Sequence
atgc intronic sequence ATGC exonic sequenceGTACATCATGGCGGTGCTGGAACAACAGCTGCTGGCCTCAAAGCAGCGgtattccctctctcccttcttagcccatctccctcctttctctctctcaaaagaaaaacctggcttaactaataaaaattggggttacacttctggattg...
Basic information
species | Oryza sativa |
transcript | LOC_Os04g04254.1 |
intron # | 12 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os04g04254.1 (Oryza sativa), 5'ss of exon 12
lower sequence: GRMZM2G021849_T02 (Zea mays), 5'ss of exon 7
GTACATCATGGCGGTGCTGGAACAACAGCTGCTGGCCTCAAAGCAGCGgtattccctctctccct-tcttagcccatctccctcctttctctctctcaaaagaaaaacctg-gcttaactaataaaaattggggttacacttctggattg
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GTGCATCATGGTGGCGCTGGAACAACAGCCGCAGGTCTCAAAGCAGCGgtaagtgctctctccatgccttatttcaatgtaaaatagttgtactcttctcaaaggcactggagagttgcaagaggaaagggagtctaagaagacatac--
upper sequence: LOC_Os04g04254.1 (Oryza sativa), 5'ss of exon 12
lower sequence: EFJ38334 (Selaginella moellendorffii), 5'ss of exon 10
GTACATCATGGCGGTGCTGGAACAACAGCTGCTGGCCTCAAAGCAGCGgtattccctctctcccttcttagcccatctccctcctttctctctctcaaaagaaaaacctggcttaactaataaaaattggggttacacttctggattg
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GTTCATCACGGTGGAGCTGGAACAACAGCTGCTGGTCTCAAAGCCGCGgtaaa--gttgtttttttctaaaa--actttgttgctttctctgttttatcttccatttttctctccatggaaacag-----------------------
upper sequence: LOC_Os04g04254.1 (Oryza sativa), 5'ss of exon 12
lower sequence: EFJ18041 (Selaginella moellendorffii), 5'ss of exon 11
GTACATCATGGCGGTGCTGGAACAACAGCTGCTGGCCTCAAAGCAGCGgtattccctctctcccttcttagcccatctccctcctttctctctctcaaaagaaaaacctggcttaactaataaaaattggggttacacttctggattg
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GTTCATCATGGAGGCGCGGGAACAACAGCTGCCGGTCTCAAAGCTGCGgtataagcaag----------agcaagagcagaggtttttttgacttaaccaggatgagtttgcgtgcttggcag-------------------------
upper sequence: LOC_Os04g04254.1 (Oryza sativa), 5'ss of exon 12
lower sequence: EFJ09619 (Selaginella moellendorffii), 5'ss of exon 11
GTACATCATGGCGGTGCTGGAACAACAGCTGCTGGCCTCAAAGCAGCGgtattccctctctcccttcttagcccatctccctcctttctctctctcaaaagaaaaacctggcttaactaataaaaattggggttacacttctggattg
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GTTCATCATGGAGGCGCGGGAACAACAGCTGCCGGTCTCAAAGCTGCGgtataagcaagagcaag----agcggaggt---ttttttgacttactgagtgtgcgtgcttggcag----------------------------------
upper sequence: LOC_Os04g04254.1 (Oryza sativa), 5'ss of exon 12
lower sequence: EFJ14885 (Selaginella moellendorffii), 5'ss of exon 10
GTACATCATGGCGGTGCTGGAACAACAGCTGCTGGCCTCAAAGCAGCGgtattccctctctcccttcttagcccatctccctcctttctctctctcaaaagaaaaacctggcttaactaataaaaattggggttacacttctggattg
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GTTCATCACGGTGGAGCTGGAACAACAGCTGCTGGTCTCAAAGCCGCGgtaaa--gttgtttttttctaaaa--aatttgctactttctctgttttatcatccatttttctctccatgcaaacag-----------------------Mapped 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|218504178|gb|FG958866.1|FG958866EST: GTACATCATGGCGGTGCTGGAACAACAGCTGCTGGCCTCAAAGCAGCG TGCCCTACAACTATTGTACCTTTCTTTGGTGACCAACCATTCTGGGGAGAC
genomic: GTACATCATGGCGGTGCTGGAACAACAGCTGCTGGCCTCAAAGCAGCGgtattccctc ... tgatttgtagTGCCCTACAACTATTGTACCTTTCTTTGGTGACCAACCATTCTGGGGAGAC
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
GTACATCATGGCGGTGCTGGAACAACAGCTGCTGGCCTCAAAGCAGCGgtattccctctctcccttcttagcccatctccctcctttctctctctcaaaagaaaaacctggcttaactaataaaaattggggttacacttctggattg
- - - - - - - GCTGGA
- - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ccctctc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctccctc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctctctct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aagaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aataaaa