Sequence
atgc intronic sequence ATGC exonic sequenceGAGAAGATGACCCAGATCATGTTCGAGAGCTTCAATGTCCCCGCCATGTATGTCGCCATCCAGGCCGTGCTCTCCCTCTACGCCAGTGGCCGCACCACAGgtaacgcaaatttaaaatttcattttcgaaatttgatttatttctttttttttttttgaggggggttgtccttaaatactatcttcgtctaaaaatataa...
Basic information
species | Oryza sativa |
transcript | LOC_Os12g06660.1 |
intron # | 3 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os12g06660.1 (Oryza sativa), 5'ss of exon 3
lower sequence: PP1S372_48V6.1 (Physcomitrella patens), 5'ss of exon 2
GAGAAGATGACCCAGATCATGTTCGAGAGCTTCAATGTCCCCGCCATGTATGTCGCCATCCAGGCCGTGCTCTCCCTCTACGCCAGTGGCCGCACCACAGgtaacgcaaatttaaaatttcattttcgaaatttgatttatttctttttttttttttgaggggggttgtccttaaatactatcttcgtctaaaaatataa
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GAGAAGATGACGCAGATCATGTTCGAGACGTTCAACGTGCCGGCGATGTACGTGGCGATCCAGGCGGTGCTGTCGCTGTACGCGAGCGGGCGAACGACGGgtgagtggggagtgagtggtgagggggtggggatggtggtggtaggatgtggaggtgggaggtgattgagaacagatg-tggcggtgcgtggaa-tgcag
upper sequence: LOC_Os12g06660.1 (Oryza sativa), 5'ss of exon 3
lower sequence: PP1S337_21V6.2 (Physcomitrella patens), 5'ss of exon 4
GAGAAGATGACCCAGATCATGTTCGAGAGCTTCAATGTCCCCGCCATGTATGTCGCCATCCAGGCCGTGCTCTCCCTCTACGCCAGTGGCCGCACCACAGgtaacgcaaatttaaaatttcattttcgaaatttgatttatttctttttttttttttgaggggggttgtccttaaatactatcttcgtc-taaaaatataa--------------------------------------------------------
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GAGAAGATGACGCAGATCATGTTCGAGACGTTCAACGTGCCGGCGATGTACGTGGCCATTCAGGCAGTGCTGTCACTATATGCCAGTGGACGAACGACCGgtgagtgatgggagaaggggtgaggtgaatgcagcatgtgcgttggttgcgaaagtggtggaggtgtgtggagaggtggggtgtttgacatgggaaggtttgtgggtcggggtaagaaactgagagcagttgtggtgatgaatgcaatgcaatgcag
upper sequence: LOC_Os12g06660.1 (Oryza sativa), 5'ss of exon 3
lower sequence: EFJ17401 (Selaginella moellendorffii), 5'ss of exon 2
GAGAAGATGACCCAGATCATGTTCGAGAGCTTCAATGTCCCCGCCATGTATGTCGCCATCCAGGCCGTGCTCTCCCTCTACGCCAGTGGCCGCACCACAGgtaacgcaaatttaaaa---tttcattttcgaaat-------ttgatttatttctttttttttttttg------aggggggttgtccttaaa-----tactatcttcgtctaaaaatataa-----------------------------
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GAGAAGATGACCCAGATCATGTTCGAGACCTTCAATGTCCCGGCCATGTACGTGGCGATCCAAGCAGTCCTTTCACTCTACGCGAGTGGACGCACTACCGgtatggagtttttttatcccttgcttgttctagacaagatggttgatgcgtgtttcttttcttcgttgcttgcgatagacatgatgcttcaagttggttctacttttgtttttccctctaacacgttgtatgatcgtggtttgtgatcag
upper sequence: LOC_Os12g06660.1 (Oryza sativa), 5'ss of exon 3
lower sequence: EFJ35077 (Selaginella moellendorffii), 5'ss of exon 2
GAGAAGATGACCCAGATCATGTTCGAGAGCTTCAATGTCCCCGCCATGTATGTCGCCATCCAGGCCGTGCTCTCCCTCTACGCCAGTGGCCGCACCACAGgtaacgcaaatttaaaatttcatt-----ttcgaaat-------ttgatttatttctttttttttttttgaggggggttgtccttaaatactatcttcgtctaaaaatataa-----------------------------------------
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GAGAAGATGACCCAGATCATGTTCGAGACCTTCAATGTCCCGGCCATGTACGTGGCAATCCAAGCAGTCCTTTCACTCTACGCGAGTGGACGCACTACCGgta-tggagttttttttttcctttgcttgttctagacaagatggttgatgcgtgtttcttttcttcgttgcttgcgatagacatgatgcttcaagttggttctacttttttttcttctctctaacacgttgtatgatcgtggtttgtgatcagMapped 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|117251245|gb|CT844082.1|CT844082EST: TGTCGCCATCCAGGCCGTGCTCTCCCTCTACGCCAGTGGCCGCACCACAG GCATCGTGCTGGACTCCGGCGACGGTGTGAGCCACACCGTGCCGATCTACG
genomic: TGTCGCCATCCAGGCCGTGCTCTCCCTCTACGCCAGTGGCCGCACCACAGgtaacgcaaa ... ttttaattagGCATCGTGCTGGACTCCGGCGACGGTGTGAGCCACACCGTGCCGATCTACG
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
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GAGAAGATGACCCAGATCATGTTCGAGAGCTTCAATGTCCCCGCCATGTATGTCGCCATCCAGGCCGTGCTCTCCCTCTACGCCAGTGGCCGCACCACAGgtaacgcaaatttaaaatttcattttcgaaatttgatttatttctttttttttttttgaggggggttgtccttaaatactatcttcgtctaaaaatataa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gaggggg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaaaata