Sequence
atgc intronic sequence ATGC exonic sequence...aacacaaagtctcctatccagaagaaaatgagtagactaatttaaagtgaactagttaactagaactggtactaactttcaatggtttattctatcaaagGGTTGTTGAGATGCAAGAAATTCTAGACCAACAGCTTGCTGAAGAAGCAGCAGAGGCTGAGGGAGAAGGTGCGATGGCATCTGTAGCAAATCCTCGAAGG
Basic information
species | Arabidopsis thaliana |
transcript | AT1G71820.2 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G71820.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: LOC_Os02g51430.2 (Oryza sativa), 3'ss of exon 7
aacacaaagtctcctatccagaagaaaatgagtagactaatttaaagtgaactagt-taactagaactggtac-taactttcaatggtttattct-atcaaagGGTTGTTGAGATGCAAGAAATTCTAGACCAACAGCTTGCTGAAGAAGCAGCAGAGGCTGAGGGAGAAGGTGCGATGGCATCTGTAGCAAATCCTCGAAGG
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-agatttagaaaattggcttgattcttttttcttatttagtttctaggtaatgggcacttatatatcttgcacataatccttaa--attcattcttatgttagGGTTGTTGAAATGCAAGAGATCCTAGATCAACAAGTTGCAGAAGAAGCAGCTGAGGCTGAGGGTGCAGGTGCTATGGCGACAATAGCAAACCAGCGTAGA
upper sequence: AT1G71820.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GRMZM2G070045_T01 (Zea mays), 3'ss of exon 3
---------------------------------------aacacaaagtctcctatccagaagaaaatgagtagacta----------atttaaagtga-actagttaactagaactggtac-taactttcaatggtttattctatcaaagGGTTGTTGAGATGCAAGAAATTCTAGACCAACAGCTTGCTGAAGAAGCAGCAGAGGCTGAGGGAGAAGGTGCGATGGCATCTGTAGCAAATCCTCGAAGG
|| | | | | |||| | ||| | | | | | || || || | | || | | | | | | | ||| | | | | || ||||||||||| |||||||| || |||| ||||| |||| ||||||||||| ||||||||||| | ||||| ||||| | || |||| | || ||
gtacatctcattcttcaatttttgctttaatataaaattgtcaatgaatatattttccaaataaaatttattttattttctattaggtatatatcatggtattcacaaatttacattattgcatcaattttgtttttggactatacatcagGGTTGTTGAAATGCAAGAGATCTTAGATCAACAAGTTGCAGAAGAAGCAGCTGAGGCTGAGGGTGCTGGTGCTATGGCGACAATAACAAACCAACGTAGA
upper sequence: AT1G71820.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA03G03120.1 (Glycine max), 3'ss of exon 9
---------------------------------------------------------------------------------------------aacacaaagtctcctatccagaagaaaatgagtagactaatttaaag---tgaactagttaactagaactggtactaactttcaatggtttattctatcaaagGGTTGTTGAGATGCAAGAAATTCTAGACCAACAGCTTGCTGAAGAAGCAGCAGAGGCTGAGGGAGAAGGTGCGATGGCATCTGTAGCAAATCCTCGAAGG
| | | | || || || | | | | | | | || ||| | | | | || || | | |||| | ||| ||||||||||| ||||||||||| || || |||||| |||| ||||||||||| |||||||| || || || || |||||||| || ||||||||||| |
gtatgttgttgatagtcaattgcactttttttttcccagtcagttcattcccttcatcttgttttagatggtaggttggatgattggaaattctagatgataggttggatgattaaaaattctaatcagccggtagaggagtttaatctttctaaaaaaatgtaatcttattttccctttgtttttcatattccagGGTTGTTGAAATGCAAGAAATCCTTGATCAACAGATTGCAGAAGAAGCAGCTGAGGCTGAAGGGGATGGCGCAATGGCATCAGTTGCAAATCCTCGTAAC
upper sequence: AT1G71820.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: Vv03s0097g00670.t01 (Vitis vinifera), 3'ss of exon 8
---aacacaaagtctcctatccagaaga--aaatgagtagactaatttaaagtgaactagttaactagaactggtactaactttcaatggtttattctatcaaagGGTTGTTGAGATGCAAGAAATTCTAGACCAACAGCTTGCTGAAGAAGCAGCAGAGGCTGAGGGAGAAGGTGCGATGGCATCTGTAGCAAATCCTCGAAGG
|| | | | | | | | | | | | |||| | |||| ||| | |||| | ||| | |||| ||| | ||||||||||| ||||||||||| || || ||||| |||||||| |||||||| ||||||||||||| ||| | |||||||| | ||||||||||| ||
tgcaatagatcactgcatgttattatgtttgaccacatggttcagttta--ctcaact--ttagtttgaacatagttttttttttctttgttttctct-ttgtagGGTTGTTGAAATGCAAGAAATCCTTGATCAACAACTTGCTGAGGAAGCAGCCGAGGCTGAGGGAGGAGGGACCATGGCATCAATTGCAAATCCTCGTAGA
upper sequence: AT1G71820.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: Vv12s0034g02360.t01 (Vitis vinifera), 3'ss of exon 8
aacacaa-agtctcctatccagaagaaaatgagtagac-taatttaaagtgaactagttaactagaactggtactaactttcaatggtttattctatcaaagGGTTGTTGAGATGCAAGAAATTCTAGACCAACAGCTTGCTGAAGAAGCAGCAGAGGCTGAGGGAGAAGGTGCGATGGCATCTGTAGCAAATCCTCGAAGG
||| || || | | | | || | || | || | |||| | | | | ||| | |||| ||| | ||||||||||| ||||||||||| || || ||||| |||||||| |||||||| ||||||||||||| ||| | |||||||| | ||||||||||| ||
-gtgcaatagatcactgcatgttattatgtttgaccacatggttcagtttgctcaagtttagtttgaacatggtttttttttctttgttttctct-ttgtagGGTTGTTGAAATGCAAGAAATCCTTGATCAACAACTTGCTGAGGAAGCAGCCGAGGCTGAGGGAGGAGGGACCATGGCATCAATTGCAAATCCTCGTAGA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.agtgaactagttaactagaactggtactaactttcaatggtttattctatcaaagGGTTGTTGAGATGCAAGAAATTCTAGACCAACAGCTTGCTGAAGAAGCAGCAGAGGCTGAGGGAGAAGGTGCGATGGCATCTGTAGCAAATCCTCGAAGG
tactaac putative branch site (score: 0)
tttattct putative PPT
tttattctatcaaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
aacacaaagtctcctatccagaagaaaatgagtagactaatttaaagtgaactagttaactagaactggtactaactttcaatggtttattctatcaaagGGTTGTTGAGATGCAAGAAATTCTAGACCAACAGCTTGCTGAAGAAGCAGCAGAGGCTGAGGGAGAAGGTGCGATGGCATCTGTAGCAAATCCTCGAAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA