Sequence
atgc intronic sequence ATGC exonic sequenceCAGGGCTGTTCATCTGGAGCCAGTGCCATTCGATATGGATCGTGACCTAATTACCCCAACTTACAAGAAGAAGCGGCCACAGCTGCTCAAATATTACCAGgtaagaacactagaaaaatatcttcctgcaatttaaggtacttggattatcatccgtctaaatctggaactctgtccgacaatctgccatttttttttag
Basic information
species | Oryza sativa |
transcript | LOC_Os01g48910.2 |
intron # | 18 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os01g48910.2 (Oryza sativa), 5'ss of exon 18
lower sequence: GRMZM2G152127_T01 (Zea mays), 5'ss of exon 18
CAGGGCTGTTCATCTGGAGCCAGTGCCATTCGATATGGATCGTGACCTAATTACCCCAACTTACAAGAAGAAGCGGCCACAGCTGCTCAAATATTACCAGgtaagaacactagaaaaatatcttcctgcaatttaaggtacttggattatcatccgtc--taaatctggaactctgtccgacaatct--gccatttttttt-tag
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CAGGGCTGTTCATCTGGACCCCGCACCGTTCGACATGGAGCGCGACCTTATCACCCCGACGTACAAGAAGAAGCGGCCACAGCTGCTGAAACACTATCAGgtatggc---------agcagtttcagataactcg-----cttgggctaacgac-gtcggtgaagcttgaccttcgtgttaatgtttttgtcgcttttcgtgcag
upper sequence: LOC_Os01g48910.2 (Oryza sativa), 5'ss of exon 18
lower sequence: GLYMA01G43470.4 (Glycine max), 5'ss of exon 18
CAGGGCTGTTCATCTGGAGCCAGTGCCATTCGATATGGATCGTGACCTAATTACCCCAACTTACAAGAAGAAGCGGCCACAGCTGCTCAAATATTACCAGgtaagaacactagaaaaatatcttc-ctgcaatttaaggtacttggattatcatccgtctaaatctgga--actctgtccgacaatctgccatttttttttag
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AAAAGCAGTTCACCTTGACTCAATTCCATTTGACATGGAACGTGACCTTATCACTCCAACATACAAGAAGAAGAGGCCACAGTTGCTTAAATACTATCAGgtacaag--ttgtcaaattctctggattgcatttcacttcatattgaatagaataggtcttgaagtggataacctttataaatggaatgttatttcccctcc-
upper sequence: LOC_Os01g48910.2 (Oryza sativa), 5'ss of exon 18
lower sequence: AT4G11030.1 (Arabidopsis thaliana), 5'ss of exon 18
CAGGGCTGTTCATCTGGAGCCAGTGCCATTCGATATGGATCGTGACCTAATTACCCCAACTTACAAGAAGAAGCGGCCACAGCTGCTCAAATATTACCAGgtaagaacactagaaaaatatcttcctgcaatttaaggtacttggattatcatccgtctaaatctggaactctgtccgacaatctgccatttttttttag
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AAAAGATGTTCATCTGGAACCAGTGGCGTTCGACATGGAACGAGACCTTCTTACTCCAACCTACAAAAAGAAGAGGCCTCAATTGCTCAAATACTATCAGgtaa-----ttttaaacat---tttaggcgatatta--tgcttataatattttcggttttaaact----ctctttcta-----ttggtgttatttaacagMapped 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|33677927|gb|CF306166.1|CF306166EST: TTACCCCAACTTACAAGAAGAAGCGGCCACAGCTGCTCAAATATTACCAG AACGTCATCGACAGCATGTATAAGAACATGAAGTAGGACTGGACTCATGGC
genomic: TTACCCCAACTTACAAGAAGAAGCGGCCACAGCTGCTCAAATATTACCAGgtaagaacac ... ttttttttagAACGTCATCGACAGCATGTATAAGAACATGAAGTAGGACTGGACTCATGGC
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
CAGGGCTGTTCATCTGGAGCCAGTGCCATTCGATATGGATCGTGACCTAATTACCCCAACTTACAAGAAGAAGCGGCCACAGCTGCTCAAATATTACCAGgtaagaacactagaaaaatatcttcctgcaatttaaggtacttggattatcatccgtctaaatctggaactctgtccgacaatctgccatttttttttag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT