Sequence
atgc intronic sequence ATGC exonic sequence...cttgagatatttaacgatgttgagattctgtccatataatgatatgatatgttcataaataacatgcataaatctgggctatttccctctcttgatacagCATGGAGACCATTATCCTGGGCGACAAAAGAATAGGGATCAAAACAAGTGTTCTAGAGGAAAAGGCCACGGCTTGTAACATGCTTTGTTGCTATGCTGAT
Basic information
species | Arabidopsis thaliana |
transcript | AT5G19820.1 |
intron # | 7 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G19820.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: LOC_Os07g38760.1 (Oryza sativa), 3'ss of exon 7
-cttgagatat-ttaacgatgttgagattctgtccatataatgatatgatatgttcataaataacatgcataaatctgggctatttccctctcttgatacagCATGGAGACCATTATCCTGGGCGACAAAAGAATAGGGATCAAAACAAGTGTTCTAGAGGAAAAGGCCACGGCTTGTAACATGCTTTGTTGCTATGCTGAT
|| |||| | | | | || | | || || | | | | | | | |||| | | || | || || ||||||||| || || |||| || ||||||||||||||||| ||| ||| ||||| ||||| || || || || ||||| |||||||| || || |||||||||
ttcagaaatatatcatccttttttatgtgaggtgtggtggttgtttttagcttcttgttggt--tctgcaatattgcccctaatctttttcactcaatacagCATTGAAACAATTACGCTTGGCGACAAAAGAATAGGTATCCGAACTAGTGTACTAGAAGAGAAAGCAACAGCTTGCAACATGCTATGCTGTTATGCTGAT
upper sequence: AT5G19820.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA05G28950.2 (Glycine max), 3'ss of exon 9
cttgagata--tttaacgatgttgagattct---gtccatataatgatatgatatgttcataaataacatgcataaatctgggctatttccctctcttgatacagCATGGAGACCATTATCCTGGGCGACAAAAGAATAGGGATCAAAACAAGTGTTCTAGAGGAAAAGGCCACGGCTTGTAACATGCTTTGTTGCTATGCTGAT
|| || || | | | |||| | | || |||| | || | |||| | ||| |||| | | ||||| | | | || |||||||| |||| || || |||||| |||| || ||||| || ||||||||||||||||| || || || |||||||||||||||||||||||||||
ctaataatgatttcattcttatggagaataagaagcacacataaaaacattttttgtttaggcgggacaaatataattaagttttatttatccat-----tgtagTATGGAGACTATTACTCTTGGGGACAAACGAATTGGAATCAAGACTAGTGTTCTAGAGGAAAAAGCTACAGCATGTAACATGCTTTGTTGCTATGCTGAT
upper sequence: AT5G19820.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA08G12120.1 (Glycine max), 3'ss of exon 7
cttgagatatttaacgatgttgagattctgtcca--tataatgatatg---atatgttcataaataacatgcataaatctgggctatttccctctcttgat-acagCATGGAGACCATTATCCTGGGCGACAAAAGAATAGGGATCAAAACAAGTGTTCTAGAGGAAAAGGCCACGGCTTGTAACATGCTTTGTTGCTATGCTGAT
| ||||||| | ||||| | || || ||||| | | || | ||| | | ||||| | || | | | || || |||||||| |||| || || ||||| |||| || ||||| || ||||||||||||||||| || || || |||||||||||||||||||||||||||
------actaataacgatttcattcttctggagaattagaagcatatgtcaaaacatttttgtttaagcaggacaaatccaactaagttttatttatccattgtagTATGGAGACTATTACTCTTGGGGACAAGCGAATTGGAATCAAGACTAGTGTTCTAGAGGAAAAAGCTACAGCATGTAACATGCTTTGTTGCTATGCTGAT
upper sequence: AT5G19820.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: Vv06s0004g00500.t01 (Vitis vinifera), 3'ss of exon 7
cttgagatatttaacgatgttgagattctgtccatataatgatatgata--tgttcataaataacatgcataaatctgg-gctatttccctctcttgatacagCATGGAGACCATTATCCTGGGCGACAAAAGAATAGGGATCAAAACAAGTGTTCTAGAGGAAAAGGCCACGGCTTGTAACATGCTTTGTTGCTATGCTGAT
| || | | | | | | | ||| | || ||| ||| |||| | || | || | | || | | || | | | ||| ||||||||||||| || || || ||| ||||||||||||| || ||||| || ||||| || ||||| ||||| |||||||| ||||||||||| |||
--tactatctagagcaagggcaatagagtgtt-gtttagccataggatcattgttgctgaaggatatttgggattttgctgacagtttttttgttcattgcagTATGGAGACCATTACTCTTGGGGATAAACGAATAGGGATCAAGACTAGTGTCCTGGAGGAGAAAGCCACCGCTTGCAACATGCTATGTTGCTATGCCGAT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gatatgttcataaataacatgcataaatctgggctatttccctctcttgatacagCATGGAGACCATTATCCTGGGCGACAAAAGAATAGGGATCAAAACAAGTGTTCTAGAGGAAAAGGCCACGGCTTGTAACATGCTTTGTTGCTATGCTGAT
ctatttccctctctt CT-rich tract
ttcataaataacat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
cttgagatatttaacgatgttgagattctgtccatataatgatatgatatgttcataaataacatgcataaatctgggctatttccctctcttgatacagCATGGAGACCATTATCCTGGGCGACAAAAGAATAGGGATCAAAACAAGTGTTCTAGAGGAAAAGGCCACGGCTTGTAACATGCTTTGTTGCTATGCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -aataaca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gcataaa