Sequence
atgc intronic sequence ATGC exonic sequencegtaagaacccttctgattcttgatattatctgggattttttttgctttgtaacttatcctaaatgttactggtgatgatttatataagGTGGTCAATGATTGCAAGCCACTTACCTGGACGAACTGACAATGAGATCAAGAATTTCTGGAATACTCATTTGAAGAAAAAGCTGATTCAGATGGGTTTT
Basic information
species | Arabidopsis thaliana |
transcript | AT5G65230.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G65230.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G159547_T01 (Zea mays), 3'ss of exon 2
-------------gtaagaacccttctgattcttgatattatctgggattttttttgctttgtaacttatcctaaatgttactggtgatgat--ttatataagGTGGTCAATGATTGCAAGCCACTTACCTGGACGAACTGACAATGAGATCAAGAATTTCTGGAATACTCATTTGAAGAAAAAGCTGATTCAGATGGGTTTT
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gctagtttgtttcactctaacttcaataactcgtatttttgacttgtacgtagtgcatgctatg-ctaatcc--agtgtcaactgttgtcatggtcaaaccagATGGTCAGCTATCGCAAAGCACCTCCCTGGGCGGACTGATAACGAGATCAAGAATTTCTGGAACACGCACCTGAAGAAGAAGCTCATCCAGATGGGCTTC
upper sequence: AT5G65230.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv11s0078g00480.t01 (Vitis vinifera), 3'ss of exon 2
-----------gtaagaacccttctgattcttgatattatctgggattttttt--tgctttgta--acttatcctaaatgttactggtgatgatttatata----agGTGGTCAATGATTGCAAGCCACTTACCTGGACGAACTGACAATGAGATCAAGAATTTCTGGAATACTCATTTGAAGAAAAAGCTGATTCAGATGGGTTTT
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gtaattcttcgaacaaaatcaatttctttaatggaatcattttaattctattgaataatgtgtattaattattttca-tatttctttttctggttttcctattgtagATGGTCAGCAATTGCTTCCCACCTTCCTGGACGGACCGACAATGAAATCAAGAATTTCCGGAACACCCATCTTAAGAAGAAGCTGATTCAGATGGGTTTC
upper sequence: AT5G65230.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv07s0141g00100.t01 (Vitis vinifera), 3'ss of exon 2
----------gtaagaacccttctgattct-tgatattatctgggattttttt--tgctttgta--acttatcctaaatgttactggtgatgatttatata----agGTGGTCAATGATTGCAAGCCACTTACCTGGACGAACTGACAATGAGATCAAGAATTTCTGGAATACTCATTTGAAGAAAAAGCTGATTCAGATGGGTTTT
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gtaattcttcgaacaaaatcaattgctttaatggaagcattttaattctattgaataatgtgtattaattattttca-tatttctttttctggttttcctattgtagATGGTCAGCAATTGCTTCTCACCTTCCTGGACGGACCGACAATGAAATCAAGAATTTCTGGAACACCCATCTTAAGAAGAAGCTGATTCAGATGGGTTTC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gattttttttgctttgtaacttatcctaaatgttactggtgatgatttatataagGTGGTCAATGATTGCAAGCCACTTACCTGGACGAACTGACAATGAGATCAAGAATTTCTGGAATACTCATTTGAAGAAAAAGCTGATTCAGATGGGTTTT
tcctaaa putative branch site (score: 2)
tgatgatttatataa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagaacccttctgattcttgatattatctgggattttttttgctttgtaacttatcctaaatgttactggtgatgatttatataagGTGGTCAATGATTGCAAGCCACTTACCTGGACGAACTGACAATGAGATCAAGAATTTCTGGAATACTCATTTGAAGAAAAAGCTGATTCAGATGGGTTTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG