Sequence
atgc intronic sequence ATGC exonic sequence...aagttcaatgagtcgattcgccaaatcttccattagctatttcaacttactttcttgattctcaacggctgaaaagtctttatctttttccttttttcagTTCAAGATGAAACCTGAAATGCACTATGCAGAGATTGATTGTCCAGTCTCAGCTCCAGAAAATTTTCCAAAAGATGATGAGCTTCATTTTGAGATTGAGT
Basic information
species | Arabidopsis thaliana |
transcript | AT3G54010.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G54010.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: LOC_Os03g25140.1 (Oryza sativa), 3'ss of exon 4
------------------------------------------aagttcaatgagtcgattcgcca--aatcttccattagctatttcaacttactttcttgattctcaacggctgaaaagtctttatctttttc-------cttttttcagTTCAAGATGAAACCTGAAATGCACTATGCAGAGATTGATTGTCCAGTCTCAGCTCCAGAAAATTTTCCAAAAGATGATGAGCTTCATTTTGAGATTGAGT
|| || | | || |||| | ||||| || | | | ||| | | | | | || | ||| | | | | | || ||||| |||||||| ||||| ||| | || |||||||||||| ||||||||||| ||||||| || ||||||||||||||||| ||||| ||||||||||||
gtatttctatacagctagtttaaaccagtgggtcaaaagaacaacaacattctaacaatgagccattactcttcttttgggtgtaacaattaaaaatgtacaggtcgtactacgcaaatatttatcattctctcatagtatcttttcgcagTTCAAAATGAAGCCTCAGATACACTATGCAGAGGAGGATTGTCCAGTTACAGCTCCTGACGGCTTTCCAAAAGATGATGAACTTCAATTTGAGATTGAGA
upper sequence: AT3G54010.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: AC216247.3_FGT005 (Zea mays), 3'ss of exon 4
---------------------------------------------aagttcaatgagtcgattcgcca-aatcttccattagctatttcaacttactttcttgattctcaacggctgaaaagtctttatctt--tttccttttttcagTTCAAGATGAAACCTGAAATGCACTATGCAGAGATTGATTGTCCAGTCTCAGCTCCAGAAAATTTTCCAAAAGATGATGAGCTTCATTTTGAGATTGAGT
| ||| | | | | | | | ||| | ||| || || | |||||| || | | | || ||||| |||| || |||| |||||||| ||| | ||| |||| ||||| || ||| ||||||||||||| |||||||||| || || ||||||||||| ||||| |||||||||||
gtatttctaatacgaagacactactcagtttcatgtagaatgcaggaattcgaaaatgcaaatgtcaacaataatacatgtgcatatt--atttacttatttagtcatttttgtctctttt-tctttgtcttacattttcttttccagTTCAAAATGCAGCCTAAAATTCACTACGCTGAGGTTGATTGTCCAGTTGCAGCTCCAGATGGCTTCCCGAAAGATGATGAACTTCAATTTGAGATTGAAA
upper sequence: AT3G54010.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv08s0007g01460.t01 (Vitis vinifera), 3'ss of exon 5
aagttcaatgagtcgattcgccaaatctt-ccattagctatttcaacttactttcttgattctcaacggctgaaaagtcttt---atctttttccttttttcagTTCAAGATGAAACCTGAAATGCACTATGCAGAGATTGATTGTCCAGTCTCAGCTCCAGAAAATTTTCCAAAAGATGATGAGCTTCATTTTGAGATTGAGT
| | | ||| | | | | || | | ||| || || || || || || ||| | ||| || | | || |||||||| ||||||||| | ||| ||||||||| ||| | ||||||| | | ||| || |||||||| || |||||||||||||||||||||||||||
--ttgcctttagtt--tctgttgatttttgttggttcatgttttaatttgtttaattatttgcttttcactttaaatttttttttatgatctcttttgtttcagTTAAAGATGAAAGCAGAACTGCACTATGGTGAGGCTAATTGTCCTCTTATGGTTCCTGATAATTTTCCGAAGGATGATGAGCTTCATTTTGAGATTGAGA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cttactttcttgattctcaacggctgaaaagtctttatctttttccttttttcagTTCAAGATGAAACCTGAAATGCACTATGCAGAGATTGATTGTCCAGTCTCAGCTCCAGAAAATTTTCCAAAAGATGATGAGCTTCATTTTGAGATTGAGT
tctttatctttttcct CT-rich tract
tttatcttttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
aagttcaatgagtcgattcgccaaatcttccattagctatttcaacttactttcttgattctcaacggctgaaaagtctttatctttttccttttttcagTTCAAGATGAAACCTGAAATGCACTATGCAGAGATTGATTGTCCAGTCTCAGCTCCAGAAAATTTTCCAAAAGATGATGAGCTTCATTTTGAGATTGAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT