Sequence
atgc intronic sequence ATGC exonic sequencegtaagtcttaatatatgactttcttttttaggtgcaacaaaatctataggactatataacaacttttttaaattaagaaattttatctttatatagtttaagaagtggaataaacaaaattttgccaatagtttgtgattattttagagatagctatatagttgcttaattttgtagaatttaaaaataaaaacgcagAAGCGAGATGGAGGTTCCGGTTGATGAGGGTCATTTCCTATCGATGCTTGTAAAGATCATGAATGCGAAAAACACTATCGAGATCGGTGTTTTCACCGGT
Basic information
species | Arabidopsis thaliana |
transcript | AT1G67980.2 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G67980.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv01s0010g03490.t01 (Vitis vinifera), 3'ss of exon 2
gtaagtcttaatatatgactttcttttttaggtgcaacaaaatctataggactatataacaacttttttaaattaagaaattttatctttatatagtttaagaagtggaataaacaaaattttgccaatagttt-gtgattattttagagatagctatatagttgcttaattttgtagaatttaaaaataaaaacgcagAAGCGAGATGGAGGTTCCGGTTGATGAGGGTCATTTCCTATCGATGCTTGTAAAGATCATGAATGCGAAAAACACTATCGAGATCGGTGTTTTCACCGGT
|| | | | || | | | | | | | | ||| || || ||| ||||| | || ||| | | | |||| ||| |||| | || || || |||||||| || ||| | || |||||| |||||||||||||||| || || || |||||| |||| || |||||||||
-----------------------------------------------------------------------------------------------gtgccaaacaaccccttaattcactctcattctcattctcattctcattcctatcctaatc-tacagtgcattaataattta--attcctatgtggca-tgcagGAGCCTGATGAATGTCCCTGTCGATGAGGGACAGTTCATTTCAATGCTTCTAAAGATCATGAATGCCAAGAAGACAATCGAGCTCGGAGTGTTCACCGGT
upper sequence: AT1G67980.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv01s0010g03510.t01 (Vitis vinifera), 3'ss of exon 2
gtaagtcttaatatatgactttcttttttaggtgcaacaaaatctataggactatataacaacttttttaaattaagaaattttatctttatatagtttaagaagtggaataaacaaaattttgccaatagtttgtgattattttagagatagctatatagttgcttaattttgtagaatttaaaaataaaaacgcagAAGCGAGATGGAGGTTCCGGTTGATGAGGGTCATTTCCTATCGATGCTTGTAAAGATCATGAATGCGAAAAACACTATCGAGATCGGTGTTTTCACCGGT
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-----------------------------------------------------------------------------atattcactctcattcccaatttctgagtgc--caaacaacccctt------aattcactctcattctc---attcctat-------cctaatct---acagtgcattaataattttgcagGAGCCTGATGAATGTCCCTGTCGATGAGGGACTGTTCATTTCAATGCTTCTAAAGATCATGAATGCCAAGAAGACAATCGAGCTCGGAGTGTTCACCGGT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttagagatagctatatagttgcttaattttgtagaatttaaaaataaaaacgcagAAGCGAGATGGAGGTTCCGGTTGATGAGGGTCATTTCCTATCGATGCTTGTAAAGATCATGAATGCGAAAAACACTATCGAGATCGGTGTTTTCACCGGT
gcttaat putative branch site (score: 4)
tatatagttgcttaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagtcttaatatatgactttcttttttaggtgcaacaaaatctataggactatataacaacttttttaaattaagaaattttatctttatatagtttaagaagtggaataaacaaaattttgccaatagtttgtgattattttagagatagctatatagttgcttaattttgtagaatttaaaaataaaaacgcagAAGCGAGATGGAGGTTCCGGTTGATGAGGGTCATTTCCTATCGATGCTTGTAAAGATCATGAATGCGAAAAACACTATCGAGATCGGTGTTTTCACCGGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC