Sequence
atgc intronic sequence ATGC exonic sequenceGCTTTGATGCCATCTCTGATTCCAAATATACTAGTGATGTCAACTGGGGCTGTATGGTCAGAAGCAGCCAAATGCTGGTTGCTCAGgtccttccctactatatttaattgaaagcgcttctcctttttttaccactgcagatgtaaataaaatggtatttggatggatttttgcag
Basic information
species | Oryza sativa |
transcript | LOC_Os03g27350.1 |
intron # | 3 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os03g27350.3 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM2G064212_T02 (Zea mays), 5'ss of exon 3
GCTTTGATGCCATCTCTGATTCCAAATATACTAGTGATGTCAACTGGGGCTGTATGGTCAGAAGCAGCCAAATGCTGGTTGCTCAGgt-----ccttccctactata------tttaattga--aagcgcttctcctttttttaccactgcagatgtaa---ataa--aatggtatttggatggatttttgcag
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GCTTTGATGCAATATCTGATTCCAAGCTAACTAGTGATGTGAACTGGGGATGCATGGTTAGAAGCAGTCAAATGCTGGTTGCTCAGgtaaactctgtccctttcaaagtgtccctttattgaccaaggatggccactgaagttgtataataagttgtaacagacaagcactggcctttgggcaaaattttgcag
upper sequence: LOC_Os03g27350.3 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM2G410085_T01 (Zea mays), 5'ss of exon 2
GCTTTGATGCCATCTCTGATTCCAAATATACTAGTGATGTCAACTGGGGCTGTATGGTCAGAAGCAGCCAAATGCTGGTTGCTCAGgtccttccctactatatttaattgaaagcgc-ttctcctttttttaccactgcagatgtaaataaaatggta-------------tttggatggatttttgcag
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GCTTTGATGCAATATCTGATTTCAAGCTAACTAGTGATGTGAACTGGGGATGCATGGTTAGAAGCAGTCAAATGCTGGTTGCTCAGgtaaactctgtccctttcaaagtgtccctttattgaccaaggatggccactgaagttgtataataagttgtaacagacaagcacctttgggcaaaattttgtag
upper sequence: LOC_Os03g27350.3 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM2G442425_T01 (Zea mays), 5'ss of exon 2
GCTTTGATGCCATCTCTGATTCCAAATATACTAGTGATGTCAACTGGGGCTGTATGGTCAGAAGCAGCCAAATGCTGGTTGCTCAGgt-----ccttccctactata------tttaattga--aagcgcttctcctttttttaccactgcagatgtaa---ataa--aatggtatttggatggatttttgcag
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-----------------------------------------------GGATGCATGGTTAGAAGCAGTCAAATGCTGGTTGCTCAGgtaaactctgtccctttcaaagtgtccctttattgaccaaggatggccactgaagttgtataataagttgtaacagacaagcattggcctttgggcaaaattttgcag
upper sequence: LOC_Os03g27350.3 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM2G458441_T01 (Zea mays), 5'ss of exon 3
--------------GCTTTGATGCCATCTCTGATTCCAAATATACTAGTGATGTCAACTGGGGCTGTATGGTCAGAAGCAGCCAAATGCTGGTTGCTCAGgt-----ccttccctactata------tttaattga--aagcgcttctcctttttttaccactgcagatgtaaataaaa-tggtatttggatggatttttgcag
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GTTAATTGTCCCAGACTTTGATGCAATATCTGATTCCAAGCTAACTAGTGATGTGAACTGGGGATGCATGGTTAGAAGCAGTCAAATGCTGGTTGCTCAGgtaaactctgtccctttcaaagtgtccctttattgaccaaggatggccactgaagttgtataataagttgtaacaagcactggcctttgggcaaaattttgcag
upper sequence: LOC_Os03g27350.3 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM2G173682_T01 (Zea mays), 5'ss of exon 2
GCTTTGATGCCATCTCTGATTCCAAATATACTAGTGATGTCAACTGGGGCTGTATGGTCAGAAGCAGCCAAATGCTGGTTGCTCAGgtccttccctactatatttaattgaaagcgcttctccttttttta-----ccactgcagatgtaaa---taaaatggtatttggatgg---atttttgcag
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GGTTTGATGCAATACCTGGTTCCAAGCTCACTAGTGATGTGAACTGGGGATGCATGGTTAGAAGTAGTCAGATGCTGGTTGCTCAGgtaaaccttc---ggacct--ctggaagtggcccttcattgaccaggattccactgcaattgtaagctgtaacaggcaagctatatggcaaaattttgcag
upper sequence: LOC_Os03g27350.3 (Oryza sativa), 5'ss of exon 4
lower sequence: GLYMA18G48380.1 (Glycine max), 5'ss of exon 3
GCTTTGATGCCATCTCTGATTCCAAATATACTAGTGATGTCAACTGGGGCTGTATGGTCAGAAGCAGCCAAATGCTGGTTGCTCAGgt------ccttccctactatatttaatt--------gaaagcgcttctcctttttttaccactgcagatgtaaataaaatggtatttggatggatttttgcag--------------------------------
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GCTTTGATGCTATTGGAGATACAAAGTATACCAGTGATGTTAATTGGGGTTGTATGCTTCGAAGCAGTCAGATGCTGGTTGCTCAGgtatgatgccttctatataatgattgcttttgacaaggaaattgttacatgataccttatattttctgtttttcttttttgcctgtttttgttgtctttcaaaataaagctactaatgtggcttccttgtgcacagMapped 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|58653596|gb|CK042276.1|CK042276EST: ATGTAAACTGGGGCTGCATGGTCAGAAGCAGCCAAATGCTGGTTGCTCAG GCATTGATTTTCCACCATCTTGGAAGGTCTTGGAGAAAGCCCTCACAGAAG
genomic: ATGTCAACTGGGGCTGTATGGTCAGAAGCAGCCAAATGCTGGTTGCTCAGgtccttccct ... atttttgcagGCATTGATTTTCCACCATCTTGGAAGGTCTTGGAGAAAGCCCTCACAGAAG
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
GCTTTGATGCCATCTCTGATTCCAAATATACTAGTGATGTCAACTGGGGCTGTATGGTCAGAAGCAGCCAAATGCTGGTTGCTCAGgtccttccctactatatttaattgaaagcgcttctcctttttttaccactgcagatgtaaataaaatggtatttggatggatttttgcag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG