Sequence
atgc intronic sequence ATGC exonic sequencegtaagttcttcagtgattcagcacagttgttatctgtgtcatataatacattagaaggttttatcttccatcgcctgagacatttatcttttgcagAAAGAATTAATCAGGACGGTTGATCTTGGTCCATTCAAGCATGTTGTGGATGACGGGCTCGAGCTGAGGAAAGCAGCTTTTGAGTGTGTGTTTACTCTGG
Basic information
species | Arabidopsis thaliana |
transcript | AT2G02560.2 |
intron # | 25 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT2G02560.2 (Arabidopsis thaliana), 3'ss of exon 25
lower sequence: LOC_Os02g07120.1 (Oryza sativa), 3'ss of exon 25
gta-agttcttcagtgattca--gcacagttgttatctgtgtcatataatacattagaaggttttatct-tccatc---gcctgagacatttatcttttgcagAAAGAATTAATCAGGACGGTTGATCTTGGTCCATTCAAGCATGTTGTGGATGACGGGCTCGAGCTGAGGAAAGCAGCTTTTGAGTGTGTGTTTACTCTGG
||| |||| | | ||| | | ||||| | || | | | | ||| || ||||| | | |||||| | | | ||| || | ||||| ||||||| ||||| || ||||| ||||| || ||||||||||||||||| || || || || || |||||||| || ||||| |||||| ||| ||
gtatagtttcttattgacttcttgttttgttgtgagctaggac-tgttatatcaagtaatgttttttgtatccatcttatcgtaatgattttttcctgtgcagCAAGAATTGATCAGAACAGTTGACCTTGGGCCTTTCAAGCATGTTGTGGACGATGGTCTTGAACTCAGGAAAGCTGCCTTTGAATGTGTGGATACATTGC
upper sequence: AT2G02560.2 (Arabidopsis thaliana), 3'ss of exon 25
lower sequence: GRMZM2G168629_T01 (Zea mays), 3'ss of exon 25
------------------gtaagttcttcagtga------ttcagcacagttgttatctgtgtcatataatacat-tagaaggttttatct-tccatcgcctga-gacatttatcttttgcagAAAGAATTAATCAGGACGGTTGATCTTGGTCCATTCAAGCATGTTGTGGATGACGGGCTCGAGCTGAGGAAAGCAGCTTTTGAGTGTGTGTTTACTCTGG
| |||| | ||| | | || | || | || | || | | | | | | ||||| |||| ||| || | | ||||||| |||| ||||||||||| ||||||||||| || ||||| |||||||| ||||| || || || || |||||||| || ||||| |||||| |||| |
gtattgtctcagttttttgagctctcttaactgagggagttgcctcataattataataaaaccgacattacagttgcattatatcttatccatccaggaagtgacgatttcctttctttgcagCAAGAGTTAATCAGGACAGTTGATCTTGGGCCTTTCAAACATGTTGTAGATGATGGTCTTGAACTCAGGAAAGCTGCCTTTGAATGTGTGGATACTTTAT
upper sequence: AT2G02560.2 (Arabidopsis thaliana), 3'ss of exon 25
lower sequence: GLYMA17G00570.1 (Glycine max), 3'ss of exon 25
-----------------------------------------------------------------------------------------gtaagttcttcagtgattcagcacagttgttatctgtgtcatataatacattagaaggttttatctt-ccatcgcctgagacattt------atcttttgcagAAAGAATTAATCAGGACGGTTGATCTTGGTCCATTCAAGCATGTTGTGGATGACGGGCTCGAGCTGAGGAAAGCAGCTTTTGAGTGTGTGTTTACTCTGG
| | || | | | | | || | | ||| || | | |||||| | || | || | | || ||||| | ||| ||| |||| | || ||||| |||||||||||||| ||||||||| |||||||||| || || || ||||||| || |||||||| ||||| || |
gtaatctgaattgtgccattctgttccatgtatttcagttgagtatatagcattacaataaaacttgactttatactccccattattctaagaatattttaatttagtaatatattttgcaatagctgcatttaccaaaatagaagatcttgtattactggaggtggactcattttaatgaaattttgacagCAAGAGCTCATAAGGACAGTTGATCTTGGTCCTTTCAAGCATATTGTGGATGATGGACTTGAATTGAGGAAGGCGGCTTTTGAATGTGTAGACACATTAC
upper sequence: AT2G02560.2 (Arabidopsis thaliana), 3'ss of exon 25
lower sequence: GLYMA07G40230.2 (Glycine max), 3'ss of exon 26
gtaagttcttcagtgattcagcacagttgttatctgtgt-catataatacattagaaggttttatcttccatcgcctgagacattt------atcttttgcagAAAGAATTAATCAGGACGGTTGATCTTGGTCCATTCAAGCATGTTGTGGATGACGGGCTCGAGCTGAGGAAAGCAGCTTTTGAGTGTGTGTTTACTCTGG
| | | | || | | | | || | | | ||| | | |||||| | || | || | || ||||| | ||| ||| |||| | || ||||| |||||||||||||| || |||||| |||||||||| || || || ||||||| || |||||||| ||||| || ||
--atactttgtaatggcttttta-atctactagaaagatgcctttaacaaaatagaagatcttgtattactggaggtgtctcattttaatgaaattttgacagCAAGAGCTCATAAGGACAGTTGATCTTGGTCCTTTTAAGCATATTGTGGATGATGGACTTGAATTGAGGAAGGCGGCTTTTGAATGTGTAGACACATTGC
upper sequence: AT2G02560.2 (Arabidopsis thaliana), 3'ss of exon 25
lower sequence: Vv12s0035g01840.t01 (Vitis vinifera), 3'ss of exon 26
------------gtaagttcttcagtgattcagcacagttgttatctgtgtcatataatacattagaaggttttatcttccatcgcctgagacatttatcttttgcagAAAGAATTAATCAGGACGGTTGATCTTGGTCCATTCAAGCATGTTGTGGATGACGGGCTCGAGCTGAGGAAAGCAGCTTTTGAGTGTGTGTTTACTCTGG
| | | || | || | ||| ||| | | || | || || |||| || ||| | | || | | ||||| |||| ||||| || || || ||||||||||| ||||||||| |||||||||| || || ||||||||||||||||||||||| ||||| || |||
tctgctactaaatttattgtttttatccttttccttttttgctattctttttattgataccaagtgacggttaaatattctgtttcatg--------tttctatgcagCAAGAGTTAATTAGAACAGTCGATCTTGGTCCTTTCAAGCATATTGTGGATGATGGTCTTGAGCTGAGGAAAGCAGCTTTTGAATGTGTAGACACACTGC
upper sequence: AT2G02560.2 (Arabidopsis thaliana), 3'ss of exon 25
lower sequence: PP1S35_209V6.1 (Physcomitrella patens), 3'ss of exon 25
gtaagttcttcagtgatt-cagcacagttgttatctgtgtcatataatacattagaaggttttatcttccatcgcctgagacatttatcttt--------tgcagAAAGAATTAATCAGGACGGTTGATCTTGGTCCATTCAAGCATGTTGTGGATGACGGGCTCGAGCTGAGGAAAGCAGCTTTTGAGTGTGTGTTTACTCTGG
|||| || || | | | || | ||| | | || | ||| | | | || | ||| ||| || || ||||||| | |||||||| || ||||||||||| ||||||||| |||||||||| ||||| || || ||||| | ||| ||||| |||||| ||| ||
---tcttctgttttgtttactccgcgtctgccttttgttcagaaca--acgatctgtggtatccgcagttgttcactaaattattcatcgttggtggatgtgtagAAAGAGCTCATCAGGACCGTGGATCTTGGTCCTTTCAAGCATATTGTGGATGATGGGCTGGAACTCAGGAAGGGAGCCTTTGAATGTGTGGATACCTTGC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tataatacattagaaggttttatcttccatcgcctgagacatttatcttttgcagAAAGAATTAATCAGGACGGTTGATCTTGGTCCATTCAAGCATGTTGTGGATGACGGGCTCGAGCTGAGGAAAGCAGCTTTTGAGTGTGTGTTTACTCTGG
tttatctttt CT-rich tract
atttatctttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagttcttcagtgattcagcacagttgttatctgtgtcatataatacattagaaggttttatcttccatcgcctgagacatttatcttttgcagAAAGAATTAATCAGGACGGTTGATCTTGGTCCATTCAAGCATGTTGTGGATGACGGGCTCGAGCTGAGGAAAGCAGCTTTTGAGTGTGTGTTTACTCTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT