Sequence
atgc intronic sequence ATGC exonic sequencegtaaaacaccattaatagtaacactctgtttccacacttttttctttgcaacccttattaactatatccctggcctctggcctatctaacagCTCGAGGCAATGGGATTTGATAGAGCCTTAGTAATAGAAGCGTTCCTCGCATGTGACCGAAATGAAGAATTGGCAGCTAACTATCTATTGGAGAACTCAG
Basic information
species | Arabidopsis thaliana |
transcript | AT1G79650.3 |
intron # | 10 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G79650.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: GLYMA08G23930.1 (Glycine max), 3'ss of exon 12
gtaaaacaccattaatagtaacactctgtttccacacttttttctttgcaacccttattaactatatccctggcctctggcctat--ctaacagCTCGAGGCAATGGGATTTGATAGAGCCTTAGTAATAGAAGCGTTCCTCGCATGTGACCGAAATGAAGAATTGGCAGCTAACTATCTATTGGAGAACTCAG
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gtatgtcactccttcttgt--cgtctaatatacgtgccgttgccattttcattttcatt---tctgctgattgatttttacttattattcgtagCTCGAGGCTATGGGATTTGATAGAGCCTCGGTGATAGAGGCATTTTTGGCATGTGACCGTGATGAGCAATTGGCAGCCAACTATTTATTGGAGAATGCTG
upper sequence: AT1G79650.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: GLYMA07G00490.1 (Glycine max), 3'ss of exon 11
gta---aaacaccattaatagtaacactctgtttccacacttttttctttgcaacccttattaactatatccctggcctctggcctatc--taacagCTCGAGGCAATGGGATTTGATAGAGCCTTAGTAATAGAAGCGTTCCTCGCATGTGACCGAAATGAAGAATTGGCAGCTAACTATCTATTGGAGAACTCAG
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gtatgtcaatgtcactcctttttgtagtctaataatatacgtgt--cattgcgattttcatt---cctgctgattgatttttacttattattcgtagCTTGAGGCTATGGGATTTGATAGAGCCTCGGTGATAGAAGCATTTTTGGCATGTGACCGTGATGAGCAATTGGCAGCCAACTATTTATTGGAGAATGCTG
upper sequence: AT1G79650.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: Vv09s0018g01400.t01 (Vitis vinifera), 3'ss of exon 11
gta-aaacaccattaatagtaacactctgtttccacacttttttctttgcaacccttattaactatatccctggcc----tctggcctatctaacagCTCGAGGCAATGGGATTTGATAGAGCCTTAGTAATAGAAGCGTTCCTCGCATGTGACCGAAATGAAGAATTGGCAGCTAACTATCTATTGGAGAACTCAG
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gtgtagactccttcctccttgatact--gtccctctcttttttgcttttaagttcattttataaattttcctaatcataatcaattcccctccccagCTTGAGGCAATGGGATTTGACAGAGCTCTTGTCATTGAGGCATTCTTAGCTTGTGATCGAAATGAAGAATTGGCAGTCAACTATCTGTTGGAGAATGCTG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttttttctttgcaacccttattaactatatccctggcctctggcctatctaacagCTCGAGGCAATGGGATTTGATAGAGCCTTAGTAATAGAAGCGTTCCTCGCATGTGACCGAAATGAAGAATTGGCAGCTAACTATCTATTGGAGAACTCAG
tattaac putative branch site (score: 1)
cctatct putative PPT
ttattaactatat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaaaacaccattaatagtaacactctgtttccacacttttttctttgcaacccttattaactatatccctggcctctggcctatctaacagCTCGAGGCAATGGGATTTGATAGAGCCTTAGTAATAGAAGCGTTCCTCGCATGTGACCGAAATGAAGAATTGGCAGCTAACTATCTATTGGAGAACTCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA