Sequence
atgc intronic sequence ATGC exonic sequenceCAAGTACGTACCCAGCAAATTCATGAAATGAAGAAAAAAGAGAAAGAATACATCAAATTGCAGgtataattgttgtctttacaaatctacgtggtgattaaatacgagttattttcatagattgaccttcagctcttttgcag
Basic information
species | Oryza sativa |
transcript | LOC_Os08g14460.3 |
intron # | 7 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os08g14460.1 (Oryza sativa), 5'ss of exon 6
lower sequence: GRMZM2G147500_T04 (Zea mays), 5'ss of exon 7
CAAGTACGTACCCAGCAAATTCATGAAATGAAGAAAAAAGAGAAAGAATACATCAAATTGCAGgtata-attgttgtctttacaaatctacgtggtgattaaatacgagtt---attttcatagattgaccttcagctcttttgcag-----------------
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CAAGTACGCACCCAGCAAATTCATGAAATGAAGAAGAAAGAGAAAGAATACATAAAGTTGCAGgtatgtatttatacctttaggccttgtttgggtattctagtattcaccccaatccacatgtattgaggtgga-ttggggtgtaaattaatttacaccccaa
upper sequence: LOC_Os08g14460.1 (Oryza sativa), 5'ss of exon 6
lower sequence: Vv11s0052g00890.t01 (Vitis vinifera), 5'ss of exon 7
CAAGTACGTACCCAGCAAATTCATGAAATGAAGAAAAAAGAGAAAGAATACATCAAATTGCAGgtataattgttgtctttacaaatctacgtggtgattaaatacgagttattttcatagattgacctt--cagctcttttgcag-----------------------------------------------------------------------------------
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CAAGTGAGGACTCAACAAATTCATGAGATGAAGAAAAAAGAGAAGGAATACATAAAATTGCAGgtaggatcctt-tccatgtgtattattatgatattatcttttaggggaaacttaaaggttgctcatgttagcaaatgggaacatctttcatgaatgacaacatatatggagaacaggagaagttcatgagtaggaaattggggaatgattgtgtttcacttgcag
upper sequence: LOC_Os08g14460.1 (Oryza sativa), 5'ss of exon 6
lower sequence: PP1S47_178V6.1 (Physcomitrella patens), 5'ss of exon 7
CAAGTACGTACCCAGCAAATTCATGAAATGAAGAAAAAAGAGAAAGAATACATCAAATTGCAGgtataa------ttgttgtctttacaaatc----tacgtggtgattaaatacgagttattttcat--agattgaccttcagctcttttgcag-----------------------------
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CAAGTGAAGACTCAGCAGATGCACGAGTTAAAGAAGAAAGAGAAGGAATACATCAAGTTGCAGgtataaggaattttcttgtcttaataatttcttttacagcgtattcctagacgactggttctcttttgcataatgtttctatcatatttgaattgaggtgaatgtatatcgtctggtacag
upper sequence: LOC_Os08g14460.1 (Oryza sativa), 5'ss of exon 6
lower sequence: PP1S91_39V6.1 (Physcomitrella patens), 5'ss of exon 9
CAAGTACGTACCCAGCAAATTCATGAAATGAAGAAAAAAGAGAAAGAATACATCAAATTGCAGgtata--attgttgtctttacaaat----------ctacgtggtgat---taaatacgagttattttcatagattgaccttcagctcttttgcag------------------------------
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CAAGTTAAAGCTCAGCAGATGCATGAACTGAAGAAGAAAGAGAAAGAGTATATCAAGTTGCAGgtatatgaagactctatttgccaacaacgatgctactacaggtcactatgtgattatgagtccttcgcatagcgcttttttttctttttttctgatgaactgtgttggtttgttggctggtccagMapped 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|58595922|gb|CK006450.1|CK006450EST: GAAATGAAGAAAAAAGAGAAAGAATACATCAAATTGCAG GAGAAGTTAAACCAGGTATTAATGGAGAAAAAGAAGGAATCATCACGTTCA
genomic: GAAATGAAGAAAAAAGAGAAAGAATACATCAAATTGCAGgtataattgt ... tcttttgcagGAGAAGTTAAACCAGGTATTAATGGAGAAAAAGAAGGAATCATCACGTTCA
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
CAAGTACGTACCCAGCAAATTCATGAAATGAAGAAAAAAGAGAAAGAATACATCAAATTGCAGgtataattgttgtctttacaaatctacgtggtgattaaatacgagttattttcatagattgaccttcagctcttttgcag
- - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - - AAAGAA