Sequence
atgc intronic sequence ATGC exonic sequencegtaaatcagttttaatgtgttaggcttgctactcatttatttagttacaaattatgtttccctcagtctttgacctgccctttttgaattttatagGCTCACTTACTCGACGGCAGGGCTAGCTCCGGTGCAAGCGTGGATTCTGCTAGACAGAATTTGGCTGCTACCTTTGTCAATGCATTCGTAAATGCTGGTT
Basic information
species | Arabidopsis thaliana |
transcript | AT2G20580.1 |
intron # | 10 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT2G20580.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: LOC_Os09g15750.1 (Oryza sativa), 3'ss of exon 12
gtaaatcagtttt-----aatg-tgttag--gcttgc---tactcatttatttagttacaaattatgtttccctcagtctttgacctgccctttttgaattttatagGCTCACTTACTCGACGGCAGGGCTAGCTCCGGTGCAAGCGTGGATTCTGCTAGACAGAATTTGGCTGCTACCTTTGTCAATGCATTCGTAAATGCTGGTT
|| || |||| |||| ||| | | |||| || | ||||||| || || | || | | | | || | | | | ||||| |||| ||| || | || ||| | | | | | || | |||||||| ||||||||| |||| || || ||||||||||||||||| |||||||| |
gttaacttgtttccccgaaatgctgtctgctgattgcatgtatctacttatttatttgtttatgaacttgctattaatgattaaaaaatgcatgct-aatttgttagGTTCATTTGATTGATGGCCGAGGGGCTACAAGCTCCAGTCTTGATTCTGCAAGACAGAATCTGGCGGCAACATTTGTCAATGCATTCGTGAATGCTGGAT
upper sequence: AT2G20580.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: LOC_Os02g05340.1 (Oryza sativa), 3'ss of exon 12
gtaaatcagttttaatgtgttaggcttgctactcatttatttagttacaaattatgtttccctcagtctttgacctgccctttttgaattttatagGCTCACTTACTCGACGGCAGGGCTAGCTCCGGTGCAAGCGTGGATTCTGCTAGACAGAATTTGGCTGCTACCTTTGTCAATGCATTCGTAAATGCTGGTT---
||| | || | | || | | | ||| | ||| | || | | | | | || | | ||| | | || ||| || ||| | || || | | | || | | || | |||||||| ||||| ||||| ||||| || ||||| |||||||||||||||||||| |
----gtcatctatattttacta---tcaatgtttattaa---ggttgc---ttttttcattcataataattaatatttgtatttaacaatctacagGTCCATTTAATTGATGGGCG---TGGTGCCAGCTCCAGTCTTGATTCTGCAAGACAAAATTTAGCTGCAACATTTGTAAATGCATTCGTAAATGCTGGATTTG
upper sequence: AT2G20580.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: LOC_Os06g48640.3 (Oryza sativa), 3'ss of exon 12
-----------gtaaatcagttttaatgtgttaggcttgc-tactcatttatttagttacaaattatgtttccctcagtctttgacctgccctttttgaattttatagGCTCACTTACTCGACGGCAGGGCTAGCTCCGGTGCAAGCGTGGATTCTGCTAGACAGAATTTGGCTGCTACCTTTGTCAATGCATTCGTAAATGCTGGTT
| | || | | || || | | | | |||||| || || | | | | | || | | | | |||| |||| ||| || | || ||| | | | | | || | ||||| || ||||||||| |||| || || ||||||||||||||||| |||||||| |
gttaacttttttttacccaaatgttatctgctgatttcatgtttctacttatttctttgtttatggacctgctattaatgattaaaaaatgcatgct-aattcattagGTTCATTTGATTGATGGCCGAGGGGCTACAAGCTCCAGTCTTGATTCCGCAAGACAGAATCTGGCGGCAACATTTGTCAATGCATTCGTGAATGCTGGAT
upper sequence: AT2G20580.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GRMZM2G155384_T02 (Zea mays), 3'ss of exon 12
gtaaatcagttttaatgtgttaggcttgctactcatttatttagttaca-aattatgtttccctcagtctttgacctgccctttttgaattttatagGCTCACTTACTCGACGGCAGGGCTAGCTCCGGTGCAAGCGTGGATTCTGCTAGACAGAATTTGGCTGCTACCTTTGTCAATGCATTCGTAAATGCTGGTT---
|| | | ||| | || ||| ||| ||| | | || | || ||||| ||| | | | ||| | |||| ||| | ||| || || | || || | | | || | | || | |||||||| ||||||||||| ||||| || ||||| |||||||| || |||||||| |
gtgatgtatattttcattattttgctgcttac-catatttgtaatagcacaattaaattttctataataattgtggttgtgttttacaatat-gcagGTCCATTTGATTGATGGTCG---TGGTGCCAGCTCCAGTCTTGATTCTGCAAGACAGAATTTAGCTGCAACATTTGTAAATGCATTTGTGAATGCTGGGTTTG
upper sequence: AT2G20580.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GLYMA06G44340.1 (Glycine max), 3'ss of exon 12
----gtaaatcagttttaatgtgttaggcttgcta-ctcatttatttagttacaaattatgtttccctcagtctt-tgacctgccctttttgaattttatagGCTCACTTACTCGACGGCAGGGCTAGCTCCGGTGCAAGCGTGGATTCTGCTAGACAGAATTTGGCTGCTACCTTTGTCAATGCATTCGTAAATGCTGGTT
||| ||||| | ||| ||| | |||| | | | || | | | ||| || | || ||| | | ||||| || || || || ||| ||||||| | |||||||| || ||||| ||||||||||| | ||||| || ||||| |||||||| ||||||||||| |
tcagaaaaaaaagtttatagatgtgctactttttgtctcaagtgtgccactttg--ttgatcagctgtgaaccttatgtttcactctggttgtttctcctagGCACATTTGCTTGATGGCCGGGCTAGTGCTGGTGCAAGTGTTGATTCAGCTAGACAGAACCTTGCTGCAACTTTTGTTAATGCATTTGTAAATGCTGGCT
upper sequence: AT2G20580.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GLYMA12G13410.1 (Glycine max), 3'ss of exon 12
----gtaaatcagttt--taatgtgttaggcttgctactcatttatttagttacaaattatgtttccctcagtctt-tgacctgccctttttgaattttatagGCTCACTTACTCGACGGCAGGGCTAGCTCCGGTGCAAGCGTGGATTCTGCTAGACAGAATTTGGCTGCTACCTTTGTCAATGCATTCGTAAATGCTGGTT
||| ||||| | ||||| || || | |||| | | | || | || | | ||| || | || ||| | ||||| ||||| || || ||| ||||||| | |||||||| || || || ||||||||||| | ||||| || ||||| |||||||| ||||||||||| |
tcagaaaaaaaagtttcttgatgtgctactttttgt-ctcaagtgtgccactttg--ttgattatctgtgaaccttatgtttcactctgcttgttactcctagGCACACTTGCTTGATGGCCGGGCTAGTGCTGGTGCAAGTGTTGACTCAGCTAGACAGAACCTTGCTGCAACTTTTGTTAATGCATTTGTAAATGCTGGCT
upper sequence: AT2G20580.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: Vv12s0028g03130.t01 (Vitis vinifera), 3'ss of exon 12
gtaaatcagttttaatgtgttaggcttgctactcatttatttagttacaaattatgtt--tccctcagtctttgacctgccctt-----tttgaatttta-tagGCTCACTTACTCGACGGCAGGGCTAGCTCCGGTGCAAGCGTGGATTCTGCTAGACAGAATTTGGCTGCTACCTTTGTCAATGCATTCGTAAATGCTGGTT
| || | ||| | |||| |||| ||| ||||| |||| | ||||| | || || ||| || | | ||| ||| ||||| ||||| || || || || ||| ||||||| | |||||||| || || ||||| |||||||| |||| ||||| |||||||||||||| |||||||||||||
acatgaaagactcaattttatagg--tgct--tcagttattcagttgaagtttatggtcatctcttagtgttaggctcatacttatttgcttggattttgctagGCACATTTGCTTGATGGCCGGGCTAGTGCTGGTGCAAGTGTTGACTCTGCCAGACAGAACCTGGCAGCTACTTTTGTCAATGCATTTGTAAATGCTGGTT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tagttacaaattatgtttccctcagtctttgacctgccctttttgaattttatagGCTCACTTACTCGACGGCAGGGCTAGCTCCGGTGCAAGCGTGGATTCTGCTAGACAGAATTTGGCTGCTACCTTTGTCAATGCATTCGTAAATGCTGGTT
ctttgac putative branch site (score: 4)
tttttgaattttata 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaaatcagttttaatgtgttaggcttgctactcatttatttagttacaaattatgtttccctcagtctttgacctgccctttttgaattttatagGCTCACTTACTCGACGGCAGGGCTAGCTCCGGTGCAAGCGTGGATTCTGCTAGACAGAATTTGGCTGCTACCTTTGTCAATGCATTCGTAAATGCTGGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG