Sequence
atgc intronic sequence ATGC exonic sequencegtaatagctttctctcagatgaaaatgatgaacaagttttggtttaaatatatatttagtctctctgcttatgattctgattcatgaatgtgctattatatagGTGGCACAAGTGCTGTTGACACTGCCATACTCGTTCTCACAGCTGGGGATGCTCTCAGGGATTCTGTTTCAGCTCTTTTATGGCATCTTAGGTAGTTGGA
Basic information
species | Arabidopsis thaliana |
transcript | AT2G21050.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT2G21050.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: LOC_Os03g14080.1 (Oryza sativa), 3'ss of exon 1
-------------------------------gtaatagctttctctc-agatgaaaatgat---gaacaagttttggtttaaatatatatttagtctctctgcttatgattctgattcatgaatgtgctattatatagGTGGCACAAGTGCTGTTGACACTGCCATACTCGTTCTCACAGCTGGGGATGCTCTCAGGGATTCTGTTTCAGCTCTTTTATGGCATCTTAGGTAGTTGGA
| ||||| | | ||| | || | |||| | || || | ||| | || | | | || ||| || |||||| || ||||||| || ||||| |||| ||||| ||||||||||| ||||||||||||||| || || ||||| |||||||| || || | || || || ||||
gtgaccacattttctgatcgacgctatgcttgcttccattttcttgcgaaatgcatgcaatctaaggtaggtttgtgccgtgatcgatgtgtagccgttcggttaa--atctgcattgctg--tgtgcttcgat-cagGTGGCCCAGGTGCTCCTGACGCTGCCCTACTCGTTCTCCCAGCTGGGGATGCTCAGCGGCATACTGTTCCAGCTCTTCTACGGGCTGTTGGGCAGCTGGA
upper sequence: AT2G21050.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: Vv03s0038g02140.t01 (Vitis vinifera), 3'ss of exon 1
gtaatagctttctctcagatgaaaatgatgaacaagttttggtttaaatatatatttagtctctctgcttatgattctgattcatgaatgtgctattatatagGTGGCACAAGTGCTGTTGACACTGCCATACTCGTTCTCACAGCTGGGGATGCTCTCAGGGATTCTGTTTCAGCTCTTTTATGGCATCTTAGGTAGTTGGA
| || | || || | | || | |||| | | || || | | | | ||| || | || | | | ||||||| || || ||| |||| |||||||||| || || |||||||||||||| || |||||||| || ||||| || |||||| | | || || ||||
-------gtctcaccatgaaaaattttgtattttgagttgagaaaaaatgaaaaaa-aggaactttagtcacccacttcatt--tgggtttggtttgtttcagGTGGCTCAGGTTCTGCTGACTTTGCCATACTCATTTTCCCAGCTGGGGATGCTGTCTGGGATTCTATTCCAGCTGTTCTATGGCTTGATGGGAAGCTGGA
upper sequence: AT2G21050.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: EFJ21839 (Selaginella moellendorffii), 3'ss of exon 1
gtaatagctttctctcagatgaaaatgatgaacaagttttggtttaaatatatatttagtctctctgcttatgattct-gattcatgaat------gtgctattatatagGTGGCACAAGTGCTGTTGACACTGCCATACTCGTTCTCACAGCTGGGGATGCTCTCAGGGATTCTGTTTCAGCTCTTTTATGGCATCTTAGGTAGTTGGA
| || | | | | || |||| ||| | | || || | ||||| |||| | | ||| | | ||| | | | ||||||| ||||||||| | || ||||||||||| ||||| |||||||| | || || ||| | || ||| |||| |||||| | | || ||||
--------gtgaggacaaacagagttttgggact--tttttttttcttcctcttcttcgttgttgtgcttgtgatcttcgcctcacggtttcttctgtggtgatttccagGTGGCTCAAGTGCTGCTCACGCTGCCATACTCCTTCTCGCAGCTGGGATTCGCGTCGGGCATTGTCTTCCAGATCTTCTATGGCCTGCTCGGGGCCTGGA
upper sequence: AT2G21050.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: EFJ36050 (Selaginella moellendorffii), 3'ss of exon 1
gtaatagctttctctcagatgaaaatgatgaacaagttttggtttaaatatatatttagtctctctgcttatgattctgattcatgaatgtgctattatatagGTGGCACAAGTGCTGTTGACACTGCCATACTCGTTCTCACAGCTGGGGATGCTCTCAGGGATTCTGTTTCAGCTCTTTTATGGCATCTTAGGTAGTTGGA
||||| | ||| | | || || || ||| | | || || | | | | || || | | | || | | |||| ||||| ||||| ||||| ||||||||||| ||||| |||||||| || | | ||| | || || | ||||| || | || || ||||
---tccactttcagtatagcgaacaccaaaaagaaacctttgttcttcttcttccttcgttgtttgtcggaacttacttgtttttctcttttcttctccacagGTCGCACAGGTGCTTTTGACGCTGCCATACTCTTTCTCGCAGCTGGGCATTGTGTGGGGGGTCACCTTCCAAGTGTTTTACGGGCTTTTGGGCTCCTGGA
upper sequence: AT2G21050.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: EFJ34222 (Selaginella moellendorffii), 3'ss of exon 1
gtaatagctttctctcagatgaaaatgatgaacaagttttggtttaaatatatatttagtctctctgcttatgattct-gattcatgaat------gtgctattatatagGTGGCACAAGTGCTGTTGACACTGCCATACTCGTTCTCACAGCTGGGGATGCTCTCAGGGATTCTGTTTCAGCTCTTTTATGGCATCTTAGGTAGTTGGA
| | | ||| | | || |||| || | | || || | ||||| |||| | | ||| | | ||| | | | ||||||| ||||||||| | || ||||||||||| ||||| |||||||| | || || ||| | || ||| |||| |||||| | | || ||||
-----gacaaacacacagtt-----ttgggacttttttttttcttcttcctcttcttcgttgttgtgcttgtgatcttcgcctcacggtttcttctgtggtgatttccagGTGGCTCAAGTGCTGCTCACGCTGCCATACTCCTTCTCGCAGCTGGGATTCGCGTCGGGCATTGTCTTCCAGGTCTTCTATGGCCTGCTCGGGGCCTGGA
upper sequence: AT2G21050.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: EFJ18760 (Selaginella moellendorffii), 3'ss of exon 1
gtaatagctttctctcagatgaaaatgatgaacaagttttggtttaaatatatatttagtctctctgcttatgattctgattcatgaatgtgctattatatagGTGGCACAAGTGCTGTTGACACTGCCATACTCGTTCTCACAGCTGGGGATGCTCTCAGGGATTCTGTTTCAGCTCTTTTATGGCATCTTAGGTAGTTGGA
| | ||| | | | || || || ||| | | || || | | | | || || | | | || | | |||| ||||| ||||| ||||| ||||||||||| ||||| |||||||| || | | ||| | || || | ||||| || | || || ||||
---gcttcgattcctccactttctgtcaaaaagaaaccttcgttcttcttcttccttcgttgtttgtcggaacttacttgtttttctcttttcttctccacagGTCGCACAGGTGCTTTTGACGCTGCCATACTCTTTCTCGCAGCTGGGCATTGTGTGGGGGGTCACCTTCCAAGTGTTTTACGGGCTTTTGGGCTCCTGGA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tatatatttagtctctctgcttatgattctgattcatgaatgtgctattatatagGTGGCACAAGTGCTGTTGACACTGCCATACTCGTTCTCACAGCTGGGGATGCTCTCAGGGATTCTGTTTCAGCTCTTTTATGGCATCTTAGGTAGTTGGA
ttctgat putative branch site (score: 3)
tattatata 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaatagctttctctcagatgaaaatgatgaacaagttttggtttaaatatatatttagtctctctgcttatgattctgattcatgaatgtgctattatatagGTGGCACAAGTGCTGTTGACACTGCCATACTCGTTCTCACAGCTGGGGATGCTCTCAGGGATTCTGTTTCAGCTCTTTTATGGCATCTTAGGTAGTTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTC