Sequence
atgc intronic sequence ATGC exonic sequenceGTGGAAAACATGAAGCAGATTGCCAAGAAAAAAGCAAATGAGGAAAGAAAGCGTCTAGAATCTGAGgtaaagttaatgcttacattgtggtgtggaaatcctgcttgtctgtggacatctgcgtggaaattgtgagcgctatgtttcattaattcattttcataca...
Basic information
species | Oryza sativa |
transcript | LOC_Os01g12670.5 |
intron # | 5 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os01g12670.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GRMZM2G401784_T01 (Zea mays), 5'ss of exon 3
GTGGAAAACATGAAGCAGATTGCCAAGAAAAAAGCAAATGAGGAAAGAAAGCGTCTAGAATCTGAGgtaaagttaatgcttacattgtggtgtggaaatcctgcttgtctgtggacatctgcgtggaaattgtgagcgctatgtttcattaattcattttcataca-----
||||||| |||| |||||||||| | || ||| |||||| |||||||||||| ||||||||||||||| || | || | | | | | |||| || | | | | | |||| || ||| | || || || | || |
GTGGAAAGCATGCAGCAGATTGCTAGAAAGAAAACAAATGTGGAAAGAAAGCGCCTAGAATCTGAGgta---ctatggaataaaatttcacgcccaggctgtgct-gtgaaagttttcttctctagggtgtttgagaactgccttttactagtt-atgtgcaagcgcatgt
upper sequence: LOC_Os01g12670.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GRMZM2G009438_T01 (Zea mays), 5'ss of exon 3
GTGGAAAACATGAAGCAGATTGCCAAGAAAAAAGCAAATGAGGAAAGAAAGCGTCTAGAATCTGAGgtaaagttaatgcttacattgtggtgtggaaatcctgcttgtctgtggacatctgcgtggaaattgtgagcgctatgtttcattaattcattttcataca-----
||||||| |||| |||||||||| | || ||| ||||||||||||||||||| ||||||||||||||| | | || | | | | | |||| || | | | | | |||| |||| ||| | || || || | || |
GTGGAAAGCATGCAGCAGATTGCTAGAAAGAAAACAAATGAGGAAAGAAAGCGCCTAGAATCTGAGgtagtatggaa---taaaatttcacgcccaggctgtgct-gtgaaagttttcttctctagggtgtttgagaactatcttttactagtt-atgtgcaagcgcatgt
upper sequence: LOC_Os01g12670.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GRMZM2G058366_T01 (Zea mays), 5'ss of exon 4
GTGGAAAACATGAAGCAGATTGCCAAGAAAAAAGCAAATGAGGAAAGAAAGCGTCTAGAATCTGAGgtaaagttaatgcttacattgtggtgtggaaatcctgcttgtctgtggacatctgcgtggaaattgtgagcgctatgtttcattaattcattttcataca-----
||||||| |||| |||||||||| | || ||| ||||||||||||||||||| ||||||||||||||| || | || | | | | | |||| || | | | | | |||| || | ||| | || || || | || |
GTGGAAAGCATGCAGCAGATTGCTAGAAAGAAAACAAATGAGGAAAGAAAGCGCCTAGAATCTGAGgta---ctatggaataaaatttcacgcccaggctgtgct-gtgaaagttttcttctctagggtgtttgagaactgtcttttactagtt-atgtgcaagcgcatgtMapped 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|29678139|gb|CB674414.1|CB674414EST: AGATTGCCAAGAAAAAAGCAAATGAGGAAAGAAAGCGTCTAGAATCTGAG CTTGAGCTTGCCCTAATGGTCGAGAAACTACAGGAGCTTCGCTCTATGAGA
genomic: AGATTGCCAAGAAAAAAGCAAATGAGGAAAGAAAGCGTCTAGAATCTGAGgtaaagttaa ... ctattttcagCTTGAGCTTGCCCTAATGGTCGAGAAACTACAGGAGCTTCGCTCTATGAGA
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
GTGGAAAACATGAAGCAGATTGCCAAGAAAAAAGCAAATGAGGAAAGAAAGCGTCTAGAATCTGAGgtaaagttaatgcttacattgtggtgtggaaatcctgcttgtctgtggacatctgcgtggaaattgtgagcgctatgtttcattaattcattttcataca
- - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - AAGAAA