Sequence
atgc intronic sequence ATGC exonic sequencegttagataacatttttacttctgaatcattatgcaaataatctgtctatctagctctttctaattaaggagaatcatttttaaacagCCATGTTTAGGAGGGGACTCAAAGACCTTAATGTTTGTGAACATATCACCTGATCCATCTTCAACTGGAGAGTCTCTATGCTCTCTTCGGTTTGCTGCTA
Basic information
species | Arabidopsis thaliana |
transcript | AT4G05190.1 |
intron # | 16 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G05190.1 (Arabidopsis thaliana), 3'ss of exon 16
lower sequence: GLYMA13G32450.1 (Glycine max), 3'ss of exon 15
--------------gttagataacatttttacttctgaatcattatg------caaataatctgtctatctagctc---tttctaattaagg---agaatcatttttaaacagCCATGTTTAGGAGGGGACTCAAAGACCTTAATGTTTGTGAACATATCACCTGATCCATCTTCAACTGGAGAGTCTCTATGCTCTCTTCGGTTTGCTGCTA
| | | |||| | ||| ||| | || || ||| | || | | || ||||| | || | ||||||||| | || ||||| || || || || |||||||||||||| ||||||||||||||||||||||||||||| || |||||||||||||||||||||
gtatgataagctatgaaaatttgcattcctcattcaaaattaacttgctttgacatatacttcagatacatgaaccaaacttgtaatttgcttttggttgtatccattggcagCCATGTCTTGGTGGGGATTCCAAAACTTTGATGTTTGTGAACATCTCACCTGATCCATCTTCAACTGGAGAGTCACTTTGCTCTCTTCGGTTTGCTGCTG
upper sequence: AT4G05190.1 (Arabidopsis thaliana), 3'ss of exon 16
lower sequence: GLYMA15G06880.1 (Glycine max), 3'ss of exon 16
---------gttagataacatttttacttctgaatcatta------tgcaaataatctgtctatctagctc---tttctaattaaggagaatcattttta-aacagCCATGTTTAGGAGGGGACTCAAAGACCTTAATGTTTGTGAACATATCACCTGATCCATCTTCAACTGGAGAGTCTCTATGCTCTCTTCGGTTTGCTGCTA
| || || |||| | ||| |||| | | || | ||| | | || ||||| | | | ||||||||| | || ||||| || || || || |||||||||||||| ||||||||||||||||||||||||||||| || ||||||||||| ||||| |||
gtatgcaaagctatgcaaaatttgcatttcgtttccatttgtttattttcattacttcagttatatgaaccaaacttgtaatttgcttatgttgtatccgtggcagCCATGTCTTGGTGGGGATTCCAAAACTTTGATGTTTGTGAACATCTCACCTGATCCATCTTCAACTGGAGAGTCACTTTGCTCTCTTCGATTTGCCGCTG
upper sequence: AT4G05190.1 (Arabidopsis thaliana), 3'ss of exon 16
lower sequence: GLYMA07G30580.1 (Glycine max), 3'ss of exon 15
------gttagataacatttttacttctgaatcattatgcaaataatctgtctatctagctctttctaa------ttaaggagaatcattttta-aacagCCATGTTTAGGAGGGGACTCAAAGACCTTAATGTTTGTGAACATATCACCTGATCCATCTTCAACTGGAGAGTCTCTATGCTCTCTTCGGTTTGCTGCTA
|| | | || | | ||| | | | ||| || | | | |||||| |||| || | | | ||||||| | | || |||||||| || || || |||||||| ||||| |||||||||| ||||||| |||| || || ||||||||||| || ||||| || |
gcttaaactattatatttgttgatcaccgaagatcttagtttacaatttgcatttacttgttcttctaatgctctttaacttatattgtatgcatggcagCCATATCTTGGTGGGGACTCCAAAACGTTGATGTTTGTCAACATCTCACCTGATCAATCTTCAGCTGGCGAATCACTATGCTCTCTACGCTTTGCAGCCA
upper sequence: AT4G05190.1 (Arabidopsis thaliana), 3'ss of exon 16
lower sequence: GLYMA08G06690.1 (Glycine max), 3'ss of exon 17
----gttagataacatt-tttacttctgaatcattatgcaaataatctgtctatctagctctttctaa-------ttaaggagaatcattttta-aacagCCATGTTTAGGAGGGGACTCAAAGACCTTAATGTTTGTGAACATATCACCTGATCCATCTTCAACTGGAGAGTCTCTATGCTCTCTTCGGTTTGCTGCTA
|| | ||| || | | ||| | | | || ||| | | | |||||| |||| || | | | ||||||| | | || ||||| || || || || |||||||| ||| |||||||||||| ||||||| |||| || || || |||||||| || ||||| || |
gcttacactattatattgttgaacacggaagatctgagtttactatttgtttttacttgttcttctaatgctcctttaacttatattgtatgcatggcagCCATATCTTGGTGGGGATTCCAAAACGTTGATGTTTGTCAACGTATCACCTGATCAATCTTCAGCTGGCGAATCACTCTGCTCTCTCCGCTTTGCAGCCA
upper sequence: AT4G05190.1 (Arabidopsis thaliana), 3'ss of exon 16
lower sequence: Vv00s0532g00020.t01 (Vitis vinifera), 3'ss of exon 16
gttagataacatttttacttctgaatcattatgcaaataatc-tgtct-atctagctctttctaattaagga------gaatcattttta--------aacagCCATGTTTAGGAGGGGACTCAAAGACCTTAATGTTTGTGAACATATCACCTGATCCATCTTCAACTGGAGAGTCTCTATGCTCTCTTCGGTTTGCTGCTA
|| | | | | || | ||| | | | || | ||| | || | | | | |||||| | |||| | ||| | ||||| || ||||| ||||| || |||||| | |||||||| ||||| || || || ||||||||| ||| ||||| |||||||||||| |||||||||| |
---agcaagtttctgttctattaaatggcatagaagtttgtcatatcttagctggttttgcatcattaagaatttctgaaatctctgttatttgtatgatcagCCTTGCTTAGGTGGGGATTCCAAGACCCTGATGTTTGTCAACATCTCTCCCGACCCATCTTCAGTTGGTGAGTCCCTATGCTCTCTTAGGTTTGCTGCCA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gcaaataatctgtctatctagctctttctaattaaggagaatcatttttaaacagCCATGTTTAGGAGGGGACTCAAAGACCTTAATGTTTGTGAACATATCACCTGATCCATCTTCAACTGGAGAGTCTCTATGCTCTCTTCGGTTTGCTGCTA
ttctaat putative branch site (score: 2)
tcattttt putative PPT
agaatcatttttaaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttagataacatttttacttctgaatcattatgcaaataatctgtctatctagctctttctaattaaggagaatcatttttaaacagCCATGTTTAGGAGGGGACTCAAAGACCTTAATGTTTGTGAACATATCACCTGATCCATCTTCAACTGGAGAGTCTCTATGCTCTCTTCGGTTTGCTGCTA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT