Sequence
atgc intronic sequence ATGC exonic sequenceGTTGCCAAGATGGTGAGGTTTACGGCGGAGGAGCTCCGCGCGAGCATGGATAAGAAGGACAACATCCGGAACATGTCTGTGATCGCGCACGTTGATCATGgtgagtgtttttcatcaagcaaaatttggattcgatcgatctgtcgctttggatctctgtgtgtgtgagtgggggatggatagtaatgtggatcgatgtgcgttttggggtgggggttggaattctgcag
Basic information
species | Oryza sativa |
transcript | LOC_Os01g52470.1 |
intron # | 2 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os01g52470.1 (Oryza sativa), 5'ss of exon 2
lower sequence: PP1S138_93V6.1 (Physcomitrella patens), 5'ss of exon 2
GTTGCCAAGATGGTGAGGTTTACGGCGGAGGAGCTCCGCGCGAGCATGGATAAGAAGGACAACATCCGGAACATGTCTGTGATCGCGCACGTTGATCATGgtgagt---gtttttcatcaagcaaaatttggattcgatcgatctgtcgctttggatctctgtgtgtgtgagtgggggatggatagtaatgtggatcgatgtgcgttttggggtgggggttggaattctgcag
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------------GTGAAGTTTTCGGCGGACGAGCTCCGCGCCATCATGGACAAGAAGCACAACATCAGGAACATGTCCGTCATCGCCCATGTCGATCACGgtatgtcgaagtccctgtctcttgcagtgtgg-tagtctgggtctggtgactagggtttgagtttgt---agtgtgcgatgatcggaagggcgactgcttgaaa-----------------------------
upper sequence: LOC_Os01g52470.1 (Oryza sativa), 5'ss of exon 2
lower sequence: EFJ28367 (Selaginella moellendorffii), 5'ss of exon 2
GTTGCCAAGATGGTGAGGTTTACGGCGGAGGAGCTCCGCGCGAGCATGGATAAGAAGGACAACATCCGGAACATGTCTGTGATCGCGCACGTTGATCATGgtgagtgtttttcatcaagcaaaatttggattcgatcgatctgtcgctttggatctctgtgtgtgtgagtgggggatggatagtaatgtggatcgatgtgcgttttggggtgggggttggaattctgcag
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------------GTGAAATTCACGGCAGAAGAGCTGCGCCGGATCATGGACAAGAAGCACAACATCCGGAACATGTCTGTGATTGCTCATGTCGATCACGgtgagtttcttc---tagattttccatccattcagtagctaaagctcgtcgatctgaaattttcgccag-------------------------------------------------------------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|88400823|gb|CI616828.1|CI616828EST: TAAGAAGGACAACATCCGGAACATGTCTGTGATCGCGCACGTTGATCATG GGAAGTCGACGCTCACTGACTCGCTGGTGGCGGCGGCCGGCATCATCGCGC
genomic: TAAGAAGGACAACATCCGGAACATGTCTGTGATCGCGCACGTTGATCATGgtgagtgttt ... aattctgcagGGAAGTCGACGCTCACTGACTCGCTGGTGGCGGCGGCCGGCATCATCGCGC
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
GTTGCCAAGATGGTGAGGTTTACGGCGGAGGAGCTCCGCGCGAGCATGGATAAGAAGGACAACATCCGGAACATGTCTGTGATCGCGCACGTTGATCATGgtgagtgtttttcatcaagcaaaatttggattcgatcgatctgtcgctttggatctctgtgtgtgtgagtgggggatggatagtaatgtggatcgatgtgcgttttggggtgggggttggaattctgcag
- - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG