Sequence
atgc intronic sequence ATGC exonic sequencegtaagttcaggacagaggcagactacctcagattcacctgctttgaacacgttagtttcataattttttgttgcattatgtggctttttgtgcatggcagCACAGCAATAAGCGAGGACCTTGGGCAAGTAGAGTACATTTTGACCGACAAAACTGGAACCCTGACAGATAACAAGATGATATTTAGAAGATGCTGTATT
Basic information
species | Arabidopsis thaliana |
transcript | AT5G44240.1 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G44240.2 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: LOC_Os11g25980.1 (Oryza sativa), 3'ss of exon 11
gtaagttcaggacagaggcagactacctcagattcacctgctttgaacacgttagtttcataattttttgttgcattatgtggctttttgtgcatggcagCACAGCAATAAGCGAGGACCTTGGGCAAGTAGAGTACATTTTGACCGACAAAACTGGAACCCTGACAGATAACAAGATGATATTTAGAAGATGCTGTATT
| | ||||| ||| | | ||| | ||| ||||| || | | || || || || | | |||||||||||| || || ||| | || ||||| || || ||||| || ||||||||||| |||||||| || ||||||||||| || || || |||||||||
---------gtaagtaggcattttacttttatcttggtaagcatgatcttgtttgtttctta------tatctaatcat----ctcttcataactaccagCACAGCAATTAGTGAAGACTTGGGTCAAGTTGAATATATTTTAACAGACAAAACTGGGACCCTGACTGAGAACAAGATGATCTTCAGGAGGTGCTGTATT
upper sequence: AT5G44240.2 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: LOC_Os04g28460.1 (Oryza sativa), 3'ss of exon 8
-------------gtaagttcaggacagaggcagactacctcagattcacctgctttgaacacgttagttt-cataattttttgttgcattatgtggctttt-----tgtgcatggcagCACAGCAATAAGCGAGGACCTTGGGCAAGTAGAGTACATTTTGACCGACAAAACTGGAACCCTGACAGATAACAAGATGATATTTAGAAGATGCTGTATT
| || | || | | |||| || || | ||| | | | | || | ||| || | | |||| ||| | ||||||||| || || || |||||||| || || |||||| |||||| |||||||||||||| |||||||| |||| ||
gtacgcctgctcattcagctaagtat-gtggcatgttatttccatatgtgtgaatttagatttttcatccaacctagctatttattttttagtacagCTTACATAAGTGTCTCTTTCAGCACAGCTATTAGTGAAGACCTTGGACAGGTTGAGTACGTTTTGAGTGACAAAACTGGAACGCTGACAGAAAACAGAAT----------------------
upper sequence: AT5G44240.2 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GRMZM2G411916_T01 (Zea mays), 3'ss of exon 2
gtaagttcaggacagaggcagactacctcagattcacctgctttgaacacgt-tagtttcataattttttgttgcattatgtggctttttgtgca-----tggcagCACAGCAATAAGCGAGGACCTTGGGCAAGTAGAGTACATTTTGACCGACAAAACTGGAACCCTGACAGATAACAAGATGATATTTAGAAGATGCTGTATT
| ||| || || | ||| | | | | || | | || | |||| | || | ||| |||| | |||||||||||| || |||||| | || || || || || |||||||| || |||||||| || |||| || ||||||||||| || ||||| |||||||||
-------------gtaagca-accacttgcatttctatcgataaggagacatacaattgttctttattttcctctgctaaatctactttaatgcaataattttcagCACAGCAATTAGTGAGGACTTGGGACAGGTTGAATATATTTTGACAGATAAAACTGGGACATTGACTGAGAACAAGATGATCTTCAGAAGGTGCTGTATT
upper sequence: AT5G44240.2 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA13G37090.1 (Glycine max), 3'ss of exon 10
gtaagttcaggacagaggcagactacct-cagattcacctgctttgaacac--gttagtttcataattttttgttgcattatgtggctttttgtgcatggcagCACAGCAATAAGCGAGGACCTTGGGCAAGTAGAGTACATTTTGACCGACAAAACTGGAACCCTGACAGATAACAAGATGATATTTAGAAGATGCTGTATT
|| ||| || || | || || | || ||| ||| | || | |||| || || | ||| | || || | || ||| || || ||||| |||||||| || ||||| ||||||||||||||||||||||| || ||||| ||||| || |||||||||||||||||||| ||||||
gtgagtgactgaaggatcctgattaataactactttgaggatcttgtacatcggcacacttttttatttattattat-taatgatgtttgttatatttgacagTACCGCGATAAGTGAGGACCTGGGACAAGTTGAGTACATTTTGACCGACAAAACAGGCACCCTCACAGAGAATAAGATGATATTTAGAAGATGTTGTATT
upper sequence: AT5G44240.2 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA12G33340.1 (Glycine max), 3'ss of exon 10
gtaagttcaggacagaggcagactacctcagattcacctgctttgaacacgt-tagtttcataattttttgttgcattatgtggctttttgtgcatggcagCACAGCAATAAGCGAGGACCTTGGGCAAGTAGAGTACATTTTGACCGACAAAACTGGAACCCTGACAGATAACAAGATGATATTTAGAAGATGCTGTATT
|| ||| ||| || | | || | | | || | |||| ||| | | || | |||||| || ||| | || || | || ||| ||||| ||||| |||||||| || ||||| |||||||||||||| |||||||| || ||||| ||||| || |||||||||||||||||||| ||||||
gtgagt----gaccgaaggatcctgattaataactactt-tgaggaactcgtacatctgcacacttttttttta----atgaagtttgttatatttgacagTACAGCGATAAGTGAGGACCTGGGACAAGTTGAGTACATTTTGACTGACAAAACAGGCACCCTCACAGAGAATAAGATGATATTTAGAAGATGTTGTATT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aacacgttagtttcataattttttgttgcattatgtggctttttgtgcatggcagCACAGCAATAAGCGAGGACCTTGGGCAAGTAGAGTACATTTTGACCGACAAAACTGGAACCCTGACAGATAACAAGATGATATTTAGAAGATGCTGTATT
ctttttgt CT-rich tract
ttagtttcataatttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagttcaggacagaggcagactacctcagattcacctgctttgaacacgttagtttcataattttttgttgcattatgtggctttttgtgcatggcagCACAGCAATAAGCGAGGACCTTGGGCAAGTAGAGTACATTTTGACCGACAAAACTGGAACCCTGACAGATAACAAGATGATATTTAGAAGATGCTGTATT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG