Sequence
atgc intronic sequence ATGC exonic sequencegtatctgttttctctgagaacatatcaacactctcagttcaaatattcttttctaatttgtctttgaaatacttatttttattttgtgatttagGGAAGGATATTAGTATTTATAGTCGAAGATGGGAGGTTGCAGCTAATCGCCGAGAAAGAAACCAAAGGAGCTGTTTATTCTCTCAATGCCTTTAATGGAA
Basic information
species | Arabidopsis thaliana |
transcript | AT4G05420.1 |
intron # | 17 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G05420.2 (Arabidopsis thaliana), 3'ss of exon 16
lower sequence: GRMZM2G402002_T01 (Zea mays), 3'ss of exon 17
------------------------------------------------------------------------gtatctgttttctctgagaacatatcaacactctcagttcaaatatt-------cttttctaattt--gtctttgaaatacttattt-ttattttgtgatttagGGAAGGATATTAGTATTTATAGTCGAAGATGGGAGGTTGCAGCTAATCGCCGAGAAAGAAACCAAAGGAGCTGTTTATTCTCTCAATGCCTTTAATGGAA
| ||| | | || | | || |||| | | | ||| |||| || || |||| ||||| | || | | ||||| |||| | |||||| ||| |||||||| || ||||| | |||| |||||||||||||||||||| |||||||| || ||||| || ||||| |
gtagtttatctgaaagcatgatgtttcactaatactagtcagttcccttttaatacgctaaaatactggttaactcccttttaatacttgtccaatttactgcttgtagtttatttctctgtgaaccttgtctatttctcgtgcacaaaatgcttatgtgttggcacatcttgtagGGCCGGATTCTTGTATTTGCAGTTGAAGATGGAAGCTTGCAATTGATCGTGGAGAAAGAAACCAAAGGAGCAGTTTATTCGCTGAATGCATTCAATGGGA
upper sequence: AT4G05420.2 (Arabidopsis thaliana), 3'ss of exon 16
lower sequence: GRMZM2G430027_T01 (Zea mays), 3'ss of exon 5
----------------------------------------------------gtatctgttttctctgagaacatatcaacactctcagttcaaatattcttttctaattt--gtctttgaaatacttattt-ttattttgtgatttagGGAAGGATATTAGTATTTATAGTCGAAGATGGGAGGTTGCAGCTAATCGCCGAGAAAGAAACCAAAGGAGCTGTTTATTCTCTCAATGCCTTTAATGGAA
|| |||| | | | | | | | | ||| | |||||||| || || |||| |||| | | | | | ||||| | || | |||||| ||| |||||||| || ||||| |||| | |||||||||||||||||||| |||||||| | ||||| || ||||| |
gtgatatatctgaaatcatgatcttttactaatgctagttaactcgtttttaatacttgttcaattt-acagcttgttttagttaatttctcagtgagccttttctatttctcgtgcacaaaatggttatgtatcggtacatcttgtagGGCCGAATCCTTGTATTTGCAGTTGAAGATGGAAGTTTGCAATTAATTGTGGAGAAAGAAACCAAAGGAGCAGTTTATTCGTTGAATGCATTCAATGGGA
upper sequence: AT4G05420.2 (Arabidopsis thaliana), 3'ss of exon 16
lower sequence: GLYMA05G30530.1 (Glycine max), 3'ss of exon 17
gtatctgttttctctgagaacatatcaacactctcagttcaaatattcttttctaatt--tgtctttgaaatacttatttttattttgtga--tttagGGAAGGATATTAGTATTTATAGTCGAAGATGGGAGGTTGCAGCTAATCGCCGAGAAAGAAACCAAAGGAGCTGTTTATTCTCTCAATGCCTTTAATGGAA
| |||||| || | | | |||| | |||||| || | | || | | | ||| ||||| | | |||||||| || | || ||| || |||||||| | | |||||||| ||||||||||| || |||||||||||||||| | ||||| |||||||| |
---------gtaagtgagaa-atttgtat-ttttcagc---attattctagtcaagcttctgatatcctgcttcctatggccattttaaaacatgtagGGAAGAATTCTTGTTTTTGCTGTTGAAGATGGAAAACTACAGCTAATTGCCGAGAAAGAGACAAAAGGAGCTGTTTATTGCTTGAATGCATTTAATGGTA
upper sequence: AT4G05420.2 (Arabidopsis thaliana), 3'ss of exon 16
lower sequence: GLYMA08G13680.1 (Glycine max), 3'ss of exon 17
gtatctgttttctctgagaacatatcaacactctcagttcaaatattcttttctaatttgtctttgaaatacttatttt---tattttgtg--atttagGGAAGGATATTAGTATTTATAGTCGAAGATGGGAGGTTGCAGCTAATCGCCGAGAAAGAAACCAAAGGAGCTGTTTATTCTCTCAATGCCTTTAATGGAA
| |||||| || | | | |||| | | |||| || || | | | ||| ||| ||||| || |||||||| || | || ||| || |||||||| | | |||||||| ||||||||||| || |||||||||||||||| | ||||| |||||||| |
--------gtaagttgagaa-atttgtattttttcagc---attgttctagtcaaagcttctgatatcctgcttcctttggccattttaaaacatgtagGGAAGAATTATTGTTTTTGCTGTTGAAGATGGAAAACTACAGCTAATTGCCGAGAAAGAGACAAAAGGAGCTGTTTATTGCTTGAATGCATTTAATGGTA
upper sequence: AT4G05420.2 (Arabidopsis thaliana), 3'ss of exon 16
lower sequence: GLYMA12G08330.1 (Glycine max), 3'ss of exon 5
gtatctgttttctctgagaacatatcaacactctcagttcaaatattcttttctaatttgtctttgaaatacttatttttattttgtg-----atttagGGAAGGATATTAGTATTTATAGTCGAAGATGGGAGGTTGCAGCTAATCGCCGAGAAAGAAACCAAAGGAGCTGTTTATTCTCTCAATGCCTTTAATGGAA
| |||||| || | | | |||| | | |||| || || | | | ||| ||| || | || |||||||| || | || ||| || |||||||| | | || ||||| ||||||||||| || |||||||||||||||| | | || |||||||| |
--------gtaagttgagaa-atttgtattttttcagc---attgttctagtcaaagcttctgatatcctgcttcctttggcctttttaaaacatgtagGGAAGAATTCTTGTTTTTGCTGTTGAAGATGGAAAACTACAACTAATTGCCGAGAAAGAGACAAAAGGAGCTGTTTATTGCTTGATGGCATTTAATGGTA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.caaatattcttttctaatttgtctttgaaatacttatttttattttgtgatttagGGAAGGATATTAGTATTTATAGTCGAAGATGGGAGGTTGCAGCTAATCGCCGAGAAAGAAACCAAAGGAGCTGTTTATTCTCTCAATGCCTTTAATGGAA
ttctaat putative branch site (score: 2)
cttatttttatttt putative PPT
ttttctaatttgtctt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatctgttttctctgagaacatatcaacactctcagttcaaatattcttttctaatttgtctttgaaatacttatttttattttgtgatttagGGAAGGATATTAGTATTTATAGTCGAAGATGGGAGGTTGCAGCTAATCGCCGAGAAAGAAACCAAAGGAGCTGTTTATTCTCTCAATGCCTTTAATGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT