Sequence
atgc intronic sequence ATGC exonic sequencegtatataatcagaaaacaatagactaggaagcgatatggataacctaattagaagatatagagtttaactattacacactataaaaccgtagttaattggtgaaatgcttactttagtcaaacatttattttaaggcacttacgtctgttgtctgtgcagAAACCATTGGGGCTGCTCTCCCTTTTGGATGAGGAATCTACATTTCCGAATGGCACAGATTTGACACTTGCAAACAAGCTAAAACAGCATCTACAGTCTA
Basic information
species | Arabidopsis thaliana |
transcript | AT3G19960.1 |
intron # | 16 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G19960.2 (Arabidopsis thaliana), 3'ss of exon 18
lower sequence: GRMZM2G113202_T01 (Zea mays), 3'ss of exon 15
gtatataatcagaaaacaatagactaggaagcgatatggataacctaattagaagatatagagtttaactattacacactataaaaccgtagttaattggtgaaatgcttac-tttagtcaaacatttattttaaggcacttacgtctgttgtctgtgcagAAACCATTGGGGCTGCTCTCCCTTTTGGATGAGGAATCTACATTTCCGAATGGCACAGATTTGACACTTGCAAACAAGCTAAAACAGCATCTACAGTCTA
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-------------------------------------------------------atgaactatcctaatttctcttgctttgtatatcttgcaaact--tgacctgcagccatgtagtaacatatatattcttgctgtctaacattc----ttaatgcagAAACCACTGGGACTATTGTCTCTGCTGGATGAGGAATCTACTTTCCCGAATGCCACAGATCTTACTTTTGCAAACAAGCTTAAGCAACATCTTGACTCGA
upper sequence: AT3G19960.2 (Arabidopsis thaliana), 3'ss of exon 18
lower sequence: GLYMA20G23660.1 (Glycine max), 3'ss of exon 16
gtatataatcagaaaacaatagactaggaagcgatatggataacctaattagaagatatagagtttaactattacacactataaaaccgtagttaattggtgaaatgcttactttagtcaaacatttattttaaggcacttacgtctgttgtctgtgcagAAACCATTGGGGCTGCTCTCCCTTTTGGATGAGGAATCTACATTTCCGAATGGCACAGATTTGACACTTGCAAACAAGCTAAAACAGCATCTACAGTCTA
|| | | | | |||| | || | | || | || || | || | | || | | | | ||||| | | | ||||||||||||| ||||||| || ||||| || ||||| || || || || || |||||||||||||| || |||| |||||||| || |||||| | | || |
-------------------------------------------------------atctgtggctaa--tatttttctcttcga--ctgtgggaaaatgttatgtctgatatgaaattggaaattcgactgtcttagactta-gcttctgacatgtgcagAAACCACTGGGGCTACTATCCCTGTTAGATGAAGAGTCAACTTTCCCTAATGGCACAGATTTAACCTTTGCTAACAAGCTTAAGCAGCATTTGAATTCCA
upper sequence: AT3G19960.2 (Arabidopsis thaliana), 3'ss of exon 18
lower sequence: GLYMA20G00320.1 (Glycine max), 3'ss of exon 16
gtatataatcagaaaacaatagactaggaagcgatatggataacctaattagaagatatagagtttaactattacacact-ataaaaccgtagttaattggtgaaatgcttactttagtcaaacatttattttaaggcacttacgtctgttgtctgtgcagAAACCATTGGGGCTGCTCTCCCTTTTGGATGAGGAATCTACATTTCCGAATGGCACAGATTTGACACTTGCAAACAAGCTAAAACAGCATCTACAGTCTA
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-------------------------------------------------------------gttgtggcaactacacttttattccttggcatggatattctgacattcatgattagaaactagaattgtgtcttatacttgacttctggtatatttgcagAGGCCACTGGGTTTATTATCCTTGTTAGATGAAGAGTCCACTTTCCCAAATGGCACAGATCTAACACTTGCTAACAAGCTTAAACAGCATTTGAATTCTA
upper sequence: AT3G19960.2 (Arabidopsis thaliana), 3'ss of exon 18
lower sequence: GLYMA09G42180.1 (Glycine max), 3'ss of exon 14
gtatataatcagaaaacaatagactaggaagcgatatggataacctaattagaagatatagagtttaactattacacactataaaaccgtagttaattggtgaaatgcttactttagtcaaacatttattttaaggcacttacgtctgttgtctgtgcagAAACCATTGGGGCTGCTCTCCCTTTTGGATGAGGAATCTACATTTCCGAATGGCACAGATTTGACACTTGCAAACAAGCTAAAACAGCATCTACAGTCTA
| || | ||| | | | | | | | | | || || | | | || ||| | || | || || | | |||| | | | |||||| ||| ||||| | | ||| | || ||||| || || || || || |||||||||||||| ||| |||| |||||||| ||||||||| | | ||||
--------------------------------------------------gtggcaactacacttttattcct-tgctttggatattctgacatatatgattagaaactagaattattgtgacttatacttga---------cttctggtatatttgcagAGGCCACTGGGGTTATTATCCTTGTTAGATGAAGAGTCCACTTTCCCAAATGGCACAGATTTAACATTTGCTAACAAGCTTAAACAGCATTTGAATTCTA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgcttactttagtcaaacatttattttaaggcacttacgtctgttgtctgtgcagAAACCATTGGGGCTGCTCTCCCTTTTGGATGAGGAATCTACATTTCCGAATGGCACAGATTTGACACTTGCAAACAAGCTAAAACAGCATCTACAGTCTA
cacttac putative branch site (score: 2)
tttagtcaaacattta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatataatcagaaaacaatagactaggaagcgatatggataacctaattagaagatatagagtttaactattacacactataaaaccgtagttaattggtgaaatgcttactttagtcaaacatttattttaaggcacttacgtctgttgtctgtgcagAAACCATTGGGGCTGCTCTCCCTTTTGGATGAGGAATCTACATTTCCGAATGGCACAGATTTGACACTTGCAAACAAGCTAAAACAGCATCTACAGTCTA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT