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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGCAAAAGTTCGGATATGGAGTATTCCTGATCATCAAGTTGTTGATTGGAATGATCTTCATGAGATGGTCACAGCTGCTTGCTACACACCGGATGGACAGgtatgccattaaaagtttttcttacattgaagtgactttgggtaaaactaaatcacgcagtaccttaataaagctctcttggtttgtaaag

Basic information

species Arabidopsis thaliana
transcript AT5G54200.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G54200.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: LOC_Os04g44700.1 (Oryza sativa), 5'ss of exon 3
TGCAAAAGTTCGGATATGGAGTATTCCTGATCATCAAGTTGTTGATTGGAATGATCTTCATGAGATGGTCACAGCTGCTTGCTACACACCGGATGGACAGgtatgc-cattaaaagtt--tttcttacattgaagtgactttgggtaaaactaaatcacgcagtaccttaataaagctctcttggtttgtaaag
|| ||| ||||| |||||||| ||||| |  | | || ||||||||||||||||||| ||||| |||||||| ||||||||||| ||||| ||||||||||| |   || || |   |  | | |   |  |||  |   ||     |   ||  ||    | ||||||        |||| |  ||| | |||
TGAAAAGGTTCGCATATGGAGCATTCCGGGACGTGAAATTGTTGATTGGAATGATCTGCATGAAATGGTCACTGCTGCTTGCTATACACCTGATGGACAGgtttctacactatatactgatgtatgtgaccgaaaaggtctttttgtatgttagctc---taataccttg-------tctcatattttctgaag

upper sequence: AT5G54200.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: LOC_Os04g58180.1 (Oryza sativa), 5'ss of exon 3
TGCAAAAGTTCGGATATGGAGTATTCCTGATCATCAAGTTGTTGATTGGAATGATCTTCATGAGATGGTCACAGCTGCTTGCTACACACCGGATGGACAGgtatgccattaaaagtttttcttacattgaagtgactttgggtaaaactaaatcacgcagtacct-taataaagctctcttggtttgtaaag
|| |||||| || || |||| | | | ||||| | |  |||  ||||||||||||||||||||||||||||| ||||| || ||| | || |||||||||||   ||      ||||| |  |  ||   | |  || | ||  |   |||| |||   || | |    || |  ||| |  |  | | |||
TGAAAAAGTACGCATTTGGAATGTACATGATCGTAAGATTGAGGATTGGAATGATCTTCATGAGATGGTCACTGCTGCGTGTTACTCCCCTGATGGACAGgttgacct-----agtttctagtgaat--gattatctattggcca---taaaacacaatgtgcttactctatatttctttgtgcctttgaag

upper sequence: AT5G54200.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GRMZM2G027049_T01 (Zea mays), 5'ss of exon 3
TGCAAAAGTTCGGATATGGAGTATTCCTGATCATCAAGTTGTTGATTGGAATGATCTTCATGAGATGGTCACAGCTGCTTGCTACACACCGGATGGACAGgtat--gccat-taaaagtttttcttacattgaagtgactttgggtaaaactaaatcacgcagtaccttaataaagctctcttggtttgtaaag
|| |||||| || |||||||| ||||   | | | || ||||||||||||| ||| | ||||| |||||||| ||||||||||| || || ||||||||||| |    ||| || |  |  |||||  ||| ||     | |   |   || |  | || ||   | ||  |    || ||| |          
TGAAAAAGTCCGCATATGGAGCATTCAAAACCGTGAAATTGTTGATTGGAAAGATTTGCATGAAATGGTCACTGCTGCTTGCTATACCCCAGATGGACAGgttttaatcatctatacataattctttgatttaatatcttcttcatgttacgatctgacacatctctttcttt---ctttctcgaag-------

upper sequence: AT5G54200.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GRMZM2G142667_T01 (Zea mays), 5'ss of exon 3
TGCAAAAGTTCGGATATGGAGTATTCCTGATCATCAAGTTGTTGATTGGAATGATCTTCATGAGATGGTCACAGCTGCTTGCTACACACCGGATGGACAGgtatgccattaaaagtttttcttacattgaagtgactttgggtaaaactaaatcacgcagtaccttaataaagctctct-tggtttgtaaag
||  ||||||||||| |||||| | | ||| | | |  |||  |||||||||||||||||||||||||| || |||||||| ||  | || |||||||||||        |  |||| || |    |  |  |  ||||     | |  |||||      | | || ||     ||||| ||| || | |||
TGAGAAAGTTCGGATTTGGAGTGTCCGTGACCGTAAGATTGAGGATTGGAATGATCTTCATGAGATGGTTACCGCTGCTTGTTATTCCCCTGATGGACAGgttga-----agtagttcttttctagtgcatattcctttttaccataa-aaatc------tgctttgattttaatctctatggcttttgaag

upper sequence: AT5G54200.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GRMZM2G017815_T01 (Zea mays), 5'ss of exon 3
TGCAAAAGTTCGGATATGGAGTATTCCTGATCATCAAGTTGTTGATTGGAATGATCTTCATGAGATGGTCACAGCTGCTTGCTACACACCGGATGGACAGgtatgccattaaaagtttttcttacattgaagtgactttgggtaaaactaaatcacgcagtaccttaataaagctctcttggtttgtaaag
|| |||||| || |||||||| ||||   | | | || ||||||||||||| ||| | ||||| ||| |||| ||||||||||| || || |||||||||||      || ||   | |    | | |    |||  | |       ||   ||| |      | | | | |  ||| |   ||| | |||
TGAAAAAGTCCGCATATGGAGCATTCAAAACCGTGAAATTGTTGATTGGAAAGATTTGCATGAAATGATCACTGCTGCTTGCTATACCCCAGATGGACAGgt------tttaatcatctatacataattttttgatctagtac----cttcttcatgttaaggcctgacatatttctttcttttt-tgaag

upper sequence: AT5G54200.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GLYMA12G35040.1 (Glycine max), 5'ss of exon 3
TGCAAAAGTTCGGATATGGAGTATTCCTGATCATCAAGTTGTTGATTGGAATGATCTTCATGAGATGGTCACAGCTGCTTGCTACACACCGGATGGACAGgtatgccattaaaagtttttcttacattgaagtgactttgggtaaaactaaatcacgcagt-accttaataaagctctcttggtttgtaaag
||| || ||||| |||||||| ||||||||||  |||||||||||||||| |||||| |||||||||||||| |||||||| || ||||| ||||| |||||  | |     ||| ||    | ||   |  |||        |||   |  |       | | ||   | ||  | ||| |    |     
TGCTAAGGTTCGCATATGGAGCATTCCTGATCGACAAGTTGTTGATTGGACTGATCTGCATGAGATGGTCACTGCTGCTTGTTATACACCTGATGGTCAGgttggtcc----aaggttaatatgcacctatttgaacactcagaaattcagtttttatgttcaactcggttaaattttctggtgcag-----

upper sequence: AT5G54200.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GLYMA13G35500.2 (Glycine max), 5'ss of exon 4
TGCAAAAGTTCGGATATGGAGTATTCCTGATCATCAAGTTGTTGATTGGAATGATCTTCATGAGATGGTCACAGCTGCTTGCTACACACCGGATGGACAGgtatgccattaaaagtttttcttacattgaagtgactttgggtaaaactaaatcacgcagtaccttaataaagctctcttggtttgtaaag
||| || ||||| |||||||| ||||||||||  ||||||||||||||||  ||||| |||||||||||||| |||||||| || ||||| ||||| |||||  | |         | | |    |||  |      |    |  ||||   | | |    | |||  | ||  | ||| |    |     
TGCTAAGGTTCGCATATGGAGCATTCCTGATCGACAAGTTGTTGATTGGACCGATCTACATGAGATGGTCACTGCTGCTTGTTATACACCTGATGGTCAGgttggtccaaggttaatatgcacctatttgaacactctaaaattcaactt--ttatgtt-caacttggttaaattttctggtgcag-----

upper sequence: AT5G54200.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GLYMA12G23110.1 (Glycine max), 5'ss of exon 6
TGCAAAAGTTCGGATATGGAGTATTCCTGATCATCAAGTTGTTGATTGGAATGATCTTCATGAGATGGTCACAGCTGCTTGCTACACACCGGATGGACAGgtatgccattaaaagtttttcttacattgaagtgactttgggtaaaactaaat---cacgcagtaccttaataaagctctcttggtttgtaaag
||| || ||||| |||||||| ||||||||||  |||||||| ||||||| |||| | |||||||||||||| |||||||| || || || ||||| |||||  |   | || | || |    |  ||  |    | |  |  |||  |  ||   || |  | |  | |||||   | ||| ||| | |  ||
TGCTAAGGTTCGTATATGGAGCATTCCTGATCGACAAGTTGTAGATTGGACTGATTTACATGAGATGGTCACTGCTGCTTGTTATACGCCTGATGGTCAGgttggt--tcaacatttatatgcatcttttatcttcat--gaaaaagttggattttcaggtcgaaattcaataatattttct-ggtctctgcag

upper sequence: AT5G54200.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GLYMA06G38170.1 (Glycine max), 5'ss of exon 3
TGCAAAAGTTCGGATATGGAGTATTCCTGATCATCAAGTTGTTGATTGGAATGATCTTCATGAGATGGTCACAGCTGCTTGCTACACACCGGATGGACAGgtatgccattaaaagtttttcttacattgaagtgactttgggtaaaactaaatcacgcagtaccttaataaagctctcttggtttgtaaag
||| || ||||| |||||||| ||||||||||  |||||||| ||||||  |||| | |||||||||||||| |||||||| || ||||| ||||| |||||  |   || ||| ||| |   |  ||||      ||  |||            |||| | |  |||||    | |  ||||   |  ||
TGCTAAGGTTCGTATATGGAGCATTCCTGATCGACAAGTTGTAGATTGGGCTGATTTACATGAGATGGTCACTGCTGCTTGTTATACACCTGATGGTCAGgttgg---ttgaaaatttataagagtttgat----tttcaggt------------cgcaattcaataata----ttttctggtccctgcag

upper sequence: AT5G54200.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: Vv19s0014g03170.t01 (Vitis vinifera), 5'ss of exon 3
TGCAAAAGTTCGGATATGGAGTATTCCTGATCATCAAGTTGTTGATTGGAATGATCTTCATGAGATGGTCACAGCTGCTTGCTACACACCGGATGGACAGgtatgccattaaaagtttttcttacattgaagtgactttgggtaaaactaaatcacgcagtaccttaataaagctctcttggtttgtaaag
||| || ||||| || ||||| || || |||| |||||||||||||||||||||||| |||||||||||||| ||||| ||||| || || ||||| |||||  | | |    | |||  ||     |    ||| | ||   ||   | | |  | ||     ||        ||  ||      | |||
TGCTAAGGTTCGCATTTGGAGCATACCCGATCGTCAAGTTGTTGATTGGAATGATCTGCATGAGATGGTCACTGCTGCCTGCTATACTCCAGATGGTCAGgttgggcgtatttaatttggctagttgttccatga-tatgcaaaagttttattggctcaaatttttt------ttcctttttcccatgaag

upper sequence: AT5G54200.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: PP1S46_235V6.1 (Physcomitrella patens), 5'ss of exon 5
TGCAAAAGTTCGGATATGGAGTATTCCTGATCATCAAGTTGTTGATTGGAATGATCTTCATGAGATGGTCACAGCTGCTTGCTACACACCGGATGGACAGgtatgccattaaaagtttttcttacattgaagtgactttggg--taaaactaaatcacgcagtaccttaataaagctctcttggtttgtaaag---------------
||  ||||| ||||| ||||| ||||| |||||||| || ||||| |||| ||||||||| || |||||||||||||  || |||||  | |||||  ||||||   |||     | ||| ||      || |   |||  |  |     |     || |  | |  || | | |   | |||| | |||| |               
TGACAAAGTGCGGATTTGGAGCATTCCCGATCATCATGTAGTTGACTGGAGTGATCTTCAAGAAATGGTCACAGCTGTATGTTACACTGCAGATGGCAAGgtattttatttcttctcttttttgtgcgtaaatccttttttgcttctgtgttggctacacgctgcggtactgaggggttattggatcgtaatggtgtttgggtttcag

upper sequence: AT5G54200.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: PP1S219_28V6.1 (Physcomitrella patens), 5'ss of exon 5
TGCAAAAGTTCGGATATGGAGTATTCCTGATCATCAAGTTGTTGATTGGAATGATCTTCATGAGATGGTCACAGCTGCTTGCTACACACCGGATGGACAGgtatgccattaaaagtttttcttacattgaagtg----------actttgggtaaaactaaatcacgcagtaccttaataaagctctcttggtttgtaaag-----
||  ||||| ||||| ||||| ||||||||||| || || ||||| |||| ||||||||| || |||||||||||||  || ||||| ||||||||  |||||| | | | |   | ||  ||      |  |           | | || ||  |  || | ||||  | |  ||||   |  | | | ||| | |         
TGACAAAGTGCGGATCTGGAGCATTCCTGATCACCATGTGGTTGACTGGAGTGATCTTCAAGAAATGGTCACAGCTGTATGTTACACTCCGGATGGGAAGgtattctaattattctcttgtttgtgcacacatcttccccctctattctgtgttcagttacaacacgtgggagattaactga-ttgtatgggtgtttgggttgtag

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGCAAAAGTTCGGATATGGAGTATTCCTGATCATCAAGTTGTTGATTGGAATGATCTTCATGAGATGGTCACAGCTGCTTGCTACACACCGGATGGACAGgtatgccattaaaagtttttcttacattgaagtgactttgggtaaaactaaatcacgcagtaccttaataaagctctcttggtttgtaaag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA