Sequence
atgc intronic sequence ATGC exonic sequencegtcagttgtactgcttgcttgcgtcttccttttattacccttaagccttaaagtactcattttcctctaacttcatcataatctctccgctcatgatctctttctttcagATGATTGATCCAGATGGAATAGCAAACTGGTCGGTCACACATGTAGATTGGTCCGAGGGCAAATGGCATCCGAAGCTGTACAATGCAAGAGACATCACTC
Basic information
species | Arabidopsis thaliana |
transcript | AT4G31350.2 |
intron # | 8 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G31350.2 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: LOC_Os06g45110.1 (Oryza sativa), 3'ss of exon 8
gtcagttgtactgcttgcttgcgtcttccttttattacccttaagcctta-aagtactcattttcctctaacttcatcataatctctccgctcatgatctctttctttcagATGATTGATCCAGATGGAATAGCAAACTGGTCGGTCACACATGTAGATTGGTCCGAGGGCAAATGGCATCCGAAGCTGTACAATGCAAGAGACATCACTC
| | || || | | | | || || | ||| | || | || | ||| | ||| ||| | || || |||||||| | ||||| | |||||| || || ||||| || |||||||| |||||||| ||||| ||||||||||||| | || | || ||| ||||
------gtcagtatttatttacaatatattgaagtgacatttgattcttttgggggcttacttgc---taaatacat----atcattttgcatat----------cttcagATGGTAGATCCTGGTGGAATTGCTAATTGGTCAGTTACACATGTTGATTGGTCTGAGGGAAAATGGCATCCGAGGTCATATAGAGCTGCAGATGTCACCT
upper sequence: AT4G31350.2 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: LOC_Os06g48700.1 (Oryza sativa), 3'ss of exon 8
gtcagttgtactgcttgcttgcgtcttccttttattacccttaagccttaaagtactcattttcctctaacttcatcataatctctccgctcatgatctctttctttcagATGATTGATCCAGATGGAATAGCAAACTGGTCGGTCACACATGTAGATTGGTCCGAGGGCAAATGGCATCCGAAGCTGTACAATGCAAGAGACATCACTC
| | | | || ||||| | | || | || | ||||| | || || | | | || | | | |||||| |||||||| |||||| ||||| ||||| || |||||||| |||||||| || || ||||||||||| || |||| || |||| |
--------------------gtaagaactctcaaaaactcttaaa---tgatgtttttcagttgtgtttacttcccagtgatttca--ggccgttattg--tacctgcagATGGTTGATCCAACTGGAATTGCAAATTGGTCAGTGACACATGTTGATTGGTCTGAAGGAAAATGGCATCCTAAAGCTTACAGGGCTGTTGACACAAGCT
upper sequence: AT4G31350.2 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: LOC_Os04g51794.1 (Oryza sativa), 3'ss of exon 7
-gtcagttgtactgcttgcttgcgtcttccttttattacccttaagccttaaagtactcattttcctctaacttcatcataatctctccgctcatgatctctttctttcagATGATTGATCCAGATGGAATAGCAAACTGGTCGGTCACACATGTAGATTGGTCCGAGGGCAAATGGCATCCGAAGCTGTACAATGCAAGAGACATCACTC
| | || || || || | ||||| | | || |||| | | | | | | | | ||| | | | || | || | | || |||||||| |||||| ||||||| || |||||||| || || ||||| || ||||| || || || ||||||||||| || |||| || | ||
tgaaatttactctatttttttaaaggaatgagtaattaca-tcatcccgtaaaatccac-------tgcagcctttttatattgtgt--acttgt-atttgtgtcaaccagATGATAGATCCAAATGGAATTGCCAACTGGTCTGTGACTCATGTTGACTGGTCTGAAGGGAAGTGGCATCCGAAAGCTTATCGGGCAAATGATGTTACAT
upper sequence: AT4G31350.2 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GRMZM2G124151_T01 (Zea mays), 3'ss of exon 8
gtcagttgtactgcttgcttgcgtcttccttttattacccttaagccttaaagtactcattttcctctaacttcatcataatctctccgctcatgatctctttctttcagATGATTGATCCAGATGGAATAGCAAACTGGTCGGTCACACATGTAGATTGGTCCGAGGGCAAATGGCATCCGAAGCTGTACAATGCAAGAGACATCACTC
|| ||| | || | || || | |||| | ||| | || | | || || | | ||| | || | || | | |||||| ||||||| | ||||| | ||||||||| |||||||| || || ||||| |||||||||||||| ||||||||||| | | || | || ||| | ||
gttagtaatccttttcaactgttatttgcctttaatttcctcgatccct----tgct--ttcttttttaagt--atagttatgttt-------tgatct-------tcagATGGTCGATCCTGGTGGAATAGCTAACTGGTCAGTGACTCATGTTGATTGGTCCGAGGGAAAATGGCATCCAAGGTCATATAGAGCTGCAGATGTTACCT
upper sequence: AT4G31350.2 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GRMZM2G138505_T01 (Zea mays), 3'ss of exon 8
gtcagttgtactgcttgcttgcgtcttccttttattacccttaagccttaaagtactcattttcctctaacttcatcataatctctccgctcatgatctctttctttcagATGATTGATCCAGATGGAATAGCAAACTGGTCGGTCACACATGTAGATTGGTCCGAGGGCAAATGGCATCCGAAGCTGTACAATGCAAGAGACATCACTC
|| | || || || || | ||||| || || | | || || ||| | || | | | | | | | | || ||||| |||| || | ||||||||| |||||||| || || ||||| |||||||||||||| ||||||||||| | | || | || ||| | ||
------gttagtaattatttttaactctgttat-ttaccttttttccctcgaccccttgcttcccttt--ttttagtacagtt------------gtgtttattctttagATGGTTGACCCTGGTGGAATAGCTAACTGGTCAGTGACTCATGTTGATTGGTCCGAGGGAAAATGGCATCCAAGGTCATATAGAGCTGCAGATGTTACAT
upper sequence: AT4G31350.2 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GRMZM2G114337_T01 (Zea mays), 3'ss of exon 8
gtcag--ttgtactgcttgcttgcgtcttccttttattacccttaa---gccttaaagtactcattttcctctaacttcatcataatct---------ctccgctcatgatctctttctttcagATGATTGATCCAGATGGAATAGCAAACTGGTCGGTCACACATGTAGATTGGTCCGAGGGCAAATGGCATCCGAAGCTGTACAATGCAAGAGACATCACTC
|| || || ||||| || | |||||| || | | | ||| || |||||| | | | | | || | | || | || | | |||||||| ||| || |||||| ||||||||||| || || || |||||||||||||| || ||||||||||| || | |||| || || | |
gtaagtgttcagaagcttgtagacgacggccttttgttctcttcgaccagccagcaaaacaacattttatttagaaaaaaaaacgaactactgaacaacactgcccttgcatttgtggcttcagATGGCTGACCCGACTGGAATTGCAAACTGGTCAGTGACGCACGTAGATTGGTCCGAAGGGAAATGGCATCCCAAAGTCTACAGGGCTGTGGATACGAGCT
upper sequence: AT4G31350.2 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GRMZM2G061465_T01 (Zea mays), 3'ss of exon 7
gtcagttgtactgcttgcttgcgtcttccttttattacccttaagccttaaagtactcattttcctctaact-tcatcataatctctccgctcatgatctctttctttcagATGATTGATCCAGATGGAATAGCAAACTGGTCGGTCACACATGTAGATTGGTCCGAGGGCAAATGGCATCCGAAGCTGTACAATGCAAGAGACATCACTC
| | | || || || | || ||| || | || | | || ||||| ||| |||||||| | ||||| | ||| || | || ||||| || |||||||| |||||||||||||| ||||||||||| | | || | ||| || |||||
-----------------------------gtcagtgttcactatctattgaaatgtcatttaacctttatttatctgggcacttgcttaattcatg--tccttgacttcagATGGTAGATCCTGGTGGCATCTCCAATTGGTCTGTTACACATGTGGATTGGTCCGAGGGAAAATGGCATCCAAGGTCATATAGTGCTGACGATGTCACTT
upper sequence: AT4G31350.2 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA17G29670.1 (Glycine max), 3'ss of exon 8
gtcagttgtactgcttgcttgcgtcttccttttattacccttaagccttaaagtactcattttcctctaacttcatcataatctctccgctcatgatctctttctttcagATGATTGATCCAGATGGAATAGCAAACTGGTCGGTCACACATGTAGATTGGTCCGAGGGCAAATGGCATCCGAAGCTGTACAATGCAAGAGACATCACTC
| | | | | || | || | | | | | || | | || || ||| | || | | | ||| ||||| ||||||| | |||||| ||||| |||||||| ||| |||| |||||||| || || ||||||||||| | | || || | || || |||
-----------------gtcagtccaccaatctgttctcttttaaatt----gcaatgataggcatttatctatctcacagctaactcgttttgtgtgtattt-----agATGCTTGATCCTGGTGGAATCGCAAATTGGTCGGTAACATATGTTGATTGGTCTGAAGGAAAATGGCATCCAAGATCATTCAGAGCTCGGGATATTACTT
upper sequence: AT4G31350.2 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA14G17110.1 (Glycine max), 3'ss of exon 8
gtcagttgtactgcttgcttgcgtcttccttttattacccttaagccttaaagtactcattttcctctaacttcatcataatctctccgctcatgatctctttctttcagATGATTGATCCAGATGGAATAGCAAACTGGTCGGTCACACATGTAGATTGGTCCGAGGGCAAATGGCATCCGAAGCTGTACAATGCAAGAGACATCACTC
| | | | | | | |||| || | || | |||| || || | | | | | ||| ||||| ||||||| | |||||| ||||| |||||| | ||| |||| |||||||| || || ||||||||||| | | | || || | || || ||
----------------gtcagtgcaccaatctgttctcttttaaattgcaatg-----ataggcatctatctcactcgcagctaactcatttggtgtgtattt-----agATGCTTGATCCTGGTGGAATCGCAAATTGGTCGATAACATATGTTGATTGGTCTGAAGGAAAATGGCATCCAAGGTCATTCAGAGCTCGGGATATTACAT
upper sequence: AT4G31350.2 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: Vv04s0008g02630.t01 (Vitis vinifera), 3'ss of exon 8
gtcagttgtactgcttgcttgcgtcttccttttattacccttaagccttaaagtactcattttcctctaacttcatcataatctctccgctcatgatctctttctttcagATGATTGATCCAGATGGAATAGCAAACTGGTCGGTCACACATGTAGATTGGTCCGAGGGCAAATGGCATCCGAAGCTGTACAATGCAAGAGACATCACTC
||||| | | | |||| | || | | | | || | ||| | || ||| || | || | || || | |||||||||||| ||||| |||||| ||||||||||| || ||||||||||||||||| || || || |||||||| || |||| | |||| ||| |
gtcagc-acattaaactttgtactctttttcccataaaaccttgtgttaaaccctcctattatttccttgtttc----caacatttcttcccactg-ctgctgctttcagATGATCGATCCTACTGGAATTGCAAACTGGTCTGTGACACATGTAGATTGGTCAGAAGGAAAGTGGCATCCAAAAGCATACAGGGGTCAAGACGTCAGTT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ctcattttcctctaacttcatcataatctctccgctcatgatctctttctttcagATGATTGATCCAGATGGAATAGCAAACTGGTCGGTCACACATGTAGATTGGTCCGAGGGCAAATGGCATCCGAAGCTGTACAATGCAAGAGACATCACTC
ctctaac putative branch site (score: 2)
tctctccgctcatgat putative PPT
atcataat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtcagttgtactgcttgcttgcgtcttccttttattacccttaagccttaaagtactcattttcctctaacttcatcataatctctccgctcatgatctctttctttcagATGATTGATCCAGATGGAATAGCAAACTGGTCGGTCACACATGTAGATTGGTCCGAGGGCAAATGGCATCCGAAGCTGTACAATGCAAGAGACATCACTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA