Sequence
atgc intronic sequence ATGC exonic sequencegtgacagattgttatgatgtttcttattattaccatggaaagcaatggaccgaagtaatgaatggaaatgatttcagGTCTGTTGGTTTGGAGTTGACTCTTGACGATTTTCAGAAAGTTAGCGATGCGGTTCCATTTCTAGCAGATCTTAAACCCAGTGGGAAGTATGTTATGGAG
Basic information
species | Arabidopsis thaliana |
transcript | AT3G23940.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G23940.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: AC234528.1_FGT005 (Zea mays), 3'ss of exon 5
gtgacagattgttatgatgtttcttattattaccatggaaagcaatggaccgaagtaatgaatggaaatgatttcagGTCTGTTGGTTTGGAGTTGACTCTTGACGATTTTCAGAAAGTTAGCGATGCGGTTCCATTTCTAGCAGATCTTAAACCCAGTGGGAAGTATGTTATGGAG
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---gtgcgttatcatcctcttgcatgtgctttctacttaggttgaaaaa---aactcatctggttgtcttctttcagGTCCGTTGGTTTGCATTTGACTCTTGATGATTTCCAGAAGGTCAGTGACCAAGTTCCTTTCCTTGCAGACCTCAAGCCCAGTGGCAAATATGTCATGGAG
upper sequence: AT3G23940.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA13G27810.1 (Glycine max), 3'ss of exon 5
----gtgacagattgttatgatgtttcttattattaccatggaaagcaatggaccgaagtaatgaatggaaatgattt---cagGTCTGTTGGTTTGGAGTTGACTCTTGACGATTTTCAGAAAGTTAGCGATGCGGTTCCATTTCTAGCAGATCTTAAACCCAGTGGGAAGTATGTTATGGAG
|||| || ||| | | || |||| || | | | || ||| | || || |||||| |||||||||||| | || ||||||||||| ||||||||||| |||||||||| |||||| ||| | ||||||||||| || |||||||| ||||| |||||
gtgagtga-agtttgatgccagagatcctatttatatac--aataaccctgagatgaaacctcaagtgtaa-tgattttggcagGTCTGTTGGCATTGATTTGACTCTTGATGATTTTCAGAAGGTTAGCGATGAGGTTCCTTTTATTGCAGATCTTAAGCCTAGTGGGAAATATGTCATGGAA
upper sequence: AT3G23940.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: Vv05s0051g00830.t01 (Vitis vinifera), 3'ss of exon 5
gtgacagattgttatgatgtttcttattattaccatggaaagcaatggaccgaagtaatgaatggaaatgatttcagGTCTGTTGGTTTGGAGTTGACTCTTGACGATTTTCAGAAAGTTAGCGATGCGGTTCCATTTCTAGCAGATCTTAAACCCAGTGGGAAGTATGTTATGGAG
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gtaagagtgtggtgagaaagttcccctgggtatgatttgcatcgctcagaattgctcatga-taagattcttggcagGTCTGTTGGTCTGCAGTTAACTCTTGATGATTTTCAGAAAGTAAGTGATGAGGTTCCATTCCTTGCTGATCTTAAGCCCAGTGGCAAATACGTCATGGAG
upper sequence: AT3G23940.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: EFJ36479 (Selaginella moellendorffii), 3'ss of exon 5
gtgacagattgttatgatgtttcttattattaccatggaaagcaatggaccgaagtaatgaatggaaatgatttc--agGTCTGTTGGTTTGGAGTTGACTCTTGACGATTTTCAGAAAGTTAGCGATGCGGTTCCATTTCTAGCAGATCTTAAACCCAGTGGGAAGTATGTTATGGAG
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--------------------------------------gtagtgaaaatctgatctttctagtttcgctagttacgcagGTCAGTAAACGTACCACTGACCTTGGACGACTTTCAGAAAGTTAGTGACGAAGTTCCGTTTATCGCTGATCTTAAACCCAGCGGGAAGTATGTAATGGAG
upper sequence: AT3G23940.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: EFJ18570 (Selaginella moellendorffii), 3'ss of exon 5
gtgacagattgttatgatgtttcttattattaccatggaaagcaatggaccgaagtaatgaatggaaatgatttcagGTCTGTTGGTTTGGAGTTGACTCTTGACGATTTTCAGAAAGTTAGCGATGCGGTTCCATTTCTAGCAGATCTTAAACCCAGTGGGAAGTATGTTATGGAG
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gtagtgaa--aatctgatctttctggttgttattgagtttcgcta---------gttacg--------------cagGTCAGTAAACGTACCACTGACCTTGGACGACTTTCAGAAAGTTAGTGACAAAGTTCCGTTTATCGCTGATCTTAAACCCAGCGGGAAGTATGTAATGGAG
upper sequence: AT3G23940.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: EFJ18571 (Selaginella moellendorffii), 3'ss of exon 6
gtgacagattgttatgatgtttcttattattaccatggaaagcaatggaccgaagtaatgaatggaaatgatttcagGTCTGTTGGTTTGGAGTTGACTCTTGACGATTTTCAGAAAGTTAGCGATGCGGTTCCATTTCTAGCAGATCTTAAACCCAGTGGGAAGTATGTTATGGAG
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----------gtagtgaaaatc----tgatctttctggttgtcattgagtttcgctagtta-----------cgcagGTCAGTAAACGTGCCACTGACCTTGGACGACTTTCAGAAAGTTAGTGACAAAGTTCCGTTTATCGCTGATCTTAAACCCAGCGGGAAGTATGTAATGGAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cttattattaccatggaaagcaatggaccgaagtaatgaatggaaatgatttcagGTCTGTTGGTTTGGAGTTGACTCTTGACGATTTTCAGAAAGTTAGCGATGCGGTTCCATTTCTAGCAGATCTTAAACCCAGTGGGAAGTATGTTATGGAG
aaatgattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgacagattgttatgatgtttcttattattaccatggaaagcaatggaccgaagtaatgaatggaaatgatttcagGTCTGTTGGTTTGGAGTTGACTCTTGACGATTTTCAGAAAGTTAGCGATGCGGTTCCATTTCTAGCAGATCTTAAACCCAGTGGGAAGTATGTTATGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT