Sequence
atgc intronic sequence ATGC exonic sequencegtaagcagtctgttgttacatgctcagagatttgttgttttgcttgatgacaagtgggctaacgtatgcaattgtgtcaaattgagcagGTTGATTTGCTGAGAGGGCAGAAGACAGACAGAGTGGATGTCAGCTTACAGCCAGAAGAGCTGGATGCTATGGAAAATGTTTTACCTGCCAAGTATGAGG
Basic information
species | Arabidopsis thaliana |
transcript | AT4G21660.2 |
intron # | 14 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G21660.2 (Arabidopsis thaliana), 3'ss of exon 14
lower sequence: GLYMA15G07760.1 (Glycine max), 3'ss of exon 15
gtaagcagtct----gttgttacatgctcagagatttgttgttttgcttgatgacaagtgggctaacgtatgcaatt--gtgtcaaattgagcagGTTGATTTGCTGAGAGGGCAGAAGACAGACAGAGTGGATGTCAGCTTACAGCCAGAAGAGCTGGATGCTATGGAAAATGTTTTACCTGCCAAGTATGAGG
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gtaagaattttttatgcggttgtttatgatgatgatatttgttttgttt--tgaagagtagcatgtttcatgcattctggctttggcactttcagGTTGATTTGCTTAGAGGTCAGAAGACAGATAAAGTGGATGTCACTTTACAGCCTGAAGAGTTGGAAGCCATGGAAAATGTTTTGCCTGCCAA--------
upper sequence: AT4G21660.2 (Arabidopsis thaliana), 3'ss of exon 14
lower sequence: GLYMA13G31550.2 (Glycine max), 3'ss of exon 15
gtaagcagtct----gttgttacatgctcagagatttgttgttttgcttgatgacaagtgggctaacgtatgcaatt--gtgtcaaattgagcagGTTGATTTGCTGAGAGGGCAGAAGACAGACAGAGTGGATGTCAGCTTACAGCCAGAAGAGCTGGATGCTATGGAAAATGTTTTACCTGCCAAGTATGAGG
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gtaagagttttttatgcggttggttatgatgatgatatttgttttgttt--tgaagagtagcatgtttcatgcattctggctttggcattttcagGTTGATCTGCTTAGAGGTCAGAAGACAGATAAAGTAGATGTCACTTTACAGCCTGAAGAGTTGGAAGCCATGGAAAATGTTTTGCCCGCGAAGTATGAAT
upper sequence: AT4G21660.2 (Arabidopsis thaliana), 3'ss of exon 14
lower sequence: GLYMA13G25110.2 (Glycine max), 3'ss of exon 15
-------gtaagcagtctgttgttacatgctcagagatttgttg--------ttttgcttgatgacaagtgggctaacgtatgcaattgtgtcaaattgagcagGTTGATTTGCTGAGAGGGCAGAAGACAGACAGAGTGGATGTCAGCTTACAGCCAGAAGAGCTGGATGCTATGGAAAATGTTTTACCTGCCAAGTATGAGG
||| | || || |||| | || || |||||| | | | | | | ||| ||| || ||||||||||| || ||||| || ||| |||| | ||||||||||| |||| |||||||||| ||||||| ||||||||||||||||| || ||
gtaaaacttaaaagagtttcctctatatttagggagaaaggggagaaggggtttctgtgtgatgata--ttgattggtgggataacatgtttcatgttttccagGTTGATTTACTTAGAGGACAAAAGTCAGATAAAGTGGATGTCACTTTACTGCCAGAAGAGTTGGATGCCATGGAAAATGTTTTACCCGCGAA--------
upper sequence: AT4G21660.2 (Arabidopsis thaliana), 3'ss of exon 14
lower sequence: GLYMA13G31550.1 (Glycine max), 3'ss of exon 15
gtaagcagtct----gttgttacatgctcagagatttgttgttttgcttgatgacaagtgggctaacgtatgcaatt--gtgtcaaattgagcagGTTGATTTGCTGAGAGGGCAGAAGACAGACAGAGTGGATGTCAGCTTACAGCCAGAAGAGCTGGATGCTATGGAAAATGTTTTACCTGCCAAGTATGAGG
||||| | | | ||| | || | |||||||| || ||| ||| | | ||||| | | | | ||||||||| |||| ||||| ||||||||||| | ||| ||||||| |||||||| |||||| |||| || |||||||||||||| || || ||
gtaagagttttttatgcggttggttatgatgatgatatttgttttgttt--tgaagagtagcatgtttcatgcattctggctttggcattttcagGTTGATCTGCTTAGAGGTCAGAAGACAGATAAAGTAGATGTCACTTTACAGCCTGAAGAGTTGGAAGCCATGGAAAATGTTTTGCCCGCGAA--------
upper sequence: AT4G21660.2 (Arabidopsis thaliana), 3'ss of exon 14
lower sequence: GLYMA07G31350.1 (Glycine max), 3'ss of exon 10
-------------gtaagcagtctgttgt-tacatgctcagagatttgttgttttgcttgatgacaagtgggctaacgtatgcaattgtgtcaaattgagcagGTTGATTTGCTGAGAGGGCAGAAGACAGACAGAGTGGATGTCAGCTTACAGCCAGAAGAGCTGGATGCTATGGAAAATGTTTTACCTGCCAAGTATGAGG
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aaaagggtaaaacttaaagagtttcctctctatatttagggagaaaagggggaggggtttcttgtgatgatattgattagtgggataacat---gttttccagGTTGATTTACTTAGAGGTCAAAAGTCAGATAAAGTGGATGTCACTTTACTGCCAGAAGAGTTGGATGCCAAGGAAAATGTTTTATCCGCAAAGTATGAAT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttgttttgcttgatgacaagtgggctaacgtatgcaattgtgtcaaattgagcagGTTGATTTGCTGAGAGGGCAGAAGACAGACAGAGTGGATGTCAGCTTACAGCCAGAAGAGCTGGATGCTATGGAAAATGTTTTACCTGCCAAGTATGAGG
ggctaac putative branch site (score: 2)
tcaaatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagcagtctgttgttacatgctcagagatttgttgttttgcttgatgacaagtgggctaacgtatgcaattgtgtcaaattgagcagGTTGATTTGCTGAGAGGGCAGAAGACAGACAGAGTGGATGTCAGCTTACAGCCAGAAGAGCTGGATGCTATGGAAAATGTTTTACCTGCCAAGTATGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA