Sequence
atgc intronic sequence ATGC exonic sequence...tttgtactgccttgatcatcatctttgctaaagatatcccatgctggttttaatctgaataatgttaactttcttgaaatgtttgctacaattttcacagACTGAAATGACAACTGCTGAAAGAGAACTTGATCAAAATACAAATTTTGATTGGAACCGTATACAAGAGAGTGGAAAAGAATTGGTGCCAGTTTTTGGAC
Basic information
| species | Arabidopsis thaliana |
| transcript | AT3G20630.1 |
| intron # | 5 |
| splice site | 3' |
| intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G20630.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: LOC_Os01g08200.1 (Oryza sativa), 3'ss of exon 5
---tttgtactgccttgatcatcat-ctttgctaaagatatcccatgctggttttaatctgaataatgttaactttcttgaaatgtttgctacaattttcacagACTGAAATGACAACTGCTGAAAGAGAACTTGATCAAAATACAAATTTTGATTGGAACCGTATACAAGAGAGTGGAAAAGAATTGGTGCCAGTTTTTGGAC
| |||| || || |||| || || | | ||||| || | ||||| || | | | | || | ||| | || ||||| || ||||| |||||||||||||| |||||||| || ||||||| ||| ||||| | |||||||| ||||| ||||| | | | | || |
tattctgtagcatctc-atgttcatactgtgttttcccctttatatgcttgtct--atctgtctagtttagaggctatttga-tgtgacccttttgttgtgcagACCGAGATGACTACTGCTGAAAGAGAGCTTGATCACAACACAAATTATGACTGGAATAGAATACAAGAAAGTGGCAAAGATGCCGAACTTTTATACGGCC
upper sequence: AT3G20630.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G107696_T02 (Zea mays), 3'ss of exon 9
tttgtactgccttgatcatcatctttgctaaagatatcccatgctggttttaatctgaataatgttaacttt---cttga----aatgtttgcta--caattttcacagACTGAAATGACAACTGCTGAAAGAGAACTTGATCAAAATACAAATTTTGATTGGAACCGTATACAAGAGAGTGGAAAAGAATTGGTGCCAGTTTTTGGAC
| || | || | || || | | | ||| || || | ||| | || ||| |||| | ||||| | || | |||||||| ||||| |||||||| || ||||||||| || ||||||| ||| ||||| | |||||||| ||||||||||| | || | |||||||
-------tatgttacagctgatgcataatacagtttttt--tcctgcttgacatgtacatagaggcaattttatgcttggccacattgtttataaatttgttcttgcagACTGAGATGACTACTGCTGAGAGGGAACTTGATGCTAACACAAATTATGACTGGAATAGAATACAAGAAAGTGGAAAAGACGCTGAGCTTCTGTTTGGAC
upper sequence: AT3G20630.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA06G39770.1 (Glycine max), 3'ss of exon 5
-----------------------------------------------------------------------------tttgtactgccttgatcatcatctttgctaaagatatcccatgctggt--tttaatctgaataatg-ttaactttc------ttgaaatg-tttgctacaattttcacagACTGAAATGACAACTGCTGAAAGAGAACTTGATCAAAATACAAATTTTGATTGGAACCGTATACAAGAGAGTGGAAAAGAATTGGTGCCAGTTTTTGGAC
||||| || | | | || |||| | ||| | || ||| | |||| || ||| | || ||||| | || | | |||||||||||||||||||||||||||||||||||||| |||||||||||||||||||| || || ||||| |||||| ||||| | | ||| |||||||||
gttaattatttatcttgaaatgatacttttcacacacacaatcaaactatattaattatttgtcttgagaataaacttttgtcttgttactccaacaggcatggcataagagcgtacttgcaattaattaaatttaaatatcacttgactcttaatattttaaaatggtccactttcttatattcagACTGAAATGACAACTGCTGAAAGAGAACTTGATCACAATACAAATTTTGATTGGAATCGAATCCAAGAAAGTGGACAAGAAGTAGATCCAATTTTTGGAC
upper sequence: AT3G20630.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA12G22240.1 (Glycine max), 3'ss of exon 5
----------------------------------------------------------------------------tttgtactgccttgatcatcatctttgc-taaagatat-cccatgctggttttaatctgaataatgttaactttcttgaaatgtt----tgctacaattttca-----cagACTGAAATGACAACTGCTGAAAGAGAACTTGATCAAAATACAAATTTTGATTGGAACCGTATACAAGAGAGTGGAAAAGAATTGGTGCCAGTTTTTGGAC
||||| || | | | || ||| | | | | | || ||| | |||| | | ||| | || || || | |||||| |||||||||||||||||||||||||||||||||||||||||||| |||||||||||||| || || ||||| |||||| ||||| | | ||| |||||||||
gttaattatttatcttgaaatgatacttttcacgcacaataaaaaatatattaattattaatcttgagtataaacttttgtcttgttactccaacaggcatggcgtaagagtgtacttaaaattaattaaatttaaatatcacttgact-cttaatattttaaactggtccaatttcttatattcagACTGAAATGACAACTGCTGAAAGAGAACTTGATCAAAATACGAATTTTGATTGGAATCGAATCCAAGAAAGTGGACAAGAAGTAGATCCAATTTTTGGAC
upper sequence: AT3G20630.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: Vv19s0014g03920.t01 (Vitis vinifera), 3'ss of exon 5
---tttgtactgccttgatcatcatctttgctaaagatatcccat-gctggttttaatctgaataatgttaactttcttgaaatgtttgctacaattttcacagACTGAAATGACAACTGCTGAAAGAGAACTTGATCAAAATACAAATTTTGATTGGAACCGTATACAAGAGAGTGGAAAAGAATTGGTGCCAGTTTTTGGAC
||| | | | || || | ||||| ||| ||| | | || || | | ||| | | || | | ||| || | || |||||||||||||| ||||||||||| |||||||| || ||||| ||||||||||||||||| || ||||| |||||| ||||| | | ||| | |||||||
ttttttttttttgataaatgatagttgttgcttgagaatcaacattgtttacttacatttcattaaaccttaagctcaatatacattttct----tgtttccagACTGAAATGACTACTGCTGAAAGGGAACTTGACCAGAATACCAATTTTGATTGGAACCGAATTCAAGAAAGTGGACAAGAAGTTGAACCACTATTTGGAC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ggttttaatctgaataatgttaactttcttgaaatgtttgctacaattttcacagACTGAAATGACAACTGCTGAAAGAGAACTTGATCAAAATACAAATTTTGATTGGAACCGTATACAAGAGAGTGGAAAAGAATTGGTGCCAGTTTTTGGAC
tgttaac putative branch site (score: 2)
ttttcac putative PPT
aataatgttaacttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tttgtactgccttgatcatcatctttgctaaagatatcccatgctggttttaatctgaataatgttaactttcttgaaatgtttgctacaattttcacagACTGAAATGACAACTGCTGAAAGAGAACTTGATCAAAATACAAATTTTGATTGGAACCGTATACAAGAGAGTGGAAAAGAATTGGTGCCAGTTTTTGGAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - -ctaaaga
- - - - - - - - - - - - - - - - - - - - - - -ggtttta
