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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCCTAGCAGCATGAAGGTGAAGGTGGTTGCTCCGCCGGAGAGGAAGTACAGTGTTTGGATTGGTGGTTCCATTCTGGCCTCCCTCAGTACCTTTCAGCAGgttgttaccctctcaaaatctaaatgagacgtttctgcttgctctgcaatctattgtatttgaaatttgacttagtcttgttattgtgttgtag

Basic information

species Zea mays
transcript GRMZM2G407517_T01
intron # 11
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G407517_T01 (Zea mays), 5'ss of exon 11
lower sequence: LOC_Os01g64630.1 (Oryza sativa), 5'ss of exon 4
CCCTAGCAGCATGAAGGTGAAGGTGGTTGCTCCGCCGGAGAGGAAGTACAGTGTTTGGATTGGTGGTTCCATTCTGGCCTCCCTCAGTACCTTTCAGCAGgttgttaccctctcaaaatctaaatgagacgtttctgcttgctctgc-aatctattgtatt-tgaaatttgacttagtcttgtt--attgtgttgtag----
|||| |||| |||||| | ||||| ||||| ||||| |||||||| |||||||| ||||||||||||||||| ||||| || ||||||||||||||||||||    |   ||||||  |  | ||       ||     ||||   | |   ||    | | ||    || |   | | ||  |  ||||| |   ||    
CCCTGGCAGTATGAAGATCAAGGTAGTTGCACCGCCAGAGAGGAAATACAGTGTCTGGATTGGTGGTTCCATCCTGGCTTCTCTCAGTACCTTTCAGCAGgtatccattgtctcaa--tgcatatacttttgtttcatctgcttaacgagattaccaaactatgtgtcttaatgcatttttagtccattgtctgcaagacac

upper sequence: GRMZM2G407517_T01 (Zea mays), 5'ss of exon 11
lower sequence: GLYMA04G39380.1 (Glycine max), 5'ss of exon 4
CCCTAGCAGCATGAAGGTGAAGGTGGTTGCTCCGCCGGAGAGGAAGTACAGTGTTTGGATTGGTGGTTCCATTCTGGCCTCCCTCAGTACCTTTCAGCAGgttgttaccctctcaaaatctaaatgagacgtttctgcttgctctgcaatct-attgtatttgaaatttgacttagtcttgttattgtgttgtag
 ||||||||||||||| | ||||| || ||||| || ||||| ||||| |||||||||||||| || || || || || |||||||| ||||| ||||||||  ||    | |  |  |  |||| |  |  |||  |  |     ||||   |||| | |  |||  ||  || || |||              
TCCTAGCAGCATGAAGATTAAGGTTGTGGCTCCACCAGAGAGAAAGTATAGTGTTTGGATTGGAGGATCAATCCTTGCATCCCTCAGCACCTTCCAGCAGgtgattgttttgtttat-tgcaaattat-ctcttccacacgtgtaccaattagattgaact--aaacatgttttggttttgcag-----------

upper sequence: GRMZM2G407517_T01 (Zea mays), 5'ss of exon 11
lower sequence: GLYMA15G05570.1 (Glycine max), 5'ss of exon 4
CCCTAGCAGCATGAAGGTGAAGGTGGTTGCTCCGCCGGAGAGGAAGTACAGTGTTTGGATTGGTGGTTCCATTCTGGCCTCCCTCAGTACCTTTCAGCAGgttgttacc----------ctctcaaaatctaaatgagacgtttctgcttgctct-------gcaatctatt-gtatttgaaat-------ttgacttagt--cttgttattgtgt-tgtag
 || || ||||||||  | ||||||||||| || || ||||| ||||||||||| |||||||||||||| ||  |||| || || || ||||| || ||||||  |||             ||   | ||| ||     |        ||| |||         ||| |||| || | || ||        |||| |  ||   ||||| |  | | |||||
ACCCAGTAGCATGAAAATCAAGGTGGTTGCACCTCCTGAGAGAAAGTACAGTGTCTGGATTGGTGGTTCTATCTTGGCATCACTTAGCACCTTCCAACAGgtttgtactgatgtttttttcctgctattctcaacatccccccctcatttgttcttacaagtaaaatgtattagtttatggaaggcaggtattgagtgtgtactttgttctcttatatgtag

upper sequence: GRMZM2G407517_T01 (Zea mays), 5'ss of exon 11
lower sequence: GLYMA06G15520.2 (Glycine max), 5'ss of exon 4
CCCTAGCAGCATGAAGGTGAAGGTGGTTGCTCCGCCGGAGAGGAAGTACAGTGTTTGGATTGGTGGTTCCATTCTGGCCTCCCTCAGTACCTTTCAGCAGgttgttaccctctcaaaatctaaatgagacgtttctgcttgctctgcaatctattgtatttgaaatttgacttagtcttgttattgtgttgtag
 ||||||||||||||| | ||||| || ||||| || ||||| ||||| ||||| |||||||| || || || || || |||||||| ||||| ||||||||  ||      |  |   | || |    | ||   || ||  |   | |  |||| ||||||| | |        | |||| | || ||| ||
TCCTAGCAGCATGAAGATTAAGGTTGTGGCTCCACCAGAGAGAAAGTATAGTGTCTGGATTGGAGGATCAATCCTTGCGTCCCTCAGCACCTTCCAGCAGgtgattgtttagtttattacaaattagctctttgacgcatgtgcca-agtagattgaatttgaactctag----aacatgttttggttttgcag

upper sequence: GRMZM2G407517_T01 (Zea mays), 5'ss of exon 11
lower sequence: GLYMA08G15480.1 (Glycine max), 5'ss of exon 4
CCCTAGCAGCATGAAGGTGAAGGTGGTTGCTCCGCCGGAGAGGAAGTACAGTGTTTGGATTGGTGGTTCCATTCTGGCCTCCCTCAGTACCTTTCAGCAGgttgttaccctctcaaaatctaaatgagacgtttctgcttgctctgcaatctattgtatttgaaatttgacttagtcttgttattgtgttgtag
 ||||||||||||||| | ||||| || ||||| || || || || || ||||| |||||||| || || || || || |||||||| ||||| ||||||||  |||   | |||  |  ||  |    ||| | |||    |        |  |  |    |||  ||   | || |||              
TCCTAGCAGCATGAAGATTAAGGTTGTAGCTCCACCAGAAAGAAAATATAGTGTCTGGATTGGAGGATCAATCCTTGCATCCCTCAGCACCTTCCAGCAGgtgattattttatcatgaattagctctttcgtgtgtgccattttcattgaatgctaaa----aaaaatgttgtggttttgcag-----------

upper sequence: GRMZM2G407517_T01 (Zea mays), 5'ss of exon 11
lower sequence: GLYMA08G19420.1 (Glycine max), 5'ss of exon 4
CCCTAGCAGCATGAAGGTGAAGGTGGTTGCTCCGCCGGAGAGGAAGTACAGTGTTTGGATTGGTGGTTCCATTCTGGCCTCCCTCAGTACCTTTCAGCAGgttgttacc-------ctctcaaaatctaaatgagacgtttctgcttgctctgcaatctattgtatttgaaatttgacttagtcttgttattgtgttgtag----------------------------------
 || |||||||||||  | ||||||||||| || || ||||| ||||||||||| ||||||||||| || ||  |||| || || || ||||| || ||||||  |||         |  |     |||      || |  |  ||  | |  |   |  || | | | |  |   | | |    | ||| | | | | |                                   
ACCCAGCAGCATGAAAATCAAGGTGGTTGCACCTCCTGAGAGAAAGTACAGTGTCTGGATTGGTGGCTCTATCTTGGCATCACTTAGCACCTTCCAACAGgtttgtactgatgttttttccccctcctattctcaacatcccccctcccacctcccccctttatgtgt-acttacaagtaaaatgtattagtttatggaaagcattgagtgtttactttgttctcttatatgcag

upper sequence: GRMZM2G407517_T01 (Zea mays), 5'ss of exon 11
lower sequence: AT1G49240.1 (Arabidopsis thaliana), 5'ss of exon 4
CCCTAGCAGCATGAAGGTGAAGGTGGTTGCTCCGCCGGAGAGGAAGTACAGTGTTTGGATTGGTGGTTCCATTCTGGCCTCCCTCAGTACCTTTCAGCAGgttg--ttaccctctcaaaatctaaatga--gacgtttctgcttgctc---tgcaatctattgtatttgaaatttgacttagtcttgttattgtgt---tgtag----
||| |||||||||||| | ||||| || || || || ||||||||||||||||| |||||||||||||| || || || |||||||| || || ||||||||    ||   || |||   ||||| |    |    || || ||| |    || |  | | |    |     |||   ||     |||   |||||   ||||     
CCCGAGCAGCATGAAGATTAAGGTCGTGGCACCACCCGAGAGGAAGTACAGTGTCTGGATTGGTGGTTCTATCCTTGCTTCCCTCAGCACTTTCCAGCAGgtaaaattggactgtcatt-tctaagtttttgcttcttgtggttgattaaatgtagacaactcctctaatggtttacattttctgtgtgtgtgtgtgtgtgtaatcag

upper sequence: GRMZM2G407517_T01 (Zea mays), 5'ss of exon 11
lower sequence: AT5G09810.1 (Arabidopsis thaliana), 5'ss of exon 4
CCCTAGCAGCATGAAGGTGAAGGTGGTTGCTCCGCCGGAGAGGAAGTACAGTGTTTGGATTGGTGGTTCCATTCTGGCCTCCCTCAGTACCTTTCAGCAGgttgttaccctctcaaaatctaaatgagacgtttctgcttgctctgcaatctatt-gtatttgaaatttgacttagtcttgttattgtgttgtag----
 ||||||||||||||| | ||||||||||| ||||| ||||| || |||||||| ||||| || || || || || || |||||||| ||||| || |||||    | ||         ||   | | || |||| |||   | |   |   ||  ||      | |   | || || |||||  |||||   |     
ACCTAGCAGCATGAAGATCAAGGTGGTTGCACCGCCAGAGAGAAAATACAGTGTCTGGATCGGAGGATCAATCCTTGCATCCCTCAGCACCTTCCAACAGgtaaaaatcccaattccgcctctttaaaac-tttcagctccatttatgaaacatgagtgaaaatactgaaattttgttttgtttgtgtgtgtgaatcag

upper sequence: GRMZM2G407517_T01 (Zea mays), 5'ss of exon 11
lower sequence: AT3G18780.2 (Arabidopsis thaliana), 5'ss of exon 3
CCCTAGCAGCATGAAGGTGAAGGTGGTTGCTCCGCCGGAGAGGAAGTACAGTGTTTGGATTGGTGGTTCCATTCTGGCCTCCCTCAGTACCTTTCAGCAGgttgttaccctctcaaaatctaaatgagacgtttctgcttgctctgcaatctattgtatttgaaatttgacttagtcttgttattgt--gttgtag
 || |||||||||||| | ||||| ||||| || || || |||||||||||||| ||||| |||||||||||||| || |||||||| || || ||||||||    |     ||| | | |   |   |   |  | | |     ||||   |||| | |  ||   ||| ||| |  |||   |||  |||  ||
ACCAAGCAGCATGAAGATTAAGGTCGTTGCACCACCTGAAAGGAAGTACAGTGTCTGGATCGGTGGTTCCATTCTTGCTTCCCTCAGCACATTCCAGCAGgtaaaaattga-tcagattttgtttcgaattctcttacat-----gcaa---attgaaatcaaaggctga-ttatttatgtatatgttggttacag

upper sequence: GRMZM2G407517_T01 (Zea mays), 5'ss of exon 11
lower sequence: Vv12s0178g00200.t01 (Vitis vinifera), 5'ss of exon 3
CCCTAGCAGCATGAAGGTGAAGGTGGTTGCTCCGCCGGAGAGGAAGTACAGTGTTTGGATTGGTGGTTCCATTCTGGCCTCCCTCAGTACCTTTCAGCAGgttg----ttaccctctcaaaatcta-aatgagacgtttctgcttgctctgcaatctattgtatttgaaatttgact-tagtcttgttattgtgttgtag
 || |||||||||||| | |||||||| || || || ||||| ||||||||||| |||||||| || || ||  | || || ||||| || || || |||||      ||    | |      | |  ||| |       || | |    | | | | |  |  ||    |  || | |  |    ||      ||| ||
TCCCAGCAGCATGAAGATCAAGGTGGTGGCACCTCCCGAGAGAAAGTACAGTGTCTGGATTGGAGGATCAATATTAGCATCTCTCAGCACATTCCAACAGgtaaaaaattgttttatttgtgcccatgatgtgggtggaatgatagtcaaggagtttgtgattgttagtctcagagtctcattccatttaaaaattgcag

upper sequence: GRMZM2G407517_T01 (Zea mays), 5'ss of exon 11
lower sequence: Vv04s0044g00580.t01 (Vitis vinifera), 5'ss of exon 5
CCCTAGCAGCATGAAGGTGAAGGTGGTTGCTCCGCCGGAGAGGAAGTACAGTGTTTGGATTGGTGGTTCCATTCTGGCCTCCCTCAGTACCTTTCAGCAGgttgttaccctctcaaaatctaaatgagacgtttctgcttgctctgcaatctattgtatttgaaatttgacttagtcttgttattgtgttgtag
 || |||||||||||| | |||||||| || || || ||||| ||||||||||| |||||||| || || ||||| || |||||||| ||||| ||||||||  ||  | | |     | |   |  |   |||     || | ||     | |  |   ||| | |    |   | |||||  |         
TCCCAGCAGCATGAAGATCAAGGTGGTGGCACCACCTGAGAGAAAGTACAGTGTCTGGATTGGAGGATCAATTCTTGCATCCCTCAGCACCTTCCAGCAGgtgattttcattt-----tttgtttttggtttttacaaatggtttgattcttttattgcatgatactaacatgctttttgttggtacag-----

upper sequence: GRMZM2G407517_T01 (Zea mays), 5'ss of exon 11
lower sequence: PP1S337_26V6.1 (Physcomitrella patens), 5'ss of exon 4
-CCCTAGCAGCATGAAGGTGAAGGTGGTTGCTCCGCCGGAGAGGAAGTACAGTGTTTGGATTGGTGGTTCCATTCTGGCCTCCCTCAGTACCTTTCAGCAGgttgttaccctctcaaaatctaaatgagacgtttc-tgcttgctctgcaatctattgta---tttgaaatttgacttagtcttgttattgtgttgtag---------
 || | | ||||||||| | |||||||| || ||||| ||||||||||||||||| ||||| || || || ||| |||| || ||||||||||| || |||||  ||   || | | | |  |  ||    ||| | ||| |  ||||   | |||  ||   |||   |||| |  |   | | ||   ||||||  |         
ACCATCG-AGCATGAAGATAAAGGTGGTGGCGCCGCCAGAGAGGAAGTACAGTGTATGGATAGGAGGGTCTATTTTGGCATCTCTCAGTACCTTCCAACAGgtattt---cttttatattacagttgcttagttgcatgcataatctgatttttatattacttttttgcattttatctg--cattttgacgtgttggggtttttgcag

upper sequence: GRMZM2G407517_T01 (Zea mays), 5'ss of exon 11
lower sequence: PP1S337_21V6.2 (Physcomitrella patens), 5'ss of exon 5
-CCCTAGCAGCATGAAGGTGAAGGTGGTTGCTCCGCCGGAGAGGAAGTACAGTGTTTGGATTGGTGGTTCCATTCTGGCCTCCCTCAGTACCTTTCAGCAGgttgt-taccctctcaaaatctaaatgagacgtttctgcttgctctgcaatctattgtatttgaaatttgacttagtcttgttatt--gtgttgtag---------------------------------------
 || | | ||||||||| | |||||||| || ||||| ||||||||||||||||| ||||| || || || ||| |||| || ||||||||||| || |||||  | ||           ||| | |   |  |      ||  | |      |  ||| ||||    || |  |  ||  |||  |    | ||||                                        
ACCATCG-AGCATGAAGATAAAGGTGGTGGCGCCGCCAGAGAGGAAGTACAGTGTATGGATAGGAGGGTCTATTTTGGCATCTCTCAGTACCTTCCAACAGgtaatgtatttgactcgtgtctgagttgcatttcgtgtttttttttatgtcttcatgtctttgtttcttcaaatgctcgcgtttgtcgaggctgtaatctttctggaatttaatccgtttacttgttgtggtgcag

upper sequence: GRMZM2G407517_T01 (Zea mays), 5'ss of exon 11
lower sequence: PP1S372_48V6.1 (Physcomitrella patens), 5'ss of exon 3
CCCTAGCAGCATGAAGGTGAAGGTGGTTGCTCCGCCGGAGAGGAAGTACAGTGTTTGGATTGGTGGTTCCATTCTGGCCTCCCTCAGTACCTTTCAGCAGgtt------gttaccctctcaaaatctaaatgagacgtttctgct--tgctctgcaatctatt--gtatttgaaatttgacttagtcttgttattgtgttgtag------------------------------------
 ||    ||||||||| | |||||||| || || ||||||||||||||||| || ||||| || || |||||  |||| |||||||| ||||| ||||||||       |||  | |   |   ||||  |  |||||      |  ||  || |  |  | |  | | | | ||||||| |  || | |  |   || |  |                                     
GCCGTCAAGCATGAAGATCAAGGTGGTGGCGCCTCCGGAGAGGAAGTACAGCGTGTGGATCGGAGGCTCCATCTTGGCATCCCTCAGCACCTTCCAGCAGgtaaactgagtttgcatgatattttctacgttggacgtggtaaatattgaacttcttttcagttagcagtcggaatttgagtatgtttcgagaggttggttaattcggtgtttgcacatattgttctttctgtggtgcag

upper sequence: GRMZM2G407517_T01 (Zea mays), 5'ss of exon 11
lower sequence: EFJ17401 (Selaginella moellendorffii), 5'ss of exon 3
CCCTAGCAGCATGAAGGTGAAGGTGGTTGCTCCGCCGGAGAGGAAGTACAGTGTTTGGATTGGTGGTTCCATTCTGGCCTCCCTCAGTACCTTTCAGCAGgttgttaccctctcaaaatctaaatgagacgtttctgcttgctctgcaatctattgtatttgaaatttgacttagtcttgttattgtgttgtag
 || |||||||||||| | |||||||||||||| ||||||||||||||||| || |||||||| ||||| || ||||| || ||||| ||||| || |||||         | ||| ||     ||   ||||| | |||  || ||  | | || | |||    |||  |  ||                   
TCCCAGCAGCATGAAGATCAAGGTGGTTGCTCCTCCGGAGAGGAAGTACAGCGTCTGGATTGGAGGTTCTATCCTGGCTTCGCTCAGCACCTTCCAACAGgt-------accacaacattcttttgct-cgttttt-ctta-tcagccttgt-ttttctttttcgtttctcgcag-------------------

upper sequence: GRMZM2G407517_T01 (Zea mays), 5'ss of exon 11
lower sequence: EFJ35077 (Selaginella moellendorffii), 5'ss of exon 3
CCCTAGCAGCATGAAGGTGAAGGTGGTTGCTCCGCCGGAGAGGAAGTACAGTGTTTGGATTGGTGGTTCCATTCTGGCCTCCCTCAGTACCTTTCAGCAGgttgttaccctctcaaaatctaaatgagacgtttctgcttgctctgcaatctattgtatttgaaatttgacttagtcttgttattgtgttgtag
 || |||||||||||| | |||||||||||||| ||||||||||||||||| || ||||| || ||||| || ||||| || ||||| ||||| || |||||    |||              |  | |   || |||| | | | |    |||     |||         ||  |||| || || | | | ||
TCCCAGCAGCATGAAGATCAAGGTGGTTGCTCCTCCGGAGAGGAAGTACAGCGTCTGGATCGGAGGTTCTATCCTGGCTTCGCTCAGCACCTTCCAACAGgt----acc--------------acaacattcttttgctcgtttttc---ttatcagccttg---------tttttctttttcttttttcgcag

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CCCTAGCAGCATGAAGGTGAAGGTGGTTGCTCCGCCGGAGAGGAAGTACAGTGTTTGGATTGGTGGTTCCATTCTGGCCTCCCTCAGTACCTTTCAGCAGgttgttaccctctcaaaatctaaatgagacgtttctgcttgctctgcaatctattgtatttgaaatttgacttagtcttgttattgtgttgtag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG