Sequence
atgc intronic sequence ATGC exonic sequencegtactttaactttcatcatcatcatttcctatacattttatttgactcccccgaggagacatatccattcctatatatgtacttactttttagtaaccttttttacctgaattaattcgttaacttcttgtttaaatgttcttaaatctggattatgcagACGTTGAGACGTTTGGCCCAAAATAGAGAAGCTGCTCGCAAAAGCCGTCTTAGGAAAAAG
Basic information
species | Arabidopsis thaliana |
transcript | AT1G08320.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G08320.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA12G30990.1 (Glycine max), 3'ss of exon 6
gtactttaactttcatcatcatcatttcctatacattttatttgactcccccgaggagacatatccattcctatatatgtacttactttttagtaaccttttttacctgaattaattcgt-taacttcttgtttaaatgttcttaaatctggattatgcagACGTTGAGACGTTTGGCCCAAAATAGAGAAGCTGCTCGCAAAAGCCGTCTTAGGAAAAAG
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-------------------------------------------------------------------------gttattgaataattttcca--aactcttttttattaaatgattttacgtaggatctaaggtaagatttttttg--ttggcct---cagACATTGAGACGTTTGGCTCAAAACAGAGAGGCTGCAAGGAAAAGCCGTCTGAGGAAAAAG
upper sequence: AT1G08320.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA12G09430.3 (Glycine max), 3'ss of exon 6
gtactttaactttcatcatcatcatttcctatacattt-tatttgactcccccgaggagacatatccattcctatatatgtacttactttttagtaaccttttttacct--gaattaattcgttaacttcttgtttaaatgttcttaaatctggattatgcagACGTTGAGACGTTTGGCCCAAAATAGAGAAGCTGCTCGCAAAAGCCGTCTTAGGAAAAAG
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--------gtgttgaatgacaca--cacaaacacatttatgtataaattcataatattaatat-tatattccaaggtatgtttttgtttttgaat---tttttttacgtgggaggtaagtcaagatattcttgtttgg-----------tttggatt---cagACACTGAGACGTTTAGCTCAAAACAGAGAAGCTGCAAGGAAAAGCCGTCTCAGGAAAAAG
upper sequence: AT1G08320.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA11G19030.1 (Glycine max), 3'ss of exon 3
gtactttaactttcatcatcatcatttcctatacattttatttgactcccccgaggagacat-atccattcctatatatgtacttactttttagtaaccttttttacctgaattaattcgttaacttcttgtttaaatgttcttaaatctggattatgcagACGTTGAGACGTTTGGCCCAAAATAGAGAAGCTGCTCGCAAAAGCCGTCTTAGGAAAAAG
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--gttttgaatatgat----acaaatacatacacatttatttataatctatgatatcaatattatatattgcaaggtatgtttttgtttttggat---tttttaaatgggaggtaagtcaagatattcttgtttgg-----------tttggatt---cagACACTGAGACGTTTAGCTCAAAACAGAGAAGCTGCAAGGAAAAGCCGTCTCAGGAAAAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cctgaattaattcgttaacttcttgtttaaatgttcttaaatctggattatgcagACGTTGAGACGTTTGGCCCAAAATAGAGAAGCTGCTCGCAAAAGCCGTCTTAGGAAAAAG
cgttaac putative branch site (score: 3)
tttaaatgttcttaaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtactttaactttcatcatcatcatttcctatacattttatttgactcccccgaggagacatatccattcctatatatgtacttactttttagtaaccttttttacctgaattaattcgttaacttcttgtttaaatgttcttaaatctggattatgcagACGTTGAGACGTTTGGCCCAAAATAGAGAAGCTGCTCGCAAAAGCCGTCTTAGGAAAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT