Sequence
atgc intronic sequence ATGC exonic sequence...tgtatgaattttctttaagtgtttagtgcgtttagctcatttcttttgcagtctattgtttgaatcatcacaactgtaattataatactttgcttcttagGTTGTGGTGGTTGATCCTGAAGCATACACTTACGATGAAGAAGTGATCAAGAAAGCTGAAGCAATGGGGAAACCGGGACTCATTGAGATCCATCCGAAAC
Basic information
species | Arabidopsis thaliana |
transcript | AT2G15400.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT2G15400.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv03s0180g00050.t01 (Vitis vinifera), 3'ss of exon 2
tgtatgaattt-tctttaagtgtttagtgcgtttagctcatttcttttgcagtctattgtttgaatcat-cacaactg--taattataatactttgcttcttagGTTGTGGTGGTTGATCCTGAAGCATACACTTACGATGAAGAAGTGATCAAGAAAGCTGAAGCAATGGGGAAACCGGGACTCATTGAGATCCATCCGAAAC
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---ttgaatgtgtggggaggaaaactcaacttccagcccatctgctgaat-gtgtttccttcagataatgcatcatgggttgtctttcatatgctctttttcagGTTGTTGTGGCTGATGCTGAGGCATACACTTATGATGATGAAGTGCTCAAGAAAGCAGAAGCTATGGGGAAGCCAGGGCTTGTGGAGATCTATGCCAAAG
upper sequence: AT2G15400.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: PP1S79_74V6.1 (Physcomitrella patens), 3'ss of exon 3
--------------------------------tgtatgaatttt--ctttaagtgtttagtgcgtttagctcatttcttttgcagtctattgtttgaatcatcacaactgtaattataatact-ttgcttct----------tagGTTGTGGTGGTTGATCCTGAAGCATACACTTACGATGAAGAAGTGATCAAGAAAGCTGAAGCAATGGGGAAACCGGGACTCATTGAGATCCATCCGAAAC
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gtagcatattcatttaactcatcttattgcagtttacaaccttaaatttcgattcgtctcgacgttcagagtattttctgagcaagtaatcgaccctatatgcggcattttaaatcacgtgttgctgcgtataaacatgctgcagGTGGTGGTGGTGGACCCTGAAGCATACACCTATGACGAAGAAGTGCTGAAGAAAGCAGAAGCCATGGGTAAGCCAGGTTTAGTGGAAATTTACAGCAAGG
upper sequence: AT2G15400.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: EFJ38153 (Selaginella moellendorffii), 3'ss of exon 3
tgtatgaattttctttaagtgtttagtgcgtttagctcatttcttttgcagtctattgtttgaatcatcacaactgtaattataatactttgcttcttagGTTGTGGTGGTTGATCCTGAAGCATACACTTACGATGAAGAAGTGATCAAGAAAGCTGAAGCAATGGGGAAACCGGGACTCATTGAGATCCATCCGAAAC
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-----------------------------------gtcag--ccagtcgagcttagagtttga----taagaaactaaagctcaaagctttgttccatagGTGGAAGTGATCGACCCAGAGGCATACACTTATGATGACGAAGTGATCAAGAAAGCCGAAGCCATGGGAAAGCCTGGCCTTGTGGAGATCTATGGCAAGG
upper sequence: AT2G15400.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: EFJ15766 (Selaginella moellendorffii), 3'ss of exon 3
tgtatgaattttctttaagtgtttagtgcgtttagctcatttcttttgcagtctattgtttgaatcatcacaactgtaattataatactttgcttcttagGTTGTGGTGGTTGATCCTGAAGCATACACTTACGATGAAGAAGTGATCAAGAAAGCTGAAGCAATGGGGAAACCGGGACTCATTGAGATCCATCCGAAAC
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-----------------------------------gtcag--ccagtcgagcttagagtttga----taagaaactaaagctcaaagctttgttccatagGTGGAAGTGGTCGACCCAGAGGCATACACTTATGATGACGAAGTGATCAAGAAAGCGGAAGCCATGGGAAAGCCTGGCCTTGTGGAGATCTATGGCAAGG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttgcagtctattgtttgaatcatcacaactgtaattataatactttgcttcttagGTTGTGGTGGTTGATCCTGAAGCATACACTTACGATGAAGAAGTGATCAAGAAAGCTGAAGCAATGGGGAAACCGGGACTCATTGAGATCCATCCGAAAC
ctttgcttctt CT-rich tract
tgtaattataatactt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tgtatgaattttctttaagtgtttagtgcgtttagctcatttcttttgcagtctattgtttgaatcatcacaactgtaattataatactttgcttcttagGTTGTGGTGGTTGATCCTGAAGCATACACTTACGATGAAGAAGTGATCAAGAAAGCTGAAGCAATGGGGAAACCGGGACTCATTGAGATCCATCCGAAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC
- - - - - - - - - -tgtttag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - tgtttga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -catcaca