Sequence
atgc intronic sequence ATGC exonic sequence...tcgttgcttcttgaaattatctgtcccttctttacatatctaaaaaccacatgttatcttgaatttttttcttatattcataatatgcaatatgctgcagCCTACAGAAAAGCAGAAGATATGAATTATCACTCCGTTTGCTTGCACGTCATATCAGATTCCATCCGCAG
Basic information
species | Arabidopsis thaliana |
transcript | AT3G12100.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G12100.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA03G30140.1 (Glycine max), 3'ss of exon 5
-tcgttgcttcttgaaattatctgtcccttctttacatatctaaaaaccacatgttatcttgaattttt-----ttcttatattcataatatgcaatatgc--tgcagCCTACAGAAAAGCAGAAGATATGAATTATCACTCCGTTTGCTTGCACGTCATATCAGATTCCATCCGCAG
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gttagtattttttgaatgttcttagattcacctgatttaaccttttccctcttttcagccttgacctgtaataatcattaaaagtttcttctggaatttgccttgcagCTTACAGAAATGCAGAAGATATGAATAATCACTCTGTTTTCCTGCATGTTGTTGCAGATTCCATTCGCAG
upper sequence: AT3G12100.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: Vv08s0007g06550.t01 (Vitis vinifera), 3'ss of exon 5
tcgttgcttcttgaaattatctgtcccttctttacatatctaaaaaccacatgt-tatcttgaatttttttcttatattcataatatgcaatat---gctgcagCCTACAGAAAAGCAGAAGATATGAATTATCACTCCGTTTGCTTGCACGTCATATCAGATTCCATCCGCAG
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----agattcttagtgttgtagtgttcagagttatgattgtcagccctaggtgcacatgctttattttttggatgttcttgtcatctttcatttttcattgcagTCTACAGGAAAGCAGAGGATATGAACTACCACTCAGTTTGCTTGCATGTTCTTGCAGATTCTATACGCAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.accacatgttatcttgaatttttttcttatattcataatatgcaatatgctgcagCCTACAGAAAAGCAGAAGATATGAATTATCACTCCGTTTGCTTGCACGTCATATCAGATTCCATCCGCAG
atgttatcttgaattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tcgttgcttcttgaaattatctgtcccttctttacatatctaaaaaccacatgttatcttgaatttttttcttatattcataatatgcaatatgctgcagCCTACAGAAAAGCAGAAGATATGAATTATCACTCCGTTTGCTTGCACGTCATATCAGATTCCATCCGCAG
- -ttgcttc
- - - - - - - - - - - - - - - - - - - - taaaaac