Sequence
atgc intronic sequence ATGC exonic sequencegttgattgatataacactttttgttttctgtttttgcttaatagtaaactcattatgttttgtctactcaaatacagTTTTCAGAGAACTTTACTATTGTTCTGTTTCATTATGATGGCGTAACAAGTGCATGGAATGATGAGTTTGAGTGGTCGAGGAATGCAATACACATAAGTG
Basic information
species | Arabidopsis thaliana |
transcript | AT1G24570.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G24570.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA05G30830.1 (Glycine max), 3'ss of exon 6
-------gttgattgatataacactttttgttttctgtttttgcttaatagta-aactcattatgttttgtctact--caaatacagTTTTCAGAGAACTTTACTATTGTTCTGTTTCATTATGATGGCGTAACAAGTGCATGGAATGATGAGTTTGAGTGGTCGAGGAATGCAATACACATAAGTG---
||| || | | | | | | | || || | | ||| || ||| | || | | |||||| |||||||||||||| || ||||| ||||||||||||||| ||||| || |||| | ||||||||||||||| | | ||||| || | ||||
gtcatctgttagtttctttttctttctgatgcataagcttgtgtatgactgtatgggtctttaaactagctccattacttgtaacagTTCTCAGAGAACTTTACAATAGTTCTATTTCATTATGATGGCAAAACAACTGAATGG---GGTGAGTTTGAGTGGTCAAAGCGGGCAATTCATGTGAGTGTCC
upper sequence: AT1G24570.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA08G14040.1 (Glycine max), 3'ss of exon 6
gttgattgata-taacactttttgttttctgtttttgcttaatagtaaactcatta--tgttttgtctactcaaatacagTTTTCAGAGAACTTTACTATTGTTCTGTTTCATTATGATGGCGTAACAAGTGCATGGAATGATGAGTTTGAGTGGTCGAGGAATGCAATACACATAAGTG---
|| || || | | ||| | | | ||| | ||| | | | | | |||| | |||||| |||||||||||||| || ||||| ||||||||||||||| |||| || |||| ||||||||||||||||| | | ||||| || | ||||
gtcatctgttagtttctttttctttctgatgtataaacttctgtatgggtctttaaactagctcaattacttgga-acagTTCTCAGAGAACTTTACAATAGTTCTATTTCATTATGATGGCCACACAACTGAATGG---GATGAGTTTGAGTGGTCAAAGCGGGCAATTCATGTGAGTGTTC
upper sequence: AT1G24570.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA11G37770.1 (Glycine max), 3'ss of exon 6
--gttgattgatataacactttttgttttctgtttttgcttaatagtaaactcattatgttttg-tctactcaaatacagTTTTCAGAGAACTTTACTATTGTTCTGTTTCATTATGATGGCGTAACAAGTGCATGGAATGATGAGTTTGAGTGGTCGAGGAATGCAATACACATAAGTG---
|| || | | || | | | || || | ||||| | | ||| | | | || || |||||||||| |||||| |||||| | || ||||||||||||||| ||| | || |||| ||||||||||| ||||| | | | || || || | ||||
gtcttaatcagttcattcctctctctgtt-tgcatatgcttgtttatgtgtcttttaactgagaatttgctttaa--cagTTTTCAGGGAACTTCACTATTCTGCTATTTCATTATGATGGCCGAACTACTGAATGG---GATGAGTTTGAATGGTCAAAGCAGGCTATTCATGTGAGTGTTC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gttttctgtttttgcttaatagtaaactcattatgttttgtctactcaaatacagTTTTCAGAGAACTTTACTATTGTTCTGTTTCATTATGATGGCGTAACAAGTGCATGGAATGATGAGTTTGAGTGGTCGAGGAATGCAATACACATAAGTG
gcttaat putative branch site (score: 4)
tctactc putative PPT
ttaatagtaaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttgattgatataacactttttgttttctgtttttgcttaatagtaaactcattatgttttgtctactcaaatacagTTTTCAGAGAACTTTACTATTGTTCTGTTTCATTATGATGGCGTAACAAGTGCATGGAATGATGAGTTTGAGTGGTCGAGGAATGCAATACACATAAGTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA