Sequence
atgc intronic sequence ATGC exonic sequencegtaagatcagttctctcatttgaaaacttcaagaatcattctttgttgtctctaaagtaatactagaaactgaattaacggtagttacgtaatcagGGTTTGACGTTGGGGAAATTTCTGAAGATGGTCATGATGATTTGGAAGGTTTAGATGCCTCAGCTTCACATATTGCTAACCTTTTGTCCTCTGAACCAGC
Basic information
species | Arabidopsis thaliana |
transcript | AT1G52700.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G52700.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA08G22420.1 (Glycine max), 3'ss of exon 4
----------gtaagatcagttctct-catttgaaaacttcaa--gaatca-ttctttgttgtctctaaagtaatactagaaactgaa--ttaacggtagttacgtaatcagGGTTTGACGTTGGGGAAATTTCTGAAGATGGTCATGATGATTTGGAAGGTTTAGATGCCTCAGCTTCACATATTGCTAACCTTTTGTCCTCTGAACCAGC
||| | | | | | | | | | | |||||| || |||| || ||| || ||| | | | || ||| | | |||||||||||||| | || ||| |||| |||||||||| ||||||| ||| ||||||||||||||||| ||||||||||| ||| | ||||| | || |||||
gtaatattaaataaaccccctcttgtgcttctactcattctgattgaatcagcactgtgtta-ctgtaagctagaacttgcagttaaaccttacttatctaaaattaatcagGGTTTGATATGGGAGAACTTTCAGAAGATGGTCCAGATGATTGGGAGGGTTTAGATGCCTCAGCATCACATATTGCCAACTTGTTGTCAACAGAGCCAGC
upper sequence: AT1G52700.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA15G01350.1 (Glycine max), 3'ss of exon 5
----gtaagatcagttctctcatttgaaaacttcaa---gaatcatt-ctttgttgtct----------ctaaagtaatactagaaactgaattaac--ggtagttacgtaatcagGGTTTGACGTTGGGGAAATTTCTGAAGATGGTCATGATGATTTGGAAGGTTTAGATGCCTCAGCTTCACATATTGCTAACCTTTTGTCCTCTGAACCAGC
|| | | || | | || | | || | |||||| || ||| || | | || | |||| | | | | | | || ||| |||||||||| || || ||| |||| |||||||||| ||||||| ||| ||||||||||||||||| |||| ||||||||| | |||||| | || |||||
gtatgtcaaaacattctttgcaccttctattttttaattaaatcatcactatgtaacctaaaacttttaccatcacaaaaaaagaagcctgacttgcttaatgggtat-taaccagGGTTTGATGTGGGAGAACTTTCAGAAGATGGTCCAGATGATTGGGAGGGTTTAGATGCCTCAGCAGCACACATTGCTAACTTGTTGTCCACAGAGCCAGC
upper sequence: AT1G52700.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA13G43990.2 (Glycine max), 3'ss of exon 5
----gtaagatcagttctctcatttgaaaacttcaag---aatcatt-ctttgttgtct-------ctaaagtaatactagaaa-------ctgaattaacggtagttacgtaatcagGGTTTGACGTTGGGGAAATTTCTGAAGATGGTCATGATGATTTGGAAGGTTTAGATGCCTCAGCTTCACATATTGCTAACCTTTTGTCCTCTGAACCAGC
|| | | || | | || | || || |||||| || ||| || || ||| ||| | ||| || ||| || ||| | |||||||||||| || || ||| |||| |||||||||| ||||||| ||| ||||||||| |||| || |||| ||||||||| | ||||| | || |||||
gtacgtcaaaacattctttgcacctactctttttaaattaaatcatcactgtgtaacctaaaacttttacagtcataaaaaaaaagtctaactagcttattgggtattat-tcatcagGGTTTGATGTGGGAGAACTTTCAGAAGATGGTCCAGATGATTGGGAGGGTTTAGATACCTCGGCAGCACACATTGCTAACTTGTTGTCAACAGAGCCAGC
upper sequence: AT1G52700.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA07G03670.2 (Glycine max), 3'ss of exon 4
------gtaagatcagttctctcatttgaaaacttcaagaatcattctttgttgtctc----taaagtaatactagaaactgaattaacggtagttac--gtaatcagGGTTTGACGTTGGGGAAATTTCTGAAGATGGTCATGATGATTTGGAAGGTTTAGATGCCTCAGCTTCACATATTGCTAACCTTTTGTCCTCTGAACCAGC
||| | | || || || | | || | | || ||| | ||| || ||| | | | || || || |||||||||||||| | || || |||| |||||||||| | ||||| ||| |||||||||||||||| ||||||||||| ||| | ||||| | || |||||
gtaatgttaaagaaactccttgtgcttctaatcattcggattgaatcagcactgtgttattgtaagctagaacttgcagttaaaccttacttatctaacattaatcagGGTTTGATATGGGAGAGCTTTCAGAAGATGGTCCAGTTGATTGGGAGAGTTTAGATGCCTCAGCATCACATATTGCCAACTTGTTGTCAACAGAGCCAGC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttgttgtctctaaagtaatactagaaactgaattaacggtagttacgtaatcagGGTTTGACGTTGGGGAAATTTCTGAAGATGGTCATGATGATTTGGAAGGTTTAGATGCCTCAGCTTCACATATTGCTAACCTTTTGTCCTCTGAACCAGC
aattaac putative branch site (score: 2)
taaagtaata 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagatcagttctctcatttgaaaacttcaagaatcattctttgttgtctctaaagtaatactagaaactgaattaacggtagttacgtaatcagGGTTTGACGTTGGGGAAATTTCTGAAGATGGTCATGATGATTTGGAAGGTTTAGATGCCTCAGCTTCACATATTGCTAACCTTTTGTCCTCTGAACCAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TCAGCT