Sequence
atgc intronic sequence ATGC exonic sequencegtatagcaaggcttcttaatgtgcccagtgatctttcaaaaccagtttcaaacaaccatttaatcttgaatctggttgtaattttttttcagGTTTGGTACAATCTTCAGCCATGATTCTGATTCAATGCCACGTGTTTGGACCGGAAAAGAGGATCTTCGAGCAATTACTAAATCAGCTCGATCTGCT
Basic information
species | Arabidopsis thaliana |
transcript | AT1G72960.1 |
intron # | 16 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G72960.1 (Arabidopsis thaliana), 3'ss of exon 16
lower sequence: GLYMA15G02780.1 (Glycine max), 3'ss of exon 17
gtatagcaaggcttcttaatgtgcccagtgatctttcaaaaccagtttcaaacaaccatttaatcttgaatctggttgtaattttttttcagGTTTGGTACAATCTTCAGCCATGATTCTGATTCAATGCCACGTGTTTGGACCGGAAAAGAGGATCTTCGAGCAATTACTAAATCAGCTCGATCTGCT
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--gtatgaaacttatgcaacat-ttaagttgacttgttagacttgtt--gagttttgctttagag--gcacttatcttaaatttcaaagcagGTTTTTGACATTGTTTAGTCATGATTCTGATTCAATGCCTCGTATTTGGACGGGAAAAGAAGATGTTCGAGCAATCACCAAGTCTGCCCGCTCTTCG
upper sequence: AT1G72960.1 (Arabidopsis thaliana), 3'ss of exon 16
lower sequence: GLYMA13G42650.1 (Glycine max), 3'ss of exon 18
gtatagcaaggcttcttaatgtgcccagtgatctttcaaaaccagtttcaaacaaccatttaatcttgaatctggttgtaattttttttcagGTTTGGTACAATCTTCAGCCATGATTCTGATTCAATGCCACGTGTTTGGACCGGAAAAGAGGATCTTCGAGCAATTACTAAATCAGCTCGATCTGCT
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--gtatgaaccttatacaacatgtaagtttacttgttgagttttactttagagg--cactta-tcttaaatttcaaag-----------cagGTTTATGACATTGTTTAGTCATGATTCTGATTCAATGCCTCGTATTTGGACGGGAAAAGAAGATGTTCGAGCCATCACCAAGTCTGCCCGCTCTTCC
upper sequence: AT1G72960.1 (Arabidopsis thaliana), 3'ss of exon 16
lower sequence: GLYMA08G20610.1 (Glycine max), 3'ss of exon 17
gtatagcaaggcttcttaatgtgcccagtgatctttcaaaaccagtttcaaacaaccatttaatcttgaatctggttgtaattttttttcagGTTTGGTACAATCTTCAGCCATGATTCTGATTCAATGCCACGTGTTTGGACCGGAAAAGAGGATCTTCGAGCAATTACTAAATCAGCTCGATCTGCT
| | ||||| | | | ||| |||| | || ||| | | | || | | | | ||| ||||||| | | || ||||||||||||||||||||||| ||||||||||| || ||||| ||| | ||||| || || || | ||||| ||| ||
---gtgtgaatcttctgcaacttctaagttgactttta---cctgttcgattgagttttacttagatgcacttaccttaactttgaaagcagGTTTACAATGTTGTTTAGCCATGATTCTGATTCAATGCCTCGTGTTTGGACGGGGAAAGAAGATATACGAGCCATCACCAAGACTGCTCGCTCTTCT
upper sequence: AT1G72960.1 (Arabidopsis thaliana), 3'ss of exon 16
lower sequence: GLYMA07G01230.1 (Glycine max), 3'ss of exon 17
gtatagcaaggcttcttaatgtgcccagtgatctttcaaaaccagtttcaaacaaccatttaatcttgaatctggttgtaattttttttcagGTTTGGTACAATCTTCAGCCATGATTCTGATTCAATGCCACGTGTTTGGACCGGAAAAGAGGATCTTCGAGCAATTACTAAATCAGCTCGATCTGCT
|||| | ||||| | | | ||| |||| | || | |||| || | | | | ||| | ||||||| | | || ||||||||||||||||||||||| ||||||||||| || ||||| ||| | ||||| || || || | ||||| ||| ||
gtatg---aatcttctgcaacttctaagttgacttttacctgttcgtttgagttttacttta--tatgcacttaccttaactttgaatgcagGTTTACGATGTTGTTTAGCCATGATTCTGATTCAATGCCTCGTGTTTGGACGGGTAAAGAAGATATACGAGCCATCACCAAGACTGCTCGCTCTTCT
upper sequence: AT1G72960.1 (Arabidopsis thaliana), 3'ss of exon 16
lower sequence: Vv09s0002g02200.t01 (Vitis vinifera), 3'ss of exon 17
---------------gtatagcaaggcttcttaatgtgcccagtgatctttcaa----aaccagtttcaaacaaccatttaatcttgaatctggttgtaatttttttt--------cagGTTTGGTACAATCTTCAGCCATGATTCTGATTCAATGCCACGTGTTTGGACCGGAAAAGAGGATCTTCGAGCAATTACTAAATCAGCTCGATCTGCT
||| || | ||| | | || | || ||| | || | | | | || || || ||| | | || |||| |||||||| ||| | || |||||||||||||| |||||||||||||| ||||| || ||||| ||| |||| ||||| || ||| | ||||| ||| ||
gttgcaactgttacattatttgaaattcttttattttccctttttatttttagattacaagaaatcgggatctactgctttggactgtatcaaatggggatggattttactgcatgcagGTTTGCGACATTGTTTAGCCATGATTCTGACTCAATGCCACGTGTCTGGACTGGGAAAGAAGATATTCGTGCAATCACCAAAACTGCTCGTTCTTCT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aaaaccagtttcaaacaaccatttaatcttgaatctggttgtaattttttttcagGTTTGGTACAATCTTCAGCCATGATTCTGATTCAATGCCACGTGTTTGGACCGGAAAAGAGGATCTTCGAGCAATTACTAAATCAGCTCGATCTGCT
atttaat putative branch site (score: 4)
ttttttttc putative PPT
ttgtaattttttttca 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatagcaaggcttcttaatgtgcccagtgatctttcaaaaccagtttcaaacaaccatttaatcttgaatctggttgtaattttttttcagGTTTGGTACAATCTTCAGCCATGATTCTGATTCAATGCCACGTGTTTGGACCGGAAAAGAGGATCTTCGAGCAATTACTAAATCAGCTCGATCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTC