Sequence
atgc intronic sequence ATGC exonic sequencegtgggtactgggtaggtgttatatataagtaattatggaccaaaagataattagattatataaacacaccctaatcacttaacttatgattaaagatataattatttacaacacaagttattatgatcttgtgatgttcatgtgatatatctgcagATTGATGGGTAAAGTTGCTTCTGATAAATGTCACAAGTGGGTTTTCAAAGAACCATCTGAATCTGAACCAAATCTTGCTAATTACTGGCAAAGTTCTTTT
Basic information
species | Arabidopsis thaliana |
transcript | AT5G53900.2 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G53900.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: LOC_Os11g25920.1 (Oryza sativa), 3'ss of exon 3
gtgggtactgggtaggtgttatatataagtaattatggaccaaaagataattagattatataaacacaccctaatcacttaacttatgattaaagatataattatttacaacacaagttattatgatcttgtgatgttcatgtgatatatctgcagATTGATGGGTAAAGTTGCTTCTGATAAATGTCACAAGTGGGTTTTCAAAGAACCATCTGAATCTGAACCAAATCTTGCTAATTACTGGCAAAGTTCTTTT
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----------------------------------------------------tggtcgctttcactttgttctactactactaccgagcttttgagcgtgat-gttggtaagacga-tgattttgatctgg-accgctggtg-ggtgctgctgcagGCTGATGGGAAAGGTGGCGTCTGATAAATGTCACAAATGGGTCTTCAAGGAACCTTCTGAATGCGAGCCCAACATCGCCAACTACTGGCAGAGCTCTTTT
upper sequence: AT5G53900.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GRMZM2G302293_T01 (Zea mays), 3'ss of exon 3
gtgggtactgggtaggtgttatatataagtaattatggaccaaaagataattagattatataaacacaccctaatcacttaacttatgattaaagatataattatttacaa---cacaagttattatgatcttgtgatgttcatgtgatatatctgcagATTGATGGGTAAAGTTGCTTCTGATAAATGTCACAAGTGGGTTTTCAAAGAACCATCTGAATCTGAACCAAATCTTGCTAATTACTGGCAAAGTTCTTTT
||| | || || || || | | | ||| | || | | || ||| || || | |||| ||| || | || |||| ||||||| || || || ||||||||||||||||| ||||| ||||| ||||| ||||||| || || || | | || |||||||| || || ||
------------------------------------------------------atttcggaggcatacaatacatacatgagtcatggacgataatgtgctaatagacagacccatgggtccgtttgat-ttggaccgtcgctcccgcat----gcagGCTGATGGGAAAGGTGGCCTCTGATAAATGTCACAAATGGGTCTTCAAGGAACCTTCTGAATGCGAGCCCAACATCTCCAACTACTGGCAGAGCTCCTTC
upper sequence: AT5G53900.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GRMZM2G132251_T01 (Zea mays), 3'ss of exon 3
gtgggtactgggtaggtgttatatataagtaattatggaccaaaagataattagattatataaacacaccctaatcacttaacttatgattaaagatataattatttacaacacaagttattatgatcttgtgatgttcatgtgatatatctgcagATTGATGGGTAAAGTTGCTTCTGATAAATGTCACAAGTGGGTTTTCAAAGAACCATCTGAATCTGAACCAAATCTTGCTAATTACTGGCAAAGTTCTTTT
|| | || |||| || ||||| | | || | || | | | | | | || | | ||| || ||||| ||||||| || || || ||||||||||||||||| ||||| ||||| ||||| ||||||| || || || | | || |||||||| || |||||
---------------------------------------------agcttttggggcatgcaaacgcatgtgaatcatgaatgatgtgctcaagaccgtgggtct----gattttgggttttggacccccttctccttcctgca-------tgcagGCTGATGGGAAAGGTGGCCTCTGATAAATGTCACAAATGGGTCTTCAAGGAACCTTCTGAATGCGAGCCCAACATCTCCAACTACTGGCAGAGCTCTTTC
upper sequence: AT5G53900.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA13G34980.1 (Glycine max), 3'ss of exon 3
gtgggtactgggtaggtgttatat-ataa-gtaattatggacca----------aaagataattagattatataaacacaccctaatc--acttaacttatgattaaagatataattatttacaacacaagtta-ttatgatcttgtga---------tgttcatgtgatat---atct-----gcagATTGATGGGTAAAGTTGCTTCTGATAAATGTCACAAGTGGGTTTTCAAAGAACCATCTGAATCTGAACCAAATCTTGCTAATTACTGGCAAAGTTCTTTT
|||||||||||||||||||| | | || || || || | || | || || | | |||| | || | |||| | | | | | | |||||| ||||| | | ||| || | ||| || || | ||| |||||||| |||||||| |||||||| || ||||||||||| || ||||| || | |||| |||||||||| | | || |||||||| || || |||
gtgggtactgggtaggtgttttgttatgttgtggttttgttctctctttctttctcagtcactttctttctctctctctctgtgaatcttgttcaatatccaattacatgtggagggactagggagttaagttacttatgcacatctgaactgtgctctgattgggtggaattggattttgggaacagGTTGATGGGGAAAGTTGCATCTGATAAGTGCCACAAGTGGGTCTTTAAAGAGCCCACAGAATGTGAACCAAATATCTCCAACTACTGGCAGAGCTCCTTT
upper sequence: AT5G53900.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA12G35490.2 (Glycine max), 3'ss of exon 2
gtgggtactgggtaggtgttatatataagtaattatggaccaaaagataattagattatataaacacaccctaatcacttaacttatgattaaagatataattatttacaacacaa-gttattatgatcttgtgatgttcatgtgatatatctgcagATTGATGGGTAAAGTTGCTTCTGATAAATGTCACAAGTGGGTTTTCAAAGAACCATCTGAATCTGAACCAAATCTTGCTAATTACTGGCAAAGTTCTTTT
|| ||| || || | ||| || | ||| || |||| ||| | || | | |||| ||| | | | | ||| |||||||| |||||||| |||||||| || ||||||||||| || ||||| || | |||| |||||||||| | | || |||||||| || || |||
-----------------------------------------------------tgttcaatatccaataccatgtggagggactagggagttaagttac--ttatgcacatctgaacagtgctctgattgggtgggaattggat--tttgggaacagGTTGATGGGGAAAGTTGCATCTGATAAGTGCCACAAGTGGGTCTTTAAAGAGCCCACAGAATGTGAACCAAATATCTCCAACTACTGGCAGAGCTCCTTT
upper sequence: AT5G53900.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv19s0014g02320.t01 (Vitis vinifera), 3'ss of exon 3
gtgggtactgggtaggtgttat-atataagtaattatggaccaaaagataattagattatataaacacaccctaa-------tcacttaactt--------------atgattaaagatataattatttacaacacaagttatt----atgatctt--gtgatgttcatgtgatatatctgcagATTGATGGGTAAAGTTGCTTCTGATAAATGTCACAAGTGGGTTTTCAAAGAACCATCTGAATCTGAACCAAATCTTGCTAATTACTGGCAAAGTTCTTTT
|||||||||||||||||||| | || | | | | | | | || | || |||| || || ||| | | | || | |||| || | |||| || || | ||| ||| | | || | ||| |||| |||||||| || ||||| |||||||| ||||| || |||||||||||||| || || || | |||||||||| | | || |||||||| |||||||||
gtgggtactgggtaggtgtttttatttgatttcatctctctctccctctctttccctctctccctcattccctccctctctctctctcaacaatagggaggaagcagaaaagtgaaaaaataaaaataaaaaacaaaaattcctctacatgggctttgataggatgaattgcttttatgagcagGTTGATGGGGAAGGTTGCATCTGATAAGTGTCATAAATGGGTTTTCAAAGAGCCTTCAGAGTGTGAACCAAATGTCTCCAACTACTGGCAGAGTTCTTTT
upper sequence: AT5G53900.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: EFJ26828 (Selaginella moellendorffii), 3'ss of exon 4
gtgggtactgggtaggtgttatatataagtaattatggaccaaaagataattagattatataaacacaccctaatcacttaacttatgattaaagatataattatttacaacacaagttattatgatcttgtgatg-ttcatgtgatatatctgcagATTGATGGGTAAAGTTGCTTCTGATAAATGTCACAAGTGGGTTTTCAAAGAACCATCTGAATCTGAACCAAATCTTGCTAATTACTGGCAAAGTTCTTTT
| || || || | | | ||||| | |||| | | | |||||||||||| |||||||| || || ||||| ||||||||||| ||| || | || || | || | || ||||||||||| || ||
-------------------------------------------------------------------------------------------------gtgcgtacttg-aaaagactccgccttccagctgtgaggactcatcttgt---tgcacagATTGATGGGAAAAGTTGCCTCAGACAAATGCCACAAGTGGGTGTTCCGGGAGTCTTCCGAGACGGAGGTCGGCCCGCTCAACTACTGGCAAAGCTCCTTC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttatttacaacacaagttattatgatcttgtgatgttcatgtgatatatctgcagATTGATGGGTAAAGTTGCTTCTGATAAATGTCACAAGTGGGTTTTCAAAGAACCATCTGAATCTGAACCAAATCTTGCTAATTACTGGCAAAGTTCTTTT
aagttattat TA-rich tract
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgggtactgggtaggtgttatatataagtaattatggaccaaaagataattagattatataaacacaccctaatcacttaacttatgattaaagatataattatttacaacacaagttattatgatcttgtgatgttcatgtgatatatctgcagATTGATGGGTAAAGTTGCTTCTGATAAATGTCACAAGTGGGTTTTCAAAGAACCATCTGAATCTGAACCAAATCTTGCTAATTACTGGCAAAGTTCTTTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG