Sequence
atgc intronic sequence ATGC exonic sequencegtagcccttgaccttagtcatttttagaactcaattcttgatttattcttgatctttttgatacctatgttctataaatatcgtaagaaaaacttgtcactctttttacttttggtattaatatgattgcttgatactatatagAATCCGCGTTTGAATTTCGGGCACTAGAGGTTGCTTTGGAAGCTATTTGTAGCTTCCTAGCTGCAAGGACAATAGAATTAGAGAAGTCTGCTTATCCTGC
Basic information
species | Arabidopsis thaliana |
transcript | AT5G09720.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G09720.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA20G35260.1 (Glycine max), 3'ss of exon 3
gtagcccttgaccttagtcatttttagaactcaattcttgattta--ttcttgatctttttgatacctatgttctataaatatcgtaagaaaaacttgtcactctttttacttttggtattaatatgat-tgcttgatacta-tatagAATCCGCGTTTGAATTTCGGGCACTAGAGGTTGCTTTGGAAGCTATTTGTAGCTTCCTAGCTGCAAGGACAATAGAATTAGAGAAGTCTGCTTATCCTGC
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---gtacgttacatta---aatgatgaaccataagtaatgaacaaacttattgattgcatctgttcct--gttataaatctatctttgta----tttgcattatctcttgctcttgttatctgagtgatctaaattacacaaatgtagAGTCACCCTTTGAATTCCGGGCCCTGGAGGTTGCTTTAGAAGCCATTTGTAGTTTTCTTGCTGCACGTACAACAGAATTGGAGATGGCTGCTTATCCTGC
upper sequence: AT5G09720.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA10G32350.1 (Glycine max), 3'ss of exon 3
gtagcccttgaccttagtcatttttagaactcaattcttgatttattcttgatctttttgat---acctatgttctataaatatcgtaagaaaaacttgtcactctttttacttttggtattaatatgat-tgcttgatactatatagAATCCGCGTTTGAATTTCGGGCACTAGAGGTTGCTTTGGAAGCTATTTGTAGCTTCCTAGCTGCAAGGACAATAGAATTAGAGAAGTCTGCTTATCCTGC
| | || | | | | |||| | || | | | | || | || ||||| | || | || | ||| | ||| |||| || ||| ||| |||| | | || | || |||| || | |||||||| ||||| || ||||||||||| ||||| |||||||| || || |||||| | ||| |||||| |||| | |||||||||||||
---gtacgctacat-acttacatttaatggtgaac-cataagtaatgaacaaactcattgattgcatctgttcctcttataaatctatctttgtatttgcattatcttttgctcttgttatctgagtgatctaaattatgcaatgtagAGTCACCCTTTGAATTCCGGGCCCTGGAGGTTGCTTTAGAAGCCATTTGTAGTTTTCTTGCTGCACGTACATCAGAATTGGAGATGGCTGCTTATCCTGC
upper sequence: AT5G09720.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv05s0020g04720.t01 (Vitis vinifera), 3'ss of exon 3
gtagcccttgaccttagtcatttttagaactcaattcttgatttattcttgatctttttgatacctatgttctataaatatcgtaagaaaaacttgtcactctttttacttttggtatta-atatgat-tgcttgatactatatagAATCCGCGTTTGAATTTCGGGCACTAGAGGTTGCTTTGGAAGCTATTTGTAGCTTCCTAGCTGCAAGGACAATAGAATTAGAGAAGTCTGCTTATCCTGC
|| | | | || | | |||||| | | ||| |||| ||| | || | || | || | || || || ||||| || | ||| || |||| || | |||||||| ||||| || ||||| ||||||||||| |||||||| || || |||||| | |||| |||| | || | |||||||||| ||
-------------------------------gtatgtctcactaatc--tagtgattttgaagg--aaataatatgaatacaagtagagatttttctgtctttcttgaaaattagttttctgaatgatctgtgtcataa-atgtagAGTCTCCCTTTGAATTCCGGGCTCTTGAGGTGGCTTTGGAAGCCATTTGTAGTTTTCTTGCTGCACGTACAACAGAACTGGAAACTGCTGCTTATCCAGC
upper sequence: AT5G09720.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: PP1S76_98V6.2 (Physcomitrella patens), 3'ss of exon 4
gtagcccttgaccttagtcatttttagaactcaattcttgatttattcttgatctttttgatacctatgttctataaatatcgtaagaaaaacttgtcactctttttacttttggtattaatatgattgcttgatactatatagAATCCGCGTTTGAATTTCGGGCACTAGAGGTTGCTTTGGAAGCTATTTGTAGCTTCCTAGCTGCAAGGACAATAGAATTAGAGAAGTCTGCTTATCCTGC
| | | || | | | || ||| | | ||| | | ||| ||| | | | || ||| | || | | || | ||||||| |||||||| || ||||| ||||||||||||||||| ||||| ||| |||| | || | || || |||| ||| ||||| ||
----------------------------------------acactgacatcttccgtgtaaatgataagttatgttaattcctttcgaattgtatgtggtacgaatgaga---agttctaacagagttaac-gttgtctggcagCTCCTCCGTTTGAGTTTCGGGCGCTGGAGGTAGCTTTGGAAGCTATTTGCAGCTTTTTAGATGCACGCACCACTGAGTTGGAGACAAATGCATATCCAGC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aaacttgtcactctttttacttttggtattaatatgattgcttgatactatatagAATCCGCGTTTGAATTTCGGGCACTAGAGGTTGCTTTGGAAGCTATTTGTAGCTTCCTAGCTGCAAGGACAATAGAATTAGAGAAGTCTGCTTATCCTGC
tttttacttttggtat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtagcccttgaccttagtcatttttagaactcaattcttgatttattcttgatctttttgatacctatgttctataaatatcgtaagaaaaacttgtcactctttttacttttggtattaatatgattgcttgatactatatagAATCCGCGTTTGAATTTCGGGCACTAGAGGTTGCTTTGGAAGCTATTTGTAGCTTCCTAGCTGCAAGGACAATAGAATTAGAGAAGTCTGCTTATCCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT