Sequence
atgc intronic sequence ATGC exonic sequencegtcagtatccttgtttctctattctatactaggatggtttaagttagtgttttgtatgttacgcttatttttgtggacttttgcttgtagGTTGATCTAGAATATTTATTGGATCGCTACCAACCTGAAAAAGAGGTTAATTGGGGTGATGAATTATCTCTTGGAGAGCAACAGAGATTGGGTATGGCCA
Basic information
species | Arabidopsis thaliana |
transcript | AT4G39850.3 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G39850.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: LOC_Os01g73530.1 (Oryza sativa), 3'ss of exon 9
-------------------------------------gtcagtatccttgtttctctattctat-actaggatggtttaagt-----tagtgttttgtatgttacgcttatttttgtggacttttgcttgtagGTTGATCTAGAATATTTATTGGATCGCTACCAACCTGAAAAAGAGGTTAATTGGGGTGATGAATTATCTCTTGGAGAGCAACAGAGATTGGGTATGGCCA
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gtaatactcataattatccacttgatagattggcatctttagctgcctcattgcacttgtttgtgactattttgtcccaagtacctagaaagtgttactggaaaaccttagtttttttcttcccttttggtagGTGGATCTGGAATATTTGCTAGAACGCTACCCTCTTGATAAGGAAGTTAACTGGGGTGATGAATTGTCTCTTGGAGAGCAACAAAGATTGGGAATGGCCC
upper sequence: AT4G39850.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: LOC_Os05g01700.1 (Oryza sativa), 3'ss of exon 6
------------gtcagtatccttgtttctctat--tctatactaggatggtttaagttagtgttttgtatgttacgcttatttttgtggacttttgct-----tgtagGTTGATCTAGAATATTTATTGGATCGCTACCAACCTGAAAAAGAGGTTAATTGGGGTGATGAATTATCTCTTGGAGAGCAACAGAGATTGGGTATGGCCA
| ||| | | | | |||| || | | || | || | | ||| | | | || | ||||| || ||||||| | ||||| || | || ||||| | | ||| || || ||||| |||||||||||||| || ||||| |||||||| ||||| || ||||| |
gtaagtaataggattcatattgatactcaattgccatttatattatgctttattgatctactactgagtacaggg-acctgctggattgtaaccttgctccttatgcagGTTGACTTGGAATACTTGCTAGAACGCTATCCTCTTGATAAGGAAGTTAACTGGGGTGATGAATTGTCCCTTGGTGAGCAACAAAGATTAGGAATGGCAA
upper sequence: AT4G39850.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA08G14480.1 (Glycine max), 3'ss of exon 6
---------------------------------gtcagtatccttgtttctctattctatacta--ggatggtttaagttagtgttttgt-atgttacgc----ttatttttgtgga---cttttgcttgta-----gGTTGATCTAGAATATTTATTGGATCGCTACCAACCTGAAAAAGAGGTTAATTGGGGTGATGAATTATCTCTTGGAGAGCAACAGAGATTGGGTATGGCCA
|| | | |||| | | | | || | || || || | | | | ||| || ||| | ||||| | || | ||| | | |||| ||||||||| || ||| |||||||||| |||| |||||||||||||| || |||||||||||| | || | || |||||||| ||||||| |||||||
gtggagctattaaaaaatgtgaaactcacatctaatcctacttctatatctcagtgccacattaatgcatagtgtatgatgattatatgtcattttaatcattattattcatctgaattgcttgtacatgtattaaagGTTGATCTTGAGTATCTATTGGATCGGTACCCGCCTGAAAAAGAGGTAAACTGGGGTGATGAACTTTCATTGGGTGAGCAACAACGATTGGGCATGGCCA
upper sequence: AT4G39850.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA05G31270.1 (Glycine max), 3'ss of exon 7
-------------gtcagtatccttgtttctctattctatactag-----gatggtttaagttagtgttttgtat--gttacgcttatttttgtgga---cttttgcttgta-----gGTTGATCTAGAATATTTATTGGATCGCTACCAACCTGAAAAAGAGGTTAATTGGGGTGATGAATTATCTCTTGGAGAGCAACAGAGATTGGGTATGGCCA
| | | ||| | |||| | | | | || || || | | | | | || | | | | ||||| | || | ||| | | |||| ||||||||| || ||| |||||||||| |||| |||||| |||||| || |||||||||||| | || | || |||||||| ||||||| |||||||
gtgaaactcacatctaatcctacttctatctcagtgccacattaatgtttagtgtttgatgattatatgttattttaatcattattattcatctgaattgcttgtacatgtattgaagGTTGATCTTGAGTATCTATTGGATCGGTACCCGTCTGAAACAGAGGTAAACTGGGGTGATGAACTTTCGTTGGGCGAGCAACAACGATTGGGCATGGCCA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ggtttaagttagtgttttgtatgttacgcttatttttgtggacttttgcttgtagGTTGATCTAGAATATTTATTGGATCGCTACCAACCTGAAAAAGAGGTTAATTGGGGTGATGAATTATCTCTTGGAGAGCAACAGAGATTGGGTATGGCCA
cttttgctt CT-rich tract
ttatttttgt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtcagtatccttgtttctctattctatactaggatggtttaagttagtgttttgtatgttacgcttatttttgtggacttttgcttgtagGTTGATCTAGAATATTTATTGGATCGCTACCAACCTGAAAAAGAGGTTAATTGGGGTGATGAATTATCTCTTGGAGAGCAACAGAGATTGGGTATGGCCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA