Sequence
atgc intronic sequence ATGC exonic sequencegtaatgaggataaacttgcgagttggaattctatgtttatgttttccatgtcagcaagtaactgggtatttcctttcttaaatttcttcgctagGAAAGAATGTGCATGCACACCAGTTAGATTCTTCGCTATCTTGTCGATGCAGAGGTCAGGAAGTGGGTGGATTGAAACATTATTGAATAGCCATGAGAAC
Basic information
species | Oryza sativa |
transcript | LOC_Os01g57550.2 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os01g57550.2 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G142507_T02 (Zea mays), 3'ss of exon 3
gtaatgaggataaac-ttgcgagttggaattctatgtttatgttttccatgtcagcaagtaactgggtatttcctttcttaaatttcttcgctagGAAAGAATGTGCATGCACACCAGTTAGATTCTTCGCTATCTTGTCGATGCAGAGGTCAGGAAGTGGGTGGATTGAAACATTATTGAATAGCCATGAGAAC
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gtaatgaagatatatactgggtcatgtgattttcctttttctatttatttccaggttagtgtctg---acttgcatgttc---tttgtctgttagGAAAGAATGTGCGTGCACAGGGGTTAGGTTCTTTGCTATCTTGTCAATGCAGAGGTCCGGGAGTGGATGGGTTGAGACGTTGTTGAATAGCCATCCTAAT
upper sequence: LOC_Os01g57550.2 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM5G877077_T02 (Zea mays), 3'ss of exon 2
gtaatgaggataaacttgcgagttggaattctatgtttatgttttccatgtcagcaagtaactgggtatttcctttcttaaatttcttcgctagGAAAGAATGTGCATGCACACCAGTTAGATTCTTCGCTATCTTGTCGATGCAGAGGTCAGGAAGTGGGTGGATTGAAACATTATTGAATAGCCATGAGAAC
|||| || |||| ||| | || ||| ||| |||| || || || | | ||| | | ||||| | | | ||||||||||||||| ||||| ||||| ||||| ||||| ||||| |||||||||||||| ||||| ||| |||| ||||| |||||||||||| ||
gtaacgaagatatact---gtgtc----ctctgattttgcctttttcaggttagtgactgact---tgtgggtgttctt-----tgtctgttagGAAAGAATGTGCGTGCACGGGGGTTAGGTTCTTTGCTATATTGTCAATGCAGAGGTCAGGGAGTGGATGGGTTGAGACATTGTTGAATAGCCATCCTAAT
upper sequence: LOC_Os01g57550.2 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM5G877077_T01 (Zea mays), 3'ss of exon 2
gtaatgaggataaacttgcgagttggaattctatgtttatgttttccatgtcagcaagtaactgggtatttcctttcttaaatttcttcgctagGAAAGAATGTGCATGCACACCAGTTAGATTCTTCGCTATCTTGTCGATGCAGAGGTCAGGAAGTGGGTGGATTGAAACATTATTGAATAGCCATGAGAAC-----
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gtaacgaagatatact---gtgtc----ctctgattttgcctttttcaggttagtgactgact---tgtgggtgttctt-----tgtctgttaggaaagAATGTGCGTGCACGGGGGTTAGGTTCTTTGCTATATTGTCAATGCAGAGGTCAGGGAGTGGATGGGTTGAGACATTGTTGAATAGCCATCCTAATATTAG
upper sequence: LOC_Os01g57550.2 (Oryza sativa), 3'ss of exon 2
lower sequence: AT3G50620.1 (Arabidopsis thaliana), 3'ss of exon 2
gtaatgaggataaacttgcgagttggaattctatgtttatgttttccatgtcagcaagtaactgggtatttcctttcttaaatttcttcg-ctagGAAAGAATGTGCATGCACACCAGTTAGATTCTTCGCTATCTTGTCGATGCAGAGGTCAGGAAGTGGGTGGATTGAAACATTATTGAATAGCCATGAGAAC
|||| | ||| | | | | | | ||| | | || | | | || | || | | |||| |||| ||||||| | | || || || | ||| || || |||||||||||||| |||||||| || ||| | |||||||| |||||||| ||| | ||
gtaactaatataccagttctgttcttgtctatgtttttgactctctttggtttgttcctttgtttaaatctttgttttgggttgtcttaaactagAGCTGAATGTGGACATAATCCGGTGAGGTACTTTGCGATATTGTCGATGCAGAGATCAGGAAGCGGTTGGTTCGAAACATTGTTGAATAGTCATAACAAT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgttttccatgtcagcaagtaactgggtatttcctttcttaaatttcttcgctagGAAAGAATGTGCATGCACACCAGTTAGATTCTTCGCTATCTTGTCGATGCAGAGGTCAGGAAGTGGGTGGATTGAAACATTATTGAATAGCCATGAGAAC
aagtaac putative branch site (score: 2)
tttcctttcttaaatt putative PPT
tttcttaaatttctt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaatgaggataaacttgcgagttggaattctatgtttatgttttccatgtcagcaagtaactgggtatttcctttcttaaatttcttcgctagGAAAGAATGTGCATGCACACCAGTTAGATTCTTCGCTATCTTGTCGATGCAGAGGTCAGGAAGTGGGTGGATTGAAACATTATTGAATAGCCATGAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA