Sequence
atgc intronic sequence ATGC exonic sequencegtaagcttgtcttccctgcaaggattattgtgtttactcaaagttctgtttcctagaactaaaagacttattttccctgtacagCGAGAGTTTTATTTGGAAGGAGGGGCCATGGTTTTGGCTGATGGTGGAGTTGTTTGTATTGATGAGTTTGACAAAATGAGGCCTGAGGACCG
Basic information
species | Oryza sativa |
transcript | LOC_Os02g55410.2 |
intron # | 10 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os02g55410.2 (Oryza sativa), 3'ss of exon 10
lower sequence: GRMZM2G075978_T01 (Zea mays), 3'ss of exon 10
gtaagcttgtcttccctgcaaggattattgtgtttactcaaagttctgtttcctagaactaaaagacttattttccctgtacagCGAGAGTTTTATTTGGAAGGAGGGGCCATGGTTTTGGCTGATGGTGGAGTTGTTTGTATTGATGAGTTTGACAAAATGAGGCCTGAGGACCG
||| | | | ||| | | | || |||| ||||| |||||| |||| | ||| || || ||| || ||||||| |||||||||||||||||||| |||||||||||||||||||||||||| |||||||| ||||| |||||||| ||||| ||||| ||| |
gtaggtctat-ttcaccaaattgtttgttgt--ttact-aaagtttggttttggaacactgtaaatatttctttttctctacagCGTGAGTTTTATTTGGAAGGAGGAGCCATGGTTTTGGCTGATGGTGGAGTAGTTTGTATCGATGAATTTGACAAGATGAGACCTGAAGACAG
upper sequence: LOC_Os02g55410.2 (Oryza sativa), 3'ss of exon 10
lower sequence: GRMZM2G450055_T01 (Zea mays), 3'ss of exon 10
gtaagcttgtcttccctgcaaggattattgtgtttactcaaagttctgtttcctagaactaaaagacttattttccctgtacagCGAGAGTTTTATTTGGAAGGAGGGGCCATGGTTTTGGCTGATGGTGGAGTTGTTTGTATTGATGAGTTTGACAAAATGAGGCCTGAGGACCG
||| | ||| ||| ||| | | || |||| ||||| | ||| |||| || || || || ||| || ||||||| |||||||||||||||||||| |||||||||||||||||||||||||| |||||||| ||||| |||||||| ||| | ||||| ||| |
gtagg-ttgatttcactgaattgtttgttgt--ttacttag-gtttagttttttaaggctgtaaccatttctttttctctacagCGCGAGTTTTATTTGGAAGGAGGAGCCATGGTTTTGGCTGATGGTGGAGTAGTTTGTATCGATGAATTTGACAAGATGCGACCTGAAGACAG
upper sequence: LOC_Os02g55410.2 (Oryza sativa), 3'ss of exon 10
lower sequence: GLYMA13G22420.1 (Glycine max), 3'ss of exon 9
------------------------------------------gtaagcttgtcttccctgc--aaggattattgt--gttt--actcaaagttctgtttcctagaactaaaagacttattttccctgtac-----agCGAGAGTTTTATTTGGAAGGAGGGGCCATGGTTTTGGCTGATGGTGGAGTTGTTTGTATTGATGAGTTTGACAAAATGAGGCCTGAGGACCG
| | | | | | || | | || || | | || |||| | || | | || | || | || ||| || || |||| ||||| ||| | ||||||||||||||||| |||||||| || || ||||| || |||||||||||||| || |||||||| || || |
gtaagttcttcccttcctaaactgtttgtattagacagtcaatttatactatactacttgttgaggtataatcataagcttgaactccatcaactttcctttttaagtctctgattcatgttctatgcaccctttagCGTGAGTTCTATCTTGAAGGAGGGGCCATGGTCTTGGCTGACGGAGGTGTTGTCTGCATTGATGAGTTTGATAAGATGAGGCCAGAAGATAG
upper sequence: LOC_Os02g55410.2 (Oryza sativa), 3'ss of exon 10
lower sequence: GLYMA17G11220.1 (Glycine max), 3'ss of exon 9
-----------------------------------------------gtaagcttgtcttccctgcaaggattattgtgtttactcaaagttctgtttcctagaactaaaagacttattttccctg-----tacagCGAGAGTTTTATTTGGAAGGAGGGGCCATGGTTTTGGCTGATGGTGGAGTTGTTTGTATTGATGAGTTTGACAAAATGAGGCCTGAGGACCG
| | | | | || || || || | | || || || | || | || ||| || | |||| ||||||||| | ||||||||||| ||||| ||||| ||||| || ||||| || ||||| |||||||| || |||||||| || ||| |
gtaagttcttaccttcctaaactgtttgtattagatcgcaaatttctactatactacttgttgaggtataatcataagcttgacctccatcaattttctttacaagtctctgattcatgttctatggtctctttagCGTGAGTTTTATCTTGAAGGAGGGGCTATGGTCTTGGCCGATGGAGGTGTTGTCTGCATTGACGAGTTTGATAAGATGAGGCCAGAAGACAG
upper sequence: LOC_Os02g55410.2 (Oryza sativa), 3'ss of exon 10
lower sequence: AT2G07690.2 (Arabidopsis thaliana), 3'ss of exon 9
gtaagcttgtcttccctgcaaggattattgtgt---ttactcaaagtt--ctgtt-tcctagaa-ctaaaagacttatt----ttccctgtacagCGAGAGTTTTATTTGGAAGGAGGGGCCATGGTTTTGGCTGATGGTGGAGTTGTTTGTATTGATGAGTTTGACAAAATGAGGCCTGAGGACCG
| |||| | || |||| || || | | || | ||| | || | | ||| || | | |||| | | | ||||||||||| ||| | ||||| || || ||||||||||||||||| || ||||| ||||||||||| |||||||| ||||| || || || |
----gtatgtcctatcttcaagtgtttttctatgatttgtttaaaagtagttgctatgacagattctcagttatttatacatatgttcattgcagCGAGAGTTCTATCTTGAAGGTGGTGCTATGGTTTTGGCTGATGGAGGTGTTGTGTGTATTGATGAATTTGACAAGATGAGACCGGAAGATAG
upper sequence: LOC_Os02g55410.2 (Oryza sativa), 3'ss of exon 10
lower sequence: Vv11s0149g00130.t01 (Vitis vinifera), 3'ss of exon 9
----------------------------------------------------------------------gtaagctt-gtcttc----cctgcaaggattattgtgtttactcaaagt--tctgtttcctagaactaaaagacttattttccctg-tacagCGAGAGTTTTATTTGGAAGGAGGGGCCATGGTTTTGGCTGATGGTGGAGTTGTTTGTATTGATGAGTTTGACAAAATGAGGCCTGAGGACCG
||||||| ||| || || | || || |||||| | | | || || | ||| | | | | | || | ||||| || |||||| | |||||||| || ||||||||||| ||||| || ||||| ||||||||||||||||||||||||||| | |||||| |
gtaagtttttgagattctctatcatgtgtgctgatcctaatgtcaattctctagctctttctttctccagataagctttgtcaatggagccgatgagtttatttaaattccctcaaaataattaggttatctgacttcaaattcaaactctacatgattcagCGTGAATTTTATCTAGAAGGAGGAGCAATGGTTTTGGCAGATGGAGGTGTTGTCTGTATTGATGAGTTTGACAAAATGAGGGCAGAGGACAG
upper sequence: LOC_Os02g55410.2 (Oryza sativa), 3'ss of exon 10
lower sequence: PP1S355_49V6.1 (Physcomitrella patens), 3'ss of exon 10
----------------------------------------------------------------------gtaagcttgtcttccct-gcaaggattattgtgtttactcaaagttctg---tttcctagaactaaaag--------acttattttccctgt-acagCGAGAGTTTTATTTGGAAGGAGGGGCCATGGTTTTGGCTGATGGTGGAGTTGTTTGTATTGATGAGTTTGACAAAATGAGGCCTGAGGACCG
| | | | ||| | || | | | | | | ||| || | || | ||| || || | | | | | |||| |||||||||| | |||||||| || |||||| | |||||||| || ||||| || ||||||||||| ||||||||| | ||||| ||| |
gtatgcaattttacatttgccccgtgtttttatctttctaccaaactctcacctgagcatgttttgcttactgaacgtttctcgtttcacatagcaaaccatctatggcaagtgttttgaaatatcgaaatgttaatagtcgcttacacctgtgtcctaaatcacagAGAGAGTTTTACCTTGAAGGAGGTGCTATGGTTCTTGCTGATGGAGGTGTTGTCTGCATTGATGAGTTCGACAAAATGCGACCTGAAGACAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gtgtttactcaaagttctgtttcctagaactaaaagacttattttccctgtacagCGAGAGTTTTATTTGGAAGGAGGGGCCATGGTTTTGGCTGATGGTGGAGTTGTTTGTATTGATGAGTTTGACAAAATGAGGCCTGAGGACCG
aactaaa putative branch site (score: 2)
cttattttccctgt putative PPT
taaaagacttatttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagcttgtcttccctgcaaggattattgtgtttactcaaagttctgtttcctagaactaaaagacttattttccctgtacagCGAGAGTTTTATTTGGAAGGAGGGGCCATGGTTTTGGCTGATGGTGGAGTTGTTTGTATTGATGAGTTTGACAAAATGAGGCCTGAGGACCG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG