Sequence
atgc intronic sequence ATGC exonic sequenceGCTGTGTCTTGGTCCATGGTCGGAGCATGGAGAACGGACTGGTGGATTTTATGCCTGTAACCGTTATGAGGCAGCAAGGCAGGAAGGAGCGgtacagttctaatctgagatattttcttaatactttattatttttatttaatattgtggttaatttgtgctgcttcgcactggttacag
Basic information
species | Oryza sativa |
transcript | LOC_Os04g41470.2 |
intron # | 9 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os04g41470.1 (Oryza sativa), 5'ss of exon 9
lower sequence: GRMZM2G006428_T01 (Zea mays), 5'ss of exon 9
GCTGTGTCTTGGTCCATGGTCGGAGCATGGAGAACGGACTGGTGGATTTTATGCCTGTAACCGTTATGAGGCAGCAAGGCAGGAAGGAGCGgta-cagttct--------aatctgagatattttcttaatactttattatttttatttaatattgtggtt----aatttgtgc-tgcttcgcactggttacag
||| ||||||||||||||||| ||||||||||| ||||||||||||||||||| |||||||| |||||| |||||||||| ||||||| |||| || |||| ||||||| || |||| | || | |||| | || | || ||||| | || || | ||| |||||
GCTATGTCTTGGTCCATGGTCAGAGCATGGAGAGAGGACTGGTGGATTTTATGCTTGTAACCGCTATGAGTCAGCAAGGCAAGAAGGAGTGgtagcaattctgagcttccaatctgatatcttttgtccggcctgcaaaatttgggtcatgtactagattttctgaatttatttatgttttgttgtggctacag
upper sequence: LOC_Os04g41470.1 (Oryza sativa), 5'ss of exon 9
lower sequence: GRMZM5G876621_T02 (Zea mays), 5'ss of exon 9
GCTGTGTCTTGGTCCATGGTCGGAGCATGGAGAACGGACTGGTGGATTTTATGCCTGTAACCGTTATGAGGCAGCAAGGCAGGAAGGAGCGgta---------cagttctaatctgagatattttcttaatactttattattt---ttatttaata-----ttgtggttaatttgtgct--gcttcgcactggttacag
||| ||||||||||||||||| ||||||||||| ||||||||||||||||||| |||||||| |||||| |||||||||| |||||||||||| | ||| ||||| | || |||| | || | ||| | || || || | || |||| || | | || | || |||||
GCTATGTCTTGGTCCATGGTCAGAGCATGGAGAGAGGACTGGTGGATTTTATGCTTGTAACCGCTATGAGTCAGCAAGGCAAGAAGGAGCGgtaggagttcttcgcttccaatctaatatcttttgtctgacctgcaaagtttgggtcatgtactagatcttctcaatttatttatgttttggtttgttgtgactacag
upper sequence: LOC_Os04g41470.1 (Oryza sativa), 5'ss of exon 9
lower sequence: AT1G65430.1 (Arabidopsis thaliana), 5'ss of exon 9
GCTGTGTCTTGGTCCATGGTCGGAGCATGGAGAACGGACTGGTGGATTTTATGCCTGTAACCGTTATGAGGCAGCAAGGCAGGAAGGAGCGgtac-agttcta-atctgagatattttcttaa-tact--ttattatttttatttaatattgtggttaatttgtgctgcttcgcactggttacag----
||| || ||||| | ||| | |||||||| || ||| ||||| |||||||| |||||||||||||| ||||||| ||| || || ||| |||||| | | ||| ||| | | || || ||| | |||||| ||| || ||| || ||| | | ||
GCTTTGCCTTGGGGCGTGGACAGAGCATGGTGAGAAGACAGGTGGCTTTTATGCTTGTAACCGTTATGAAGCAGCAAAGCAAGATGGCATTgtatgagttctgtacattgtttatgttcctgactaacaactaatatgtctatttatctttgaacatattttttgtc-tttcataatctttctgtgcag
upper sequence: LOC_Os04g41470.1 (Oryza sativa), 5'ss of exon 9
lower sequence: Vv00s0207g00090.t01 (Vitis vinifera), 5'ss of exon 9
GCTGTGTCTTGGTCCATGGTCGGAGCATGGAGAACGGACTGGTGGATTTTATGCCTGTAACCGTTATGAGGCAGCAAGGCAGGAAGGAGCGgtacagttctaatctgagatattttcttaatactttattatttttattt-aatattgtggttaatttgtgctgcttcgcactggttacag----------
||| ||||||||| ||||||| || ||||| || |||| ||||| |||||||| ||||||||||||||| |||||| ||| || |||| |||| || | | | | | | | ||||| || ||||| ||| ||| | || | | | || | || |
GCTTTGTCTTGGTGCATGGTCAGATCATGGTGAGAGGACAGGTGGTTTTTATGCATGTAACCGTTATGAGACAGCAAAGCAAGAGGGAGTGgtaagatttttttttccctcgatatttacacactttttttttttttttttgataaataagcaaaagaattgtattacgaagaggcactaaaatagcgactMapped EST sequences
Showing partial alignments of ESTs and genomic sequences. See full alignments
ATGC EST sequence
ATGC genomic sequence (exon)
ATGC genomic sequence (truncated intron)
EST:
gi|29681156|gb|CB677431.1|CB677431EST: GTGGATTTTATGCCTGTAACCGTTATGAGGCAGCAAGGCAGGAAGGAGCG TATGATGAATCTGAAAGGAGAAGAGAAATGGCAAAGAACTCGCTTGAGAGA
genomic: GTGGATTTTATGCCTGTAACCGTTATGAGGCAGCAAGGCAGGAAGGAGCGgtacagttct ... ctggttacagTATGATGAATCTGAAAGGAGAAGAGAAATGGCAAAGAACTCGCTTGAGAGA
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
GCTGTGTCTTGGTCCATGGTCGGAGCATGGAGAACGGACTGGTGGATTTTATGCCTGTAACCGTTATGAGGCAGCAAGGCAGGAAGGAGCGgtacagttctaatctgagatattttcttaatactttattatttttatttaatattgtggttaatttgtgctgcttcgcactggttacag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG