Sequence
atgc intronic sequence ATGC exonic sequence...accttctagactgttgtctcatcatgtgttcaattacgaatttagagatatttgactcttgttcccattcctatttatagaatcttgctgttatttacagGCTTTACTACACAAAGGTTAAACTTGGGACACCACCAAGAGAATTTAATGTTCAAATTGACACTGGAAGTGATGTTTTGTGGGTTAGCTGCACTTCCTGC
Basic information
species | Arabidopsis thaliana |
transcript | AT1G08210.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G08210.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA11G19640.2 (Glycine max), 3'ss of exon 1
accttctagac--tgttgtctcatc--atgtgttcaattacgaatttagagatatttgactcttgttcccattcctatttatagaatcttgctgttatttacagGCTTTACTACACAAAGGTTAAACTTGGGACACCACCAAGAGAATTTAATGTTCAAATTGACACTGGAAGTGATGTTTTGTGGGTTAGCTGCACTTCCTGC
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--attccaatccttgttgttttgcttaatgttttttgctctcaattcaatgctttattattcgggaaa--aattatatattaaaatttgtgaatttttccacagGCTTTACTATACAAAGGTGAAATTGGGTACTCCACCAAGGGAATTGTATGTGCAGATTGACACTGGCAGTGATGTTCTCTGGGTTAGTTGTGGGTCCTGC
upper sequence: AT1G08210.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA12G08870.1 (Glycine max), 3'ss of exon 1
accttctagactgttgtctcatcatgtgttcaattacgaatttagagatatttgactct-tgttcccattcctatttat--agaatcttgctgttatttacagGCTTTACTACACAAAGGTTAAACTTGGGACACCACCAAGAGAATTTAATGTTCAAATTGACACTGGAAGTGATGTTTTGTGGGTTAGCTGCACTTCCTGC
| | || | | || || || || || | |||| | | | | | || ||| ||| | ||| ||| | | ||||||||||||| |||||||| ||| | || || || ||||| ||||| |||| || ||||||||||| ||||||||| | |||||||| || ||||||
---tctcaattcaatgatttcttatttggaaaaaggaatatatatatatatatatatatatatatatatatatatatattaaaaattttggcttcttccacagGCTTTACTATACAAAGGTGAAATTGGGTACTCCTCCAAGGGAATTCTATGTGCAGATTGACACTGGCAGTGATGTTCTCTGGGTTAGTTGTGGGTCCTGC
upper sequence: AT1G08210.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA12G30430.1 (Glycine max), 3'ss of exon 1
--accttctagactgttgtctcatcatg-tgttcaattacgaatttagagatatttgactcttgttcccattc--ctatttatagaatcttgctgttatttacagGCTTTACTACACAAAGGTTAAACTTGGGACACCACCAAGAGAATTTAATGTTCAAATTGACACTGGAAGTGATGTTTTGTGGGTTAGCTGCACTTCCTGC
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ttatctgttaa--tatcgttttgatgcgctattttatttt--attgattaatttgtggccttcctttaaattatattgattttggaat-taatgacttattgcagGCTCTACTATACAAAAGTGCAGTTGGGTACTCCTCCAGTGGAATTTAATGTGCAGATTGACACTGGTAGTGATGTTCTCTGGGTTAGTTGCAACTCCTGC
upper sequence: AT1G08210.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA17G05490.1 (Glycine max), 3'ss of exon 1
---------accttctagactgttgtctcatcatgtgttcaattacgaatttagagatatttgactcttgttcccattcctatttatagaatcttgctgttatttacagGCTTTACTACACAAAGGTTAAACTTGGGACACCACCAAGAGAATTTAATGTTCAAATTGACACTGGAAGTGATGTTTTGTGGGTTAGCTGCACTTCCTGC
||| | || | | | | | | ||| ||||| | ||| |||| | || || || | || | |||| | | || |||||| ||||| ||||| || | | || || || ||| ||||||||||| || ||||||||||| ||||||||| | |||||||| || | ||||||
tgtgttattttctttttgattaatttatggccttccgttaaattatacaatta-----attt---ttttatttgtgttttaaattttggaat-taatgacttattgcagGCTCTACTATACAAAAGTGCAGTTGGGTACTCCTCCAGTGGAATTTAATGTGCAGATTGACACTGGCAGTGATGTTCTCTGGGTTAGTTGTAACTCCTGC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.agatatttgactcttgttcccattcctatttatagaatcttgctgttatttacagGCTTTACTACACAAAGGTTAAACTTGGGACACCACCAAGAGAATTTAATGTTCAAATTGACACTGGAAGTGATGTTTTGTGGGTTAGCTGCACTTCCTGC
atttgac putative branch site (score: 4)
tatttatagaatctt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
accttctagactgttgtctcatcatgtgttcaattacgaatttagagatatttgactcttgttcccattcctatttatagaatcttgctgttatttacagGCTTTACTACACAAAGGTTAAACTTGGGACACCACCAAGAGAATTTAATGTTCAAATTGACACTGGAAGTGATGTTTTGTGGGTTAGCTGCACTTCCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - -ctcatca