Sequence
atgc intronic sequence ATGC exonic sequenceGAAGATGGCTGAAGCAGGATGCGAATATATCACTGTCTTAGGTGTTGATTTTATGTCAGAAAATGTTCGTGCAATACTTGATCAAGCTGGATATAGCAAGgtatttatgtgtttatatcactgattgtcattaagtttgaagaatttctattctactgtctccattgtttactggaaggactaagttacagaactcattg...
Basic information
species | Oryza sativa |
transcript | LOC_Os12g19304.1 |
intron # | 3 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os12g19304.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G142836_T01 (Zea mays), 5'ss of exon 1
GAAGATGGCTGAAGCAGGATGCGAATATATCACTGTCTTAGGTGTTGATTTTATGTCAGAAAATGTTCGTGCAATACTTGATCAAGCTGGATATAGCAAGgtatttatgtgtttatatcactgattgtcattaagtttgaagaatttctattctactgtctccattgtttactggaaggactaagttacagaactcattg-
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TAAAATGGCTGAAGCAGGATGTGACTATATTACAGTTTTAGGTGTTGACTTCATGTCAGAAAATGTTCGGGCAGTACTTGATCAAGCAGGATTTAATAAGgtattttta-attagtgtttccagaagtctaattgtcatgccattttcactaagagcatactgtgagaataaagctaagagtaggtttgtatatgcactta
upper sequence: LOC_Os12g19304.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GLYMA05G02710.1 (Glycine max), 5'ss of exon 2
GAAGATGGCTGAAGCAGGATGCGAATATATCACTGTCTTAGGTGTTGATTTTATGTCAGAAAATGTTCGTGCAATACTTGATCAAGCTGGATATAGCAAGgtatttatgtgtttatatcactgattgtcatta-agtttgaagaatttctattctactgtctccattgtttactggaaggactaagttacagaactcattg-----------------------------------------------------------------------------------------
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CAAAATGGCAAAAGCCGGATGCCAGTTCATAACAGTTCTAGGTGTGGATTTTATGTCAGAAAATGTGCGTGCCATCCTTGATCAAGCTGGTTTCAGTGAGgtatgcctttctctcctaagttaagtctgtctagaagatggactctattaagtttcccatttataaacattggtgaatggcttgtatgaagcaggtcacacgtgctgcagtaaaatatattagtaaaattggtatttgtgctacatgttaatccttagtccttaatttttcttctggtaattatttgcag
upper sequence: LOC_Os12g19304.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GLYMA17G13410.1 (Glycine max), 5'ss of exon 1
-----GAAGATGGCTGAAGCAGGATGCGAATATATCACTGTCTTAGGTGTTGATTTTATGTCAGAAAATGTTCGTGCAATACTTGATCAAGCTGGATATAGCAAGgtatttatgtgtttatatcactgattgtcattaagtttgaagaatttctattctactgtctccattgtttactggaaggactaagttacagaactcattg-----------------------------
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GCAGTCAAAATGGCAAAAGCTGGATGCCAATTCATAACAGTTCTAGGTGTCGATTTTATGTCAGAAAATGTGCGTGCCATCCTTGATCAAGCTGGTTTTAgtgagttatgcctttctctattttgaagatagccatca-gcaggcaaaatatgtgatgataagttaagtctgtcttgaagatggactctattaagtttccaatttataaatattggtgaatggctcgtatgaag
upper sequence: LOC_Os12g19304.1 (Oryza sativa), 5'ss of exon 3
lower sequence: AT5G50210.1 (Arabidopsis thaliana), 5'ss of exon 2
GAAGATGGCTGAAGCAGGATGCGAATATATCACTGTCTTAGGTGTTGATTTTATGTCAGAAAATGTTCGTGCAATACTTGATCAAGCTGGATATAGCAAGgt-atttatgtgtttatatcactgat-tgtcattaagtttgaagaatttctattctactgtctccattgtttactggaaggactaagttacagaactcattg
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CACGATGGCTAAAGCTGGATGTCAGTTTATAACAGTTCTTGGTGTTGATTTCATGTCCGAAAATGTTCGTGCCATCCTAGATCAAGCTGGGTTTGAAAAGgttagagaagggtttttttctcttatattttgttttgtgatagtgagtctttacatattat-tcggttttgtag----------------------------
upper sequence: LOC_Os12g19304.1 (Oryza sativa), 5'ss of exon 3
lower sequence: Vv17s0000g09490.t01 (Vitis vinifera), 5'ss of exon 2
GAAGATGGCTGAAGCAGGATGCGAATATATCACTGTCTTAGGTGTTGATTTTATGTCAGAAAATGTTCGTGCAATACTTGATCAAGCTGGATATAGCAAGgtatttatgtgtttatatcactgattgtcattaagtttgaagaatttctattctactgtctccattgtttactggaaggactaagttacagaactcattg--
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CAAGATGGCAAAAGCTGGATGTCAATTCATTGCAGTTTTGGGCGTAGATTTTATGGCAGAAAATGTGCGTGCCATCCTTGATCAAGCTGGCTTTGGAGAGgtacccttttattactcatgcct-tttctgtaatcatttggcaatttgtatatggaattctgagctgctc-tcattcattctagataacagagtagatgaagMapped 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|33796673|gb|CF324204.1|CF324204EST: TTATGTCAGAAAATGTTCGTGCAATACTTGATCAAGCTGGATATAGCAAG GTTGGTGTTTATAGAATGTCAAGTGATCAAATTGGCTGTTCATTGGCAGAC
genomic: TTATGTCAGAAAATGTTCGTGCAATACTTGATCAAGCTGGATATAGCAAGgtatttatgt ... atttatgcagGTTGGTGTTTATAGAATGTCAAGTGATCAAATTGGCTGTTCATTGGCAGAC
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
GAAGATGGCTGAAGCAGGATGCGAATATATCACTGTCTTAGGTGTTGATTTTATGTCAGAAAATGTTCGTGCAATACTTGATCAAGCTGGATATAGCAAGgtatttatgtgtttatatcactgattgtcattaagtttgaagaatttctattctactgtctccattgtttactggaaggactaagttacagaactcattg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG