Sequence
atgc intronic sequence ATGC exonic sequencegtcagtttatgtacattgaacaacaataagttgtttatatcttctagttccttttactaaagtatagattttggtgttgtttccagAGACCGATTCAAACTCTCAGTGGTGGTCAGAAACAAAGAATTGCCATTGCTGGTGCTTTAGCTGAAGCGTGCAAAGTGCTATTGTTGGATGAGCTCACAA
Basic information
species | Arabidopsis thaliana |
transcript | AT4G33460.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G33460.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: LOC_Os01g56400.1 (Oryza sativa), 3'ss of exon 3
gtcagtttatgtacattgaacaacaataagttgtttatatcttctagttccttttactaaagtatagattttggtgttgtttccagAGACCGATTCAAACTCTCAGTGGTGGTCAGAAACAAAGAATTGCCATTGCTGGTGCTTTAGCTGAAGCGTGCAAAGTGCTATTGTTGGATGAGCTCACAA
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------gtaggca-gctgacatgctccttttggattataatctattgtctgcacaaggttcacaaacatcctt-catccaacacagAGGCCAATCCAAACTCTGAGTGGCGGGCAGAAGCAGAGAGTTGCAATTGCCGGTGCTTTAGCTGAAGCATCCAAAGTACTACTACTGGATGAGCTGACCA
upper sequence: AT4G33460.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GRMZM2G111511_T05 (Zea mays), 3'ss of exon 1
gtcagtttatgtacattgaacaacaataagttgtttatatcttctagttccttttactaaagtatagattttggtgttgtttccagAGACCGATTCAAACTCTCAGTGGTGGTCAGAAACAAAGAATTGCCATTGCTGGTGCTTTAGCTGAAGCGTGCAAAGTGCTATTGTTGGATGAGCTCACAA
|| | | || || | | | ||| | ||| || || | || | | | | ||||| || || |||||||| |||||||| |||||||| ||| |||| ||||||||||| ||||||||||| | |||||| || || |||| || || || |
------gtaggctt-ctaaattccagcttttggatcataatctaaagtc---ttcacaatgttaataaccct--tcattcaaacagAGGCCAATCCAAACTCTGAGTGGTGGGCAGAAACAGAGAGTTGCAATTGCTGGTGCGTTAGCTGAAGCATCCAAAGTATTACTGCTGGACGAACTGACCA
upper sequence: AT4G33460.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA06G15900.1 (Glycine max), 3'ss of exon 4
---gtcagtttatgtacattgaacaa-caataagttgtttatatcttctagttccttttactaaagtatagattttggtgttgtttccagAGACCGATTCAAACTCTCAGTGGTGGTCAGAAACAAAGAATTGCCATTGCTGGTGCTTTAGCTGAAGCGTGCAAAGTGCTATTGTTGGATGAGCTCACAA
| || | || |||| || ||| | ||| | || | | | | | || | | || || | | | |||||| | | |||||||| |||||||||||||| || || ||||||||||||||||| | |||||||| || ||||| || |||||||||||||||||||
gtattaaggatgacaaccttgagcactcaaacaaatgtgtgaattatacaata------aatgaactttcc-ttctgttacaatattcagAGATCTGTCCAAACTCTGAGTGGTGGTCAGAAGCAGAGGGTTGCCATTGCTGGTGCTCTTGCTGAAGCTTGTAAAGTTCTGTTGTTGGATGAGCTCACAA
upper sequence: AT4G33460.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv04s0044g01320.t01 (Vitis vinifera), 3'ss of exon 4
----gtcagtttatgtacattgaacaacaataa-gttgtttatatcttctagttccttttactaaagtatagattttggtgttgtttccagAGACCGATTCAAACTCTCAGTGGTGGTCAGAAACAAAGAATTGCCATTGCTGGTGCTTTAGCTGAAGCGTGCAAAGTGCTATTGTTGGATGAGCTCACAA
|| | | | | | || | | | | |||||| || | || ||||| || || || ||| ||| |||| |||| || || |||||||||||||||||||| ||||||||||||||||||| || |||||||| ||||| |||||| | |||||||||||||
gtaggttgtatattatgctctcaattatagaagcataaattatattttatgattacttttc------------ttctgttgaacttttcagCGACCTGTTCAGACACTAAGTGGTGGTCAGAAACAAAGGGTTGCCATTGCTGGTGCTTTGGCAGAAGCGTGTAAAGTACTATTGCTAGATGAGCTCACAA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgtttatatcttctagttccttttactaaagtatagattttggtgttgtttccagAGACCGATTCAAACTCTCAGTGGTGGTCAGAAACAAAGAATTGCCATTGCTGGTGCTTTAGCTGAAGCGTGCAAAGTGCTATTGTTGGATGAGCTCACAA
tactaaa putative branch site (score: 1)
ttgtttcc putative PPT
ttttactaaagtatag 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtcagtttatgtacattgaacaacaataagttgtttatatcttctagttccttttactaaagtatagattttggtgttgtttccagAGACCGATTCAAACTCTCAGTGGTGGTCAGAAACAAAGAATTGCCATTGCTGGTGCTTTAGCTGAAGCGTGCAAAGTGCTATTGTTGGATGAGCTCACAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA