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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tggaactatttactgagtatcaattgtagcttcttgacaattgacattcttctcatttctctagttttcatttttcgcttgtttattcatggtgctatagGCTCGTCGTGGTGGAGTTGATGAGCCGTTTGCATGGGAAAGCAGAGAGTTTCTGAGGAAGCTCTGCATAGGGAAG

Basic information

species Zea mays
transcript GRMZM2G136296_T03
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G136296_T02 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os02g32350.2 (Oryza sativa), 3'ss of exon 2
----tggaactatttactgagtatcaattgtagcttcttgacaattgacattcttctcatttctctagttttcatttttcgcttgtttattcatggtgctatagGCTCGTCGTGGTGGAGTTGATGAGCCGTTTGCATGGGAAAGCAGAGAGTTTCTGAGGAAGCTCTGCATAGGGAAG
    | |     || |     ||| |||| ||  |||||           ||   |||  || | |  |||   | ||     |     ||  || ||||  ||||||| ||||||||||| ||||| || ||||| ||||||||||| |||||||| ||||| ||||||||||| |||
tttctcgtgtagttcaaaacttatgaatt-ta--ttcttattctccagtctttccctccctttt-tgctttatgtattgaaactaaaactttgtgctgctcaagGCTCGCCGTGGTGGAGTGGATGAACCATTTGCTTGGGAAAGCAGGGAGTTTCTAAGGAAACTCTGCATAGGAAAG

upper sequence: GRMZM2G136296_T02 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA04G38010.1 (Glycine max), 3'ss of exon 2
--------------tggaactatttactgagtatcaattgtagcttcttgacaatt---gacattcttctcatttctctagttttcatttttcgcttgtttattcatggtgctatagGCTCGTCGTGGTGGAGTTGATGAGCCGTTTGCATGGGAAAGCAGAGAGTTTCTGAGGAAGCTCTGCATAGGGAAG
              | ||  | ||| |   | || ||||  | |   |  | ||||   | |  | |  | ||| || |||| ||  |||||   || ||| | |    |  | ||||| ||| | ||||| || || ||||| ||||||||||||||||||||||||||||||||||||||||||||||||
gtacttttagttatttgactttttttcattggattaatta-atcaattaaataatttaaggctctgtgttaattgctttagtgttgtttttt---ttttttttgcgaattattgtagGCGCGTAGAGGTGGTGTGGACGAGCCTTTTGCATGGGAAAGCAGAGAGTTTCTGAGGAAGCTCTGCATAGGGAAG

upper sequence: GRMZM2G136296_T02 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA05G33320.1 (Glycine max), 3'ss of exon 2
---------------------------------------------------------------------------------tggaactatttactgagtatcaattgtagcttcttgacaattgacattcttctcatttctctagttttcatttttcgct-----tgtttattcatggtgcta--tagGCTCGTCGTGGTGGAGTTGATGAGCCGTTTGCATGGGAAAGCAGAGAGTTTCTGAGGAAGCTCTGCATAGGGAAG
                                                                                 |   | | ||| | | ||   ||||      |  ||| |||||   ||  |   | ||||   || || |  || || |     | ||| || |      |   ||||| ||| | ||||| || ||||||||||||||||||||||| |||||||||||  ||||||||||||| ||||||
gtaattttacttgattcatggatattttgttgtaactatgaactgaaattgttttgaaatgcttctgtatcgattttgtgttaataatgttttccgtgttctaatttcgaaat--tgaaaattgctttttgtgctacttctggggtgtttacattacgttaaagctctttgtttaaaaaatttgctagGCGCGTAGAGGTGGTGTAGATGAGCCGTTTGCATGGGAAAGTAGAGAGTTTCTACGGAAGCTCTGCATTGGGAAG

upper sequence: GRMZM2G136296_T02 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA06G17050.4 (Glycine max), 3'ss of exon 2
--------------tggaactatttactgagtatcaattgtagcttcttgacaattgacattctt---ctcatttctctagttttcatttttcgcttgtttattcatggtgctatagGCTCGTCGTGGTGGAGTTGATGAGCCGTTTGCATGGGAAAGCAGAGAGTTTCTGAGGAAGCTCTGCATAGGGAAG
              | ||  | ||| |   | || ||||  | |   |  | |||| | |   ||    | ||| || |||| ||  |||||   || |||    || |||   ||||| ||| | ||||| || || ||||||||||||||||||||||||||||||||||||||||||||||||||||||
gtagttttagttatttgactttttttcattggattaatta-atcaattaaataatttaaagctttgtgttaattgctttagtgttttttttttttttttttgcgaattgtg--gtagGCGCGTAGAGGTGGTGTGGACGAGCCGTTTGCATGGGAAAGCAGAGAGTTTCTGAGGAAGCTCTGCATAGGGAAG

upper sequence: GRMZM2G136296_T02 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA08G00910.1 (Glycine max), 3'ss of exon 2
------------------------------------------------------------------------------tggaactatttactgagtatca-attgtagcttcttgac---aattgacattcttctcatttctctagttttcatttttcgcttgtttattcatggtgct--atagGCTCGTCGTGGTGGAGTTGATGAGCCGTTTGCATGGGAAAGCAGAGAGTTTCTGAGGAAGCTCTGCATAGGGAAG
                                                                              | |   | | |  ||  |  |  ||| ||  |||   |    || ||   |   |   | | ||   || || |  ||    || ||| || |      |  |||||| ||| | ||||| || |||||||||||||| |||||||| |||||||||||  ||||||| ||||| ||||||
gtaattttacttggttcatggaattgaaattgctgtgactgtgaattgaaattcttttgaaattctgttgtaccgattttgtggtttatgatgttttccgtattctaatttcaaaattgaaaatgctttctgtgctactgctgaggtgtttacattaaagttctttgtttaaaaattttgatagGCGCGTAGAGGTGGTGTAGATGAGCCGTTTGCGTGGGAAAGTAGAGAGTTTCTACGGAAGCTTTGCATTGGGAAG

upper sequence: GRMZM2G136296_T02 (Zea mays), 3'ss of exon 2
lower sequence: AT5G07350.2 (Arabidopsis thaliana), 3'ss of exon 2
---------------------------------------------------------------------------------------------tggaactatttactgagtatcaattgtagcttcttga-caattgacattcttctcatttctctagttttcatttt---tcgcttgtttattcatggtgctatagGCTCGTCGTGGTGGAGTTGATGAGCCGTTTGCATGGGAAAGCAGAGAGTTTCTGAGGAAGCTCTGCATAGGGAAG
                                                                                             ||    | ||   |   ||    || |    |||| | |    ||   | || |  ||| |     ||  || |    | | |||||| ||| |     | ||||||||  | || ||  | |||||||| |||||||||||||||| ||| ||| ||||||| || |||||||| |||
gtgagttttaatctcaagttttttttaccagatattagtgtttgaaacaaaagcttgtgatcatcacaaccaatcaaaaaatctttttgatattgatttttttcttttcatactgcttatgaagtcttaaaccgcagattatattattttttgttggaattaaatgtcatgttgtttgttttttcct--ctttttagGCTCGCAGAGGAGGTATAGATGAGCCTTTTGCATGGGAAAGCAAAGAATTTTTGAGGAAACTTTGCATAGGAAAG

upper sequence: GRMZM2G136296_T02 (Zea mays), 3'ss of exon 2
lower sequence: AT5G61780.1 (Arabidopsis thaliana), 3'ss of exon 2
--tggaactatttactgagtatcaattgtagc----ttcttgacaattgacattcttctcatttct--ctagttttcatttttcgc-ttgttta--ttcatggtgctatagGCTCGTCGTGGTGGAGTTGATGAGCCGTTTGCATGGGAAAGCAGAGAGTTTCTGAGGAAGCTCTGCATAGGGAAG
    |   | || |   || ||   || |  |     | || || |   | | | |||   ||  |  ||| || | || |||| | ||||||   ||     || |  |||||||  | || ||  | |||||||| ||||||||||||||||| |||||||| |||||||| ||||| || |||
gtcagctttgttaaaaaagcattccttttcacaactctttttactaacaaaagttttcaatttcatagctacttattatgtttctcattgtttggtttgcctttgtttcagGCTCGCAGAGGAGGTATAGATGAGCCTTTTGCATGGGAAAGCAGGGAGTTTCTAAGGAAGCTTTGCATTGGAAAG

upper sequence: GRMZM2G136296_T02 (Zea mays), 3'ss of exon 2
lower sequence: Vv00s0283g00020.t01 (Vitis vinifera), 3'ss of exon 2
----------tggaactatttactgagtatcaattgtagcttcttgacaattgacattcttctcatttctctagttttcatttttcgcttgtttattcatggtgctatagGCTCGTCGTGGTGGAGTTGATGAGCCGTTTGCATGGGAAAGCAGAGAGTTTCTGAGGAAGCTCTGCATAGGGAAG
            ||||  |||  |  || |||  |||   |  |  |   |    |||   || ||  ||     | || ||||   ||   | |||| |        |||| ||| | ||||||||||||||||||||||||||||| |||||||||| | | |||||||||||||| || |||
ggattttgttaagaacattttgttttgt-tcagctgtga-taataaatggtattgattagacttatgactgggagtctctttttctcctctctcattcct--------agGCCCGTAGGGGTGGAGTTGATGAGCCGTTTGCATGGGACAGCAGAGAGTATTTAAGGAAGCTCTGCATTGGAAAG

upper sequence: GRMZM2G136296_T02 (Zea mays), 3'ss of exon 2
lower sequence: Vv14s0068g00720.t01 (Vitis vinifera), 3'ss of exon 1
--tggaactatttactgagtatcaattg--tagcttcttgacaattgacattcttctcatttctctagttttcatttttcgcttgtttattcatggtgctatagGCTCGTCGTGGTGGAGTTGATGAGCCGTTTGCATGGGAAAGCAGAGAGTTTCTGAGGAAGCTCTGCATAGGGAAG
  ||| | || | |      |    ||   |   ||||  | | |  | | |||| |  | |  |  |   | ||||||   |||  |||  || |  |||||||| ||| | |||||  ||||||| || ||||||||||| || ||||||| | ||||||| ||||||||||| |||
tttggcattactaataccacactttttaaatgaattctctatattccatactcttattctgtaccctgacctgattttt---ttgaatatctattg-actatagGCCCGTAGAGGTGGTATTGATGAACCATTTGCATGGGATAGTAGAGAGTATTTGAGGAAACTCTGCATAGGAAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attcttctcatttctctagttttcatttttcgcttgtttattcatggtgctatagGCTCGTCGTGGTGGAGTTGATGAGCCGTTTGCATGGGAAAGCAGAGAGTTTCTGAGGAAGCTCTGCATAGGGAAG
                tagttttcattttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tggaactatttactgagtatcaattgtagcttcttgacaattgacattcttctcatttctctagttttcatttttcgcttgtttattcatggtgctatagGCTCGTCGTGGTGGAGTTGATGAGCCGTTTGCATGGGAAAGCAGAGAGTTTCTGAGGAAGCTCTGCATAGGGAAG

- - - - tttactg
- - - - - - - - - - - - tgtagct