactctgtttgtaactttcacttataccatttgagcagAGAAAGCGAAAATGGGGGAGAAGGAGTGGTACTTCTTCACACTAAGAGACCGTAAATACCCAACGGGACTGAGAACGAACAGAGCAACAGAAGCTGGTTA

upper sequence: Vv19s0014g02200.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: PP1S327_64V6.1 (Physcomitrella patens), 3'ss of exon 1
-------------------------------gttggtaccacctacctacccttctacattttctctcaaac--acccacacaatccattaatttatagccattttttttaacatacaa-------acagAAAAAGCAAAGATGGGAGAGAAGGAGTGGTACTTCTTCAGCCTCCGCGATCGGAAGTATCCAACTGGCCTCCGAACCAACCGGGCCACAGAAGCTGGCTA
                                 ||||      | | |  ||| | |  ||     |||     ||  | |    ||      ||  |   | |||  |        ||        |||| ||||| ||| | || |||||||||||||||||||||||||| || ||||| |||||||| || ||  | ||||| ||  | ||||| |||   || ||
gtgacacaaactcccaatccttccagtatcatctggtgtagtgtgc-tgtcctccgaatttggtgatcatgtgaactgagatggaccgaatcattgaaattagtttcctcggtgggaaatgatcttgcagAGAAAGCGAAGTTAGGGGAGAAGGAGTGGTACTTCTTCAGCCTGCGGGATCGCAAGTATCCGACGGGAATGCGAACAAATAGAGCCACCGAAAAGGGTTA

upper sequence: Vv19s0014g02200.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: EFJ22540 (Selaginella moellendorffii), 3'ss of exon 1
--------------------------------------------------------------------------------------------------gttggtaccacctacctacccttctacattttctctcaaacacccacacaa---tccattaa----tttatagccattttttttaacatacaaacagAAAAAGCAAAGATGGGAGAGAAGGAGTGGTACTTCTTCAGCCTCCGCGATCGGAAGTATCCAACTGGCCTCCGAACCAACCGGGCCACAGAAGCTGGCTA
                                                                                                  |    | | |   || |    |    || ||      |    ||   || |   |||  |||     |        || |||||    | |   |||| |||||||| |||||||||||||| ||||||||||| ||| |  | || |||||||| || || ||  | || || || ||||| || || || |||||
gtaaggaggaactctcccatcttctctcgcattcgtttctatgatttcctctcactctctcgacgttcttgggcttgaatttgctgcattgcattcatggcattccaaggaacttggaatcgatcacttgggtcgagttgcctggacgaaattcctctaaaaatctctcctttgttcttttttctttcccggcagAGAAAGCAAACATGGGAGAGAAGGAATGGTACTTCTTTAGCTTGAGGGACCGGAAGTACCCGACGGGGATGCGTACGAATCGGGCAACCGAGGCCGGCTA

upper sequence: Vv19s0014g02200.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: EFJ11746 (Selaginella moellendorffii), 3'ss of exon 1
--------------------------------------------------------------------------------------------------gttggtaccacctacctacccttctacattttctctcaaacacccacacaa---tccattaa----tttatagccattttttttaacatacaaacagAAAAAGCAAAGATGGGAGAGAAGGAGTGGTACTTCTTCAGCCTCCGCGATCGGAAGTATCCAACTGGCCTCCGAACCAACCGGGCCACAGAAGCTGGCTA
                                                                                                  |    | | |   || |    |    || ||      |    ||   || |   |||  |||     |        || |||||    | |   |||| |||||||| |||||||||||||| ||||||||||| ||| |  | || || ||||| || || ||  | || || || ||||| || || || |||||
gtaaggaggaactctctcatcttctctcgcattcgcttctatcatttcctctcactctctcgacgttcttgggcttgaatttgctgcattgcattcatggcattccaaggaacttggaatcgatcacttgggtcgagttgcctggacgaaattcctctaaaaatctctcctttgttcttttttctttcccggcagAGAAAGCAAACATGGGAGAGAAGGAATGGTACTTCTTTAGCTTGAGGGACCGTAAGTACCCGACGGGGATGCGTACGAATCGGGCAACCGAGGCCGGCTA

upper sequence: Vv19s0014g02200.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: EFJ37734 (Selaginella moellendorffii), 3'ss of exon 1
--------gttggtac-cacctacctacccttctac-attttctctcaaacacccacacaatccattaat-ttatagccattttttttaacatacaaacagAAAAAGCAAAGATGGGAGAGAAGGAGTGGTACTTCTTCAGCCTCCGCGATCGGAAGTATCCAACTGGCCTCCGAACCAACCGGGCCACAGAAGCTGGCTA
         | | | | ||    | |  |    | | || |  |         ||       | | |||   | | |   ||   | |  | | || ||||| || || ||||||||||||||||| |||||||||||||  || || || || |||||||| || ||  | || || ||||| ||||| || || || ||
ttctatgcatcgtttctcataatcttggctagatgctatctatttcttggagtccgtgagcactactaacactttcgtttttggctcttgc-tccacacagACAAGGCCAAGATGGGAGAGAAGGAATGGTACTTCTTCACGCTGCGAGACCGAAAGTATCCTACGGGAATGCGCACAAACCGAGCCACCGAGGCCGGATA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcaaacacccacacaatccattaatttatagccattttttttaacatacaaacagAAAAAGCAAAGATGGGAGAGAAGGAGTGGTACTTCTTCAGCCTCCGCGATCGGAAGTATCCAACTGGCCTCCGAACCAACCGGGCCACAGAAGCTGGCTA
                                      ttttaac  putative branch site (score: 2)
                   attaatttatagccat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttggtaccacctacctacccttctacattttctctcaaacacccacacaatccattaatttatagccattttttttaacatacaaacagAAAAAGCAAAGATGGGAGAGAAGGAGTGGTACTTCTTCAGCCTCCGCGATCGGAAGTATCCAACTGGCCTCCGAACCAACCGGGCCACAGAAGCTGGCTA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG