Sequence
atgc intronic sequence ATGC exonic sequencegtacccctcaaggcctcaacttttgttattttaaggatataaattggaaaaatctttgatcttttgatgcctacataagaactaatgaaccattcactcttttcacttttggtattgaagtgtttgtttgttactatatagAATCCCCGTTTGAATTCCGGGCGCTAGAGGTGGCCTTGGAAGCTATTTGTAGTTTTCTAGCTGCAAGGACAACAGAACTAGAGAAGTTTGCTTATCCTGC
Basic information
species | Arabidopsis thaliana |
transcript | AT5G09690.4 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G09690.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA20G35260.1 (Glycine max), 3'ss of exon 3
gtacccctcaaggcctcaacttttgttattttaaggatataaattggaaaaatct-ttgatc-ttttgatgcctacataagaactaatgaaccattcactct---tttcacttttggtattgaagtgttt--gtttgttactatatagAATCCCCGTTTGAATTCCGGGCGCTAGAGGTGGCCTTGGAAGCTATTTGTAGTTTTCTAGCTGCAAGGACAACAGAACTAGAGAAGTTTGCTTATCCTGC
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----------gtacgttacattaaatgatg--aaccataagtaatgaacaaacttattgattgcatctgttcctgttataaatctatctttgtatttgcattatctcttgctcttgttatctgagtgatctaaattacacaaatgtagAGTCACCCTTTGAATTCCGGGCCCTGGAGGTTGCTTTAGAAGCCATTTGTAGTTTTCTTGCTGCACGTACAACAGAATTGGAGATGGCTGCTTATCCTGC
upper sequence: AT5G09690.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA10G32350.1 (Glycine max), 3'ss of exon 3
gtacccctcaaggcctcaacttttgttattttaaggatataaattggaaaaatctttgat--cttttgatgcctacataagaactaatgaaccattcactct---tttcacttttggtattgaagtg-tttgtttgttactatatagAATCCCCGTTTGAATTCCGGGCGCTAGAGGTGGCCTTGGAAGCTATTTGTAGTTTTCTAGCTGCAAGGACAACAGAACTAGAGAAGTTTGCTTATCCTGC
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gtacgctacatacttacatttaatggtgaaccataagta---atgaacaaactcattgattgcatctgttcctcttataa-atctatctttgtatttgcattatcttttgctcttgttatctgagtgatctaaattatgcaatgtagAGTCACCCTTTGAATTCCGGGCCCTGGAGGTTGCTTTAGAAGCCATTTGTAGTTTTCTTGCTGCACGTACATCAGAATTGGAGATGGCTGCTTATCCTGC
upper sequence: AT5G09690.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv05s0020g04720.t01 (Vitis vinifera), 3'ss of exon 3
gtacccctcaaggcctcaacttttgttattttaaggatataaattggaaaaatctttgatcttttgatgcctacataagaactaatgaaccattcactcttttcacttttggtattgaagtgtttgtttgttactatatagAATCCCCGTTTGAATTCCGGGCGCTAGAGGTGGCCTTGGAAGCTATTTGTAGTTTTCTAGCTGCAAGGACAACAGAACTAGAGAAGTTTGCTTATCCTGC
|| | | | | | || || | | || | | ||| | || | || |||| | || | |||| | ||| | || || |||| || || |||||||||||||| || |||||||| |||||||| |||||||||||||| |||||| | ||||||||||| || | ||||||||| ||
------------------------------gtatgtctcactaatctagtgattttgaaggaaataatatgaatacaagtagagatttttctgtctttcttgaaaattagttttctgaatgatctgtgtcataa-atgtagAGTCTCCCTTTGAATTCCGGGCTCTTGAGGTGGCTTTGGAAGCCATTTGTAGTTTTCTTGCTGCACGTACAACAGAACTGGAAACTGCTGCTTATCCAGC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gaaccattcactcttttcacttttggtattgaagtgtttgtttgttactatatagAATCCCCGTTTGAATTCCGGGCGCTAGAGGTGGCCTTGGAAGCTATTTGTAGTTTTCTAGCTGCAAGGACAACAGAACTAGAGAAGTTTGCTTATCCTGC
tttgttactatata 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtacccctcaaggcctcaacttttgttattttaaggatataaattggaaaaatctttgatcttttgatgcctacataagaactaatgaaccattcactcttttcacttttggtattgaagtgtttgtttgttactatatagAATCCCCGTTTGAATTCCGGGCGCTAGAGGTGGCCTTGGAAGCTATTTGTAGTTTTCTAGCTGCAAGGACAACAGAACTAGAGAAGTTTGCTTATCCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT