Sequence
atgc intronic sequence ATGC exonic sequencegtaaagattcttatgatataattgtcttttttcccgcttgagagaaacataagagtctcaagagaaaatgcatcttaatgtcttgcagGTTCTTCAGAGAAAAACAGAAGAAGCAGCAATGGCTACCAAAAGACTTAAAGAGCTGCTAGAAGCCCGCAAGTCTTCACCTCATGATATATCAG
Basic information
species | Arabidopsis thaliana |
transcript | AT3G50240.1 |
intron # | 16 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G50240.1 (Arabidopsis thaliana), 3'ss of exon 16
lower sequence: GLYMA05G15750.1 (Glycine max), 3'ss of exon 18
-----gtaaagattcttatgatataattgtcttttttcccgc--ttgagagaaacataagagtctcaagagaaaatgcatcttaatgtcttgcagGTTCTTCAGAGAAAAACAGAAGAAGCAGCAATGGCTACCAAAAGACTTAAAGAGCTGCTAGAAGCCCGCAAGTCTTCACCTCATGATATATCAG
||||||| || || || | || | || ||| | | || ||| | ||| | || | || ||||||||||||| || || ||||| |||||| |||||||||| ||||| || ||||| || | ||||||||||| ||||| |||| ||| | || |
gtaagttaaagata--taaaattagatgggaaattggcgcgtgattgttatgga-atgagaatgaagtgagtaggtggttaactattatctgcagGTTCTTCAAAGGAAGACAGAGGAAGCAACAATGGCTACGAAAAGGCTAAAAGAATTGTTGGAAGCCCGCAAATCTTCTCCTCGTGACAACTCTG
upper sequence: AT3G50240.1 (Arabidopsis thaliana), 3'ss of exon 16
lower sequence: GLYMA17G18540.1 (Glycine max), 3'ss of exon 13
----gtaaagattcttatgatataattgtcttttttcccgcttgagagaaacataa-gagtctcaagagaaaatgcatcttaatgtc--ttgcagGTTCTTCAGAGAAAAACAGAAGAAGCAGCAATGGCTACCAAAAGACTTAAAGAGCTGCTAGAAGCCCGCAAGTCTTCACCTCATGATATATCAG
|| || ||| | | || | | || ||| ||| | | || ||| | ||| ||| | | | | | | |||||||||||||| || || ||||| |||||| |||||||||| ||||| || ||||| || | || |||||||| ||||| || | ||||| || |
gtaagttaaagatctaaagttagatgggaaattg---ccgtgtgattgctatggaatgagaatgaagtgaataggtggttaactattatttgcagGTTCTTCAAAGGAAGACAGAGGAAGCAACAATGGCTACGAAAAGGCTAAAAGAATTGTTGGAGGCCCGCAAATCTTCTCCCCGTGATAACTCTG
upper sequence: AT3G50240.1 (Arabidopsis thaliana), 3'ss of exon 16
lower sequence: Vv07s0031g00130.t01 (Vitis vinifera), 3'ss of exon 17
-------------gtaaagattcttatgatataattgtcttttttcccgcttgagagaaacataagagtctcaagagaaaatgcatcttaatgtcttgcagGTTCTTCAGAGAAAAACAGAAGAAGCAGCAATGGCTACCAAAAGACTTAAAGAGCTGCTAGAAGCCCGCAAGTCTTCACCTCATGATATATCAG
| || ||| || | ||| || | | | ||| || | | || | | | | | || | |||| ||||||||||| |||||||||||||| || ||| | ||||||||||| || |||||| | |||||||| ||||| |||||| | | ||||| || |
ctccggcccttctttggcttgtcctattatttggttgctaggatttcatagaaacacaaagatttgtggctaattattggaagaagctcctt-tctttcagGTTCTTCAAAGAAAAACAGAAGAGGCTGCAGTAGCTACCAAAAGGCTGAAAGAGTTACTAGAAGCTCGCAAATCTTCAGCACGTGATAATTCCG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ccgcttgagagaaacataagagtctcaagagaaaatgcatcttaatgtcttgcagGTTCTTCAGAGAAAAACAGAAGAAGCAGCAATGGCTACCAAAAGACTTAAAGAGCTGCTAGAAGCCCGCAAGTCTTCACCTCATGATATATCAG
tcttaat putative branch site (score: 3)
aaacataa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaaagattcttatgatataattgtcttttttcccgcttgagagaaacataagagtctcaagagaaaatgcatcttaatgtcttgcagGTTCTTCAGAGAAAAACAGAAGAAGCAGCAATGGCTACCAAAAGACTTAAAGAGCTGCTAGAAGCCCGCAAGTCTTCACCTCATGATATATCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC