Sequence
atgc intronic sequence ATGC exonic sequenceAACAGGTTATATAGTGATGCTGGATGACGGAACATTTGACGTTGATGCAAATACATCAATAGACCACCTATCTGAAGAACTTGGTGTTAAAATACCAGAGgtgttatttcttgtttggtctttgctttttctacagttgctgtttacttctacagtcactataagtgttattttggacattgccatggcaatcaaattgg...
Basic information
species | Oryza sativa |
transcript | LOC_Os03g39640.1 |
intron # | 12 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os03g39640.2 (Oryza sativa), 5'ss of exon 12
lower sequence: GRMZM2G153928_T02 (Zea mays), 5'ss of exon 6
AACAGGTTATATAGTGATGCTGGATGACGGAACATTTGACGTTGATGCAAATACATCAATAGACCACCTATCTGAAGAACTTGGTGTTAAAATACCAGAGgtgttatttcttgtttggtcttt-gctttttctacagttgctgtttacttctacagtcac-tataagtgttattttggacattgccatggcaatcaaattgg
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AACAGGCTATATAGTAAGGCGGGGGGATGGAACATTTGATGTTGATGCAAACACATCGATAGATCACCTATCTGAAGAGCTTGGTATCAAAATACCAGAGgtgttgtttctcattagatatttagctttctctacagttgctatggattcccttggacatgtgtgcctgttgtacactgtatgatcatcaaaagttgact--
upper sequence: LOC_Os03g39640.2 (Oryza sativa), 5'ss of exon 12
lower sequence: AT3G13070.1 (Arabidopsis thaliana), 5'ss of exon 12
AACAGGTTATATAGTGATGCTGGATGACGGAACATTTGACGTTGATGCAAATACATCAATAGACCACCTATCTGAAGAACTTGGTGTTAAAATACCAGAGgtgttatt-tcttgtttggtctttgctttttctacagttgctgtttacttctacagtcactataagtgttat-tttggacattgccatggcaatcaaattgg------------------------------------------
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AACAGGATATATTGTCATGAGAGATGAGGGCATATATGATGTTGATGCTAATACATCAATTGACCAGCTATCTGAAGAACTGAATATGAAAATGCCAGAGgtaatgttattttcagcagtctcttttattcctct--ttattgcgt-cctcaagagcattcctcagggttatcttttaactttgtaaatgtgaacatgttctttaaaagttgaaacccacaatgtttgttcatttgggaaacagMapped 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|58603218|gb|CK013746.1|CK013746EST: ACTTGGTGTTAAAATACCAGAG GGTCATCAGTATGAGACGGTGTCTGGTTTTGTCTGTGAATCCTTTGGTTAT
genomic: ACTTGGTGTTAAAATACCAGAGgtgttatttc ... ttgtttgcagGGTCATCAGTATGAGACGGTGTCTGGTTTTGTCTGTGAATCCTTTGGTTAT
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
AACAGGTTATATAGTGATGCTGGATGACGGAACATTTGACGTTGATGCAAATACATCAATAGACCACCTATCTGAAGAACTTGGTGTTAAAATACCAGAGgtgttatttcttgtttggtctttgctttttctacagttgctgtttacttctacagtcactataagtgttattttggacattgccatggcaatcaaattgg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC