Sequence
atgc intronic sequence ATGC exonic sequencegtaacttcttatttctccattccactattatgatcttgcttccaccagcttttatttatttgttctgtttttctgtagCTCGGTGAGACCATTTGTCCGATGAAGGAAGATTTTATAATGGTTCATTTGCAACATTGCTGCAAGCATTGTACCACTCTCATGGTATCTGGAAACCGGT
Basic information
species | Arabidopsis thaliana |
transcript | AT1G55970.1 |
intron # | 11 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G55970.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: LOC_Os02g04490.1 (Oryza sativa), 3'ss of exon 12
-------------------------------------------------------------------------------gtaacttcttatttctccattccactattatgatcttgcttc-caccagcttt--tatttatttgttctgtttttctgtagCTCGGTGAGACCATTTGTCCGATGAAGGAAGATTTTATAATGGTTCATTTGCAACATTGCTGCAAGCATTGTACCACTCTCATGGTATCTGGAAACCGGT
|| | || | || ||| | || | | || || || |||| || | ||| | |||| | || |||| || || ||||||| ||| |||||||||||||| || |||||||||||||| ||| || | || ||| || || ||||| |||||||| || |
gtaggattgtacagtggtttgcgtgctccttattttgatagatcacatggctgctagcactctacccctctttccctttctatcatccttgctcagtattt-gtttttttcactttactggatggcatctttaccatgaacttgatttgttatg-tgcagCTTGGGGAAACCATTTATCCAATGAAGGAAGATTTCATTATGGTTCATTTGCAGTATTCGTGTAGTCACTGTTGTACCCTTATGGTGTCTGGAAAACGTT
upper sequence: AT1G55970.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: GLYMA07G00230.1 (Glycine max), 3'ss of exon 12
------------------gtaactt--cttatttctccattccactattatgat--cttgcttccaccagcttttatttatttgttctgtttttctgtagCTCGGTGAGACCATTTGTCCGATGAAGGAAGATTTTATAATGGTTCATTTGCAACATTGCTGCAAGCATTGTACCACTCTCATGGTATCTGGAAACCGGT
| |||| || |||| ||| || ||| | | ||| | | || | | | | | | ||||| |||| ||||| |||||||| |||||||||||||||||||| |||||||||||||| ||| || | ||| | | | ||||| ||||| ||||| |
aaacatcactattgtttccttactttactgctttcaatatttatctgttaggttcccttatgtttgataatttcttataaaattctggatctttctccagCTTGGTGAAACCATTTGCCCGATGAAGGAAGATTTTATTATGGTTCATTTGCAGCATGCATGTACTAGCTGTTGTATTTTAATGGTGTCTGGCAACCGTT
upper sequence: AT1G55970.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: GLYMA15G00250.1 (Glycine max), 3'ss of exon 12
------gtaacttcttattt-ctccattccactattat---gatcttgctt------------ccaccagcttttatttatttgttctgtttttctgtagCTCGGTGAGACCATTTGTCCGATGAAGGAAGATTTTATAATGGTTCATTTGCAACATTGCTGCAAGCATTGTACCACTCTCATGGTATCTGGAAACCGGT
|| ||||| | || | |||| || |||| | || ||| | | ||| || | | || | | | | |||| ||||| |||||||| || ||||||||||||||||| |||||||||||||| ||| |||| ||||| | ||| ||||| ||||| ||||| |
caaattatatcttctcacttattgcatttaacatttatatggggtttccttgagtggaaatagcaatttccttgtaataaagcttttgatctctatccagCTTGGTGAAACCATTTGCCCAATGAAGGAAGATTTTATCATGGTTCATTTGCAGCATGCATGCACTCATTGCTGTATTCTAATGGTGTCTGGCAACCGTT
upper sequence: AT1G55970.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: GLYMA08G24290.1 (Glycine max), 3'ss of exon 14
-------------------gtaacttcttatttct--ccattccactattatgatc-ttgcttccaccagcttttatttatttgttctgtttttctgtagCTCGGTGAGACCATTTGTCCGATGAAGGAAGATTTTATAATGGTTCATTTGCAACATTGCTGCAAGCATTGTACCACTCTCATGGTATCTGGAAACCGGT
|| || | || ||| || ||| | || || | | || | | | | | | ||||| |||| ||||| ||||||| || ||||||||||||||||| |||||||||||||| ||| || | ||| | | | ||||| ||||| ||||| |
aaacattaatattgtttccttactttactgctttcaaatatttatctgttaggttccttatgtttgataatttcttataaaattcttgatctttctccagCTTGGTGAAACCATTTCCCCAATGAAGGAAGATTTTATTATGGTTCATTTGCAGCATGCATGTACTAGCTGTTGTATTTTAATGGTGTCTGGCAACCGTT
upper sequence: AT1G55970.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: Vv09s0054g01780.t01 (Vitis vinifera), 3'ss of exon 11
-----------------------gtaacttcttatttctccattccactattatgatcttgcttccaccagcttttatttatttgttctgtttttctgtagCTCGGTGAGACCATTTGTCCGATGAAGGAAGATTTTATAATGGTTCATTTGCAACATTGCTGCAAGCATTGTACCACTCTCATGGTATCTGGAAACCGGT
|| |||| | | | || || | | | ||| | | |||| | | | || || |||| |||| ||||| ||||| | || |||||||||||||||||||||||||| ||||||||| || | |||||| ||| ||||||||||||||||| |
tttcaaacgtcttcactgatattatattttctcctgacacttttgaacaaatgaaagtcaatttctgtttgttcttatgaagctat-ctattcttctccagCTTGGTGAAACCATAAGCCCAATGAAGGAAGATTTTATAATGGTTCACTTGCAACATGCATGTACTCATTGTTGTCATCTGATGGTATCTGGAAACCGTT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.actattatgatcttgcttccaccagcttttatttatttgttctgtttttctgtagCTCGGTGAGACCATTTGTCCGATGAAGGAAGATTTTATAATGGTTCATTTGCAACATTGCTGCAAGCATTGTACCACTCTCATGGTATCTGGAAACCGGT
tttgttctgtttttct CT-rich tract
ttttatttatttgttc 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaacttcttatttctccattccactattatgatcttgcttccaccagcttttatttatttgttctgtttttctgtagCTCGGTGAGACCATTTGTCCGATGAAGGAAGATTTTATAATGGTTCATTTGCAACATTGCTGCAAGCATTGTACCACTCTCATGGTATCTGGAAACCGGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC