Sequence
atgc intronic sequence ATGC exonic sequencegtgagtttacctcgtataagaaactagattatgaacctaataacgttgagacatgtaacaatgattgaattagctagaaaaaacttgatacttgtcgcctgattctctctcttctctcgttctttgatctctaaatagGGAACTGAGAGAGATTTTGTGCGTGCGGCAGAAGCATACATGCATGCTAAATCACAGTCCAATGCGCAAGCAATGTTCAACCTCGGTTACATGCATGAAC
Basic information
species | Arabidopsis thaliana |
transcript | AT1G18260.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G18260.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM2G146386_T01 (Zea mays), 3'ss of exon 2
gtgagtttacctcgtataagaaactagattatgaacctaataacgttgagacatgtaacaatgattgaattagctagaaaaaacttgatacttgtcgcctgattctctctcttctctcgttctttgatctctaaatagGGAACTGAGAGAGATTTTGTGCGTGCGGCAGAAGCATACATGCATGCTAAATCACAGTCCAATGCGCAAGCAATGTTCAACCTCGGTTACATGCATGAAC
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-----------------aagaaagtgaaatat---cttcatg----tgatatttcttggaaaatatgcatttgctgagaaa---ctggcaatagggtgttacctacctgtattttctctgttt-----------acagGGCGTCGCAAGGGACTATGAACGTGCAGCAGAGGCATATATGCATGCTCGGTCACAGTCTAATGCTCAAGCTATTTTTAACCTTGGGTACATGCATGAGC
upper sequence: AT1G18260.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA05G33770.2 (Glycine max), 3'ss of exon 2
gtgagtttacctcgtataagaaactagattatgaacctaataacgttgagaca-tgtaacaatgattgaattagctagaaaaaacttgatacttgtcgcctgattctctctcttctctcgttctttgatctctaaatagGGAACTGAGAGAGATTTTGTGCGTGCGGCAGAAGCATACATGCATGCTAAATCACAGTCCAATGCGCAAGCAATGTTCAACCTCGGTTACATGCATGAAC
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---------------gtatgtggtttgacgatgcgc--aatgctgtgaattcaatttattggccattgtgctctcttttgcctactacac-cttttcactttctcgtgtttttcccccccttctgt----------cagGGTACTGCCAGGGATTATGAGCGAGCTGCTGAGGCTTATATGCATGCTAAATCACAATCGAATGCACAAGCCATGTTCAATCTTGGATACATGCATGAGC
upper sequence: AT1G18260.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA08G05930.1 (Glycine max), 3'ss of exon 2
gtgagtttacctcgtataagaaactagattatgaacctaataacgttgagacatgtaacaatgattgaatt-agctagaaaaaacttgata-cttgtcgcctgattctctctcttctctcgt-----tctttgatctctaaatagGGAACTGAGAGAGATTTTGTGCGTGCGGCAGAAGCATACATGCATGCTAAATCACAGTCCAATGCGCAAGCAATGTTCAACCTCGGTTACATGCATGAAC
| | | | | ||| |||||| | | | | || | ||| | ||||| || | | |||||| |||| || |||| |||| || |||| || ||| || || || || || ||||||||||||||||| | || |||||||| |||||||| || || ||||||||||| |
---------------------------------------------gtatgtggtttggcgatggatgaattcaatttaagccattgtgctctctttttgcctgcaccttttcactttctcgtgtttccctttttccttctgccagGGTACTGCCAGGGATTATGAGCGAGCTGCTGAGGCTTATATGCATGCTAAATCACAATTGAACGCGCAAGCCATGTTCAATCTTGGATACATGCATGAGC
upper sequence: AT1G18260.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA08G05930.2 (Glycine max), 3'ss of exon 2
gtga-gtttacctcgtataagaaactagattatgaacctaataacgttgagacatgta-----acaatgattgaatt-agctagaaaaaacttgata-cttgtcgcctgattctctctcttctctcgt-----tctttgatctctaaatagGGAACTGAGAGAGATTTTGTGCGTGCGGCAGAAGCATACATGCATGCTAAATCACAGTCCAATGCGCAAGCAATGTTCAACCTCGGTTACATGCATGAAC
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gtaatgaacatgctgctttactcattggag-atgcatattactatggtcgggtatgtggtttggcgatggatgaattcaatttaagccattgtgctctctttttgcctgcaccttttcactttctcgtgtttccctttttccttctgccagGGTACTGCCAGGGATTATGAGCGAGCTGCTGAGGCTTATATGCATGCTAAATCACAATTGAACGCGCAAGCCATGTTCAATCTTGGATACATGCATGAGC
upper sequence: AT1G18260.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv17s0000g02280.t01 (Vitis vinifera), 3'ss of exon 4
--------------gtgagtttacctcgtataagaaactagattatgaacctaataacgttgagacatgtaacaatgattgaattagctagaaaaaacttgatacttgtcgcctgattctctctcttctctcgttctttgatctctaaatagGGAACTGAGAGAGATTTTGTGCGTGCGGCAGAAGCATACATGCATGCTAAATCACAGTCCAATGCGCAAGCAATGTTCAACCTCGGTTACATGCATGAAC
|| ||| | | || || |||| | | || | | | | | | | | | | || ||| || || | | ||| | | ||||| || | | | |||| ||||||||||||| || || || ||| | |||||||||||||| || || || |||||||| ||||| ||||||||||| || ||||||||||| |
gtatgtgtctataaatgggttaatcctgtcggagct-ctaggtccaggacttc-tgattctagtatgcatttatgttctccatacaatgtaaattttcttaatttttatttatttattgtttaccttctttccctttct----------cagGGTACTGAGAGAGATTATGATCGAGCTGCAAAGGCATACATGCATGCCAAGTCCCAATCCAATGCACAAGCCATGTTCAACCTTGGGTACATGCATGAGC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cttgatacttgtcgcctgattctctctcttctctcgttctttgatctctaaatagGGAACTGAGAGAGATTTTGTGCGTGCGGCAGAAGCATACATGCATGCTAAATCACAGTCCAATGCGCAAGCAATGTTCAACCTCGGTTACATGCATGAAC
cctgattctctctctt CT-rich tract
tctaaata 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgagtttacctcgtataagaaactagattatgaacctaataacgttgagacatgtaacaatgattgaattagctagaaaaaacttgatacttgtcgcctgattctctctcttctctcgttctttgatctctaaatagGGAACTGAGAGAGATTTTGTGCGTGCGGCAGAAGCATACATGCATGCTAAATCACAGTCCAATGCGCAAGCAATGTTCAACCTCGGTTACATGCATGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA