Sequence
atgc intronic sequence ATGC exonic sequencegtaagccttcgaacctttcttctgtatgatgttatgcctaatttttgaatatcacacaaatgcatatctgatagtttagtagctgaaacttatttgttgctgccaacacacacaaaagagttgtgcttgttaagtgcaaaggcttcatctatgaatctaaatatgtttaaaactttttatccagAGTTGAAGTACTTGATGAAGAACCAGGAGATGATGAAGAAGGAAGCGGTCAGAG
Basic information
species | Arabidopsis thaliana |
transcript | AT5G40550.2 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G40550.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM5G862959_T04 (Zea mays), 3'ss of exon 6
gtaagccttcgaacctttcttctgtatgatgttatgcctaatttttgaatatcacacaaatgcatatctgatagtttagtagctgaaacttatttgttgctgccaacacacacaaaagagttgtgcttgttaagtgcaaaggcttcatc-tatgaatctaaatatgtttaaaactttt---tatccagAGTTGAAGTACTTGATGAAGAACCAGGAGATGATGAAGAAGGAAGCGGTCAGAG
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---------------------------------------------------------------------------------------attaccatgtacatgcacattttcgtgtgcctgttactgttgccttatatgtgaccatcatcctgtaagtatcact-catttaatattgatgcacgtgcagGTATGAAGTACTTGATGAAGAACCAGGTGATGACGAAGAG---AGCACTCAAAA
upper sequence: AT5G40550.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA16G07460.1 (Glycine max), 3'ss of exon 5
gtaagccttcgaacctttcttctgtatgatgttatgcctaatttttgaatatcacacaaatgcatatctgatagtttagtagctgaaacttatttgttgctgccaacacacacaaaagagttgtgcttgttaagtgcaaaggcttcatctatgaatctaaatatgtt--taaaacttt-ttatccagAGTTGAAGTACTTGATGAAGAACCAGGAGATGATGAAGAAGGAAGCGGTCAGAG
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-----------------------------------------------------------------------------------tgtaa-tcattgacagaaagaatagtacccattatgacattgatcttt---tgtaattgtccttttcattattttatttgttctcctgtaacatgattttacagATTTGAAGTACTGGATGAGGAACCAGGCGATGATGAAGAAAGCAGTGGCCAAAG
upper sequence: AT5G40550.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA19G08050.1 (Glycine max), 3'ss of exon 6
gtaagccttcgaacctttcttctgtatgatgttatgcctaatttttgaatatcacacaaatgcatatctgatagtttagtagctgaaacttatttgttgctgccaacacacacaaaagagttgtgcttgttaagtgcaaaggcttcatctatgaatcta-aatatgtttaaaactttttatccagAGTTGAAGTACTTGATGAAGAACCAGGAGATGATGAAGAAGGAAGCGGTCAGAG
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------------------------------------------------------------------tgtaatcattgacagaaagagtagtatccatt-ttgacatta-atcttttgtaattgtccttgtcatt-------attttatttgttctcctgtgacatgatttga----------cagATTTGAAGTACTAGATGAGGAACCAGGTGATGATGAAGAAAGCAGTGGCCAAAG
upper sequence: AT5G40550.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: Vv14s0066g00210.t01 (Vitis vinifera), 3'ss of exon 6
gtaagccttcgaacctttcttctgtatgatgttatgcctaatttttgaatatcacacaaatgcatatctgatagtttagtagctgaaacttatttgttgctgccaacacacacaaaagagttgtgcttgttaagtgcaaaggcttcatctatgaatctaaatatgtttaaaactttttatccagAGTTGAAGTACTTGATGAAGAACCAGGAGATGATGAAGAAGGAAGCGGTCAGAG
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------------------------------------------------------------------------aacttttttataacagtgcgattgattgtgccctttaataaaattcagc-atacatgccttgta--------ttgttcataaatattgatgga---acaactatatatgcagATTTGAAGTACTTGATGAGGAACCTGGTGATGATGAAGAGAGTAGTGGCCAAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttaagtgcaaaggcttcatctatgaatctaaatatgtttaaaactttttatccagAGTTGAAGTACTTGATGAAGAACCAGGAGATGATGAAGAAGGAAGCGGTCAGAG
atctaaa putative branch site (score: 3)
ctttttatcc putative PPT
atctatgaatctaaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagccttcgaacctttcttctgtatgatgttatgcctaatttttgaatatcacacaaatgcatatctgatagtttagtagctgaaacttatttgttgctgccaacacacacaaaagagttgtgcttgttaagtgcaaaggcttcatctatgaatctaaatatgtttaaaactttttatccagAGTTGAAGTACTTGATGAAGAACCAGGAGATGATGAAGAAGGAAGCGGTCAGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA