Sequence
atgc intronic sequence ATGC exonic sequencegtaagttgttgcttaaccactagtttaaccttttcaatcaaatgctagtctctaaactcttgtctattatcagGTCATCCGCGTATCATTCACAGGGACATCAAGTCGTCTAACATTCTTTTAGAGGACAACTTTGATGCTCGG
Basic information
species | Arabidopsis thaliana |
transcript | AT1G68690.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G68690.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GRMZM2G028731_T01 (Zea mays), 3'ss of exon 3
-----------gta-agttgttgcttaacca--ctagtttaaccttttcaatcaaatg----ctagtctc------taaactcttgtctattat---cagGTCATCCGCGTATCATTCACAGGGACATCAAGTCGTCTAACATTCTTTTAGAGGACAACTTTGATGCTCGG
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gtaagatgcatgcatggaagctgcttaattatattagtttgaactactcagaataatggagcttgatcttacttaataaatgtttgcttatcgtacgtagGTCATCCAAGGATCATTCACAGGGATATCAAGTCGTCAAACATCTTGCTTGATGACCAGTTTGAGGCTCAG
upper sequence: AT1G68690.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA01G23180.1 (Glycine max), 3'ss of exon 3
-------------------------------gtaagttgttgcttaaccactagtttaaccttttcaatcaaatgctagtctctaaactcttgtctattatcagGTCATCCGCGTATCATTCACAGGGACATCAAGTCGTCTAACATTCTTTTAGAGGACAACTTTGATGCTCGG
||| | ||| || | ||| ||| ||| | | | | | || ||| ||||| | || | |||||||||||||| |||||||| || |||||||||||||| ||| | ||| || |
catcaattgatgtagctacttgaaccatcttgtagaatactgcatagatgttgtattattaatttattattgatgtaattgtatg---ttatgcacatt-tcagGCAACCCTAGGATCATTCACAGGGATATCAAGTCATCAAACATTCTTTTAGATTTCAATTATGAAGCCAAG
upper sequence: AT1G68690.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA02G14310.1 (Glycine max), 3'ss of exon 3
-------------------------------gtaagttgttgcttaaccactagtttaaccttttcaatcaaatgctagtctctaaactcttgtctattatcagGTCATCCGCGTATCATTCACAGGGACATCAAGTCGTCTAACATTCTTTTAGAGGACAACTTTGATGCTCGG
||| | | ||| || | ||| ||| ||| || | | | | || ||| ||||| | || | |||||||||||||| |||||||| || |||||||| ||||| ||| ||||| || |
catcaattgatgcaggtacttgactcatctagtaggataatgcatagaagttgtattattaatttactgttgatgttattttatg---ttatgcgcatt-tcagGCAACCCTAGGATCATTCACAGGGATATCAAGTCATCAAACATTCTCTTAGATTTCAATTTTGAAGCCAAG
upper sequence: AT1G68690.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: EFJ19888 (Selaginella moellendorffii), 3'ss of exon 2
gtaagttgttgcttaaccactagtttaaccttttcaatcaaatgctagtctctaaactcttgtctattatcagGTCATCCGCGTATCATTCACAGGGACATCAAGTCGTCTAACATTCTTTTAGAGGACAACTTTGATGCTCGG
| | | | || | | | || || ||| || || | || |||| ||||| || |||||||| ||||||| |||||||||||||||||||| || |||| ||||| |||| |
----------------gtaagatctctatctctccgttggaac-ttaatctaaaagtcattcgttcttg-cagGCCATCCTCGAATCATTCATCGGGACATAAAGTCGTCTAACATTCTTTTGGATAACAATTTTGACGCTCAG
upper sequence: AT1G68690.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: EFJ20011 (Selaginella moellendorffii), 3'ss of exon 2
gtaagttgttgcttaaccactagtttaaccttttcaatcaaatgctagtctctaaactcttgtctattatcagGTCATCCGCGTATCATTCACAGGGACATCAAGTCGTCTAACATTCTTTTAGAGGACAACTTTGATGCTCGG
| | || | || | | | || || ||| || || | || |||| ||||| || |||||||| ||||||| |||||||||||||||||||| || | || ||||| |||| |
----------------gtaagatttctatctctccgttggaac-ttaatctaaaagtcattcgttcttg-cagGCCATCCTCGAATCATTCATCGGGACATAAAGTCGTCTAACATTCTTTTGGATAATAATTTTGACGCTCAG
upper sequence: AT1G68690.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: EFJ07415 (Selaginella moellendorffii), 3'ss of exon 2
gtaagttgttgcttaaccactagtttaaccttttcaatcaaatgctagtctctaaactcttgtctattatcagGTCATCCGCGTATCATTCACAGGGACATCAAGTCGTCTAACATTCTTTTAGAGGACAACTTTGATGCTCGG
| | | | || | | | || || ||| || || | || |||| ||||| || |||||||| ||||||| |||||||||||||||||||| || | || ||||| |||| |
----------------gtaagatctctatctctccgttggaac-ttaatctaaaagtcattcgttcttg-cagGCCATCCTCGAATCATTCATCGGGACATAAAGTCGTCTAACATTCTTTTGGATAATAATTTTGACGCTCAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.actagtttaaccttttcaatcaaatgctagtctctaaactcttgtctattatcagGTCATCCGCGTATCATTCACAGGGACATCAAGTCGTCTAACATTCTTTTAGAGGACAACTTTGATGCTCGG
ctctaaa putative branch site (score: 3)
ctcttgtct CT-rich tract
ttttcaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagttgttgcttaaccactagtttaaccttttcaatcaaatgctagtctctaaactcttgtctattatcagGTCATCCGCGTATCATTCACAGGGACATCAAGTCGTCTAACATTCTTTTAGAGGACAACTTTGATGCTCGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA