Sequence
atgc intronic sequence ATGC exonic sequence...taggctacaataataaagttaactaatgcagtaataaatgagttaggatctcagttctgacagttttgtttttgtattttatttgtataataatggacagACAGACAAGGCATCGATGCTCGATGAGATCATAGATTATGTCAAGTTTTTACAACTCCAAGTCAAG
Basic information
species | Arabidopsis thaliana |
transcript | AT2G24260.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT2G24260.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: LOC_Os02g55250.1 (Oryza sativa), 3'ss of exon 4
----------taggctacaa-taataaagttaa-ctaatgcagtaataaatgagttaggatctcagttctgacagttttgtttttgtattttatttgtataataatggacagACAGACAAGGCATCGATGCTCGATGAGATCATAGATTATGTCAAGTTTTTACAACTCCAAGTCAAG
| | | ||| ||| | | || | || | ||||| | || | | | | | | |||| ||| ||||| |||||||||||||||||||| |||||||| |||||||| ||||| | || ||||||||||||
catccatcttcatatcttagctgatagggttgctccagcacaa-agtagagtgacacggatcactgtcactgaaatgacgatgtggaatttcgtttt-----------gcagACCGACAAGGCATCGATGCTCGACGAGATCATTGATTATGTGAAGTTCCTCCAGCTCCAAGTCAAG
upper sequence: AT2G24260.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: LOC_Os09g25040.1 (Oryza sativa), 3'ss of exon 4
-----------taggctacaataataaagtta--actaatgcagtaataaatgagttaggatctcagttctgacagttttgtttttgtattttatttgtataataatggacagACAGACAAGGCATCGATGCTCGATGAGATCATAGATTATGTCAAGTTTTTACAACTCCAAGTCAAG-------------------------
| | || | | || | ||| | | ||| | | ||||| || | ||| | ||| | | || | | | | ||||| |||||||| || ||||| || |||||||| || || |||||||| |||||||||||||||||
cgacgctcgctttcttttcagttccccatttgagattaacctcttcgtgaattgctca---tctcatctcaagtgtgtgtgtgtgtgtgtgtctttcttggagTTGATG-CAGACGGACAAGGCTTCCATGCTGGACGAGATCATCGACTACGTCAAGTTCCTACAACTCCAAGTCAAGGCAAGCACGTACACTAAATTACTAA
upper sequence: AT2G24260.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: LOC_Os06g08500.1 (Oryza sativa), 3'ss of exon 3
taggctacaataataaagttaactaatgcagtaataaatgag-ttaggatctcagttctgacagttttgtttttgtat----tttatttgtataataatg--gacagACAGACAAGGCATCGATGCTCGATGAGATCATAGATTATGTCAAGTTTTTACAACTCCAAGTCAAG
| | | ||| || || | || |||| | || | | || ||| || || || | | || || ||||| |||||||| |||||||| || |||||||| || || |||||||| | || ||||||||||||
-------tgggcgcattcgtgcccaattttgtcatcgtttttcttgacatcttgatgaagaaaatgaagtgattgaatggagttctttgatttgattttgcttgcagACGGACAAGGCGTCGATGCTGGACGAGATCATCGACTACGTCAAGTTCCTGCAGCTCCAAGTCAAG
upper sequence: AT2G24260.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GRMZM2G067654_T01 (Zea mays), 3'ss of exon 4
------------------------tagg-ctacaataataaagttaactaatgcagtaataaatgagttaggatctcagttctgacagttttgtttttgt--attttatttgtataataatggacagACAGACAAGGCATCGATGCTCGATGAGATCATAGATTATGTCAAGTTTTTACAACTCCAAGTCAAG
||| | | | | || | || | ||| | | | | | || | | || | || | | |||| | | ||||| |||||||| |||||||| || |||||||| || || |||| ||| || || ||||||||||||
gtcggcatcccccctctagctagctagctcctttctcttctctctcgctcgcgtcgtcaacaatcaacagacaacactgaaatggcgacgtggtgtgggtcggtcgtcgttgtttgtggttttgcagACGGACAAGGCGTCGATGCTGGACGAGATCATCGACTACGTCAGGTTCTTGCAGCTCCAAGTCAAG
upper sequence: AT2G24260.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GRMZM2G316758_T01 (Zea mays), 3'ss of exon 3
taggctacaat-aataaagttaactaatgcagtaataaatgagttaggatctcagttctgacagttttgtt-tttgtattttatttgtataataatggacagACAGACAAGGCATCGATGCTCGATGAGATCATAGATTATGTCAAGTTTTTACAACTCCAAGTCAAG
| || || | | || | | | ||| || ||| || | || | || | || | ||| | | | || | | ||||| ||||||||||||||||| |||||||| || || || || ||||| | || ||||||||||||
-cgtctttgatcgacagagctt-ccatggcacaaactaataagactcattgtcgctgaaaacgatcgtgccgtgtgtcatcgtatggaattttgttttgcagACCGACAAGGCATCGATGCTTGATGAGATTATTGACTACGTGAAGTTCCTCCAGCTCCAAGTCAAG
upper sequence: AT2G24260.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA09G14380.2 (Glycine max), 3'ss of exon 4
taggctacaataataaagt-taactaatgcagtaataa--atgagttaggatctcagttctgacagttttgtttttgtattttatttgtataataatggacagACAGACAAGGCATCGATGCTCGATGAGATCATAGATTATGTCAAGTTTTTACAACTCCAAGTCAAG----------------------------------
|| ||| | | | || || | || || | || |||| || | | | | || |||| || || | | ||||||||||||||||||| ||||| ||||||||||| ||||| || ||||| | || ||||||||||||
---attataatgtttatttgcaaatattattgtcattattatatgttaacattatatgggtcaatcgctaattgaaatattcgtttggtttgtggaatgacagACAGACAAGGCATCCATGCTAGATGAGATCATCGATTACGTGAAGTTCCTGCAGCTCCAAGTCAAGGTGCGCATCCCGCGTTTTTCTCTTGTACTAGCAT
upper sequence: AT2G24260.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA17G08300.1 (Glycine max), 3'ss of exon 4
------taggctacaataataaagttaactaatgcagtaataaatgagttaggatctcagttctgacagttttgtttttgtattttatttgtataataatggacagACAGACAAGGCATCGATGCTCGATGAGATCATAGATTATGTCAAGTTTTTACAACTCCAAGTCAAG
| | | || |||| ||| || || |||| | || || | | | | | |||| | || | || || ||||||| |||||||| || ||||| ||||||||||| |||||||| ||||| |||| ||||||||||||
tcaacatctatctctcttttagtattaaa-aatacacaaacaaatacaatttcttc-cattgttaaaatatgtgttcattgggttggctcgtg----gattgacagACTGACAAGGCCTCCATGCTGGATGAGATCATCGATTATGTGAAGTTCCTACAGCTCCAAGTCAAG
upper sequence: AT2G24260.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA15G33020.1 (Glycine max), 3'ss of exon 4
taggctacaataataaagttaactaatgcagtaataaatgagttagg---atctcagttctgacagt--tttgtttttgtattttatttgtataataatggacagACAGACAAGGCATCGATGCTCGATGAGATCATAGATTATGTCAAGTTTTTACAACTCCAAGTCAAG
|| || |||| ||| | || || | | || | | || | | | | | | || | | || |||| || || | | ||||||||||||||||||| ||||| ||||||||||| ||||| || ||||| | || ||||||||||||
----tcactattataatgtttatta-tgtaattattattatcctatgctaacattaaatgggtcaatccctaattgaaatattcgtttggtttgtggaatgacagACAGACAAGGCATCCATGCTAGATGAGATCATCGATTACGTGAAGTTCCTGCAGCTCCAAGTCAAG
upper sequence: AT2G24260.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA09G14380.1 (Glycine max), 3'ss of exon 4
taggctacaataataaagt-taactaatgcagtaataa--atgagttaggatctcagttctgacagttttgtttttgtattttatttgtataataatggacagACAGACAAGGCATCGATGCTCGATGAGATCATAGATTATGTCAAGTTTTTACAACTCCAAGTCAAG
|| ||| | | | || || | || || | || |||| || | | | | || |||| || || | | ||||||||||||||||||| ||||| ||||||||||| ||||| || ||||| | || ||||||||||||
---attataatgtttatttgcaaatattattgtcattattatatgttaacattatatgggtcaatcgctaattgaaatattcgtttggtttgtggaatgacagACAGACAAGGCATCCATGCTAGATGAGATCATCGATTACGTGAAGTTCCTGCAGCTCCAAGTCAAG
upper sequence: AT2G24260.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv11s0037g00040.t01 (Vitis vinifera), 3'ss of exon 4
--taggctacaataataaagttaactaatgcagtaataaatgagttaggatctcagttctgacagttttgtttttgtattttatttgtataataatggacagACAGACAAGGCATCGATGCTCGATGAGATCATAGATTATGTCAAGTTTTTACAACTCCAAGTCAAG
| || | | | | | | |||| ||| | || | | | || | | || || || |||| |||||| |||||||| || ||||| ||||||||||| || |||||||| || | || |||||||| |||
cccggtctcgagcagtgcggc-gagtcatgcgtagcgaaaccacctattttatttttactttaatacgaaatcgataatgttgggtggggtggaatg-acagACGGACAAGGCTTCAATGCTGGATGAGATCATTGACTATGTCAAATTCCTGCAGCTCCAAGTGAAG
upper sequence: AT2G24260.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: PP1S173_83V6.1 (Physcomitrella patens), 3'ss of exon 3
taggctaca-ataataaagttaactaatg-cagtaataaatgagttaggatctcagttctgacagttttgtttttgtattttatttgtataataatggacagACAGACAAGGCATCGATGCTCGATGAGATCATAGATTATGTCAAGTTTTTACAACTCCAAGTCAAG
| || | || | | | ||| | || | | ||| |||| | | | | | | | || ||| | || |||||| || ||||| |||||||| ||||| ||||| ||||| |||||||| | ||||||||||| |||
gaaacttcgtgtatttttttcatctactttcacttgggcttattttaaaatctaattagaagaaatgatccaatcctcttactgctgtctgtggat--acagACGGATAAGGCGTCGATGCTGGATGAAATCATCGATTACGTCAAGTTCCTGCAACTCCAAGTAAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ggatctcagttctgacagttttgtttttgtattttatttgtataataatggacagACAGACAAGGCATCGATGCTCGATGAGATCATAGATTATGTCAAGTTTTTACAACTCCAAGTCAAG
ttctgac putative branch site (score: 2)
acagttttgtttttgt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
taggctacaataataaagttaactaatgcagtaataaatgagttaggatctcagttctgacagttttgtttttgtattttatttgtataataatggacagACAGACAAGGCATCGATGCTCGATGAGATCATAGATTATGTCAAGTTTTTACAACTCCAAGTCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA
- - - acaataa
- - - - - - - - - -taactaa
- - - - - - - - - - - - - - - - aataaat
- - - - - - - - - - - - - - - - - - - - - - - -atctcag