Sequence
atgc intronic sequence ATGC exonic sequenceTGGATCCCACTATTCGAGCTGAAGTTTGGGAATTTCTTCTTGGCTGCTATGCCTTGAGTAGTACCTCAGAGTATAGGAGGAAACTAAGAGCTGTTAGAAGgtttgacactttcctgttttcagtaccaggataccttttttgtacaagcataagaccgtaagagcataaatgaattgcatttattatctagaataaaatc...
Basic information
species | Oryza sativa |
transcript | LOC_Os01g01010.1 |
intron # | 4 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os01g01010.1 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM2G031043_T01 (Zea mays), 5'ss of exon 5
TGGATCCCACTATTCGAGCTGAAGTTTGGGAATTTCTTCTTGGCTGCTATGCCTTGAGTAGTACCTCAGAGTATAGGAGGAAACTAAGAGCTGTTAGAAGgtttgacactttcc----tgttttca-gtaccaggat----accttttttgtacaagcataagaccgtaagagcataaatgaattgcatttattatctagaataaaatc
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TGGATCCTTCTATTCGAGCGGAAGTTTGGGAATTTCTTATTGGCTGCTACACCTTAAGTACTACAGCGGAATATAGGGGAAAACTAAGAGCTGCTCGAAGgtttgaagttttctcttttgtcttctcgtaatatgatgtttacattttattttctaaaaaagaatcttgtg-gtaggcatcagtttggttacttttatatt--------
upper sequence: LOC_Os01g01010.1 (Oryza sativa), 5'ss of exon 4
lower sequence: AT3G59570.1 (Arabidopsis thaliana), 5'ss of exon 4
TGGATCCCACTATTCGAGCTGAAGTTTGGGAATTTCTTCTTGGCTGCTATGCCTTGAGTAGTACCTCAGAGTATAGGAGGAAACTAAGAGCTGTTAGAAGgtttgacacttt-cctgttttca----gtaccaggataccttttttgtacaagcataagacc---gtaagagcataaatgaattgcatttattatctagaataaaatc
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TCGATCCATCCATAAGAGCTGAAGTTTGGGAATTTCTCCTTGGCTGTTATGCATTAAGCAGCACCTCTGAGTATCGTACGCAACTCAGGGTAGCTCGAAGgttgggcagtttgtttgctttcatgttgtatcgtgatggagtgctatgtgaaactcaagttttatggaaaaagcttaataagctgttcataatttatgcag-------
upper sequence: LOC_Os01g01010.1 (Oryza sativa), 5'ss of exon 4
lower sequence: AT2G43490.2 (Arabidopsis thaliana), 5'ss of exon 4
TGGATCCCACTATTCGAGCTGAAGTTTGGGAATTTCTTCTTGGCTGCTATGCCTTGAGTAGTACCTCAGAGTATAGGAGGAAACTAAGAGCTGTTAGAAGgtttgacactttcct----gttttcagtaccaggataccttttttgta---caagcataagaccgtaagagcataaatga-attgcatttattatctagaataaaatc
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TCGACCCATCTATTAGAGCTGAAGTTTGGGAATTTCTCCTTGGTTGTTATGCGTTGAGCAGCACCTCTGAGTACCGTAATCAACTCAGGGTAGCTCGAAGgttagactgtttgatcacagcttagagtgagaaagagtgctaatagcaagttaagtttaat-caaaaagcttacaagcgttattggaattttcacgcag---------
upper sequence: LOC_Os01g01010.1 (Oryza sativa), 5'ss of exon 4
lower sequence: Vv00s0226g00160.t01 (Vitis vinifera), 5'ss of exon 4
TGGATCCCACTATTCGAGCTGAAGTTTGGGAATTTCTTCTTGGCTGCTATGCCTTGAGTAGTACCTCAGAGTATAGGAGGAAACTAAGAGCTGTTAGAAGgtttgacactttcctgttttcagtac--caggataccttttttgtacaagcataagaccgtaagagcataaatgaattgcatttat-tatctagaataaaatc
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TGGATCCATCTATAAGGGCTGAAGTTTGGGAATTTCTTCTTGGTTGTTATGCAGTTGACAGCACCGCAGAGCATCGGAGGCAACTAAGGACAGCCAGGAGgttgagctctcttcattctaatgtatttccagataataattttttttcctgatttttttgtctgattttt--ttgactg-attcatgcaaagagaactatttcMapped 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|29675456|gb|CB671731.1|CB671731EST: GCCTTGAGTAGTACCTCAGAGTATAGGAGGAAACTAAGAGCTGTTAGAAG GGAAAAATATCAAATTTTAGTTAGACAGTGCCAGAGCATGCACCCAAGCAT
genomic: GCCTTGAGTAGTACCTCAGAGTATAGGAGGAAACTAAGAGCTGTTAGAAGgtttgacact ... ttctatgcagGGAAAAATATCAAATTTTAGTTAGACAGTGCCAGAGCATGCACCCAAGCAT
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
TGGATCCCACTATTCGAGCTGAAGTTTGGGAATTTCTTCTTGGCTGCTATGCCTTGAGTAGTACCTCAGAGTATAGGAGGAAACTAAGAGCTGTTAGAAGgtttgacactttcctgttttcagtaccaggataccttttttgtacaagcataagaccgtaagagcataaatgaattgcatttattatctagaataaaatc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT