Sequence
atgc intronic sequence ATGC exonic sequencegtaactaaacactaatacgcctcacagttttgtgactttcaaactaagccatctagagaaactgtagttaatgtcttttgattttgagatttgcagCTACTGTTTTTGGACAGAATCTAAGATTAGAACCATTGGAGATAGAGCAGAAGACGACGTGGAAGAGAGAAATGAATTGCCTTCTCTCTGTGTGTGACTA
Basic information
species | Arabidopsis thaliana |
transcript | AT1G01700.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G01700.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA03G01560.1 (Glycine max), 3'ss of exon 3
gtaactaaacactaatacgcctcacagttttgtgactttcaaactaagccatctagagaaactgtagttaatgtcttttgattttgagatttgcagCTACTGTTTTTGGACAGAATCTAAGATTAGAACCATTGGAGATAGAGCAGAAGACGACGTGGAAGAGAGAAATGAATTGCCTTCTCTCTGTGTGTGACTA
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--------------------gtaatttttttttaatagtagcaatag--cataagatatggctatggtttaacttatttgaatagggaatttgcagCAACTGCTTTTGGACAAAATTTAAAGTTGGAGCCTCTCAAGCCTGAGAAGAAGGCTATGTGGAAAAGAGAAATGAATTGTCTTCTATCTGTGTGTGATTA
upper sequence: AT1G01700.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: EFJ07173 (Selaginella moellendorffii), 3'ss of exon 1
gtaactaaacactaatacgcctcacagttttgtgactttcaaactaagccatctagagaaactgtagttaatgtcttttgattttgagatttgcagCTACTGTTTTTGGACAGAATCTAAGATTAGAACCATTGGAGATAGAGCAGAAGACGACGTGGAAGAGAGAAATGAATTGCCTTCTCTCTGTGTGTGACTA
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------------------------------gttcgttttcgatctagacttgtcatgg----tacggtgtaaccgtgtgggtcttcgctgttgcagCTTCGGTGTTTGGAAACTTGTGGAAGCTAGAACCTTTAGCCACGAGCCGGAGGAGAATGTGGAAGAGAGAAATGAATTGGCTTGTCTCTGTGACAGACTA
upper sequence: AT1G01700.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: EFJ09188 (Selaginella moellendorffii), 3'ss of exon 1
gtaactaaacactaatacgcctcacagttttgtgactttcaaactaagccatctagagaaactgtagttaatgtcttttgattttgagatttgcagCTACTGTTTTTGGACAGAATCTAAGATTAGAACCATTGGAGATAGAGCAGAAGACGACGTGGAAGAGAGAAATGAATTGCCTTCTCTCTGTGTGTGACTA
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------------------------------gttcgttttcgatctagacttgtcatgg----tacggtgtaaccgtgtggattttcgctgttgcagCGTCGGTGTTTGGAAACTTGTGGAAGCTAGAACCTTTAGCCACGAGCCGGAGGAGAATGTGGAAGAGAGAAATGAATTGGCTTGTCTCTGTGACAGACTA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aactaagccatctagagaaactgtagttaatgtcttttgattttgagatttgcagCTACTGTTTTTGGACAGAATCTAAGATTAGAACCATTGGAGATAGAGCAGAAGACGACGTGGAAGAGAGAAATGAATTGCCTTCTCTCTGTGTGTGACTA
ttttgat putative branch site (score: 4)
ttttgatttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaactaaacactaatacgcctcacagttttgtgactttcaaactaagccatctagagaaactgtagttaatgtcttttgattttgagatttgcagCTACTGTTTTTGGACAGAATCTAAGATTAGAACCATTGGAGATAGAGCAGAAGACGACGTGGAAGAGAGAAATGAATTGCCTTCTCTCTGTGTGTGACTA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA