Sequence
atgc intronic sequence ATGC exonic sequenceGAATGGATTGCATGGGCAGAGCCTCAATATAATTTTAACCCGATGATAGATGAATGGTGCAAGGAGGCACCAAAGGAACTTGATTTCAACCATGAGGCAGgtaattacccctttcagttctcatactcctctctccatataaaagaacatgcatgctcttgtgactcatccatattttttttaaaagtaaaggtctagtcactaatgaacatatcatcctgataatgtatgctataaaatccttaattttag
Basic information
species | Oryza sativa |
transcript | LOC_Os06g48770.1 |
intron # | 6 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os06g48770.2 (Oryza sativa), 5'ss of exon 6
lower sequence: GRMZM2G140917_T01 (Zea mays), 5'ss of exon 7
GAATGGATTGCATGGGCAGAGCCTCAATATAATTTTAACCCGATGATAGATGAATGGTGCAAGGAGGCACCAAAGGAACTTGATTTCAACCATGAGGCAGgtaattacccctttcagttctcatactcctctctccatataaaagaacatgcatgctcttgtgactcatccatattttttttaaaagtaaaggtctagtcactaatgaacatatcatcctgataatgtatgctataaaatccttaattttag
|||||||| || |||||||||||||| ||| ||||||| |||||||| |||||||||||||||||||| |||||||||||||||||||||||||| ||||||| || || |||| | |||||||| | | |||||| | | || | ||| | ||||| | ||| || | ||||| || ||||| | | || ||||||||| || |||||| || | ||||||||
GAATGGATAGCGTGGGCAGAGCCTCAGTATGATTTTAATCCGATGATTGATGAATGGTGCAAGGAGGCTCCAAAGGAACTTGATTTCAACCATGAAGCAGgtattttccttgctcaggt-tcatactcatattgccatatgcttctctgcacgattttccatgtcctgtccctctttttaaatagagtcaaagcctagtggctcatgaagaggttgtcttgataatgtgtggtataaattcttcaattttag
upper sequence: LOC_Os06g48770.2 (Oryza sativa), 5'ss of exon 6
lower sequence: GLYMA17G24420.1 (Glycine max), 5'ss of exon 5
GAATGGATTGCATGGGCAGAGCCTCAATATAATTTTAACCCGATGATAGATGAATGGTGCAAGGAGGCACCAAAGGAACTTGATTTCAACCATGAGGCAGgtaattacccctttcagttctcatactcctctctccatataaaaga---acatgcatgctcttgtgactcatccatattttttttaaaagtaaaggtctagtcactaatgaacatatcatcctgataatgtatgctataaaatccttaattttag
|| |||||||||||||| ||||| |||||||| ||||| || ||||| |||||||||||||| || || || ||||||||||| ||||| ||||| || |||| || | | | |||| | | | | | | || ||| ||| | || ||||| || | | | |||| | || ||| ||| |
GACTGGATTGCATGGGCTGAGCCGCAATATAACTTTAATCCTATGATCGATGAATGGTGCAAAGAAGCTCCTAAGGAACTTGACTTCAATCATGAAGCTGgtattttcagatctt--ttctaaaatttgtat-ttgatgtaatagatataaatttatgcttggaaatatctttggtgtattttgttggagataagttcttgga----------------------------------------------------
upper sequence: LOC_Os06g48770.2 (Oryza sativa), 5'ss of exon 6
lower sequence: GLYMA14G20110.1 (Glycine max), 5'ss of exon 6
GAATGGATTGCATGGGCAGAGCCTCAATATAATTTTAACCCGATGATAGATGAATGGTGCAAGGAGGCACCAAAGGAACTTGATTTCAACCATGAGGCAGgtaattacccctttcagttctcatactcctctctccatataaaagaac---atgcatgctcttgtgactcatccatattttttttaaaagtaaaggtctagtcactaatgaacatatcatcctgataatgtatgctataaaatccttaattttag
|| |||||||||||||| ||||| |||||||| ||||| || ||||| |||||||||||||| || || || ||||||||||| ||||| ||||| || |||| || | | | || | | | | | || ||| ||| | || ||||| || | | | |||| | || ||| ||| |
GACTGGATTGCATGGGCTGAGCCACAATATAACTTTAATCCTATGATCGATGAATGGTGCAAAGAAGCTCCTAAGGAACTTGACTTCAATCATGAAGCTGgtattttcggatct---tttataaaatttgcatttgatgtaatagatctaaattaatgcttgaaaatatctttggtgtattttgttggagataagttcttgga----------------------------------------------------
upper sequence: LOC_Os06g48770.2 (Oryza sativa), 5'ss of exon 6
lower sequence: AT5G24810.2 (Arabidopsis thaliana), 5'ss of exon 6
GAATGGATTGCATGGGCAGAGCCTCAATATAATTTTAACCCGATGATAGATGAATGGTGCAAGGAGGCACCAAAGGAACTTGATTTCAACCATGAGGCAGgtaattacccctttcagttctcatactcctctctccatataaaagaacatgcatgctcttgtgactcatccatattttttttaaaagtaaaggtctagtcactaatgaacatatcatcctgataatgtatgctataaaatccttaattttag
|| |||||||| ||||| || || || || |||||||| || ||||||||||||||||||||||| || |||| ||||| || ||||| ||| || |||| | ||| || | | || | | || | | | ||||| | | | ||| | ||| | | | | | |||| || |
GACTGGATTGCGTGGGCGGAACCACAGTACAATTTTAATCCCATGATAGATGAATGGTGCAAGGAAGCTCCAAGAGAACTAGACTTCAATATTGAAGCTGgtatgcttcacttgcattaataatgaatagccttaaatttca--------------ttctgtga-taaactataatagcaccaaagcttgtgatt--gccttccatgatcaagttca-----------------------------------
upper sequence: LOC_Os06g48770.2 (Oryza sativa), 5'ss of exon 6
lower sequence: Vv04s0008g02740.t01 (Vitis vinifera), 5'ss of exon 5
GAATGGATTGCATGGGCAGAGCCTCAATATAATTTTAACCCGATGATAGATGAATGGTGCAAGGAGGCACCAAAGGAACTTGATTTCAACCATGAGGCAGgtaattacccctttcagttctcatactcctctctccatataaaagaacatgcatgct-----cttgtgactcatccatattttttttaaaagtaaag--gtctagtcactaatgaacatatcatcctgataatgtatgct-ataaaatccttaattttag---------
|| ||||| ||||||||||| || |||||| | || ||||| ||||| ||||||||||||| || ||||| || ||||||||||| | ||||| || |||| | | ||| || || | | | | | | | || | |||| | | |||| ||| | || || | | || || || || | | || | ||| ||| | | | |
GACTGGATAGCATGGGCAGAACCACAATATGACTTCAACCCTATGATTGATGAATGGTGCAGAGAAGCACCTAAAGAACTTGATTTTGATCATGAAGCTGgtatgctctggtctcatggaatatttatttcagtgcttttttatggtcttgtgattgggaaacaagtgattgttttctattactttcagtggtttagcaaatttattttagattttcactacactatgcttttatagcttgatatcatcacttgtctctgtgcctgtagMapped 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|86498768|gb|CI141401.1|CI141401EST: CACCAAAGGAACTTGATTTCAACCATGAGGCAG AGAACACAAAGGCTGTCTCCAGTAATCTTAGTCGAAAAACCAATTGCGAGA
genomic: CACCAAAGGAACTTGATTTCAACCATGAGGCAGgtaattaccc ... ttaattttagAGAACACAAAGGCTGTCTCCAGTAATCTTAGTCGAAAAACCAATTGCGAGA
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
GAATGGATTGCATGGGCAGAGCCTCAATATAATTTTAACCCGATGATAGATGAATGGTGCAAGGAGGCACCAAAGGAACTTGATTTCAACCATGAGGCAGgtaattacccctttcagttctcatactcctctctccatataaaagaacatgcatgctcttgtgactcatccatattttttttaaaagtaaaggtctagtcactaatgaacatatcatcctgataatgtatgctataaaatccttaattttag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA