Sequence
atgc intronic sequence ATGC exonic sequencegttagggtacttataatttattatagcccttcatgtgtaatttgaagcagaaacttattttgttttcattttgcagCCAAATTTAAGTGCATCATGGTTGTTCCAAAGAGCAATGTCAGCAAGGCCGCAGATCGATGTTTCCCCAACTTTTATCAATGAGCTTCTCTTTGCTAATT
Basic information
species | Oryza sativa |
transcript | LOC_Os08g32630.2 |
intron # | 13 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os08g32630.5 (Oryza sativa), 3'ss of exon 12
lower sequence: GRMZM5G851815_T01 (Zea mays), 3'ss of exon 11
gttagggtacttataatttattatagcccttcatgtgtaatttgaagcagaaacttattttgttttcattttgcagCCAAATTTAAGTGCATCATGGTTGTTCCAAAGAGCAATGTCAGCAAGGCCGCAGATCGATGTTTCCCCAACTTTTATCAATGAGCTTCTCTTTGCTAATT
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---------gttagtgtatgccatagccatttcgatacaatttgaagtggaagcttattcggttttggtattgcagCCAAACTTAAGTGCATCATGGTTGTTCCAACGAGCGATGTCAGTAAGGCCACATGTCAATGTTTCACCAACCTTTATCAATGAGCTTCTCTTTGCTAATT
upper sequence: LOC_Os08g32630.5 (Oryza sativa), 3'ss of exon 12
lower sequence: GLYMA14G05100.1 (Glycine max), 3'ss of exon 14
------gttagggtacttataatttattatagcc-cttcatgtgtaatttgaagcagaaacttattttgttttcattttgcagCCAAATTTAAGTGCATCATGGTTGTTCCAAAGAGCAATGTCAGCAAGGCCGCAGATCGATGTTTCCCCAACTTTTATCAATGAGCTTCTCTTTGCTAATT
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gtactttccaacttctctaaagactgtttcagcaactgtagatgaaactaaatacctgg-ccaatattgtgt--ataatgcagCCCAACTTGAGTGCTTCATGGTTGTTCCAAAGAGCAATGTCAGCAAAGAAACAGTCCAATGTTCCCGCAGATTTTATTAATGAACTTCTATATACCAATT
upper sequence: LOC_Os08g32630.5 (Oryza sativa), 3'ss of exon 12
lower sequence: GLYMA02G43820.1 (Glycine max), 3'ss of exon 7
-------gttagggtacttataatttattatagcccttcatgtgtaatttgaagcagaaacttattttgtttt----cattttgcagCCAAATTTAAGTGCATCATGGTTGTTCCAAAGAGCAATGTCAGCAAGGCCGCAGATCGATGTTTCCCCAACTTTTATCAATGAGCTTCTCTTTGCTAATT-----------
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gtgtgtctttgagtcaattaaagcatgtgat----ttttatattacaattaaagcatgaatatgtgtgtctttgaatcaatatatgtgtgtctttgagTGCTTCGTGGTTGTTCCAAAGAGCAATGTCAGCAAAGAAACAATCCAATGTTCCTGCAGATTTTATTAATGAACTTCTTTATACGAATTTTAGTTGTATG
upper sequence: LOC_Os08g32630.5 (Oryza sativa), 3'ss of exon 12
lower sequence: AT2G32640.2 (Arabidopsis thaliana), 3'ss of exon 13
--------gttagggtacttataatttattatagcccttcatg-tgtaatttgaagcagaaacttattttgttttcattttgcagCCAAATTTAAGTGCATCATGGTTGTTCCAAAGAGCAATGTCAGCAAGGCCGCAGATCGATGTTTCCCCAACTTTTATCAATGAGCTTCTCTTTGCTAATT
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gtaatatagctttgtggttctcagctaaatatctttctccctgctattaacttcactg--aatccatttggcttttgaacgacagCCAAACTTGAGCGCATCATGGCTGTTTCAAAGAGCAATGTCTGCAAAGCAACAGCTCGATGTTTCCCGTGGCTTCACCAATGAGCTTCTCCATGTAAATT
upper sequence: LOC_Os08g32630.5 (Oryza sativa), 3'ss of exon 12
lower sequence: Vv12s0059g01150.t01 (Vitis vinifera), 3'ss of exon 13
gttagggtact-tataatttatt--atagcccttcatgtgtaatttgaagcagaaacttattttgttttcattttgcagCCAAATTTAAGTGCATCATGGTTGTTCCAAAGAGCAATGTCAGCAAGGCCGCAGATCGATGTTTCCCCAACTTTTATCAATGAGCTTCTCTTTGCTAATT
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gttcgtgttttctgtaattgatttagcaacttctaccacacaatt---agctcaa--tgaatatttgttcaa--tgcagCCCAACCTTAGTGCAGCATGGTTGTTTCAAAGGGCAATGTCAGCAAAGCAACAGTATGATGTTTCTCCTGATTTCATCAGTGAGCTTCTTTATGTCAATTMapped 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|29642655|gb|CB647662.1|CB647662EST: ATGCACGTAGTTTGCAGCTGCTGAACCCTTATATG CCAAATTTAAGTGCATCATGGTTGTTCCAAAGAGCAATGTCAGCAAGGCCG
genomic: ATGCACGTAGTTTGCAGCTGCTGAACCCTTATATGgttagggtac ... cattttgcagCCAAATTTAAGTGCATCATGGTTGTTCCAAAGAGCAATGTCAGCAAGGCCG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tatagcccttcatgtgtaatttgaagcagaaacttattttgttttcattttgcagCCAAATTTAAGTGCATCATGGTTGTTCCAAAGAGCAATGTCAGCAAGGCCGCAGATCGATGTTTCCCCAACTTTTATCAATGAGCTTCTCTTTGCTAATT
ttttgttttcatttt CT-rich tract
aaacttattttgtttt TA-rich tract
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttagggtacttataatttattatagcccttcatgtgtaatttgaagcagaaacttattttgttttcattttgcagCCAAATTTAAGTGCATCATGGTTGTTCCAAAGAGCAATGTCAGCAAGGCCGCAGATCGATGTTTCCCCAACTTTTATCAATGAGCTTCTCTTTGCTAATT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT