Sequence
atgc intronic sequence ATGC exonic sequence...ttgtaagctgggagtatttaaacccttgacctccatatctatattggttcttgcgattgatggctgatattccaacctgtaaaactgttttgacatccagGGCTGGAAGACATTTTTTGAGGAACCAGTTATGTTAATAGCTTTTGTATTGCTGGGAAGGAATCTTGAACAGAGAGCTAAAATAAAAGCCACCAGTGATA
Basic information
species | Arabidopsis thaliana |
transcript | AT4G33520.2 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G33520.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: LOC_Os08g37950.1 (Oryza sativa), 3'ss of exon 5
ttgtaagctgggagtatttaaacccttgacctccatatctatattggttcttgcgattgatggctgatattccaacctgtaaaactgttttgacatc---cagGGCTGGAAGACATTTTTTGAGGAACCAGTTATGTTAATAGCTTTTGTATTGCTGGGAAGGAATCTTGAACAGAGAGCTAAAATAAAAGCCACCAGTGATA
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attcattctgcatctgctctattttacgcacgttagtttaatctaggtatatgtgatgcat---tgtcataatagtttgttttacggtttaagtttcttgcagGGGTGGAAGACATTTTTTGAGGAGCCGGTTATGTTAGTAGCTTTTGTTCTTCTTGGGAAGAACCTTGAGCAGAGGGCGAAGCTAAAAGCTACTAGTGATA
upper sequence: AT4G33520.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G315931_T01 (Zea mays), 3'ss of exon 5
------------------------------------------------------------ttgtaagctggg---agtatttaaaccc------ttgacctccatatctatattg-gttcttgcgattg-----atggc---------tgatattccaa-------cctgtaaaactgttttgacatccagGGCTGGAAGACATTTTTTGAGGAACCAGTTATGTTAATAGCTTTTGTATTGCTGGGAAGGAATCTTGAACAGAGAGCTAAAATAAAAGCCACCAGTGATA
|||| || | | ||||||| | || |||| | |||||| | |||| ||| ||||| | |||| || | | || | || || | ||||| |||||||||||||||||||||||||||||||| ||||||||||| | || || | |||||| || ||||| || ||| | ||||| ||||||||||
gtagctcctactctatttttccaaaagattttttttggtttgttgcatgctttgcagatattgttggccagtttcatcgtttaaactcctttagttaccctctagctctataatatgttccgttaatttgcatcatggcatatcgccttaatatgtcagtagcttgcttatatcgttccatttacctgcagGGGTGGAAGACATTTTTTGAGGAACCAGTTATGTTGATAGCTTTTGTTCTTCTAGGGAAGAATCTGGAGCAGAGGGCAAAACTTAAAGCTACCAGTGATA
upper sequence: AT4G33520.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G315931_T02 (Zea mays), 3'ss of exon 5
ttgtaagctgggagtatttaaacccttgacctccatatctatattggttcttgcgattgatggctgatattccaacctgtaaaactgttttgacatccagGGCTGGAAGACATTTTTTGAGGAACCAGTTATGTTAATAGCTTTTGTATTGCTGGGAAGGAATCTTGAACAGAGAGCTAAAATAAAAGCCACCAGTGATA------------------------------------------------------------
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----------------------------------------------------------tatgtcagtagctt--gcttatatcgttccatttacctgcaggggtggaagacattttttgaggaaccagttatgttgatagcttttgttcttctagggaagAATCTGGAGCAGAGGGCAAAACTTAAAGCTACCAGTGATATGACTGGACTGCTTAGTATTCTTCCATCTAAAGCACGCCTAATGGTGGATAATGATGCTG
upper sequence: AT4G33520.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA05G24520.1 (Glycine max), 3'ss of exon 1
ttgtaagctgggagtatttaaacccttgacctccatatctatattggttcttgcgattgatggctgatattccaacctgtaaaa----ctgttttgacatc----cagGGCTGGAAGACATTTTTTGAGGAACCAGTTATGTTAATAGCTTTTGTATTGCTGGGAAGGAATCTTGAACAGAGAGCTAAAATAAAAGCCACCAGTGATA
| ||||| | | | | | |||| | | | || | ||| | ||| ||| || |||| | | ||||| |||||| | || || ||||||||| ||||| |||| || ||||| ||| | |||||||||||||||||||||||||| || ||||| ||||||||||
-------gaaagtatatttgttttgtgaaattatgcaattggattg-tgataatgtatgtaaatataaatttaattgtgttaaatgatcttttttaatgtttttgcagGGTTGGAAGGCCTTCTTCGAGGAACCAATTATGCTAATTGCATTTGTTTTGTTAGGAAGGAATCTTGAACAGAGAGCTAAGATTAAAGCAACCAGTGATA
upper sequence: AT4G33520.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA08G07710.1 (Glycine max), 3'ss of exon 5
ttgtaagctgggagtatttaaacccttgacctccatatctatattggttcttgcgattgatggctgatattccaacctgtaaaa----ctgttttgacatc----cagGGCTGGAAGACATTTTTTGAGGAACCAGTTATGTTAATAGCTTTTGTATTGCTGGGAAGGAATCTTGAACAGAGAGCTAAAATAAAAGCCACCAGTGATA
| ||||| | | | | | ||| || | | | || | ||| | ||| ||| || |||| | | ||||| |||||| | || |||||||||||| ||||| |||| || ||||| ||| | ||||||||||| |||||||||||||| || ||||| |||||||||
--------aaagtatatttgttttgtgaaattatgcagttggatttgtgatagtgtatgtaaatataaatttaattgtgttaaatgatcttttttaatgtttatgcagGGTTGGAAGGCCTTCTTTGAGGAACCAATTATGCTAATTGCATTTGTCTTGTTAGGAAGGAATCTCGAACAGAGAGCTAAGATTAAAGCAGCCAGTGATA
upper sequence: AT4G33520.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: Vv12s0142g00400.t01 (Vitis vinifera), 3'ss of exon 2
ttgtaagctg-ggagtatttaaacccttgacctccatatctatattggttcttgcgattgatggctgatattccaacctgtaaaac---tgttttga-catccagGGCTGGAAGACATTTTTTGAGGAACCAGTTATGTTAATAGCTTTTGTATTGCTGGGAAGGAATCTTGAACAGAGAGCTAAAATAAAAGCCACCAGTGATA
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----aggatatagggtagtagttgccttgaaatggaaag-taagcttgtggaagacaaagttggttgatgctgttgtctgttgaatgaatatgttgttcgtgcagGGCTGGAAGGCATTTTTTGAAGAACCAATCATGTTAATAGCATTTGTCTTGCTAGGAAGGAATCTGGAACAGAGAGCTAAAATTAAAGCTACCAGTGATA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ggttcttgcgattgatggctgatattccaacctgtaaaactgttttgacatccagGGCTGGAAGACATTTTTTGAGGAACCAGTTATGTTAATAGCTTTTGTATTGCTGGGAAGGAATCTTGAACAGAGAGCTAAAATAAAAGCCACCAGTGATA
ttttgac putative branch site (score: 3)
ctgtttt CT-rich tract
tgatatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttgtaagctgggagtatttaaacccttgacctccatatctatattggttcttgcgattgatggctgatattccaacctgtaaaactgttttgacatccagGGCTGGAAGACATTTTTTGAGGAACCAGTTATGTTAATAGCTTTTGTATTGCTGGGAAGGAATCTTGAACAGAGAGCTAAAATAAAAGCCACCAGTGATA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT