Sequence
atgc intronic sequence ATGC exonic sequence...gaaccatgcattgtatctcaagggtttgtatttccaatttatattgtttcatgctccttaactaatttgcaggtattgaacttttcatccatgattacagGTTGGCTACATTGTTACATCTTGCTTGCTCAATGAGAACCATGACTTTTTGAAGTTGGCAATAAATACAGTGCGGAACGATATTATTGGTCGGAATGAGA
Basic information
species | Arabidopsis thaliana |
transcript | AT5G22770.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G22770.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA17G05410.1 (Glycine max), 3'ss of exon 2
------------------------------------------------------------------------------------------gaaccatgcattgtatctcaag--ggtttgtatttccaatttatattgt-ttcatgctccttaactaatttgcaggtattgaacttttcatccatgattacagGTTGGCTACATTGTTACATCTTGCTTGCTCAATGAGAACCATGACTTTTTGAAGTTGGCAATAAATACAGTGCGGAACGATATTATTGGTCGGAATGAGA
| | ||| | | || ||| || | | | | | | || | | | || | | | | || ||| |||| | |||||||| |||||||| ||||| | ||||| ||||| || ||||||||| | | |||||| |||||||||||||| || ||||| |||||||| ||||| |
gtattttgttctccttcatgacacctttttataatgatttgtttctctctctctctctctctctctctctctcaatatattactttattctggtgaagtatttcagtttcagttcatttacatacctagcagagaaaatatctatagactgtgaagaagt----aattctaatattgccataaatgactgcagGTTGGGTACATTGTAACATCAAGTTTGCTTAATGAAAATCATGACTTTCTCAGGTTGGCTATAAATACAGTGCGCAATGATATCATTGGTCGTAATGAAA
upper sequence: AT5G22770.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA12G30520.1 (Glycine max), 3'ss of exon 2
-gaaccatgcattgtatctcaag--ggtttgtatttccaatttatattgtttc-atgctccttaactaatttgcaggtattgaacttttcatccatgattacagGTTGGCTACATTGTTACATCTTGCTTGCTCAATGAGAACCATGACTTTTTGAAGTTGGCAATAAATACAGTGCGGAACGATATTATTGGTCGGAATGAGA
| | || | | || ||| || || | | | | || || | | | || | | | || ||| |||| | |||||||| |||||||| ||||| | ||||| ||||| || ||||||||| | | |||||| |||||||||||||| || ||||| |||||||| ||||| |
ctggtgaagtgtttcagtttcagttcatttacatgtctagcagagaaaatatctatagactgtgaagaag----gaattctaatattgccataaatgactgcagGTTGGGTACATTGTAACATCAAGTTTGCTTAATGAAAATCATGACTTTCTCAGGTTGGCTATAAATACAGTGCGCAATGATATCATTGGTCGTAATGAAA
upper sequence: AT5G22770.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv06s0061g01170.t01 (Vitis vinifera), 3'ss of exon 2
gaaccatgcattgtatctcaagggtttgtatttccaatttat-attgtttcatgctccttaactaatttgcaggtattgaacttttcatccatgattacagGTTGGCTACATTGTTACATCTTGCTTGCTCAATGAGAACCATGACTTTTTGAAGTTGGCAATAAATACAGTGCGGAACGATATTATTGGTCGGAATGAGA
|||| | | |||| | | | || || || | || || | | | || ||| || | | | | || || | ||||| || |||||||| || || || || ||||||||||||||||||||||||| ||| ||||||||||| ||||| || ||||||||||| || ||||| |
-ttttgtgcagttcactgcaagtttattaactttcatcacattacaattggttggttcattacacttttattaactttcatcatattataattggctgcagGTGGGGTACATTGTAACGTCATGTTTACTCAATGAGAACCATGACTTTTTGAGGTTAGCAATAAATACTGTGCGCAATGATATTATTGGCCGAAATGAAA
upper sequence: AT5G22770.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: PP1S26_36V6.1 (Physcomitrella patens), 3'ss of exon 2
gaaccatgcattgtatctcaagggtttgtatttccaatttatatt-gtttcatgctccttaactaatttgcaggtattgaacttttcatccatgattacagGTTGGCTACATTGTTACATCTTGCTTGCTCAATGAGAACCATGACTTTTTGAAGTTGGCAATAAATACAGTGCGGAACGATATTATTGGTCGGAATGAGA
| | | |||| | |||| | | || | ||| || ||| | | || | || || | || | | |||||||||||||| || ||||||||| |||||||||||||||| || |||||| ||| || || || || || || || || ||||||||||||||||
----------gtatgtatcaaatatcgatattccttgcaaccgtcagtgacttgcctctgcactgttacactgg-gtctaatgattggt--attaat-cagGTTGGCTACATCGTCACATCTTGCCTGCTCAATGAGAACCACGATTTTTTGCGACTGGTCATTAACACTGTCCGTAATGACATCATTGGTCGGAATGAGA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gtttcatgctccttaactaatttgcaggtattgaacttttcatccatgattacagGTTGGCTACATTGTTACATCTTGCTTGCTCAATGAGAACCATGACTTTTTGAAGTTGGCAATAAATACAGTGCGGAACGATATTATTGGTCGGAATGAGA
aactaat putative branch site (score: 2)
ttaactaattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gaaccatgcattgtatctcaagggtttgtatttccaatttatattgtttcatgctccttaactaatttgcaggtattgaacttttcatccatgattacagGTTGGCTACATTGTTACATCTTGCTTGCTCAATGAGAACCATGACTTTTTGAAGTTGGCAATAAATACAGTGCGGAACGATATTATTGGTCGGAATGAGA
gaaccat
- - - - - - - atctcaa
- - - - - - - - - - - ggtttgt
- - - - - - - - - - - - - - - - - - - - - - - - - atgctcc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - taactaa