Sequence
atgc intronic sequence ATGC exonic sequencegtatgggttcacatagcaagttcagagtgtttgtaatataggttcaatcttaattaattaaaaattgatcttgttttagGAGAGGTTAAACCAAGTGTTGATGGAGAAAAAGAAGGAAACGAGATCAGGCATGGAGATTATGAATCTACTCCAG
Basic information
species | Arabidopsis thaliana |
transcript | AT2G18876.2 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT2G18876.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: LOC_Os08g14460.1 (Oryza sativa), 3'ss of exon 6
gtatgg--gttcacatagcaagttcagagtgtttgtaatataggttcaatcttaattaattaaaaattgatcttgttttagGAGAGGTTAAACCAAGTGTTGATGGAGAAAAAGAAGGAAACGAGA---TCAGGCATGGAGATTATGAATCTACTCCAG
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gtataattgttgtctttacaaatctac-gtggtgattaaatacgagttattttcatagattgaccttcagctcttttgcagGAGAAGTTAAACCAGGTATTAATGGAGAAAAAGAAGGAATCATCACGTTCAGGAATGGAAATAATGAACTTGTTGCAG
upper sequence: AT2G18876.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA13G00980.1 (Glycine max), 3'ss of exon 7
---------------------------------------------------------gtatgggttcacatagca--agttcagagtgtttgtaatataggttcaatcttaattaattaaaaattgatcttgttt-------tagGAGAGGTTAAACCAAGTGTTGATGGAGAAAAAGAAGGAAACGAGATCAGGCATGGAGATTATGAATCTACTCCAG
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gtgtgacatctttgattttttattttttttattctgatgagaaccatatttggtgattagtgctcttacatgataggaacttacacaagtccacctattattagatttggaaatgaataagggctggtattttttgtatttgcagGAGAGGCTAAACCAAGTGTTGATGGAGAAGAAGAAAGAGTCTAGGTCAGGCATGGAGATAATGAATTTGCTTCAG
upper sequence: AT2G18876.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA17G07040.2 (Glycine max), 3'ss of exon 7
----------------------------------------------------gtatgggttcacatagcaag--ttcagagtgtttgtaatataggttcaatcttaattaattaaaaattg--atcttgtttt---agGAGAGGTTAAACCAAGTGTTGATGGAGAAAAAGAAGGAAACGAGATCAGGCATGGAGATTATGAATCTACTCCAG
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gtgtgatatctttgattttgtttttattctgatgagaaccatatttggtgattagtgcttttacatgataggaacttacgcgggtccacatattattagatttggaaatgatgaagggctggtattttgtatttgcagGAGAGGCTAAACCAAGTGTTGATGGAGAAGAAGAAAGAGTCTAGGTCAGGCATGGAGATAATGAATTTGCTTCAG
upper sequence: AT2G18876.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: Vv11s0052g00890.t01 (Vitis vinifera), 3'ss of exon 7
-----------------------------------------------------------------------gtatgggttcacatagcaagtt---cagagtgtttgtaatatagg-----ttcaatcttaattaattaaaaattgatcttgtttta------gGAGAGGTTAAACCAAGTGTTGATGGAGAAAAAGAAGGAAACGAGATCAGGCATGGAGATTATGAATCTACTCCAG
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gtaggatcctttccatgtgtattattatgatattatcttttaggggaaacttaaaggttgctcatgttagcaaatgggaacatctttcatgaatgacaacatatatggagaacaggagaagttcatgagtaggaaattggggaatgattgtgtttcacttgcagGAGAGGCTTAACCAAGTTTTGATGGAGAAAAAGAAGGAATCGAGGTCTGGCATGGAGATAATGAATCTTCTTCAG
upper sequence: AT2G18876.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: EFJ06947 (Selaginella moellendorffii), 3'ss of exon 7
gtatgggttcacatagcaagttcagagtgtttgtaatataggttcaatcttaattaattaaaaattgatcttgttttagGAGAGGTTAAACCAAGTGTTGATGGAGAAAAAGAAGGAAACGAGATCAGGCATGGAGATTATGAATCTACTCCAG
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----------------------gtatgagcttgcagtttc--ttca--tttgatt--ctacttatcgat-tcattctagGAACGGTTAAACCAAGTGCTTATGGAGAAGAAAAAGGAGACAAAAGCAGGCATGGAGATAATGAACCTCTTGCAG
upper sequence: AT2G18876.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: EFJ09125 (Selaginella moellendorffii), 3'ss of exon 5
gtatgggttcacatagcaagttcagagtgtttgtaatataggttcaatcttaattaattaaaaattgatcttgttttagGAGAGGTTAAACCAAGTGTTGATGGAGAAAAAGAAGGAAACGAGATCAGGCATGGAGATTATGAATCTACTCCAG
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----------------------------gtatgcacttgcagtttcttcatttgattctacttatcgat-tcattctagGAACGGTTAAACCAAGTGCTTATGGAGAAGAAAAAGGAGACAAAAGCAGGCATGGAGATAATGAACCTCTTGCAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gagtgtttgtaatataggttcaatcttaattaattaaaaattgatcttgttttagGAGAGGTTAAACCAAGTGTTGATGGAGAAAAAGAAGGAAACGAGATCAGGCATGGAGATTATGAATCTACTCCAG
tcttgtttt CT-rich tract
tttgtaatataggttc 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatgggttcacatagcaagttcagagtgtttgtaatataggttcaatcttaattaattaaaaattgatcttgttttagGAGAGGTTAAACCAAGTGTTGATGGAGAAAAAGAAGGAAACGAGATCAGGCATGGAGATTATGAATCTACTCCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT