Sequence
atgc intronic sequence ATGC exonic sequenceGATTGGACCAAAATGGTACCGTGGTGTCCGAAGGCATGGCCTGATTATGGGATGCTCTGTGACGGGCGTCAAAAGAGAACATGGAGACTCCCCTTTGCAGgtttttttttttgctaatttgccttgcaagttgcaaattcacataagcctcctttgttcggatgactctttttgtcgttacttttatttcttactgatttatatgttgattattactcatggattggcaacgcaacacctgggtatgacgaatgttgaag
Basic information
species | Oryza sativa |
transcript | LOC_Os12g42090.3 |
intron # | 2 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os12g42090.3 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G099206_T01 (Zea mays), 5'ss of exon 1
GATTGGACCAAAATGGTACCGTGGTGTCCGAAGGCATGGCCTGATTATGGGATGCTCTGTGACGGGCGTCAAAAGAGAACATGGAGACTCCCCTTTGCAGgtttt--tttttttgctaatttgccttgcaagttgcaaattca-------cataagcctcctttgttcggatgactctttttgtcgttacttttatttcttactgatttatatgttgattattactcatggattggcaacgcaacacctgggtatgacgaatgttgaag
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GATCGGACCGAAGTGGTACCGTGGTGTCTGAAGGCATGGCCTCATCATGGGTTGCTCTGTCACAGGCGTCAAGAGAGAGCGTGGAGACTCTCCCTTGGAGgtaccacttctttttttcatttttctaatagaaagcgtagctatcaggttcgtagttgtgtgcttttggcacatctcgttcagactttagattgttcatttcccgtcgtacctgc-aagcaacattcaggggttt-tggtataagttttcggttttgtttttcatgcag
upper sequence: LOC_Os12g42090.3 (Oryza sativa), 5'ss of exon 2
lower sequence: GLYMA10G03590.1 (Glycine max), 5'ss of exon 2
GATTGGACCAAAATGGTACCGTGGTGTCCGAAGGCATGGCCTGATTATGGGATGCTCTGTGACGGGCGTCAAAAGAGAACATGGAGACTCCCCTTTGCAGgtttttttttttgctaatttgccttgcaagttgcaaattcacataagcctcctttgttcggatgactctttttgtcgttacttttatttcttactgatttatatgttgattattactcatggattggcaacgcaacacctgggtatgacgaatgttgaag
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GATTGGCCCAAAATGGTACCGTGGTGTTCGCCGACATGGCTTGATTATGGGTTGTTCAGTGACCGGTGTTAAGCCTGCATCTGGAGATTCTCCTTTGCAGgtatttgtcgtc-tcagcttcttaatctatctatatttggttgtatgtttgttttccct---tgttttatttgggggatgttattatttttt--taacttgaatca------------------------------------------------------
upper sequence: LOC_Os12g42090.3 (Oryza sativa), 5'ss of exon 2
lower sequence: Vv05s0020g04430.t01 (Vitis vinifera), 5'ss of exon 2
GATTGGACCAAAATGGTACCGTGGTGTCCGAAGGCATGGCCTGATTATGGGATGCTCTGTGACGGGCGTCAAAAGAGAACATGGAGACTCCCCTTTGCAGgtttttttttttgctaatttgc-cttgcaagttgcaaattcacataagcctcctttgttcggatgactctttttgtcgttacttttatttcttactgatttatatgttgattattactcatggattggcaacgcaacacctgggtatgacgaatgttgaag
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AATTGGTCCGAAATGGTACCGTGGTGTGCGGCGGCATGGCTTGATTATGGGATGCTCTGTGACAGGTGAAAAGCCTTTTACAGGGGATTCTCCCCTACAGgtaactaacttcttggaccttcatttgtcatataggaagactaataaaaatacattaatttcgttgctgattt-gcctctctatttgtggtttcctaattt------------------------------------------------------------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|88489784|gb|CI427056.1|CI427056EST: GATGCTCTGTGACGGGCGTCAAAAGAGAACATGGAGACTCCCCTTTGCAG AGTGAACATGTCAATATTTTTCTCACTTGCATGAGATTAATGAACATTGTA
genomic: GATGCTCTGTGACGGGCGTCAAAAGAGAACATGGAGACTCCCCTTTGCAGgttttttttt ... aatgttgaagAGTGAACATGTCAATATTTTTCTCACTTGCATGAGATTAATGAACATTGTA
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
GATTGGACCAAAATGGTACCGTGGTGTCCGAAGGCATGGCCTGATTATGGGATGCTCTGTGACGGGCGTCAAAAGAGAACATGGAGACTCCCCTTTGCAGgtttttttttttgctaatttgccttgcaagttgcaaattcacataagcctcctttgttcggatgactctttttgtcgttacttttatttcttactgatttatatgttgattattactcatggattggcaacgcaacacctgggtatgacgaatgttgaag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA