Sequence
atgc intronic sequence ATGC exonic sequencegttagtgcaagaatatgaagtgatctttagttcggtttgtttttttacagttttgctgaaatagtaagatatgtttacattagatagaacaaaaatctaaaatgagatgtggtgaatgtaaagttgagtatatgatccattgtaatgtatttgaaaaacttttggcaacagCTGAAACTGTAATATACAGAATATATTACTACATAAATAGGAGTGGAAATGGGCATCTTACCTTGAGAGAGCTTAAGCGAGGAAATTTAGTTGACGCAAT
Basic information
species | Arabidopsis thaliana |
transcript | AT1G54450.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G54450.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: LOC_Os10g33680.1 (Oryza sativa), 3'ss of exon 6
gttagtgcaagaatatgaagtgatctttagttcggtttgtttttttacagttttgctgaaatagtaagatatgtttacattagatagaacaaaaatctaaaatgagatgtggtgaatgtaaagttgagtatatgatccattgtaatgtatttgaaaaacttttggcaacagCTGAAACTGTAATATACAGAATATATTACTACATAAATAGGAGTGGAAATGGGCATCTTACCTTGAGAGAGCTTAAGCGAGGAAATTTAGTTGACGCAAT
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------------------------------------------------------------tgaggattctacgattggacctggtc-aatgactattggtagtgatttgctggatgcctgcatctcattc----atctgcta-atcgtttattatgtaatttt-----cagCTGAGACTGTAATATACAGAATCTTTTATTCCATAAATAGAGCTGGAAATGGCCATCTTACCCTCAGAGAGCTAAAACGTGGGAATTTAATTGCTGCGAT
upper sequence: AT1G54450.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GRMZM2G148323_T01 (Zea mays), 3'ss of exon 6
gttagtgcaagaatatgaagtgatctttagttcggtttgtttttttacagttttgctgaaatagtaagatatgtttacattagatagaacaaaaatctaaaatgagatgtggtgaatgtaaagttgagtatatgatccattgtaatgtatttgaaaaacttttggcaacagCTGAAACTGTAATATACAGAATATATTACTACATAAATAGGAGTGGAAATGGGCATCTTACCTTGAGAGAGCTTAAGCGAGGAAATTTAGTTGACGCAAT
| | | ||| ||| ||| ||| || | | |||| || || ||| ||| | | | | || |||| | |||| | |||| || ||||||||||||||||| | ||||| ||||||||| ||| ||||| ||||| || |||||||||| || || ||||||||| ||| ||| |
---------------------------------------------------------aactcaactatctat-tttgtttta---agatcagatttgctgaatgttttgaactgttgctaatgtttgctgtgtcac--------attcatttcttgatgtttt--cttcagCGGAGACTGTAATATACAGAATCTTTTACTCCATAAATAGATCTGGGAATGGTCATCTGACTCTGAGAGAGCTCAAACGTGGAAATTTAATTGCTGCACT
upper sequence: AT1G54450.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA03G41180.1 (Glycine max), 3'ss of exon 6
gttagtgcaagaatatgaagtgatctttagttcggtttgtttttttacagttttgctgaaatagtaagatatgtttacattagatagaacaaaaatctaaaatgagatgtggtgaatgtaaagttgagtatatgatccattgtaatgtatttgaaaaacttttggcaacagCTGAAACTGTAATATACAGAATATATTACTACATAAATAGGAGTGGAAATGGGCATCTTACCTTGAGAGAGCTTAAGCGAGGAAATTTAGTTGACGCAAT
|||| ||| | | | | | || | |||| | | || | | || || | | ||| | | ||| | |||| ||||||||||||| ||||||||||||||||||||||| ||||| |||||||| | ||||||| |||| ||||||||||| ||||| || |||| |||||
----------------------------------------------------------------cttcatatatttgagt--gttgggaaaatcagttaaaggattgttttgtctttttgtgtgtg-gtgcaatgttcataactgtttgtttttt---ccaatggcc-cagCTGAAACTGTCATATACAGAATATATTACTACATTAATAGATCAGGAAATGGCCGTCTTACCCTGAGGGAGCTTAAGCGTGGAAACATAATTGATGCAAT
upper sequence: AT1G54450.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA10G30930.1 (Glycine max), 3'ss of exon 6
gttagtgcaagaatatgaagtgatctttagttcggtttgtttttttacagttttgctgaaatagtaagatatgtttacattagatagaacaaaaatctaaaatgagatgtggtgaatgtaaagttgagtatatgatccattgtaatgtatttgaaaaacttttggcaacagCTGAAACTGTAATATACAGAATATATTACTACATAAATAGGAGTGGAAATGGGCATCTTACCTTGAGAGAGCTTAAGCGAGGAAATTTAGTTGACGCAAT
| || |||| | || | | | | | || || | | | || | || | || | | | ||||| || | ||||||||||||||||||||||||| ||||| ||||| ||||| ||||||||| | ||| ||| |||| ||||| ||||| ||||| || |||| |||||
------------------------------------------------------------------tgcta-gttttctttcaactggtctttggtttctggtgtaatactttttttttt---ttttgcattgagtgcaatattcttaatttgttttttcaatgtcc-cagCTGAAACTGTAATATACAGAATCTATTATTACATTAATAGATCTGGAAATGGTCGTCTCACCCTGAGGGAGCTGAAGCGTGGAAACATAATTGATGCAAT
upper sequence: AT1G54450.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA19G43790.1 (Glycine max), 3'ss of exon 6
gttagtgcaagaatatgaagtgatctttagttcggtttgtttttttacagttttgctgaaatagtaagatatgtttacattagatagaacaaaaatctaaaatgagatgtggtgaatgtaaagttgagtatatgatccattgta---atgtatttgaaaaacttttggcaacagCTGAAACTGTAATATACAGAATATATTACTACATAAATAGGAGTGGAAATGGGCATCTTACCTTGAGAGAGCTTAAGCGAGGAAATTTAGTTGACGCAAT
| | | || | | | | | | || || ||| | ||| || | | || | || ||| | |||||| | |||| ||||||||||||| ||||||||||||||||||||||| ||||| |||||||| | ||||||| |||| ||||| || || ||||| || |||| |||||
-------------------------------------------------------------------gttgggcataggctggtcatcatag---tttatggtgtaatgctct---tgttttgtcttttgtgtggtgcaatgttcataactatttgtttttccaatggcc-cagCTGAAACTGTCATATACAGAATATATTACTACATTAATAGATCAGGAAATGGTCGTCTTACCCTGAGGGAGCTGAAACGTGGAAACATAATTGATGCAAT
upper sequence: AT1G54450.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA20G36530.1 (Glycine max), 3'ss of exon 6
gttagtgcaagaatatgaagtgatctttagttcggtttgtttttttacagttttgctgaaatagtaagatatgtttacattagatagaacaaaaatctaaaatgagatgtggtgaatgtaaagttgagtatatg-atccattgtaatgtatttga--aaaacttttggcaac--agCTGAAACTGTAATATACAGAATATATTACTACATAAATAGGAGTGGAAATGGGCATCTTACCTTGAGAGAGCTTAAGCGAGGAAATTTAGTTGACGCAAT
|| || | | ||| || | | | ||| | | | | || | | || ||| || ||| | || | | ||| | | |||||||||||||||||||||||| ||||| ||||| ||||| ||||||||| ||| ||| |||| ||||| ||||| ||||| || |||| |||||
--------------------------------------------------------------------------ctagtttggtttcaactggtatttggtttctgctgtaat--actttattttatttttttgcatctggtgcaatattcttaatttgatttttcaacgtcccagCTGAAACTGTAATATACAGAATCTATTATTACATTAATAGATCTGGAAATGGTTGTCTCACCCTGAGGGAGCTGAAGCGTGGAAACATAATTGATGCAAT
upper sequence: AT1G54450.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: PP1S7_163V6.2 (Physcomitrella patens), 3'ss of exon 6
gttagtgcaagaatatgaagtgatctttagttcggtttgtttttttacagttttgctgaaatagtaagatatgtttacattagatagaacaaaaatctaaaatgagatgtggtgaatgtaaagttgagtatatgatccattgtaatgtatttgaaaaacttttggcaacagCTGAAACTGTAATATACAGAATATATTACTACATAAATAGGAGTGGAAATGGGCATCTTACCTTGAGAGAGCTTAAGCGAGGAAATTTAGTTGACGCAAT
||||| | | | | ||| || | | ||||| | || | || | | | | | |||| || || | | ||| | | || | | |||| | | | | |||||||||||||||||||||||||||| ||| | ||||||| ||| ||||| | || | |||||| | ||||| | |||||| ||| || |
------------gcatgaattcttaaccgactttgcatgtgacattcagactcatttcgaatag-atgacaaaaatatttgctccatgctggtattattaaattt-atcctgtacaccacatcctgattctctgcacttgcatgatgttct------atggtggtggacagCTGAAACTGTAATATACAGAATATTCTACCATGTAAATAGAGCTGGGAATGGTCGGCTACAACTTAGAGAGTTAAAGCGGAGTAATTTAATTGCTGCTCT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgtaaagttgagtatatgatccattgtaatgtatttgaaaaacttttggcaacagCTGAAACTGTAATATACAGAATATATTACTACATAAATAGGAGTGGAAATGGGCATCTTACCTTGAGAGAGCTTAAGCGAGGAAATTTAGTTGACGCAAT
ctttt CT-rich tract
taatgtatttgaaaaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttagtgcaagaatatgaagtgatctttagttcggtttgtttttttacagttttgctgaaatagtaagatatgtttacattagatagaacaaaaatctaaaatgagatgtggtgaatgtaaagttgagtatatgatccattgtaatgtatttgaaaaacttttggcaacagCTGAAACTGTAATATACAGAATATATTACTACATAAATAGGAGTGGAAATGGGCATCTTACCTTGAGAGAGCTTAAGCGAGGAAATTTAGTTGACGCAAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT