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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTGTTAGGAGTTGTTATGATGAGGGTAAGCGTGTAGCTGAGACGTTGATGTTTGACTATCACAAGCAGCATGGCATTGgtaacacttcatctttcacttaaacttcaatattagtagctcatagtcctctttgttatgtgataactctgggcttatgattttttttcttaacagtgtttatcatctatgtctgtag

Basic information

species Zea mays
transcript GRMZM2G300412_T01
intron # 14
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G300412_T01 (Zea mays), 5'ss of exon 14
lower sequence: LOC_Os03g16980.5 (Oryza sativa), 5'ss of exon 8
GTGTTAGGAGTTGTTATGATGAGGGTAAGCGTGTAGCTGAGACGTTGATGTTTGACTATCACAAGCAGCATGGCATTGgtaacacttcatctttcacttaaacttcaatattagtagctcatagtcctctttgttatgtgataactctgggcttatgattttttttcttaacagtgtttatcatctatgtctgtag
| || |||||||| ||||| |||||||||||||| || || ||  |||||||||||||||||| |||||||||||||||||| | ||                           ||| |||||  ||| |||||  ||||||   |   || || |  || |  ||  |||   | |||   |||||| |||||||
GAGTCAGGAGTTGCTATGACGAGGGTAAGCGTGTCGCAGAAACACTGATGTTTGACTATCACAGGCAGCATGGCATTGgtaatatttt--------------------------tagttcata--cctttttgtcttgtgatg--tactggattgtagttctccttaataagtat-tttccaatctatctctgtag

upper sequence: GRMZM2G300412_T01 (Zea mays), 5'ss of exon 14
lower sequence: GLYMA12G06990.1 (Glycine max), 5'ss of exon 8
GTGTTAGGAGTTGTTATGATGAGGGTAAGCGTGTAGCTGAGACGTTGATGTTTGACTATCACAAGCAGCATGGCATTGgtaacacttcatctttcacttaaacttcaatattagtagctcatagtcctctttgttatgtgataactctgggcttatgattttttttcttaacagtgtttatcatctatgtctgtag----
| ||| | ||||| ||||||||||| || ||||| ||||| || ||||||||||| ||||| | ||||||||| || |||||   ||| ||| |   ||   |||||    |||| |    |  | ||| |||||||     |    | |   | |   | | |   ||||| | ||||   || | | | |  |     
GAGTTCGTAGTTGCTATGATGAGGGGAAACGTGTGGCTGAAACTTTGATGTTTGATTATCATAGGCAGCATGGAATAGgtaat--ttcttctcttcttttttcttca----tagttgtctgt--tgctccttgttata----actggtagaaatttttctctgtaatttaactgagttttctatatttctttcaacatag

upper sequence: GRMZM2G300412_T01 (Zea mays), 5'ss of exon 14
lower sequence: GLYMA12G06980.3 (Glycine max), 5'ss of exon 8
GTGTTAGGAGTTGTTATGATGAGGGTAAGCGTGTAGCTGAGACGTTGATGTTTGACTATCACAAGCAGCATGGCATTGgtaacacttcatctttcactt------aaacttcaatattagtagctca--tagtcct--ctttgttatgt-gataactctgggcttatgattttttttcttaacagtgtttatcatctatgtctgtag
| ||| ||||||||||||||||||| |||||||| || || || ||||||||||| ||||| | |||||| || || |||||  | | ||||||           | |  ||| | ||    || ||   |||      ||||   ||  | |||||        || | |   | |  |     | || ||  | | | |||  ||
GAGTTCGGAGTTGTTATGATGAGGGCAAGCGTGTTGCAGAAACTTTGATGTTTGATTATCATAGGCAGCACGGAATCGgtaattccttatcttttctccttggcaacatctcattgttgagggcacaaacagtagaagttttgcactgccgttaactaataagcaataactcaatgtgatgcttattttcattttttttctct-cag

upper sequence: GRMZM2G300412_T01 (Zea mays), 5'ss of exon 14
lower sequence: GLYMA11G15010.1 (Glycine max), 5'ss of exon 8
GTGTTAGGAGTTGTTATGATGAGGGTAAGCGTGTAGCTGAGACGTTGATGTTTGACTATCACAAGCAGCATGGCATTGgtaacacttcatctttcacttaaacttcaata-ttagtagctcatagtcctctttgttatgtgataactctgggcttatgattttttttcttaaca-gtgtttatcatctatgtctgtag--------------------
| ||| ||||||||||||||||||| |||||||| || || || ||||||||||| ||||| | ||||||||| || |||||  | | ||||||   ||   |||   |  || | | |   |  |    |  |       | |   |  |  ||    |  | ||   ||| | |   | |     | ||    |                      
GAGTTCGGAGTTGTTATGATGAGGGCAAGCGTGTTGCAGAAACTTTGATGTTTGATTATCATAGGCAGCATGGAATCGgtaattccttatctttattttttccttttctccttggcaacatctcattgattgagggcacaaacagtacacgttttgcactgctgttaactaataagcaataactcaatgtgatgcttattttcatatttttctctcag

upper sequence: GRMZM2G300412_T01 (Zea mays), 5'ss of exon 14
lower sequence: GLYMA15G04500.2 (Glycine max), 5'ss of exon 9
GTGTTAGGAGTTGTTATGATGAGGGTAAGCGTGTAGCTGAGACGTTGATGTTTGACTATCACAAGCAGCATGGCATTGgtaacacttcatctttca---cttaaacttcaatattagtagctcatagtcctctttgttatgtgataactctgggcttatgattttttttcttaacagtgtttatcatctatgtctgtag--
| ||| | ||||| ||||||||||| || || || |||||||| ||||||||||| || || | ||||||||| ||||||||    |  |||||     |||| | ||   | |   |   |   || | | |    || | |||   |||    || |  |||   | ||| |  ||||||||      | ||   |   
GAGTTCGTAGTTGCTATGATGAGGGGAAACGGGTGGCTGAGACATTGATGTTTGATTACCATAGGCAGCATGGAATTGgtaatttattgtctttttttccttataatttcttctcgttttgtttaaggcatatccaata-gagatttttct----ttgttttttaactccttga-ggtgtttatatatcctttcaacatag

upper sequence: GRMZM2G300412_T01 (Zea mays), 5'ss of exon 14
lower sequence: GLYMA13G40960.1 (Glycine max), 5'ss of exon 9
GTGTTAGGAGTTGTTATGATGAGGGTAAGCGTGTAGCTGAGACGTTGATGTTTGACTATCACAAGCAGCATGGCATTGgtaacacttcatctttcacttaaacttcaatattagtagctcatagtcctctttgttatgtgataactctgggcttatgatttttt-ttcttaacagtgtttatcatctatgtctgtag--
| ||| | ||||| ||||||||||| || || || || ||||| ||||||||||| || || | ||||||||| ||||||||    |  ||||    |    |||   || |     |||||  |  |      |||    ||    |     | || || ||   || |    ||||||||      | ||   |   
GAGTTCGTAGTTGCTATGATGAGGGGAAACGGGTGGCCGAGACATTGATGTTTGATTACCATAGGCAGCATGGGATTGgtaatttcttgtcttcttttc---ctt--gtaatttcttctcattttgtttacacatatccagtagagatttatctttgtttcttaactccttgtggtgtttatgtctcctttcaacatag

upper sequence: GRMZM2G300412_T01 (Zea mays), 5'ss of exon 14
lower sequence: GLYMA11G15020.1 (Glycine max), 5'ss of exon 8
GTGTTAGGAGTTGTTATGATGAGGGTAAGCGTGTAGCTGAGACGTTGATGTTTGACTATCACAAGCAGCATGGCATTGgtaacacttcatctt--tcacttaaacttcaatattagtagct-----------catagtcctctttgttatgtgataactctgggcttatgattttttttc-----ttaacagtgtttatcatctatgtctgtag----
| ||| | ||||| ||||||||||| || ||||| ||||| || ||||||||||| ||||| | ||||||||| || |||||    |  ||||  |  ||| |   |   | ||  | | |           ||||||  |||||  |   |  | |     ||   |  ||||| |||      ||||| | |||| | || | | | |  |     
GAGTTCGTAGTTGCTATGATGAGGGGAAACGTGTGGCTGAAACTTTGATGTTTGATTATCATAGGCAGCATGGAATAGgtaatttctgctcttcttttcttcatagttgttgttgattgttgttgttttcttcatagttgtcttttgttccttgttatagctggtagaaaattttcttttgtaagttaactgagttttttatatttctttcaacatag

upper sequence: GRMZM2G300412_T01 (Zea mays), 5'ss of exon 14
lower sequence: AT5G59290.2 (Arabidopsis thaliana), 5'ss of exon 7
GTGTTAGGAGTTGTTATGATGAGGGTAAGCGTGTAGCTGAGACGTTGATGTTTGACTATCACAAGCAGCATGGCATTGgtaacacttcatctttcacttaaacttcaatattagtagctcatagtcctctttgttatgtgataactctgggcttatgattttttttcttaacagtgtttatcatctatgtctgtag
| ||| ||||||| ||||| || || ||||| ||||| || || |||||||||||||| ||||  || |||||||||||| |       | ||  ||||   |   ||  | | |   |||   |  ||||| |   |||||  || |  | || | |||    |  ||  || |  |                  
GGGTTCGGAGTTGCTATGACGAAGGCAAGCGGGTAGCCGAAACCTTGATGTTTGACTACCACAGACAACATGGCATTGgtca------gttttctactt---ccctaaactcactgcatcacttttttctttatccagtgattcctttaagattctcattggcctgtttgtcatttgtag----------------

upper sequence: GRMZM2G300412_T01 (Zea mays), 5'ss of exon 14
lower sequence: AT3G46440.1 (Arabidopsis thaliana), 5'ss of exon 7
GTGTTAGGAGTTGTTATGATGAGGGTAAGCGTGTAGCTGAGACGTTGATGTTTGACTATCACAAGCAGCATGGCATTGgtaacacttcatctttcacttaaacttcaatattagtagctcatagtcctctttgttatgtg-ataactctgggcttatgatttttt-ttcttaacagtgtttatcatctatgtctgtag
|||||||||| ||||||||||| || |||||||| |||||||| |||||||||||||| |||| ||| ||||| ||||||||   | ||| ||   || |  ||              |||   | |||  ||| || || || |   |   || ||  |  ||| ||| | | | ||||| |  |   | | |||||
GTGTTAGGAGCTGTTATGATGAAGGCAAGCGTGTTGCTGAGACCTTGATGTTTGACTACCACAGGCAACATGGAATTGgtaa-gttgcatttt---ctcaggctctcgc--------ttcaactttctccctgtaatttgcatcaacatattctcattgtcctttattccttaaattgtttttgtttcttctttgtag

upper sequence: GRMZM2G300412_T01 (Zea mays), 5'ss of exon 14
lower sequence: Vv06s0004g04390.t01 (Vitis vinifera), 5'ss of exon 8
GTGTTAGGAGTTGTTATGATGAGGGTAAGCGTGTAGCTGAGACGTTGATGTTTGACTATCACAAGCAGCATGGCATTGgtaacacttcatctttcacttaaacttcaatattagtagctcatagtcctctttgttatgtgataactctgggcttatgattttttttcttaacagtgtttatcatctatgtctgtag
||||  |||| || ||||||||||| |||||||| |||||||| ||||||||||| ||||| | ||| ||||| || ||||||  ||  | |||   ||    || |||  |        | |  | ||  ||  || |||    |       ||||   || |||||| | | | |  |                
GTGTGCGGAGCTGCTATGATGAGGGGAAGCGTGTGGCTGAGACTTTGATGTTTGATTATCATAGGCAACATGGGATAGgtaac-ttttgtgtttttttt----tttaatcctga------acaaacttcaatga-atatgaagttttaatatgtatg---ttgtttctttatattttggacag-------------

upper sequence: GRMZM2G300412_T01 (Zea mays), 5'ss of exon 14
lower sequence: Vv13s0019g00840.t01 (Vitis vinifera), 5'ss of exon 8
GTGTTAGGAGTTGTTATGATGAGGGTAAGCGTGTAGCTGAGACGTTGATGTTTGACTATCACAAGCAGCATGGCATTGgtaaca-----cttcatctttc--acttaaac-ttcaatat-tagtagctcatagtcctctttg---ttatgtgataactctgggcttatg---attttttttcttaacagtgtttatcatctatgtctgtag-----------------------------------------------------
| || |||||||| ||||||||||| ||||| || ||||| ||  |||||||||| ||||||| ||||||||| || ||||| |     || | ||| ||  |   | ||   ||| |   ||   | |  |  |||        | |     | |||   ||  | ||   | || ||  ||         |     ||| | |||| |                                                      
GAGTCAGGAGTTGCTATGATGAGGGAAAGCGAGTGGCTGAAACTCTGATGTTTGATTATCACAGGCAGCATGGAATAGgtaaaattgggctccctctctctgatccatacacccaacacacagacacccccacacctacacacattcactcagtcactgatgggatgtgtaaaattgttcactcccttcccctccctctctctatctgaaactctactttccaatgcactctcactttattttgaaatggtgatcctataacag

upper sequence: GRMZM2G300412_T01 (Zea mays), 5'ss of exon 14
lower sequence: PP1S189_118V6.1 (Physcomitrella patens), 5'ss of exon 8
GTGTTAGGAGTTGTTATGATGAGGGTAAGCGTGTAGCTGAGACGTTGATGTTTGACTATCACAAGCAGCATGGCATTGgta-acac-ttcatctttcacttaaacttcaatattagtagctcatagtcctctttgtta-tgtgata---actctgggcttatgattttttttcttaacagtgtttatcatctatgtctgtag
| || || || || ||||| ||||| |||||||| ||||||||  | ||||||||||| || | |||||||||| |||||| | || ||| || |    |     ||| |  |||  |     ||  | | | |||   |   ||    |||    || ||  || |||   | |  |                        
GAGTAAGAAGCTGCTATGACGAGGGAAAGCGTGTTGCTGAGACTCTTATGTTTGACTACCATAGGCAGCATGGCGTTGgtatatacattcctcgtgttgtatcttttctaagttaacacgctctacgcttttatgtcggtccaatgtgtactagaagcgtaaaatatttaaacctggc------------------------

upper sequence: GRMZM2G300412_T01 (Zea mays), 5'ss of exon 14
lower sequence: EFJ17446 (Selaginella moellendorffii), 5'ss of exon 7
GTGTTAGGAGTTGTTATGATGAGGGTAAGCGTGTAGCTGAGACGTTGATGTTTGACTATCACAAGCAGCATGGCATTGgtaacacttcatctttcacttaaacttcaatattagtagctcatagtcctctttgttatgtgataactctgggcttatgattttttttcttaacagtgtttatcatctatgtctgtag
|||||||||| || || || ||||| || || || || || |||||||||||||||||||||| |||||| || ||||||     ||  ||  |  ||| | |||  ||     | | ||  |   |   |  || |  |                                                        
GTGTTAGGAGCTGCTACGACGAGGGAAAACGCGTGGCCGAAACGTTGATGTTTGACTATCACAGGCAGCACGGGATTGgt-----ttgctcgattgctttagctt-gatgacgctggttctgacgtccagtaattctcag--------------------------------------------------------

upper sequence: GRMZM2G300412_T01 (Zea mays), 5'ss of exon 14
lower sequence: EFJ35029 (Selaginella moellendorffii), 5'ss of exon 7
GTGTTAGGAGTTGTTATGATGAGGGTAAGCGTGTAGCTGAGACGTTGATGTTTGACTATCACAAGCAGCATGGCATTGgtaacacttcat--ctttcacttaa--acttcaatattagtagctcatagtcctctttgttatgtgataactctgggcttatgattttttttcttaacagtgtttatcatctatgtctgtag
|||||||||| || || || ||||| || || || || || |||||||||||||||||||||| |||||| || ||||||    ||  ||  ||||  ||| |  ||     |  |     |   || | |||                                                                   
GTGTTAGGAGCTGCTACGACGAGGGAAAACGCGTGGCCGAAACGTTGATGTTTGACTATCACAGGCAGCACGGGATTGgtg-tgctcgattgctttagcttgatgacgctggttctgacgtccagtaattctcag-----------------------------------------------------------------

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTGTTAGGAGTTGTTATGATGAGGGTAAGCGTGTAGCTGAGACGTTGATGTTTGACTATCACAAGCAGCATGGCATTGgtaacacttcatctttcacttaaacttcaatattagtagctcatagtcctctttgttatgtgataactctgggcttatgattttttttcttaacagtgtttatcatctatgtctgtag

- - - - - - - - - - - - - - - - - AGCTGA