Sequence
atgc intronic sequence ATGC exonic sequenceACAGTTGCTGATTCACAATGGCAAGGTTTTGAAAGATGAAAGTACATTGGAAGAGAACAAAGTCAGTGAAGTTGGGTTTTTAGTTGTCATGCTTAGTAAGgtaggccgcgtatgtgctgtatataatttaaatggtgatgttatttattacgcttcatttaattcttttctgactggatgctgggtgtaacggtgcagca...
Basic information
species | Oryza sativa |
transcript | LOC_Os02g08300.1 |
intron # | 2 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os02g08300.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G143462_T06 (Zea mays), 5'ss of exon 2
ACAGTTGCTGATTCACAATGGCAAGGTTTTGAAAGATGAAAGTACATTGGAAGAGAACAAAGTCAGTGAAGTTGGGTTTTTAGTTGTCATGCTTAGTAAGgtaggccgcgtatgtgctgtatataatttaaatggtgatgttatttattacgcttcatttaattcttttctgactggatgctg-ggtgtaacggtgcagca-
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ACAACTGCTGATTTTCAATGGAAAGGTCTTGAAAGATGAAAGTACATTGGAAGAGAATAAAGTCAATGAGGATGGGTTTCTAGTTGTCATGCTTAGTAAGgttgggttctaatacatc-tctgtactacacattttca-gatagatatgatgttttactgaagtatttttcattttagtctgataatgttaccacttgattt
upper sequence: LOC_Os02g08300.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GLYMA13G44910.1 (Glycine max), 5'ss of exon 2
ACAGTTGCTGATTCACAATGGCAAGGTTTTGAAAGATGAAAGTACATTGGAAGAGAACAAAGTCAGTGAAGTTGGGTTTTTAGTTGTCATGCTTAGTAAGgtaggccgcgtatgtgctgtatataatttaaatggtgatgttatttattacgcttcatttaattcttttc-tgactggatgctgggtgtaacggtgcagca--
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GCAATTGCTCATTCACAATGGTAAGGTTTTGAAAGATGAAACTACTTTATCCGACAATAAGGTCTCTGAGGATGGTTTTCTTGTTGTCATGCTTAGTAAGgta---cctttactttcttccttcaccttaactttttttttttttttttttatcttatacaaaccatcaaaccattacaattcctatttcctcaccctgcatt
upper sequence: LOC_Os02g08300.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GLYMA07G00490.1 (Glycine max), 5'ss of exon 2
ACAGTTGCTGATTCACAATGGCAAGGTTTTGAAAGATGAAAGTACATTGGAAGAGAACAAAGTCAGTGAAGTTGGGTTTTTAGTTGTCATGCTTAGTAAGgtaggccgcgtatgtgctgtatataat-ttaaatggtgatgttatttattacgcttcatttaattcttttctgactggatgctgggtgtaacggtgcagca
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GCAATTGCTGATTCACAATGGTAAGGTTTTGAAAGATGAAACTACATTAGTAGAGAACAAAGTCTCTGAAGATGGTTTTCTTGTTGTTATGCTTAGTAAGgtatatttctttcttcaagaataccttgccaaacaattgcttaggcaagtcacctccatccagatgtagtgct-ctacttgttgatagtgaaattttattt
upper sequence: LOC_Os02g08300.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GLYMA08G23930.2 (Glycine max), 5'ss of exon 2
ACAGTTGCTGATTCACAATGGCAAGGTTTTGAAAGATGAAAGTACATTGGAAGAGAACAAAGTCAGTGAAGTTGGGTTTTTAGTTGTCATGCTTAGTAAGgtaggccgcgtatgtgctgtatataat-ttaaatggtgatgttatttattacgcttcat-ttaattcttttctgactggatgctgggtgtaacggtgcagca
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GCAATTGTTGATTCACAATGGCAAGGTTTTGAAAGATGAAACTACATTAGTAGAGAATAAAGTCTCTGAAGATGGCTTTCTTGTTGTTATGCTTAGTAAGgtatatttctttcttcaagaatactttgtcaaacaattgcttaggcaagtcaccttcatactgactgtcatttga--gctctcatatttttatcctgtatca
upper sequence: LOC_Os02g08300.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GLYMA13G44910.2 (Glycine max), 5'ss of exon 2
--------------------------------------------------------------ACAGTTGCTGATTCACAATGGCAAGGTTTTGAAAGATGAAAGTACATTGGAAGAGAACAAAGTCAGTGAAGTTGGGTTTTTAGTTGTCATGCTTAGTAAGgtaggccgcgtatgtgctgtatataatttaaatggtgatgttatttattacgcttcatttaattcttttctgactggatgctgggtgtaacggtgcagca
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ATTATGGCAGTCAAGAAGAATATCGAAGATGTACAAGGCAAAGACAATTACCCATGTGGACAGCAATTGCTCATTCACAATGgtaaggttttgaaagatgaaactactttatccgacaataaggtctctgaggatggttttcttgttgtcatgcttagtaaggtacctttactttcttcctt--------------------------------------------------------------------------------
upper sequence: LOC_Os02g08300.1 (Oryza sativa), 5'ss of exon 2
lower sequence: AT1G79650.1 (Arabidopsis thaliana), 5'ss of exon 2
ACAGTTGCTGATTCACAATGGCAAGGTTTTGAAAGATGAAAGTACATTGGAAGAGAACAAAGTCAGTGAAGTTGGGTTTTTAGTTGTCATGCTTAGTAAGgtaggccgcgtatgtgctgtatataatttaaatggtgatgttatttattacgcttcatttaattcttttctgactggatgctgggtgtaacggtgcagca--
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GCAATTGTTGATTCACAATGGAAAAGTTTTGAAAGATGAAACTAGCCTGGTGGAGAACAAAGTTACGGAGGAAGGATTTCTCGTCGTTATGCTTAGCAAGgtaa-cagttcaaat-ctggctactgcaaagatcatacttcttttatcttcaacaaatcagtcttcttatttaccttaaacaaggataaaagctgatgaata
upper sequence: LOC_Os02g08300.1 (Oryza sativa), 5'ss of exon 2
lower sequence: AT1G16190.1 (Arabidopsis thaliana), 5'ss of exon 2
ACAGTTGCTGATTCACAATGGCAAGGTTTTGAAAGATGAAAGTACATTGGAAGAGAACAAAGTCAGTGAAGTTGGGTTTTTAGTTGTCATGCTTAGTAAGgtaggccgcgtatgtgctgtatataatttaaatggtgatgttatttattacgcttcatttaattcttttctgactgga-tgctgggtgtaac--ggtgcagca
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GCAATTACTGATTCACAATGGAAAGGTTTTGAAAGATGAAACTACCTTGGTGGAGAACAAGGTTACCGAGGAGGGTTTTCTTGTCGTGATGCTTAGCAAGgtacctatctgatttcttttatg-atcctagatagtgct-tagtgtgagtcactctaagcaacctggatttatatatccttcttagtcccattagatatagt-
upper sequence: LOC_Os02g08300.1 (Oryza sativa), 5'ss of exon 2
lower sequence: Vv09s0018g01400.t01 (Vitis vinifera), 5'ss of exon 2
ACAGTTGCTGATTCACAATGGCAAGGTTTTGAAAGATGAAAGTACATTGGAAGAGAACAAAGTCAGTGAAGTTGGGTTTTTAGTTGTCATGCTTAGTAAGgtaggccgcgtatgtgctgtatataatttaaatggtgatgttatttattacgcttcatttaattcttttctgactggatgctgggtgtaacggtgcagca----
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ACAATTATTGATTCATAATGGAAAGGTCTTGAAAGATGAAACTACACTGGTGGAGAACAAAGTTACAGAAGATGGTTTTCTAGTGGTCATGCTTAGCAAGgtaggt----ttttttttttttttctttctatctttgggctttttaacaactgttggtgctgcacttgcatagttgtataataaatttaatgtttaggtatcatMapped 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|88351863|gb|CI624668.1|CI624668EST: AGAGAA-AAAGGTCAGTGAAGTTGGGTTTTTAGTTGTCATGCTTAGTAAG AGTAAAGCTTCTGGTTCCAGTGGAGCTTTAAGTTCACTG
genomic: AGAGAACAAAG-TCAGTGAAGTTGGGTTTTTAGTTGTCATGCTTAGTAAGgtaggccgcg ... ttctctgcagAGTAAAGCTTCTGGTTCCAGTGGAGCTTTAAGTTCACTG
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ACAGTTGCTGATTCACAATGGCAAGGTTTTGAAAGATGAAAGTACATTGGAAGAGAACAAAGTCAGTGAAGTTGGGTTTTTAGTTGTCATGCTTAGTAAGgtaggccgcgtatgtgctgtatataatttaaatggtgatgttatttattacgcttcatttaattcttttctgactggatgctgggtgtaacggtgcagca
- - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA