Sequence
atgc intronic sequence ATGC exonic sequencegttagtctcgtattcaatttttaattttgtaattcatcaggctgtcaaaaatattatgtctgtgatttaactctaacccttgcggggctgaaacaattgcagTTTAAAATGCGGGAGGCACAAATGTGCAATATTCTCGGCCGGGTCACTCTTGATGCCAAGACAGCTAAAGCGTTTAAAGAAAAGATCGATGATGAGTACC
Basic information
species | Arabidopsis thaliana |
transcript | AT5G10840.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G10840.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA04G06420.1 (Glycine max), 3'ss of exon 2
---gttagtctcgtattcaatttttaattttgtaattcatcaggct--gtcaaaaatattatgtctgtgatttaactctaacccttgcggggctgaaacaattgcagTTTAAAATGCGGGAGGCACAAATGTGCAATATTCTCGGCCGGGTCACTCTTGATGCCAAGACAGCTAAAGCGTTTAAAGAAAAGATCGATGATGAGTACC
| | ||| | || | ||| ||| || | | | || | | ||| | ||| | | | | | || | ||||||||||||||||| ||| ||||||||||||||||||| | | | |||||||| || || ||||| | ||| ||||| |||||| ||||||||| |
attttcaagctctttttttttcccattctttttaaactttcgagttcccttaattttgtcatggttatgaactgatttctgactcagtggtatt-------ttgcagTTTAAAATGCGTGAGCCACAAATGTGCAATATTCTGTGTAATCTTAAACTTGATGCTAAAACTGCTAAGGAGTTCAAAGAGAAGATCAGTGATGAGTATC
upper sequence: AT5G10840.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA06G06460.1 (Glycine max), 3'ss of exon 2
gttagtctcgtattcaa-tttttaattttgtaattcatcaggctgtcaaaaatattatgtctgt---gatttaactctaacccttgcggggctgaaacaattgcagTTTAAAATGCGGGAGGCACAAATGTGCAATATTCTCGGCCGGGTCACTCTTGATGCCAAGACAGCTAAAGCGTTTAAAGAAAAGATCGATGATGAGTACC
| | || | ||| |||| ||| | || | | | | | ||| | ||| | || || | || ||| | ||||||||||||||||| ||| ||||||||||||||||||| | | | |||||||| || || ||||| | ||| ||||| |||||| ||||||||| |
-----ttttgtttccaagctttttattccattctttttaaacttttgagttcccttaattttgtcatggttatgaactgatttctgactcagtgatatt-ttgcagTTTAAAATGCGCGAGCCACAAATGTGCAATATTCTGTGTAATCTTAAACTTGATGCTAAAACTGCTAAGGAGTTCAAAGAGAAGATCAGTGATGAGTATC
upper sequence: AT5G10840.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA14G11780.1 (Glycine max), 3'ss of exon 2
gttagtctcgtattcaatttttaattttgtaattcatcaggctgtcaaaaatattatgtctgtgatttaactctaacccttgcggggctgaaacaattgcagTTTAAAATGCGGGAGGCACAAATGTGCAATATTCTCGGCCGGGTCACTCTTGATGCCAAGACAGCTAAAGCGTTTAAAGAAAAGATCGATGATGAGTACC
|||| | | | | || |||||| | ||| || || ||||| | | | | | || | ||| | ||||||||||||||||| || ||||||||||||||||| | | | | | ||||||||||| || || |||||||| ||||| ||||| ||||||||||| |
---------gtatgttttatatgaaattttaattc-ttgccttgttaattatgttatggttaccaacttattt--actc-------agtgacgtatttgcagTTTAAAATGCGTGAACCACAAATGTGCAATATTGTGTGTAAGCTTAAACTTGATGCCAAAACTGCAAAAGCGTTCAAAGAGAAGATTGATGATGAGTATC
upper sequence: AT5G10840.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA17G34020.1 (Glycine max), 3'ss of exon 2
gttagtctcgtattcaatttttaattttgtaattcatcaggctgtcaaaaatattatgtctgtgatttaactctaacccttgcggggctgaaacaattgcagTTTAAAATGCGGGAGGCACAAATGTGCAATATTCTCGGCCGGGTCACTCTTGATGCCAAGACAGCTAAAGCGTTTAAAGAAAAGATCGATGATGAGTACC
|||| | | | | || |||||| | | ||| || || ||||| | | |||| |||| |||| | | |||||||||||||||| || ||||||||||||||||| | | | | | ||||||||||| || || |||| ||| || || ||||| |||||||| || |
---------gtatgttttatatgaaattttaattc-ttgtgttgttaattatgttatgct----aatcaactta----tttgct---ctgacatatatgcagTTTAAAATGCGTGAACCACAAATGTGCAATATTGTGTGTAAGCTTAAACTTGATGCCAAAACTGCAAAAGAGTTCAAGGAGAAGATTGATGATGAATATC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aaaatattatgtctgtgatttaactctaacccttgcggggctgaaacaattgcagTTTAAAATGCGGGAGGCACAAATGTGCAATATTCTCGGCCGGGTCACTCTTGATGCCAAGACAGCTAAAGCGTTTAAAGAAAAGATCGATGATGAGTACC
ctctaac putative branch site (score: 2)
tgatttaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttagtctcgtattcaatttttaattttgtaattcatcaggctgtcaaaaatattatgtctgtgatttaactctaacccttgcggggctgaaacaattgcagTTTAAAATGCGGGAGGCACAAATGTGCAATATTCTCGGCCGGGTCACTCTTGATGCCAAGACAGCTAAAGCGTTTAAAGAAAAGATCGATGATGAGTACC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA