Sequence
atgc intronic sequence ATGC exonic sequencegtaagagttctgtttctttaagttctgtttctttatgccatattaatcttgtttaaagaagaacattcttgttgtaaacggaggaagtaatgatacgttgatgttcgtagATGCTAGCGAAGAAGGTGGAAACATTAACAAAGGCAATGGAGGTTGAAGCAAAGAAGATGAGACGGGAAGTAGCTGCAATGGAAAAAGAAGTTGCTGCAA
Basic information
species | Arabidopsis thaliana |
transcript | AT1G24764.1 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G24764.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: LOC_Os02g50320.1 (Oryza sativa), 3'ss of exon 9
gtaagagttctgtttctttaagttctgtttctttatgccatattaatcttgtttaaagaagaacattcttgttgtaaacggaggaagtaatgatacgttgatgttcgtagATGCTAGCGAAGAAGGTGGAAACATTAACAAAGGCAATGGAGGTTGAAGCAAAGAAGATGAGACGGGAAGTAGCTGCAATGGAAAAAGAAGTTGCTGCAA
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---------------------gtatggcactagaattcctgtttattatggatttaatgggaccaat---gctgtgggtcatgcctttgctaactgcctcttgtttacagATGTTGGCAAAAAAGGTAGATACATTAACCAAGGCTATGGAAGTGGAGGCTAAAAAGATGAGGCGAGAGGTAGCTGCTATGGAGAAGGAAGTTGCTGCTA
upper sequence: AT1G24764.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA07G26540.1 (Glycine max), 3'ss of exon 9
gtaagagttctgtttctttaagttctgtttctttatgccatattaat-cttgtttaaagaagaacattcttgttgtaaacggaggaagtaatgatacgttgatgttcgtagATGCTAGCGAAGAAGGTGGAAACATTAACAAAGGCAATGGAGGTTGAAGCAAAGAAGATGAGACGGGAAGTAGCTGCAATGGAAAAAGAAGTTGCTGCAA
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gtaaatgtttggtctattta--ttgtatttggatataatccttgacttcttatttataaatgatagtccttgct--aattgtttccaatggccat-catctat-----cagATGTTAGCAAAGAAGGTAGATACATTGACCAAAGCCATGGAAGTTGAGGCAAAGAAGATGAGAAGGGAAGTAGCTGCTATGGAGAAGGAGGTAGCTGCTA
upper sequence: AT1G24764.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA02G09390.1 (Glycine max), 3'ss of exon 9
gtaagagttctgtttctttaagttctgtttctttatgccatattaat-cttgtttaaagaagaacattcttgttgtaaacggaggaagtaatgatacgttgatgttcgtagATGCTAGCGAAGAAGGTGGAAACATTAACAAAGGCAATGGAGGTTGAAGCAAAGAAGATGAGACGGGAAGTAGCTGCAATGGAAAAAGAAGTTGCTGCAA
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gtaagtgtttggtctattta--ttgtgtttggatataatccttgacttcttatgtataaatgatagtccttgct--aattgtttccaatggtcat-catctat-----cagATGTTAGCAAAGAAGGTAGATACATTGACCAAAGCCATGGAAGTTGAGGCAAAGAAGATGAGAAGGGAAGTAGCTGCTATGGAGAAGGAGGTAGCTGCTA
upper sequence: AT1G24764.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA08G05100.1 (Glycine max), 3'ss of exon 9
gtaagagttctgtttctttaagttctgtttctttatgccatattaatcttg--tttaaagaagaacattcttgttgtaaacggaggaagtaatgatacgttgatgttcgt-agATGCTAGCGAAGAAGGTGGAAACATTAACAAAGGCAATGGAGGTTGAAGCAAAGAAGATGAGACGGGAAGTAGCTGCAATGGAAAAAGAAGTTGCTGCAA
| ||| | ||| || | ||||||||||| ||| | || ||| | | || | | |||| |||| | | || ||||||| || ||||| || || ||||| || || || ||||| ||||| ||||||||||||||| | ||||||||| | ||||| || || || |||||||
-----------------gttagtatttttttgttcttggatattaatcttagatttctaattgataattataatcttagctaattgttgcaatg----gttgttatctgtcagATGCTGGCAAAGAAAGTAGATACATTGACCAAAGCCATGGAAGTTGAGGCAAAGAAGATGAGAAGAGAAGTAGCTTCCATGGAGAAGGAGGTAGCTGCAA
upper sequence: AT1G24764.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA05G34560.1 (Glycine max), 3'ss of exon 9
gtaagagttctgtttctttaagttctgtttctttatgccatattaatcttg--tttaaagaagaacattcttgttgtaaacggaggaagtaatgatacgttgatgttcgt-agATGCTAGCGAAGAAGGTGGAAACATTAACAAAGGCAATGGAGGTTGAAGCAAAGAAGATGAGACGGGAAGTAGCTGCAATGGAAAAAGAAGTTGCTGCAA
||| | | ||| ||| || ||||||||||| ||| | || ||| | | || | | |||| |||| | | || ||||||| || ||||| || || ||||| || || || ||||| ||||| ||||||||||||||| | ||||||||| | ||||| || || || ||||| |
----------------gttagtatttatttgtttttgg-atattaatcttagatttctaattgataattataatcttagctaactgttgcaatg----gttgttatctgtcagATGCTGGCAAAGAAAGTAGATACATTGACCAAAGCCATGGAAGTTGAGGCAAAGAAGATGAGAAGAGAAGTAGCTTCCATGGAGAAGGAGGTAGCTGCGA
upper sequence: AT1G24764.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: Vv01s0011g05790.t01 (Vitis vinifera), 3'ss of exon 9
gtaagagttctgtttctttaagttctgtttctttatgccatattaatcttgtttaaagaagaacattcttgttgtaaacggaggaagtaatgatacgttgatgttcgtagATGCTAGCGAAGAAGGTGGAAACATTAACAAAGGCAATGGAGGTTGAAGCAAAGAAGATGAGACGGGAAGTAGCTGCAATGGAAAAAGAAGTTGCTGCAA
|| |||| | || | || | | ||| | ||||| | | || | |||| ||| | | | | || |||||||||| |||||||| || |||||||| ||||||||||| ||||| || |||||||||||| ||||||| ||||| ||||| || || || ||||| |
---------------gttggtattct-tgtcctcat-ctgtcttatgatgctttaattcatatttttgctcatgtatttggatgtaattct------------ttttcagATGCTAGCTAAGAAGGTAGATACATTAACCAAGGCAATGGAAGTTGAGGCTAAGAAGATGAGAAGGGAAGTTGCTGCCATGGAGAAGGAGGTAGCTGCCA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aagaagaacattcttgttgtaaacggaggaagtaatgatacgttgatgttcgtagATGCTAGCGAAGAAGGTGGAAACATTAACAAAGGCAATGGAGGTTGAAGCAAAGAAGATGAGACGGGAAGTAGCTGCAATGGAAAAAGAAGTTGCTGCAA
cgttgat putative branch site (score: 5)
taatgata 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagagttctgtttctttaagttctgtttctttatgccatattaatcttgtttaaagaagaacattcttgttgtaaacggaggaagtaatgatacgttgatgttcgtagATGCTAGCGAAGAAGGTGGAAACATTAACAAAGGCAATGGAGGTTGAAGCAAAGAAGATGAGACGGGAAGTAGCTGCAATGGAAAAAGAAGTTGCTGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
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- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC