Sequence
atgc intronic sequence ATGC exonic sequence...agacttgtgtagaatttgttctagctggatcagtgtctactagagaaagtagccttgactatattcatggacttacgattctttttactggcacttttagGTTTATATGTCGTTCGTCCAGGCTCTGTATGGTGGAGGAGGGTGGCCACTGTCGGTATTCCTTTCACCTGATTTAAAGCCGTTGATGGGTGGAACCTACT
Basic information
| species | Arabidopsis thaliana |
| transcript | AT4G03200.2 |
| intron # | 3 |
| splice site | 3' |
| intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G03200.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA03G36910.1 (Glycine max), 3'ss of exon 5
agacttgtgtagaatttgttctagctggatcagtgtctactagagaaagtagccttgactat--attcatggactta--cgattctttttactggcacttttagGTTTATATGTCGTTCGTCCAGGCTCTGTATGGTGGAGGAGGGTGGCCACTGTCGGTATTCCTTTCACCTGATTTAAAGCCGTTGATGGGTGGAACCTACT
| | | ||||||| || || || |||| ||| | || ||| | | ||| | ||||| | | ||||||| || ||||||| || |||||| |||||||||||||||| ||||| ||| || || ||||||||||| || || || || ||||||||||| ||||
-agttcctttggaatttgaatggttaaga--gatgctta-tagaaaaattgaggttttctaccggtaacaaggtttagtaaaggatttttttttccttctttagGTGTACATGTCGTATGTGCAGGCTTTGTATGGTGGAGGAGGTTGGCCCCTGAGTGTGTTTCTTTCACCTGACTTGAAACCTTTAATGGGTGGAACTTACT
upper sequence: AT4G03200.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA19G39560.2 (Glycine max), 3'ss of exon 5
------------------------------------------------------------------------------------------------------agacttgtgtagaatttgttctagctggatcagtgtctactagagaaagtagcct-tgactatattcatggacttacgattctttttactggcacttttagGTTTATATGTCGTTCGTCCAGGCTCTGTATGGTGGAGGAGGGTGGCCACTGTCGGTATTCCTTTCACCTGATTTAAAGCCGTTGATGGGTGGAACCTACT
| | | | | ||||||| | ||| | | | || || || | || || ||| | | | ||||| | | ||||||| || ||||||| || |||||| |||||||||||||||| ||||| ||| || || ||||||||||| || || || || ||||||||||| ||||
gtatatttttggaggcatgtcagctgagagtacctacaaggatattatttccaaaaattattctattttaaggaacaaaaaatggtgtttataaattatccaaaattcctttggaatttgaatgattgagatggttatggaaagtttaaggttttctactagtaacaagttgtactaaaggatatttttcc---cttctttagGTGTACATGTCGTATGTGCAGGCTTTGTATGGTGGAGGAGGTTGGCCCCTGAGTGTGTTTCTTTCACCTGACTTGAAACCTTTAATGGGTGGAACTTACT
upper sequence: AT4G03200.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: Vv07s0104g01480.t01 (Vitis vinifera), 3'ss of exon 5
agacttgtgtagaatttgtt-ctagctggatcagtgtctactagagaaagtagcc-ttgactatattcatggacttacgattctttttactggcacttttagGTTTATATGTCGTTCGTCCAGGCTCTGTATGGTGGAGGAGGGTGGCCACTGTCGGTATTCCTTTCACCTGATTTAAAGCCGTTGATGGGTGGAACCTACT
|| || ||||| || | | | || | | || | | ||| | |||| | | || || | | |||| || ||| | | || |||||| | ||||||||||| || |||||| || || ||||||||||||||||| || || |||||||||||||| ||||
--tgtttcgtttcttttgtcactcttcagtttgctaactttcaaaattgttaactgctaactgttttcaagtaaggctgagaaaattgtttcatctctccagGTATACATGACATATGTGCAGGCTTTATATGGTGGAGGGGGTTGGCCATTGAGTGTCTTCCTTTCACCTGATTTGAAACCTTTGATGGGTGGAACTTACT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aaagtagccttgactatattcatggacttacgattctttttactggcacttttagGTTTATATGTCGTTCGTCCAGGCTCTGTATGGTGGAGGAGGGTGGCCACTGTCGGTATTCCTTTCACCTGATTTAAAGCCGTTGATGGGTGGAACCTACT
gacttac putative branch site (score: 2)
cactttt putative PPT
attcttttta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
agacttgtgtagaatttgttctagctggatcagtgtctactagagaaagtagccttgactatattcatggacttacgattctttttactggcacttttagGTTTATATGTCGTTCGTCCAGGCTCTGTATGGTGGAGGAGGGTGGCCACTGTCGGTATTCCTTTCACCTGATTTAAAGCCGTTGATGGGTGGAACCTACT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
