Sequence
atgc intronic sequence ATGC exonic sequencegtatgtcgttttttacttcatttaagctcggttagttgtgtacctttgtcttgaagctgtggcctatgatttctgaatcattctttttggaatttgttacgaagGTTTCGTTGTTTAGAAGACTGCTGCTTATGGTGAGAAACTTGAGAGCAGAATCGGACAGGATGCACGCATTAGCCTGTATCTGTCGGACAGCTCTCTGTG
Basic information
species | Arabidopsis thaliana |
transcript | AT3G01780.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G01780.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: LOC_Os11g07470.1 (Oryza sativa), 3'ss of exon 1
gtatgtcgttttttacttcatttaagctcggttagttgtgtacctttgtcttgaagctgtggcctatgatttctgaatcattctttttggaatttgttacga---agGTTTCGTTGTTTAGAAGACTGCTGCTTATGGTGAGAAACTTGAGAGCAGAATCGGACAGGATGCACGCATTAGCCTGTATCTGTCGGACAGCTCTCTGTG
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-----cagtttcttcccttctgtgcatgccttctgaagaatatgtgagtgtcataatgttaatttat--tccaagatcaatttacaaaagcatgttttatgacacagGTGTCTCTGTTCAAAAGACTTCTTCAGATGGTGAGAAACTTGAGAGCCGAATCAGATCGTATGCATGCATTGGCATGTATTTGTCGGACTGCTCTTTGTG
upper sequence: AT3G01780.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: LOC_Os02g55010.1 (Oryza sativa), 3'ss of exon 1
gtatgtcgttttttacttcatttaagctcggttagttgtgtacctttgtcttgaagctgtggcctatgatttc-tgaatcattctttttggaatttgttacgaagGTTTCGTTGTTTAGAAGACTGCTGCTTATGGTGAGAAACTTGAGAGCAGAATCGGACAGGATGCACGCATTAGCCTGTATCTGTCGGACAGCTCTCTGTG
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---tcacgatattagttgccactatattcc-ctagcatta-accggcgatctgtgttacatgcatataataacatggatttacaaaagtatgttttgtgatgcagGTGTCTCTGTTCAAAAGGCTGCTTCAAATGGTGAGGAATTTGAGAGCAGAATCAGATCGTATGCATGCATTGGCATGTATTTGTCGGACTGCTCTTTGTG
upper sequence: AT3G01780.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GRMZM2G162286_T01 (Zea mays), 3'ss of exon 1
gtatgtcgttttttacttcatttaagctcggttagttgtgtacctttgtcttgaagctgtggcctatgatttctgaatcattctttttggaatttgttacga---agGTTTCGTTGTTTAGAAGACTGCTGCTTATGGTGAGAAACTTGAGAGCAGAATCGGACAGGATGCACGCATTAGCCTGTATCTGTCGGACAGCTCTCTGTG
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-----agatatgttactgtgtttggaacaa--tagcttttaatatagtagataatattgcgaatttatgttcaagatgtatttacttgaacatgtgctatgacacagGTCTCTCTATTCAAAAGACTGCTTCAGATGGTGAGAAACTTGAGAGCAGAATCAGATCGAATGCATGCTTTGGCATGTATTTGTCGGACTGCTCTTTGTG
upper sequence: AT3G01780.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: Vv14s0171g00280.t01 (Vitis vinifera), 3'ss of exon 1
-gtatgtcgttttttact---tcatttaagctcggttagttgtgtacctttgtcttgaagctgtggcctatgatttctgaatcattctttttggaatttgttacgaagGTTTCGTTGTTTAGAAGACTGCTGCTTATGGTGAGAAACTTGAGAGCAGAATCGGACAGGATGCACGCATTAGCCTGTATCTGTCGGACAGCTCTCTGTG
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aatatacaagatgccaataaatcttttctgtagtgctaattatttgtttcaagggcatagctgcaaac-atgattt---gatgatataactt--aactgctttc--agGTTTCATTATTTAAAAGGTTGCTTCTAATGGTGAGAAACTTGAGAGCAGAATCGGACCGTATGCATGCTTTAGCCTGTATTTGTCGCACTGCACTTTGTG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cttgaagctgtggcctatgatttctgaatcattctttttggaatttgttacgaagGTTTCGTTGTTTAGAAGACTGCTGCTTATGGTGAGAAACTTGAGAGCAGAATCGGACAGGATGCACGCATTAGCCTGTATCTGTCGGACAGCTCTCTGTG
attcttttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatgtcgttttttacttcatttaagctcggttagttgtgtacctttgtcttgaagctgtggcctatgatttctgaatcattctttttggaatttgttacgaagGTTTCGTTGTTTAGAAGACTGCTGCTTATGGTGAGAAACTTGAGAGCAGAATCGGACAGGATGCACGCATTAGCCTGTATCTGTCGGACAGCTCTCTGTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTC