Sequence
atgc intronic sequence ATGC exonic sequenceGTGGCGGCTCTAGCAATGGAGGATATGCTATCTTGGATGCAGGAAGGTGGTCAGgtaagttagaagttttggtgatattctgttattacgctggataatttattcttctttctggtccatag
Basic information
species | Oryza sativa |
transcript | LOC_Os03g18310.2 |
intron # | 9 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os03g18310.3 (Oryza sativa), 5'ss of exon 9
lower sequence: GRMZM5G824405_T02 (Zea mays), 5'ss of exon 8
GTGGCGGCTCTAGCAATGGAGGATATGCTATCTTGGATGCAGGAAGGTGGTCAGgtaagttagaagttttggtgatattctgttattacgctg-gataatttattcttctttctggtccatag
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GTGGCTGCATTAGCAATGGAAGATATGCTATCTTGGATGCAGGAGGGTGGTCAGgtaggccactgatt--ggtagcactgcgttagagctcttcaatgattaa--ctttcagctggtctgcag
upper sequence: LOC_Os03g18310.3 (Oryza sativa), 5'ss of exon 9
lower sequence: GLYMA14G37520.3 (Glycine max), 5'ss of exon 10
GTGGCGGCTCTAGCAATGGAGGATATGCTATCTTGGATGCAGGAAGGTGGTCAGgtaagttagaagttttggtgatattctgtta-ttacgctggat----aatttattcttctt----tctggtccatag----
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GTAGCAAAGATGGCATTTGAAGATATGATATCTTGGATGCAAGAAGGTGGCCAGgtaaattcattcttttagata-actttgttacttaagccttctttcaaattttttcaacttaagttttaatttggatatag
upper sequence: LOC_Os03g18310.3 (Oryza sativa), 5'ss of exon 9
lower sequence: GLYMA02G39390.1 (Glycine max), 5'ss of exon 10
GTGGCGGCTCTAGCAATGGAGGATATGCTATCTTGGATGCAGGAAGGTGGTCAGgtaagttagaagttttgg-tgatattctgttattacgctggataatttattcttctttctggtccatag----------------
|| || | ||| | || |||||| ||||||||||||| |||||||| ||||||| || |||| | | | || | ||| || | || || || | |
GTAGCAAAGATGGCATTTGAAGATATGATATCTTGGATGCAAGAAGGTGGCCAGgtaaattcattcttttagataacttttttactttaagccttctttcaagttttttttcttaacttaagttttaatttggatttag
upper sequence: LOC_Os03g18310.3 (Oryza sativa), 5'ss of exon 9
lower sequence: AT1G07110.1 (Arabidopsis thaliana), 5'ss of exon 10
GTGGCGGCTCTAGCAATGGAGGATATGCTATCTTGGATGCAGGAAGGTGGTCAGgtaagt---tagaagttttggtgatattctgttattacgctggataat-ttattcttctttctggtccatag
|| || || || || |||||||| ||| || |||||||||| ||||||||||| |||||| | |||| | || | | | || | | | || | | || | | |||
GTAGCAGCACTTGCTATGGAGGACATGATAGCTTGGATGCAAGAAGGTGGTCAAgtaagtatctttcggtttagatgtaagttcctggtttctatatcttgcattgtaaatagtttttagctgtag
upper sequence: LOC_Os03g18310.3 (Oryza sativa), 5'ss of exon 9
lower sequence: Vv06s0004g06920.t01 (Vitis vinifera), 5'ss of exon 10
GTGGCGGCTCTAGCAATGGAGGATATGCTATCTTGGATGCAGGAAGGTGGTCAGgtaagttagaagttttggtgatattctgttat-tacgctggataattt--------attcttctttctggtccatag
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GTAGCAGCCCTGGCAATGGATGATATGATATCTTGGATGCAAGAGGGCGGCCAGgtaagttattttatgtca-gatattgtgatgcatgtgcctaatcctttcattttaaattattctaattggattgtag
upper sequence: LOC_Os03g18310.3 (Oryza sativa), 5'ss of exon 9
lower sequence: PP1S215_89V6.1 (Physcomitrella patens), 5'ss of exon 11
GTGGCGGCTCTAGCAATGGAGGATATGCTATCTTGGATGCAGGAAGGTGGTCAGgtaag---ttagaagttttggtgatattctgttattacgctgga--taatttattcttctttctggtccatag---------------------------
||||| |||||||||||||| || ||||| |||||||| | ||||||||||||||| | | |||| || | || || | ||| ||| || || ||| | |
GTGGCTGCTCTAGCAATGGAAGACATGCTTGCTTGGATGGAAGAAGGTGGTCAGgtataattctctacaatttgacgaagtcctacaatctccaaggagtcaatataagtttatttaaatacagcggtgggtcgagtcctttttagtgattattMapped 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|58689570|gb|CK078257.1|CK078257EST: CGGCTCTAGCAATGGAGGATATGCTATCTTGGATGCAGGAAGGTGGTCAG GTAGGTATCTTTGATGCCACAAACAGCACAAGAAACCGGAGAAATATGCTG
genomic: CGGCTCTAGCAATGGAGGATATGCTATCTTGGATGCAGGAAGGTGGTCAGgtaagttaga ... tggtccatagGTAGGTATCTTTGATGCCACAAACAGCACAAGAAACCGGAGAAATATGCTG
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
GTGGCGGCTCTAGCAATGGAGGATATGCTATCTTGGATGCAGGAAGGTGGTCAGgtaagttagaagttttggtgatattctgttattacgctggataatttattcttctttctggtccatag
- - - - - - - - TGGAGG
- - - - - - - - GGAGGA
- - - - - - - - - GAGGAT