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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtataaggcagtattctttacatctatggttctttctgattatccactaaattacatttcttctaaagtgattaaatacttagctgttataaacatgcattcaggtgtaccatccaaatattgatttggaaGGCAATGTCTGTCTGAACATTCTGCGTGAAGATTGGAAGCCTGTTCTCAACATCAACACCGTTATTTATGGCCTGAATCTTCTTTTTACG

Basic information

species Zea mays
transcript GRMZM2G115939_T02
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G115939_T02 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os10g11260.2 (Oryza sativa), 3'ss of exon 4
-----gtataaggc---agtattctttacatctatg-gttctttctgattatccactaaattacatttcttctaaagtgattaaatacttagctgttataaacatgcattcaggtgtaccatccaaatattgatttggaaGGCAATGTCTGTCTGAACATTCTGCGTGAAGATTGGAAGCCTGTTCTCAACATCAACACCGTTATTTATGGCCTGAATCTTCTTTTTACG
     ||  ||| |    ||||    |    || |   | || | |  ||  ||| | ||| |  || | ||| ||   |||       ||    |||||| | ||||||||||| |||||||||||||||||||||||||| ||||| || ||||||||| ||||||||||||||||||||||||||||||||||||| |||||||||||||                 
gtgaagtgcaagaccaaggtataagatggggctttctatgctatatattttcccagtgaat-atgttgcctcttaaccaatt-----tctatgcattataa-cttgcattcagGTATACCATCCAAATATTGATTTGGAAGGAAATGTATGCCTGAACATTTTGCGTGAAGATTGGAAGCCTGTTCTCAACATCAACACTGTTATTTATGGCC-----------------

upper sequence: GRMZM2G115939_T02 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os10g11260.3 (Oryza sativa), 3'ss of exon 4
gtataaggcagtattctttacatctatggttctttctgattatccactaaattacatttcttctaaagtgattaaatacttagctgttataaacatgcattcaggtgtaccatccaaatattgatttggaaGGCAATGTCTGTCTGAACATTCTGCGTGAAGATTGGAAGCCTGTTCTCAACATCAACACCGTTATTTATGGCCTGAATCTTCTTTTTACG
|||||||   |   | | ||   ||||   | || |   |          | ||  || | ||| ||   |||       ||    |||||| | ||||||||||| |||||||||||||||||||||||||| ||||| || ||||||||| ||||||||||||||||||||||||||||||||||||| |||||||||||||                 
gtataagatggggctttctatg-ctatatattttcccagt---------gaatatgttgcctcttaaccaatt-----tctatgcattataa-cttgcattcagGTATACCATCCAAATATTGATTTGGAAGGAAATGTATGCCTGAACATTTTGCGTGAAGATTGGAAGCCTGTTCTCAACATCAACACTGTTATTTATGGCC-----------------

upper sequence: GRMZM2G115939_T02 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA11G06830.1 (Glycine max), 3'ss of exon 4
-------gtataaggcagtattctttac----atctatggttct-ttctgattatccactaaattacatttcttctaaagtgattaaatacttagctgttataaa----catgcattcaggtgtaccatccaaatattgatttggaaGGCAATGTCTGTCTGAACATTCTGCGTGAAGATTGGAAGCCTGTTCTCAACATCAACACCGTTATTTATGGCCTGAATCTTCTTTTTACG
       |     |    | || |||||    ||   || ||   || || | |     |   || | | |  | |    |  | | | | |||  |||   |      | |  ||  |||| || |||||||||||||| |||||||| ||||| ||||| |||||  | || ||||||||||| ||||| || || || ||||| || || ||||||                  
gtaggatggtcttgattatcttttttactctaattcgtgctttagttttggtaagtgtgttgttttcttgttctgtttcatcttcataaatttatttgtagcattatctcgtatatgaagGTCTATCATCCAAATATTGACTTGGAAGGAAATGTTTGTCTCAACATCTTACGAGAAGATTGGAAACCTGTCCTTAATATAAACACTGTCATCTATGGCT-----------------

upper sequence: GRMZM2G115939_T02 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA01G38470.1 (Glycine max), 3'ss of exon 4
--------gtataaggcagtattctttac----atctatggttct-ttctgatta-tccactaaattacatttcttctaaagtgattaaatacttagctgttataaa----catgcattcaggtgtaccatccaaatattgatttggaaGGCAATGTCTGTCTGAACATTCTGCGTGAAGATTGGAAGCCTGTTCTCAACATCAACACCGTTATTTATGGCCTGAATCTTCTTTTTACG
        || |     |   || ||| |    ||   || ||   || || | | |    |   ||    ||||  |  ||      ||   |||  |||   |      | |  || ||||| || |||||||||||||| |||||||| ||||| ||||| |||||  | || ||||||||||| ||||| || || || ||||| || || ||||||                  
gtaggatggtcttgattatcttttttttctctaattcgtgctttagttttggtaagtgtgttgttttcttgttctgtttcagcatcataaattttatttgtagcattatctcctatatgcagGTCTATCATCCAAATATTGACTTGGAAGGAAATGTTTGTCTCAACATCTTACGAGAAGATTGGAAACCTGTCCTTAATATAAACACTGTCATCTATGGCT-----------------

upper sequence: GRMZM2G115939_T02 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA02G06580.1 (Glycine max), 3'ss of exon 6
-----------------------------------------------------gtataaggcagtattctttacatctatggttctttctgattatccactaaattacatttcttctaaagtgattaaatacttagctgttataaacatgcattcaggtgtaccatccaaatattgatttggaaGGCAATGTCTGTCTGAACATTCTGCGTGAAGATTGGAAGCCTGTTCTCAACATCAACACCGTTATTTATGGCCTGAATCTTCTTTTTACG
                                                      | ||   || ||    ||  |||| || || | ||  |||      |        | | ||  ||||| ||||| || ||   ||| ||   |||  ||  |||| |||||||||||||| || |||||||| ||||| || || ||||| || || ||||||||||| ||||| ||||| || ||| |  | || || |||                  
gtaggaactaggagatcttggttatctttggtattattaactcattcttttttatgtacatca-tacgtgtttaatct-tgcttgtgtcatatttgtggtttttccttgtctgtttcaaagtcattaattaatt---tgtcatgt-catatatgtagGTCTACCATCCAAATATAGACTTGGAAGGAAATGTTTGCCTTAACATCCTACGAGAAGATTGGAAACCTGTCCTCAATATAAACTCTATCATCTACGGCT-----------------

upper sequence: GRMZM2G115939_T02 (Zea mays), 3'ss of exon 5
lower sequence: AT2G18600.1 (Arabidopsis thaliana), 3'ss of exon 4
gtataaggcagtattctttacatctatggttctttctgattatccactaaattacatttcttctaaagtgattaaatacttagctgttataaacatgcatt-caggtgtaccatccaaatattgatttggaaGGCAATGTCTGTCTGAACATTCTGCGTGAAGATTGGAAGCCTGTTCTCAACATCAACACCGTTATTTATGGCCTGAATCTTCTTTTTACG
                 |||    |    || || || | | ||       ||  || |  ||| |  || ||| | |    |||     |        ||  ||||||| ||||| ||||| ||| | ||||| || ||||||||||||||  |||||||||| ||||| || ||||||||||| ||||| ||||| || || |                 
----------------gttaggctt----tttttcctcagtctctgaagcgttttatgttgtctgatatgtttatacagaatgctaaagaatgtcaatgttgtagGTGTATCATCCGAATATCGATCTAGAAGGAAACGTCTGTCTGAACATCTTGCGTGAAGACTGGAAACCGGTTCTCAACATAAACACAGTTATCTACGGTC-----------------

upper sequence: GRMZM2G115939_T02 (Zea mays), 3'ss of exon 5
lower sequence: AT4G36800.1 (Arabidopsis thaliana), 3'ss of exon 4
gtataaggcagtattctttacatctatggttctttctgattatccactaaattacatttcttctaaagtgattaaatacttagctgttataaacatgcattcaggtgtaccatccaaatattgatttggaaGGCAATGTCTGTCTGAACATTCTGCGTGAAGATTGGAAGCCTGTTCTCAACATCAACACCGTTATTTATGGCCTGAATCTTCTTTTTACG
   || | |  |  || ||  |  |    |   |  |    | |  |||  | | |  || | |    ||   |||  ||| | || | |         || |||| || ||||| ||||| ||||||||||| || || || ||||||||  |||||||||||||||| |||||||| ||||| ||||| ||||| || || |                 
--gtaggcctctcctccttttacatgccttatatagtttacagcttctacttca-aaatcgtttgtgttgtagaaactctttgttggtttt----cttgtttagGTTTATCATCCCAATATCGATTTGGAAGGAAACGTTTGCCTGAACATCTTGCGTGAAGATTGGAAACCTGTTCTTAACATTAACACAGTTATCTACGGAC-----------------

upper sequence: GRMZM2G115939_T02 (Zea mays), 3'ss of exon 5
lower sequence: Vv18s0001g12010.t01 (Vitis vinifera), 3'ss of exon 3
--gtataaggcagtattctttacatctatggttctttctgattatccactaaattacatttcttctaaagtgattaaatacttagctgttataaacatgcatt-----caggtgtaccatccaaatattgatttggaaGGCAATGTCTGTCTGAACATTCTGCGTGAAGATTGGAAGCCTGTTCTCAACATCAACACCGTTATTTATGGCCTGAATCTTCTTTTTACG
  |   ||  |    |  |  |  | | |   | ||  |  |  |  ||||||||  | |  |  | | || ||     |  ||  || ||  |   ||   |     ||||| |||||||| || ||||| |||| ||| ||||||||||| |||||||| || || || ||||| ||||| || ||||| |||||  | || ||||| |                 
gtgggcaaaccccagtagtccatttttgttaatgttcattctcctttactaaattgtactattaatcatgttatcctgcaagtaattgctaacattgtgtcctacctgcagGTCTACCATCCTAACATTGACTTGGCAGGAAATGTCTGTCTTAACATTCTTCGGGAGGACTGGAACCCTGTCCTAAACATAAACACTATCATCTATGGAC-----------------

upper sequence: GRMZM2G115939_T02 (Zea mays), 3'ss of exon 5
lower sequence: Vv04s0023g01280.t01 (Vitis vinifera), 3'ss of exon 3
---------gtataaggc--agtattctttacatcta----tggttctttctgattatccactaaattacatttct-------tctaaagtgat---taa--atacttagctgttataaac-atgca---ttcaggtgtaccatccaaatattgatttggaaGGCAATGTCTGTCTGAACATTCTGCGTGAAGATTGGAAGCCTGTTCTCAACATCAACACCGTTATTTATGGCCTGAATCTTCTTTTTACG
         | | ||     | | |  ||| | |||     || |||  | | || |    ||  ||   |||| |       | ||  ||| |   |||   |  | |  | | |||  | || ||   |  |||| |||||||| || ||||| |||||||| ||||| || || |||||| | || ||||||||||| ||||| || || || || ||  ||||||||||                   
gtggagaaagcacaatctttaatttcttttgcttctggctctgtttcccttttatcagtttcttgatagtatttttgtccatatatatggtgttgtataatggtgttaaattctcatagtccatccaacttgtagGTCTACCATCCCAACATTGACTTGGAAGGAAATGTTTGCCTCAACATTTTACGAGAAGATTGGAAACCTGTCCTTAATATAAATACGATTATTTATGGAT-----------------

upper sequence: GRMZM2G115939_T02 (Zea mays), 3'ss of exon 5
lower sequence: PP1S61_126V6.1 (Physcomitrella patens), 3'ss of exon 4
--gtataaggcagtattctttacatctatggttctttctgattatccactaaattacatttcttctaaagtgattaaatacttagctgttataaacatgcattcaggtgtaccatccaaatattgatttggaaGGCAATGTCTGTCTGAACATTCTGCGTGAAGATTGGAAGCCTGTTCTCAACATCAACACCGTTATTTATGGCCTGAATCTTCTTTTTACG
  ||| |   |   | |   || ||  ||| || |      | ||| |   |||   |    | || ||||  |||| |||||  ||  || ||   ||  |  |||| || ||||||||||| ||| ||||||||||||| |||||||| ||||| ||||| |||||||||||||| || |   | ||| |  | || ||||| |                 
gagtagacaccgacactgagtagattcatgattttgaaacgtcatcaatctaatgtaacgattgctcaagtc-ttaactacttgact--tacaa---tgtgtgtagGTTTATCATCCAAATATAGATCTGGAAGGCAATGTGTGTCTGAATATTCTTCGTGAGGATTGGAAGCCTGTGCTGAGTGTAAACTCTATCATATATGGTC-----------------


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tacttagctgttataaacatgcattcaggtgtaccatccaaatattgatttggaaGGCAATGTCTGTCTGAACATTCTGCGTGAAGATTGGAAGCCTGTTCTCAACATCAACACCGTTATTTATGGCCTGAATCTTCTTTTTACG
                                          tattgat  putative branch site (score: 3)
                                       aaatattgattt  TA-rich tract