Sequence
atgc intronic sequence ATGC exonic sequence...tagtcaaagggaccatcttgaagcattatttggtgacactgtctgcatttgtgctttgaataggacgctaatgcagttttctcaatgaaatgctatgtagGTGGTCTCTTGGTGCTATAATGTACGAAATGCTAGTAGGATATCCGCCGTTTTATTCAGATGATCCTATGTCAACCTGTAGAAAG
Basic information
species | Arabidopsis thaliana |
transcript | AT2G20470.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT2G20470.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: LOC_Os10g33640.1 (Oryza sativa), 3'ss of exon 6
tagtcaaagggaccatcttgaagcattatttggtgacactgtctgcatttgtgctttgaataggacgctaatgcagttttctcaatgaaatgctatgtagGTGGTCTCTTGGTGCTATAATGTACGAAATGCTAGTAGGATATCCGCCGTTTTATTCAGATGATCCTATGTCAACCTGTAGAAAG
| | | | | || | | ||| | ||| || | | | ||| | || | || ||| | | | |||| |||| ||||||||| ||||| || || ||||| ||||||||||| || ||||| || || ||||| ||||| |||||| |||| || ||||||
-----gtaagcatcgt-ttacataaatatctcgtgccatggacctc--ttgagtttgcagtaaaga---aattgaataatttcaa-------ctatctagGTGGTCACTTGGAGCAATCATGTATGAAATGCTAGTGGGCTATCCCCCATTCTATTCTGATGAGCCTATGACAACTTGCAGAAAG
upper sequence: AT2G20470.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: EFJ29515 (Selaginella moellendorffii), 3'ss of exon 6
tagtcaaagggaccatcttgaagcattatttggtgacactgtctgcatttgtgctttgaataggacgctaatgcagttttctcaatgaaatgctatgtagGTGGTCTCTTGGTGCTATAATGTACGAAATGCTAGTAGGATATCCGCCGTTTTATTCAGATGATCCTATGTCAACCTGTAGAAAG
|||||| || || || | | | | || | || | || | ||||||||||||||| |||||||||||||| |||||||| || |||||||| || ||||| || || || ||||| || || | |||
-------------------------------------gtaagaggcatttctgattgaaa----atatctac-cggcttgattgattta-tggtgcctagGTGGTCTCTTGGAGCTATAATGTACGAGATGCTAGTCGGGTATCCGCCCTTCTATTCCGACGAACCGATGTCTACTTGCCGGAAG
upper sequence: AT2G20470.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: EFJ28086 (Selaginella moellendorffii), 3'ss of exon 6
tagtcaaagggaccatcttgaagcattatttggtgacactgtctgcatttgtgctttgaataggacgctaatgcagttttctcaatgaaatgctatgtagGTGGTCTCTTGGTGCTATAATGTACGAAATGCTAGTAGGATATCCGCCGTTTTATTCAGATGATCCTATGTCAACCTGTAGAAAG
||| || || || || | | | | || | || | || | ||||||||||||||| |||||||||||||| |||||||| || |||||||| || ||||| || || || ||||| || || | |||
-------------------------------------gtaagaggcacttctgattgaaa----atatctac-cggcttgattgattta-tggtgcctagGTGGTCTCTTGGAGCTATAATGTACGAGATGCTAGTCGGGTATCCGCCCTTCTATTCCGACGAACCGATGTCTACTTGCCGGAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.catttgtgctttgaataggacgctaatgcagttttctcaatgaaatgctatgtagGTGGTCTCTTGGTGCTATAATGTACGAAATGCTAGTAGGATATCCGCCGTTTTATTCAGATGATCCTATGTCAACCTGTAGAAAG
cgctaat putative branch site (score: 3)
tttgaata 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tagtcaaagggaccatcttgaagcattatttggtgacactgtctgcatttgtgctttgaataggacgctaatgcagttttctcaatgaaatgctatgtagGTGGTCTCTTGGTGCTATAATGTACGAAATGCTAGTAGGATATCCGCCGTTTTATTCAGATGATCCTATGTCAACCTGTAGAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG
-agtcaaa
- - - - - - - - - - - - - tatttgg
- - - - - - - - - - - - - - - - - - - ctgtctg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aatgaaa