Sequence
atgc intronic sequence ATGC exonic sequencegtatataatttcttcttttccctattcattagttaatactcaacaaggtgattaattaaatttttaattatcatcagGTGATTACAGAGACACTGAGAATGGGAAATGTTATAATTGGAGTGATGAGAAAGGCGATGAAAGATGTTGAAATAAAAGGATATGTGATACCAAAAGGAT
Basic information
species | Arabidopsis thaliana |
transcript | AT3G13730.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G13730.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA08G20690.1 (Glycine max), 3'ss of exon 5
---------gtata-taatttcttcttttccctattcat---tagttaatactcaac---aaggtgattaattaaatttttaattatcatcagGTGATTACAGAGACACTGAGAATGGGAAATGTTATAATTGGAGTGATGAGAAAGGCGATGAAAGATGTTGAAATAAAAGGATATGTGATACCAAAAGGAT
||| | | ||| | | | ||| | |||| || | || | | | |||| | | || || |||| || || || || |||| ||||||||| ||||||||||||| ||||||||||| | |||||||||||||||||||| | | ||||||||||| |
gtaagacaaccatagctactggttcctcatcaaagacatgtaaaaataatccttagttttcagctaacttattatgtgctctatctgtat-agGTCATCACTGAAACTTTGAGGATGGGAAATATTATAATTGGAGTCATGAGAAAGGCCTTAAAAGATGTTGAAATAAAAGGGCACTTAATACCAAAAGGGT
upper sequence: AT3G13730.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA07G01280.1 (Glycine max), 3'ss of exon 8
---------gtata-taatttcttcttttccctattcattagttaatactcaaca------aggtgattaattaaatttttaattatcatcagGTGATTACAGAGACACTGAGAATGGGAAATGTTATAATTGGAGTGATGAGAAAGGCGATGAAAGATGTTGAAATAAAAGGATATGTGATACCAAAAGGAT
||| ||| ||| | | | || |||| || | | || | | | |||| | | | | || |||| || | || || | || ||||||||| ||||||||||||| ||||||||||| | |||||||||||||||||||| | | ||||||||||| |
gtaaggaaaccatagctattggttcctcgtcaaagaaatataaaaataatccatagttttcagctaacttattatgtgctctacttgtat-agGTCATCAGTGAAACTTTAAGGATGGGAAATATTATAATTGGAGTTATGAGAAAGGCCTTAAAAGATGTTGAAATAAAAGGGCACTTAATACCAAAAGGGT
upper sequence: AT3G13730.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv09s0002g02080.t01 (Vitis vinifera), 3'ss of exon 5
-------------------------------gtatataatttcttcttttccctattcattagttaatactcaacaaggtgattaattaaatttttaattatcatcagGTGATTACAGAGACACTGAGAATGGGAAATGTTATAATTGGAGTGATGAGAAAGGCGATGAAAGATGTTGAAATAAAAGGATATGTGATACCAAAAGGAT
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gtaagttcttggactgattcatgattagatagaagaggaaatgaggacatata-agttataaatgcatatacagtaagatg--taaatgatgcttttatca--aacagGTGATCACAGAAACACTAAGGTTGGGAAACGTTATTATAGGGGTGATGAGGAAGGCCATGAAGGATGTGGAGATAAAGGGACATAGGATACCAAAAGGAT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tattcattagttaatactcaacaaggtgattaattaaatttttaattatcatcagGTGATTACAGAGACACTGAGAATGGGAAATGTTATAATTGGAGTGATGAGAAAGGCGATGAAAGATGTTGAAATAAAAGGATATGTGATACCAAAAGGAT
ttttaat putative branch site (score: 3)
aacaaggtgattaatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatataatttcttcttttccctattcattagttaatactcaacaaggtgattaattaaatttttaattatcatcagGTGATTACAGAGACACTGAGAATGGGAAATGTTATAATTGGAGTGATGAGAAAGGCGATGAAAGATGTTGAAATAAAAGGATATGTGATACCAAAAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG