Sequence
atgc intronic sequence ATGC exonic sequencegtagcacctttagcctgagtattgacccaagcccaccttgtgatagtggtgatgaatgataataatcaggaaatgaatctgactgagattatttgcttgtgctgtgtaagCTTTTTATCGAAGAGATTTGCCGGGATGTACATCGTTCTGACTCGGAATGGAAGATCATATTGCTTAGATACTTCAACCCTGTTGGTGCACATCCTAGTG
Basic information
species | Arabidopsis thaliana |
transcript | AT4G23920.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G23920.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM2G079803_T01 (Zea mays), 3'ss of exon 1
gtagcacctttagcctgagtattgacccaagcccaccttgtgatagtggtgatgaatgataataatcaggaaatgaatctgactgagattatttgcttgtgctgtgtaagCTTTTTATCGAAGAGATTTGCCGGGATGTACATCGTTCTGACTCGGAATGGAAGATCATATTGCTTAGATACTTCAACCCTGTTGGTGCACATCCTAGTG
| | ||| || || ||| || | || || ||||||| | || || | || |||| || | || || |||||||||||| | | ||||| | | |||||||||||||| || ||||| |||||||| || |||||||| ||||||||||
-----------------------gtctgctgcctctttttcaatgtgaaaacctgctgaagattgttagctctctaagttgactgaaaagtttcaaatg-gttgc---agCTCGTTGTTGAGGATATTTGCCGGGATATCTACCGTTCAGGTCCTGAATGGAAGATCATTTTACTTAGGTACTTCAATCCAGTTGGTGCTCATCCTAGTG
upper sequence: AT4G23920.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA05G36850.1 (Glycine max), 3'ss of exon 4
gtagcacctttagcctgagtattgacccaagcccaccttgtgatagtggtgatgaatgataataatcaggaaatgaatctgactgagattatttgcttgtgctgtgtaagCTTTTTATCGAAGAGATTTGCCGGGATGTACATCGTTCTGACTCGGAATGGAAGATCATATTGCTTAGATACTTCAACCCTGTTGGTGCACATCCTAGTG
|| ||| | | | ||| | || ||||| ||| ||| | |||| | ||||| | ||| | | | ||||| | |||||||| ||||| || ||| | | ||| | || || || ||||| | ||| || | |||||||||||||| |||||||||||||| ||||
------------------gttttgcattttaatttcataattataatt-tgttgaatactaacaatgat-------atctaa-tgagagtttttctcttttc------agCTTATCATCGAAGAAATTTGTCGTGATATCTACCGTGCAGATTCTGATTGGAAAGTTATACTGTTGAGATACTTCAACCCAGTTGGTGCACATCCCAGTG
upper sequence: AT4G23920.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA08G02690.2 (Glycine max), 3'ss of exon 4
gtagcacctttagcctgagtattgacccaagcccaccttgtgatagtggtgatgaatgataataatcaggaaatgaatctgactgagattatttgcttgtgctgtgtaagCTTTTTATCGAAGAGATTTGCCGGGATGTACATCGTTCTGACTCGGAATGGAAGATCATATTGCTTAGATACTTCAACCCTGTTGGTGCACATCCTAGTG
|| |||| | | | | ||| | | || | | || | | || |||||| ||||| | ||| | | | ||||||| |||||||| ||||| || ||| | || ||| | || || || |||| | ||| | | |||||||||||||| |||||||||||||| ||||
------------------gttttgattttaattt-cataattataataatt-tgttgaacagtactgaacaatgatatctga-tgagagtttttctcttttc------agCTTTTCATCGAAGAAATTTGTCGCGATATCCACCGTGCAGATTCAGATTGGACAGTTATACTATTGAGATACTTCAACCCAGTTGGTGCACATCCCAGTG
upper sequence: AT4G23920.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv02s0025g01580.t01 (Vitis vinifera), 3'ss of exon 4
---------------------------gtagcacc--tttagcctgagtattgacccaagcccaccttgtgatagtggtgatgaatgataataatcaggaaat---------gaatctgactgag--attatttgcttgtgctgtgtaagCTTTTTATCGAAGAGATTTGCCGGGATGTACATCGTTCTGACTCGGAATGGAAGATCATATTGCTTAGATACTTCAACCCTGTTGGTGCACATCCTAGTG
||| | || || | | || || || | | | |||| | ||| | | |||| | | | ||||| | | | | | | | ||||| |||| ||||| || ||||| ||| | | |||| || || |||||||| || | ||||| |||||||||||||| |||||||||||| ||||||
gtatgctttgggcaatgaacagaggcaatagtttcggttcaggcatactaaagaaacagattgcacataaaggaatggtta-gaacctttacaatctgtttcttctttattagcatctgttctaacaactgatgaggttgatcctttcagCTTGTTATTGAAGATATATGCCGTGATATTTACGGTTCAGATTCTGAATGGAAAATAGTGTTGCTGAGATACTTCAACCCGGTTGGTGCACATTCTAGTG
upper sequence: AT4G23920.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv02s0025g01560.t01 (Vitis vinifera), 3'ss of exon 4
gtagcacctttagcctgagtattgacccaagcccaccttgtgatagtggtgat--gaatgataataatcaggaaatgaatctgactgagattatttgcttgtgctgtgtaagCTTTTTATCGAAGAGATTTGCCGGGATGTACATCGTTCTGACTCGGAATGGAAGATCATATTGCTTAGATACTTCAACCCTGTTGGTGCACATCCTAGTG
||||| |||| | | || ||| | | |||| | || | | || || | || ||| | | | || | ||| | | | ||||||| || ||||| || ||||| ||| | || || ||||| || |||||||| || | ||||| ||||| |||||||| ||||| |||||||||||||
------tagttagca-aagtactccttccttttcattttg-aactttcttgattaggatcctctttattagcatctgt-tctagc--aactgatgaggttg-attctttcagCTTTTCATTGAAGATATATGCCGTGATATCCACCGCTCTGATTCTGAATGGAAAATTGTGTTGCTGAGATATTTCAACCCAGTTGGGGCACATCCTAGTG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atgataataatcaggaaatgaatctgactgagattatttgcttgtgctgtgtaagCTTTTTATCGAAGAGATTTGCCGGGATGTACATCGTTCTGACTCGGAATGGAAGATCATATTGCTTAGATACTTCAACCCTGTTGGTGCACATCCTAGTG
atctgac putative branch site (score: 3)
agattattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtagcacctttagcctgagtattgacccaagcccaccttgtgatagtggtgatgaatgataataatcaggaaatgaatctgactgagattatttgcttgtgctgtgtaagCTTTTTATCGAAGAGATTTGCCGGGATGTACATCGTTCTGACTCGGAATGGAAGATCATATTGCTTAGATACTTCAACCCTGTTGGTGCACATCCTAGTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA