Sequence
atgc intronic sequence ATGC exonic sequenceATTCGTCCAGATCGCCAAACATTATATTGGAGTGCTACTTGGCCAAAGGAAGTTGAACAGCTAGCAAGGAACTTTCTTTTCGACCCATACAAGgtggttatttttgccaatgcatcattttgcagatgaatttatggcagactacggtatctgcttcatgtgaactcaattgctttttttgtgctgcag
Basic information
species | Oryza sativa |
transcript | LOC_Os01g10050.1 |
intron # | 6 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os01g10050.2 (Oryza sativa), 5'ss of exon 6
lower sequence: GRMZM2G143246_T01 (Zea mays), 5'ss of exon 6
ATTCGTCCAGATCGCCAAACATTATATTGGAGTGCTACTTGGCCAAAGGAAGTTGAACAGCTAGCAAGGAACTTTCTTTTCGACCCATACAAGgtggttatttttgccaatgcatcattttgcagatgaatttatggcagactacggtatctgcttcatgtgaactcaattgctttttttgtgctgcag
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ATTCGTCCAGATCGCCAAACACTTTACTGGAGTGCTACCTGGCCGAAGGAAGTTGAGCAGCTAGCAAGGAATTTCCTTTTTGACCCATACAAGgtacttgctatagtccacccaacattttgcag-tgcatcttt---------ccatttctactgtatgtcaacactgctgaatttaatatgatgcag
upper sequence: LOC_Os01g10050.2 (Oryza sativa), 5'ss of exon 6
lower sequence: GLYMA07G01260.1 (Glycine max), 5'ss of exon 6
ATTCGTCCAGATCGCCAAACATTATATTGGAGTGCTACTTGGCCAAAGGAAGTTGAACAGCTAGCAAGGAACTTTCTTTTCGACCCATACAAGgtg-gttatttt-----------tgccaatgcatcattttgcagatgaatttatggcagactacggt-atctgcttcatg---tgaactcaattgctttttttgtgctgcag----------------------------------------------------------------------------
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ATTCGTCCAGATCGTCAAACTTTGTATTGGAGTGCTACCTGGCCAAAGGAGGTCGAACAATTGGCAAGGAAGTTCCTTTATAACCCATACAAAgtaagatattttatgttgggatatgtaactgtagtttttttcttttaaattt-cgttcctctatgatgaaatgatttttggtctgaaatgaattgtcttttaagaagcatgtatgatgtttatgtatagtattgtattttgtgagaactttatttatttaagcaacaatttctgtaatcattgtgcag
upper sequence: LOC_Os01g10050.2 (Oryza sativa), 5'ss of exon 6
lower sequence: GLYMA08G20670.1 (Glycine max), 5'ss of exon 6
ATTCGTCCAGATCGCCAAACATTATATTGGAGTGCTACTTGGCCAAAGGAAGTTGAACAGCTAGCAAGGAACTTTCTTTTCGACCCATACAAGgtg-gttatttt------------tgccaatgcatcattttgcagatgaatttatggcagactacggtatctgcttca-tgtgaactcaattgctttttttgtgctgcag----------------------------------------------------------------------------
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ATTCGTCCAGATCGTCAAACTTTGTATTGGAGTGCTACCTGGCCAAAGGAGGTTGAACAATTGGCAAGGAAGTTCCTTTATAACCCATACAAAgtaagatattttcatgttgggatatgcaactgtatttttttcttttaaatttcattcctctatgctgaatggttttcggtctgaaatgaattgtcttttaagaagaatgtatgatgtttatgtatagtattgtattttgtgagaactttatatatttaagtaacaatttctgtaatcattgtgcag
upper sequence: LOC_Os01g10050.2 (Oryza sativa), 5'ss of exon 6
lower sequence: GLYMA07G11880.1 (Glycine max), 5'ss of exon 6
ATTCGTCCAGATCGCCAAACATTATATTGGAGTGCTACTTGGCCAAAGGAAGTTGAACAGCTAGCAAGGAACTTTCTTTTCGACCCATACAAGgtgg------ttatttttgccaatgcatca-----ttttgcagatgaatttatggcagactacggt-atctgcttcatg---tgaactcaattgctt---tttttgtgctgcag--------
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ATTCGTCCAGATCGTCAAACTTTGTATTGGAGTGCTACCTGGCCAAAGGAGGTCGAACAATTGGCAAGGAAGTTCCTTTATAACCCATACAAAgtaagatattttatgttgggatatgtaacggtagtttttttcttttaaatttcgttcctctatgatgaaatggtttttggtctgaaatgaattgtcgaagcatgtatgatgtttatgtatagMapped 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|218490551|gb|FG953048.1|FG953048EST: CAAAGGAAGTTGAACAGCTAGCAAGGAACTTTCTTTTCGACCCATACAAG GTCATAATTGGTTCTGAGGAGTTGAAAGCTAATCATGCCATTTCTC
genomic: CAAAGGAAGTTGAACAGCTAGCAAGGAACTTTCTTTTCGACCCATACAAGgtggttattt ... tgtgctgcagGTCATAATTGGTTCTGAGGAGTTGAAAGCTAATCATGCCATTTCTC
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ATTCGTCCAGATCGCCAAACATTATATTGGAGTGCTACTTGGCCAAAGGAAGTTGAACAGCTAGCAAGGAACTTTCTTTTCGACCCATACAAGgtggttatttttgccaatgcatcattttgcagatgaatttatggcagactacggtatctgcttcatgtgaactcaattgctttttttgtgctgcag
- - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA