Sequence
atgc intronic sequence ATGC exonic sequencegttggagcaattttcttttattcaattgctatgtaattgctattttgtttgccattgcgaagctacctattgcctattccattgagacactttgttgtgatattgtatgtggatatgctgaaattcttaattctaagctcgacgggcttgtatgctcagttcaactctaatgctgctctgttcctttacacatttcagCTTCTCTGGGTAAATCTAATCATGGATACACTGGGAGCTCTGGCTTTAGCAACTGAACCACCGACGGATAACCTTATGAAGAGACAGCCTGTTGGTCGAA
Basic information
species | Oryza sativa |
transcript | LOC_Os08g40530.1 |
intron # | 12 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os08g40530.1 (Oryza sativa), 3'ss of exon 12
lower sequence: GRMZM2G132712_T03 (Zea mays), 3'ss of exon 28
gttggagcaattttcttttattcaattgctatgtaattgctattttgtttgccattgcgaagctacctattgcctattccattgagacactttgttgtgatattgtatgtggatatgctgaaattcttaattctaagctcgacgggcttgtatgctcagttcaactctaat-gctgctctgttcct-ttacacatttcagCTTCTCTGGGTAAATCTAATCATGGATACACTGGGAGCTCTGGCTTTAGCAACTGAACCACCGACGGATAACCTTATGAAGAGACAGCCTGTTGGTCGAA
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-------------------------------------------------------------------------------------------------tcagat-acatatagcttaacaacgacacagcatttta--cctgagacacatgtatttccaggctgtttctcatcagtatcatatacttctttcacttctcagCTTCTGTGGGTGAACCTCATAATGGACACACTTGGAGCTCTTGCATTAGCAACCGAGCCTCCAACAGACAACCTTATGAAGAGAAATCCTGTTGGTCGAA
upper sequence: LOC_Os08g40530.1 (Oryza sativa), 3'ss of exon 12
lower sequence: EFJ22392 (Selaginella moellendorffii), 3'ss of exon 23
gttggagcaattttcttttattcaattgctatgtaattgctattttgtttgccattgcgaagctacctattgcctattccattgagacactttgttgtgatattgtatgtggatatgctgaaattcttaattctaagctcgacgggcttgtatg-ctcagttcaactctaatgctgctctgttcctttacacatttcagCTTCTCTGGGTAAATCTAATCATGGATACACTGGGAGCTCTGGCTTTAGCAACTGAACCACCGACGGATAACCTTATGAAGAGACAGCCTGTTGGTCGAA
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---------------------------------------------------------------------------------------------------------------------------------------------gtgagtcgttatctctcgtttcatctgttcagtttataagtcgttttcta-----cagCTGCTTTGGGTAAATCTTATTATGGATACTTTGGGAGCGCTCGCTTTAGCCACTGAACCACCTACAGACGACTTAATGGATAGGCCGCCCGTGGGACGCA
upper sequence: LOC_Os08g40530.1 (Oryza sativa), 3'ss of exon 12
lower sequence: EFJ25508 (Selaginella moellendorffii), 3'ss of exon 24
gttggagcaattttcttttattcaattgctatgtaattgctattttgtttgccattgcgaagctacctattgcctattccattgagacactttgttgtgatattgtatgtggatatgctgaaattcttaattctaagctcgacgggcttgtatg-ctcagttcaactctaatgctgctctgttcctttacacatttcagCTTCTCTGGGTAAATCTAATCATGGATACACTGGGAGCTCTGGCTTTAGCAACTGAACCACCGACGGATAACCTTATGAAGAGACAGCCTGTTGGTCGAA
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---------------------------------------------------------------------------------------------------------------------------------------------gtgagtcggtatctctcgtttcatctgttcagtttataagtcgttttcta-----cagCTGCTTTGGGTAAATCTTATTATGGATACTTTGGGAGCGCTCGCTTTAGCCACTGAGCCACCTACAGACGACTTAATGGATAGGCCGCCCGTGGGACGCAMapped 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|29665351|gb|CB661626.1|CB661626EST: ATGTTGTTGCAGCTGTGTCCTCTGGTGACGTGCCTCTAAATGCTGTTGAG CTTCTCTGGGTAAATCTAATCATGGATACACTGGGAGCTCTGGCTTTAGCA
genomic: ATGTTGTTGCAGCTGTGTCCTCTGGTGACGTGCCTCTAAATGCTGTTGAGgttggagcaa ... cacatttcagCTTCTCTGGGTAAATCTAATCATGGATACACTGGGAGCTCTGGCTTTAGCA
EST:
gi|29681421|gb|CB677696.1|CB677696EST: ATGTTGTTGCAGCTGTGTCCTCTGGTGACGTGCCTCTAAATGCTGTTGAG CTTCTCTGGGTAAATCTAATCATGGATACACTGGGAGCTCTGGCTTTAGCA
genomic: ATGTTGTTGCAGCTGTGTCCTCTGGTGACGTGCCTCTAAATGCTGTTGAGgttggagcaa ... cacatttcagCTTCTCTGGGTAAATCTAATCATGGATACACTGGGAGCTCTGGCTTTAGCA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gggcttgtatgctcagttcaactctaatgctgctctgttcctttacacatttcagCTTCTCTGGGTAAATCTAATCATGGATACACTGGGAGCTCTGGCTTTAGCAACTGAACCACCGACGGATAACCTTATGAAGAGACAGCCTGTTGGTCGAA
ctctaat putative branch site (score: 3)
ctctgttcctttac putative PPT
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttggagcaattttcttttattcaattgctatgtaattgctattttgtttgccattgcgaagctacctattgcctattccattgagacactttgttgtgatattgtatgtggatatgctgaaattcttaattctaagctcgacgggcttgtatgctcagttcaactctaatgctgctctgttcctttacacatttcagCTTCTCTGGGTAAATCTAATCATGGATACACTGGGAGCTCTGGCTTTAGCAACTGAACCACCGACGGATAACCTTATGAAGAGACAGCCTGTTGGTCGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA