Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATTGTTTTCATTCATGCAGATTGCAGATCATTTAACATAAATGGCTGACGCAGAGGACATTCAGCCCCTAGTCTGTGACAATGGAACTGGAATGGTCAAGgtaactgtagtcgcttggcatcatattctctaatgattcctctttttccatacagcttttagattttcagtcaatgttaagcactttttccatctcttatag

Basic information

species Zea mays
transcript GRMZM2G030169_T03
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G030169_T03 (Zea mays), 5'ss of exon 1
lower sequence: LOC_Os10g36650.1 (Oryza sativa), 5'ss of exon 2
ATTGTTTTCATTCATGCAGATTGCAGATCATTTAACATAAATGGCTGACGCAGAGGACATTCAGCCCCTAGTCTGTGACAATGGAACTGGAATGGTCAAGgtaact----gtagtcgcttggcatcatattctctaatga---ttcctctttttccatacagcttttagattttcagtcaatgttaagca----ctttttccatctcttatag
                          |||| |||| ||||||||||||||||||||||||||||||||| ||||||||||||||||| ||||||||||||||||      ||  |  |||||||||  ||| |  ||  |   |||  | |  |    |    | ||| | ||          | ||| |    || ||| ||| | | ||||
--------------------------ATCAGTTAAAATAAATGGCTGACGCAGAGGACATTCAGCCCCTTGTCTGTGACAATGGAACCGGAATGGTCAAGgtaataaaaagtgatgacttggcatcgcattgttgaacaaaatttctacctgatggtaattattgttacaattgagaagctcatcaagtattaactgttttcatttttcatag

upper sequence: GRMZM2G030169_T03 (Zea mays), 5'ss of exon 1
lower sequence: GLYMA04G39380.2 (Glycine max), 5'ss of exon 2
ATTGTTTTCATTCATGCAGATTGCAGATCATTTAACATAA-ATGGCTGACGCAGAGGACATTCAGCCCCTAGTCTGTGACAATGGAACTGGAATGGTCAAGgtaactgtagtcgcttggcatcatattctctaatgattcctctttttccatacagcttttagattttcagtcaatg-ttaagcactttttccatctct-tatag
                           |  |||   | || |||||||| || ||||| ||||| ||||| |||||||||||||||||||||||||| |||||     ||||  ||| |||   | |||| | ||| |     |   || ||  ||  |     |  | |   || | || |   || |    |||| | || ||
---------------------------TAGTTTGGTAAAAGATGGCTGATGCTGAGGATATTCAACCCCTTGTCTGTGACAATGGAACTGGAATGGTGAAGgt-----tagt-actttgcagtttcttctgttatg-tgtaattgcatctat-tagtctcggtttcgttatcaaacgatttatttctataatgatctgtgtacag

upper sequence: GRMZM2G030169_T03 (Zea mays), 5'ss of exon 1
lower sequence: GLYMA15G05570.1 (Glycine max), 5'ss of exon 2
ATTGTTTTCATTCATGCAGATTGCAGATCATTTAACATAAATGGCTGACGCAGAGGACATTCAGCCCCTAGTCTGTGACAATGGAACTGGAATGGTCAAGgt----aactgt------agtcgcttggcatcatattctctaatga----------ttcctctttttccatacagcttttagattttcagtcaatgttaa-----gcactttttccatctcttatag
                              ||| | | | |||||||| || ||||||||||| || || ||   ||| |||||||||||||||||||||||    |  |||      | | | |  |  |    |   | | |||          |  |||| |        ||  || |   ||  |    || || |       | ||||  |     ||  ||
-----------------------------GTTTTAAA-AGATGGCTGATGCTGAGGACATTCAACCTCTTGTTGTTGATAATGGAACTGGAATGGTCAAGgttagaagatgttttgccaattgatgagtgtttcttgtgccattgaagaagactgttcactctgtgcttgcttagtattcattgttaaatatgatattgatatatatatttttctcgatgtttgcag

upper sequence: GRMZM2G030169_T03 (Zea mays), 5'ss of exon 1
lower sequence: GLYMA05G32220.1 (Glycine max), 5'ss of exon 1
--ATTGTTTTCATTC-ATGCAGATTGCAGATCATTTAACATAAATGGCTGACGCAGAGGACATTCAGCCCCTAGTCTGTGACAATGGAACTGGAATGGTCAAGgtaactgtagtcgcttggcatcatattctctaatgattcctctttttccatacagcttttagattttcagtcaatgttaagcactt--tttccatctcttatag
   ||  |  ||  | ||||   |||||| |   ||   | | ||||| || || ||||| ||||| ||||| || |||||||||||||||||||||||||||||     ||||  ||| ||  | |  | | |  || ||| | |  ||   | || ||  |||  ||    |||    | |    ||  |||  || |   | ||
TATTTCATGGCACCCTATGCTTTTTGCAGGT---TTGTAAAAGATGGCCGATGCTGAGGATATTCAACCCCTTGTTTGTGACAATGGAACTGGAATGGTCAAGgt-----tagt-acttagcggctttgttttt--tgtttcatgtgctt--gtgcatctgctagccttgagttcataactgaatctttgattttaatatggaacag

upper sequence: GRMZM2G030169_T03 (Zea mays), 5'ss of exon 1
lower sequence: GLYMA08G15480.1 (Glycine max), 5'ss of exon 2
ATTGTTTTCATTCATGCAGATTGCAGATCATTTAACATAAATGGCTGACGCAGAGGACATTCAGCCCCTAGTCTGTGACAATGGAACTGGAATGGTCAAGgtaactgtagtcgcttggcatcatattctctaatgattcctctttttccatacagcttttagattttcagtcaatgttaagcactttttccatctcttatag
                              |||   | | ||||| || || ||||| ||||| ||||| || || ||||||||||||||||||||||||||     ||||  ||| |     | || | |  |      |   | | ||   ||  || || |  | ||| |||  |      | |||  || |   | ||
-----------------------------GTTTGTAAAAGATGGCAGATGCCGAGGATATTCAACCCCTTGTTTGCGACAATGGAACTGGAATGGTCAAGgt-----tagt-acttcgtggatttttgttttgttgcatgtgcatatgca---agtcttgagttcataagtgaataat-----ttattttaatatggaacag

upper sequence: GRMZM2G030169_T03 (Zea mays), 5'ss of exon 1
lower sequence: GLYMA04G39380.1 (Glycine max), 5'ss of exon 2
ATTGTTTTCATTCATGCAGATTGCAGATCATTTAACATAA-ATGGCTGACGCAGAGGACATTCAGCCCCTAGTCTGTGACAATGGAACTGGAATGGTCAAGgtaactgtagtcgcttggcatcatattctctaatgattcctctttttccatacagcttttagattttcagtcaatg-ttaagcactttttccatctct-tatag
                              |||   | || |||||||| || ||||| ||||| ||||| |||||||||||||||||||||||||| |||||     ||||  ||| |||   | |||| | ||| |     |   || ||  ||  |     |  | |   || | || |   || |    |||| | || ||
------------------------------TTTGGTAAAAGATGGCTGATGCTGAGGATATTCAACCCCTTGTCTGTGACAATGGAACTGGAATGGTGAAGgt-----tagt-actttgcagtttcttctgttatg-tgtaattgcatctat-tagtctcggtttcgttatcaaacgatttatttctataatgatctgtgtacag

upper sequence: GRMZM2G030169_T03 (Zea mays), 5'ss of exon 1
lower sequence: GLYMA06G15520.2 (Glycine max), 5'ss of exon 2
ATTGTTTTCATTCATGCAGATTGCAGATCATTTAACATAAA-TGGCTGACGCAGAGGACATTCAGCCCCTAGTCTGTGACAATGGAACTGGAATGGTCAAGgtaactgtagtcgcttggcatcatattctctaatgattcctctttttccatacagcttttagattttcagtcaatgttaagcactttttccatctcttatag
                              |||   | ||| ||||||| || ||||| ||||| ||||| || ||||||||||||||||||||||| |||||     ||||   |||   |    |  |    | ||| |   | ||   |   | ||| |  || |   ||||| |||   |  |  ||       || ||
------------------------------TTTGGTAAAAAATGGCTGATGCTGAGGATATTCAACCCCTTGTTTGTGACAATGGAACTGGAATGGTGAAGgt-----tagtactttgcagtttcttgttagtgtaattgcatctatttagtcttggtttca--ttattgctcaat-ttatttaaatgatcatctgtgtacag

upper sequence: GRMZM2G030169_T03 (Zea mays), 5'ss of exon 1
lower sequence: GLYMA05G32220.2 (Glycine max), 5'ss of exon 2
ATTGTTTTCATTCATGCAGATTGCAGATCATTTAACATAAATGGCTGACGCAGAGGACATTCAGCCCCTAGTCTGTGACAATGGAACTGGAATGGTCAAGgtaactgtagtcgcttggcatcatattctctaatgattcctctttttccatacagcttttagattttcagtcaatgttaagcactt--tttccatctcttatag
                              |||   | | ||||| || || ||||| ||||| ||||| || |||||||||||||||||||||||||||||     ||||  ||| ||  | |  | | |  || ||| | |  ||   | || ||  |||  ||    |||    | |    ||  |||  || |   | ||
-----------------------------GTTTGTAAAAGATGGCCGATGCTGAGGATATTCAACCCCTTGTTTGTGACAATGGAACTGGAATGGTCAAGgt-----tagt-acttagcggctttgttttt--tgtttcatgtgctt--gtgcatctgctagccttgagttcataactgaatctttgattttaatatggaacag

upper sequence: GRMZM2G030169_T03 (Zea mays), 5'ss of exon 1
lower sequence: GLYMA08G19420.1 (Glycine max), 5'ss of exon 2
ATTGTTTTCATTCATGCAGATTGCAGATCATTTAACATAAATGGCTGACGCAGAGGACATTCAGCCCCTAGTCTGTGACAATGGAACTGGAATGGTCAAGgtaa-----------ctgtagtcgcttggcatcatattctctaatgattcctctttttccataca-gctt--ttagattttcagtcaatgttaagcactttttccatctcttatag
                              ||| | | |||||||||| || ||||||||||| || || ||   ||| ||||||||||||||||||||||| |            |  | | | |  |       |   ||| |||         |||  |    ||||  ||| || |    | ||| | |     ||| ||||    ||  ||
-----------------------------GTTTTAAA-AAATGGCTGATGCTGAGGACATTCAACCTCTTGTTGTTGATAATGGAACTGGAATGGTCAAGgttagaacatgttttttccaattgatgagtgcttcttgtgctattgaagtagacagttcgctctgtgcttgcttaaatatgatattaatat-atattttttctccaatgtttgcag

upper sequence: GRMZM2G030169_T03 (Zea mays), 5'ss of exon 1
lower sequence: AT5G09810.1 (Arabidopsis thaliana), 5'ss of exon 2
ATTGTTTTCATTCATGCAGATTGCAGATCATTTAACATAAATGGCTGACGCAGAGGACATTCAGCCCCTAGTCTGTGACAATGGAACTGGAATGGTCAAGgtaactgtagtcgcttggcatcatattctctaatgatt-cctctttttccatacagcttttagattttcagtcaatgttaagcactttttccatctcttatag
                                    | ||||||| || |  ||||| |||||||| || |||||||||||||||||||||||||| ||||| | |      | ||      ||| | | |  |  |  |||  |||    ||||  | | ||| |     |||           |||||  || | | | ||
----------------------------------TGAAAAATGGCCGATGGTGAGGATATTCAGCCACTTGTCTGTGACAATGGAACTGGAATGGTGAAGgtgagttagactgtttatttagatactgtatggttctaaccttctttgttgtacatgtgtaagactactgatca--------tgatttttgtatat-taacag

upper sequence: GRMZM2G030169_T03 (Zea mays), 5'ss of exon 1
lower sequence: Vv04s0044g00580.t01 (Vitis vinifera), 5'ss of exon 3
ATTGTTTTCATTCATGCAGATTGCAGATCATTTAACATAAATGGCTGACGCAGAGGACATTCAGCCCCTAGTCTGTGACAATGGAACTGGAATGGTCAAGgtaactgtagtcgcttggcatcatattctctaatgattcctctttttccatacagctttt-agattttcagtcaatgttaagcactttttccatctcttatag----
                              |   | |   ||||| ||  | || || || |||||||| |||||||||||||||||||||||||| |||||  |||| ||  |||    |    |  | |   ||||  |  | ||   | | |||  | | ||  ||| |     | |        |   ||   |||||     
-----------------------------GTAATAAAAGGATGGCCGATACTGAAGATATCCAGCCCCTCGTCTGTGACAATGGAACTGGAATGGTGAAGgt--ctgttgtttctt--tcttgcttgatatgcagatttgttgtgttgtttgctgctcctcaaatgctcaatttgaataagctttccatgttatgctttatatgcag

upper sequence: GRMZM2G030169_T03 (Zea mays), 5'ss of exon 1
lower sequence: Vv12s0178g00200.t01 (Vitis vinifera), 5'ss of exon 1
ATTGTTTTCATTCATGCAGATTGCAGATCATTTAACATAAATGGCTGACGCAGAGGACATTCAGCCCCTAGTCTGTGACAATGGAACTGGAATGGTCAAGgtaactgtagtcgcttggcatcatattctctaatgattcctctttttccatacagcttttagattttcagtcaatgttaagcactttttccatctcttatag---
                              ||| | | | ||||| || || ||||| || ||||| || || |||||||||||||||||||||||||||||     | |||  ||    | || |  |  ||||| | |   | ||     | ||  ||   |    |       ||| | | |||    |     | |     
---------------------------AGGTTTTAGA-AGATGGCCGATGCCGAGGATATCCAGCCTCTTGTGTGTGACAATGGAACTGGAATGGTCAAGgt-----ttgtcagttattcttatttatttcaatgagttcatatgtttgtgtctgcacttgtttagataaagggctttagggattttacaaaatgaatttgactc

upper sequence: GRMZM2G030169_T03 (Zea mays), 5'ss of exon 1
lower sequence: PP1S337_21V6.2 (Physcomitrella patens), 5'ss of exon 3
ATTGTTTTCATTCATGCAGATTGCAGATCATTTAACATAAATGGCTGACGCAGAGGACATTCAGCCCCTAGTCTGTGACAATGGAACTGGAATGGTCAAGgtaactgtagtcgcttggcatcatattctctaatgattcctctttttccatacagcttttagattttcagtcaatgttaagcactttttccatc-tcttatag
                           ||  |    | ||||||||||||  |||||  | |||||| | || || |||||||||||||||||||||||||| |    | ||   |   | |  |     |||   ||||    ||     |  |  || |    |||  | ||| || |||   |  |  |   | || || 
--------------------------GTCGGTATTAAGAAATGGCTGACGGTGAGGAAGTACAGCCCTTGGTGTGCGACAATGGAACTGGAATGGTCAAGgtgaggtcactcttctaaaacc-cagagattaacttttccgaacttggttcattggattcaaggattctat-aatcttgagcttctgctgaaaaatattcta-

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATTGTTTTCATTCATGCAGATTGCAGATCATTTAACATAAATGGCTGACGCAGAGGACATTCAGCCCCTAGTCTGTGACAATGGAACTGGAATGGTCAAGgtaactgtagtcgcttggcatcatattctctaatgattcctctttttccatacagcttttagattttcagtcaatgttaagcactttttccatctcttatag

- - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA