Sequence
atgc intronic sequence ATGC exonic sequencegtatatttgtaacgcctcatagaacatcatactttggcctcttccctccttgatctatagtagaacttatgctggagtttatgcagGTACTGGAACTTGGTATGAATTTTCTCGCAGCAGATGATATGAGTGCAATACTTGCTGTGAAATTAAGGAAAAGGCTTGGTTTTGGGATGTGGACAAAGT
Basic information
species | Arabidopsis thaliana |
transcript | AT1G53590.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G53590.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA13G33580.1 (Glycine max), 3'ss of exon 4
------gtatatttgt-aacgcctcata------gaacatcatactttggcctctt--------ccctccttgatctatagtagaacttatgctggagtttatgcagGTACTGGAACTTGGTATGAATTTTCTCGCAGCAGATGATATGAGTGCAATACTTGCTGTGAAATTAAGGAAAAGGCTTGGTTTTGGGATGTGGACAAAGT
| | |||| | || || |||| ||| | | | || | | | | |||| ||| || || ||| |||| ||||| | || |||||||||||| |||| |||||||||||||||||||||||||||||| |||| ||||| | || ||||| |||||| ||||
gtatgtgaaaatttttcaaagcagcataccaagggaatgttttgttctgcatctgtgaatgaaattttgttcaggttgatttagatattaatgtgtgattcatgtagGTTCTGGAGTTAGGAATGAATTTTCTCACAGCTGATGATATGAGTGCAATACTTGCTGTGAAACTAAGAAAAAGATTGGGCTTTGGAATGTGGGCAAAAC
upper sequence: AT1G53590.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA15G39380.1 (Glycine max), 3'ss of exon 4
----gtatatttgtaacgcctcata-----gaacatcatactttggcctcttc--------cctccttgatctatagtagaac-ttatgctggagtttatgcagGTACTGGAACTTGGTATGAATTTTCTCGCAGCAGATGATATGAGTGCAATACTTGCTGTGAAATTAAGGAAAAGGCTTGGTTTTGGGATGTGGACAAAGT
|| | || ||| || |||| | | | || || ||| | || || | | | || ||| || ||| ||| |||| ||||| | || ||||||||||| | || |||||||||||||| ||||||||||||||| |||| |||||| | || ||||| |||||| ||||
gtatgtgaaattttaaagcagcataccaagggattgtgttgttctgcatctgtgaatgaaattttgttcattttgatttatacattaccgtgtcgttcatgtagGTTCTGGAGTTAGGATTGAATTTTCTCACGGCTGATGATATGAGTGCTATACTTGCTGTGAAACTAAGAAAAAGGTTGGGCTTTGGAATGTGGGCAAAAC
upper sequence: AT1G53590.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv19s0138g00140.t01 (Vitis vinifera), 3'ss of exon 4
----------------gtatatttgtaacgcctcatagaacatcatactttggcctcttccctccttgatctatagtagaacttatgctggagtttatgcagGTACTGGAACTTGGTATGAATTTTCTCGCAGCAGATGATATGAGTGCAATACTTGCTGTGAAATTAAGGAAAAGGCTTGGTTTTGGGATGTGGACAAAGT
| | | || ||| | | | || |||| | | | | | | ||| || | | || |||||||| ||| | || |||||||||||| | || |||||||||||||||||||| ||| | ||| | |||| ||| | || ||||| |||||| |||| |
gtatgtttgactagccctggaatggtggaaccttactg--tgttatctattgggatactattgacataagtcttcagagattcagtgattcaattaatgcagGTTTTGGGGTTGGGAATGAATTTTCTCACTGCTGATGATATGAGTGCAATACTAGCTATAAAACTGAGGAGAAGATTGGGATTTGGAATGTGGGCAAAAT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ctttggcctcttccctccttgatctatagtagaacttatgctggagtttatgcagGTACTGGAACTTGGTATGAATTTTCTCGCAGCAGATGATATGAGTGCAATACTTGCTGTGAAATTAAGGAAAAGGCTTGGTTTTGGGATGTGGACAAAGT
ccttgat putative branch site (score: 5)
atctata 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatatttgtaacgcctcatagaacatcatactttggcctcttccctccttgatctatagtagaacttatgctggagtttatgcagGTACTGGAACTTGGTATGAATTTTCTCGCAGCAGATGATATGAGTGCAATACTTGCTGTGAAATTAAGGAAAAGGCTTGGTTTTGGGATGTGGACAAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA