Sequence
atgc intronic sequence ATGC exonic sequencegtaaactttaattcagcatttttctttcacaacttgaagctttgtggccattacactgataaattgaaagtttttaatttcagTATTGGACTGACTGAGAGAGAGGAAGGTGACCTTGGACCCGTTTATGGATTTCAGTGGAGACACTTTGGTGCTAA
Basic information
species | Arabidopsis thaliana |
transcript | AT4G34570.1 |
intron # | 8 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G34570.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: LOC_Os11g29390.1 (Oryza sativa), 3'ss of exon 6
--gtaaactttaattcagcatttttctttcacaacttgaagct-----ttgtggccat--tacactgataaatt--gaaagttttta----atttcagTATTGGACTGACTGAGAGAGAGGAAGGTGACCTTGGACCCGTTTATGGATTTCAGTGGAGACACTTTGGTGCTAA
| | || || || | || | | | || | | ||| | | | ||||| ||| | || ||||| || ||| |||| | | | || || |||||||| || || || |||||||||||||| ||| |||||||||||||| |
gtatttatcttggatccacactagtcgagaaacaatggatattgctgttcttggttctcgtgctctgatccatttggcaaaattttactgtgttctagTGTTGGCTTAGCACATAGGGAAGAAGGTGATCTAGGTCCAGTTTATGGATTTCAATGGCGACACTTTGGTGCTGA
upper sequence: AT4G34570.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GRMZM2G139880_T01 (Zea mays), 3'ss of exon 5
gtaaactttaattcagcatttttctttcacaacttgaagctttgtggccattacactgataaattgaaagtttttaatttcagTATTGGACTGACTGAGAGAGAGGAAGGTGACCTTGGACCCGTTTATGGATTTCAGTGGAGACACTTTGGTGCTAA
||| | | || || | | || || || ||| || | || | ||| | |||||||| || | | || ||||||||||| || || || |||||||||||||| ||| ||||||||||||| |
gtatttatcagttggatataagctgtaaataaattatttctctgttattgatatctaatccacctggtcatcttt---tctagTATTGGCTTGGCACACAGGGAGGAAGGTGATCTAGGTCCAGTTTATGGATTTCAATGGCGACACTTTGGTGCCGA
upper sequence: AT4G34570.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA11G12280.1 (Glycine max), 3'ss of exon 5
------------gtaaacttta--attcagcatttttctttcacaacttgaagctttgtggccattacactgataaattgaa---agtttttaatttcagTATTGGACTGACTGAGAGAGAGGAAGGTGACCTTGGACCCGTTTATGGATTTCAGTGGAGACACTTTGGTGCTAA
| || | | | || | | ||| || | | | ||| | | | || | || || || | ||| |||| | ||| ||||| |||| || || ||||| |||||| | ||||| |||||||| ||||||||||| |||||||| || ||
gtaccttgataggcaagcatgaccatctactaatttgtattaattgca-aattttttcttttctatgcagttattaactggatttagtatttatatacagCATTGGTTTGACAGACAGGGAGGAGGGTGACTTAGGACCTGTTTATGGGTTTCAGTGGAGGCACTTTGGAGCCAA
upper sequence: AT4G34570.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA06G01280.1 (Glycine max), 3'ss of exon 6
----gta-aactttaattcagcatttttctttcacaacttgaag--ctttgtggccattacactgataaattga----aagtttttaatttcagTATTGGACTGACTGAGAGAGAGGAAGGTGACCTTGGACCCGTTTATGGATTTCAGTGGAGACACTTTGGTGCTAA
| | ||| || | | |||| |||| ||| | ||| | ||| || | ||||| | ||||| ||| |||| |||| |||| ||| | ||||| |||||| | ||||| |||||||| ||||| ||||| ||||||||||| |
gcaagcatgactatatatttcaactttttaagtacaatttgtacatttttctttatattgcagtttgtaattggctttacattttttattgcagTGTTGGTTTGACAGAGCGGGAGGAGGGTGACTTGGGACCTGTTTATGGGTTTCAATGGAGGCACTTTGGTGCCAG
upper sequence: AT4G34570.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA04G01240.1 (Glycine max), 3'ss of exon 6
------gtaaactttaattcagcatttttcttt----cacaacttgaagctttgtggcca--ttacactgataaattg-----aaagtttttaatttcagTATTGGACTGACTGAGAGAGAGGAAGGTGACCTTGGACCCGTTTATGGATTTCAGTGGAGACACTTTGGTGCTAA
| || | | | | | ||| |||| |||| ||| | ||| | | || || | ||||| | | ||||| ||| |||| |||| |||| ||||| ||||| || ||| | ||||| |||||||| ||||| ||||| ||||||||||| |
tgatgggcaagcatgactatatattttaacttttaagtacaaattgtacatttttctttatgttgcagtttgtaattggctttacatttttttattgcagTGTTGGTTTGACAGAGAGGGAGGAGGGCGACTTGGGACCTGTTTATGGGTTTCAATGGAGGCACTTTGGTGCCAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.acaacttgaagctttgtggccattacactgataaattgaaagtttttaatttcagTATTGGACTGACTGAGAGAGAGGAAGGTGACCTTGGACCCGTTTATGGATTTCAGTGGAGACACTTTGGTGCTAA
ttttaat putative branch site (score: 3)
ttttt CT-rich tract
tgataaattgaaagtt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaaactttaattcagcatttttctttcacaacttgaagctttgtggccattacactgataaattgaaagtttttaatttcagTATTGGACTGACTGAGAGAGAGGAAGGTGACCTTGGACCCGTTTATGGATTTCAGTGGAGACACTTTGGTGCTAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA