Sequence
atgc intronic sequence ATGC exonic sequenceTGCGATGAACAAGCTGTTGATGGAGGAGAATGACAGGCTGCAGAAGCAGGTGTCCCGCCTCGTTTACGAGAACGGGTACATGCGGCAGCAGCTCCATAATgtgagattcatcatctttgctaatctcatcagacataactcatgatatgcaagtgtttgcctcagaggcatgatctgagtctgagttctacaatggcaag...
Basic information
species | Oryza sativa |
transcript | LOC_Os03g43930.1 |
intron # | 2 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os03g43930.2 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G023291_T01 (Zea mays), 5'ss of exon 2
TGCGATGAACAAGCTGTTGATGGAGGAGAATGACAGGCTGCAGAAGCAGGTGTCCCGCCTCGTTTACGAGAACGGGTACATGCGGCAGCAGCTCCATAATgtgagattcatcatctttgctaatctcatcagacataactcatgatatgcaagtgtttgcctcagaggcatgatctgagt----ctgagttctac--aatggcaag--------------------------------------------------------------------------------
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TGCGATGAACAAGCTGTTGATGGAGGAGAATGACAGGCTGCAGAAGCAGGTCTCCCGACTCGTCTACGAGAATGGATACATGCGACAGCAGCTTCACAATgtgagatccatctcccttgctcattccccagaacat--cttatt-tatat---ttttttttctagataaatcagctgaatggcacaaagtatcatgtagtagtgaatggtgctgttttatgtaagttttgatgcgaaccttgtcgcatgattccacgtctaataccgtgtgttttgatatttgcag
upper sequence: LOC_Os03g43930.2 (Oryza sativa), 5'ss of exon 2
lower sequence: GLYMA08G13110.1 (Glycine max), 5'ss of exon 2
TGCGATGAACAAGCTGTTGATGGAGGAGAATGACAGGCTGCAGAAGCAGGTGTCCCGCCTCGTTTACGAGAACGGGTACATGCGGCAGCAGCTCCATAATgtgagattca-tcatctttgctaat-ctcatcaga---cataactca-tgatatgcaagtgtttgcctcagaggcatgatctgagtctgagttctacaatggcaag
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TGCAATGAACAAGTTGTTGATGGAAGAGAACGACCGACTGCAGAAGCAGGTCTCACAGTTGGTTTATGATAATGGATTCATGAAACAACAAATACATACTgtgagtctcaattatcattctgaatgttcattgaagaatataatttagtgttattgaagaacctatgtcatttactggtttcttaacag-----------------
upper sequence: LOC_Os03g43930.2 (Oryza sativa), 5'ss of exon 2
lower sequence: GLYMA15G13640.1 (Glycine max), 5'ss of exon 2
TGCGATGAACAAGCTGTTGATGGAGGAGAATGACAGGCTGCAGAAGCAGGTGTCCCGCCTCGTTTACGAGAACGGGTACATGCGGCAGCAGCTCCATAATgtgagattcatcatctttgctaatctcatcagacataactcatgatatgcaag-tgtttgcctcagaggcatgatctga-gtctgagttctacaatggcaag------------
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TGCAATGAACAAGCTGTTAATGGAGGAGAATGACCGTTTGCAGAAGCAGGTTTCTCATCTGGTGTATGAGAATGGTTACATGAAGCAACAGATACACACTgtgatattctctatctctctctctgtctttcttctc--ttcattttgtgaatgctttttgtattttctgaatatattaatggctgaaccatgttttggtttgaactttgaacag
upper sequence: LOC_Os03g43930.2 (Oryza sativa), 5'ss of exon 2
lower sequence: Vv10s0003g04670.t01 (Vitis vinifera), 5'ss of exon 2
TGCGATGAACAAGCTGTTGATGGAGGAGAATGACAGGCTGCAGAAGCAGGTGTCCCGCCTCGTTTACGAGAACGGGTACATGCGGCAGCAGCTCCATAATgtgagattcatcat----ctttgctaatctcatcagacataactcatgatatgcaagtgtttgcctcagaggcatgatctgagtctgagttctacaatggcaag
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TGCAATGAACAAGCTGTTGATGGAAGAGAATGACCGGTTACAGAAGCAGGTCTCGCAGTTGGTTTATGAAAATGGATACATGAGACAGCAGCTGCAGAGTgtaagctcctccactccaccttcttgctagcataaaagtggcatcatcacttggttatttctgtccctaatatctgaag-gggcttttataatcaaatcgt---Mapped 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|58665470|gb|CK054156.1|CK054156EST: TGTCCCGCCTCGTTTACGAGAACGGGTACATGCGGCAGCAGCTCCATAAT CCTTCTGTGGCAACTACAGACACGAGCTGTGAGTCTGTGGTTACAAGTGGT
genomic: TGTCCCGCCTCGTTTACGAGAACGGGTACATGCGGCAGCAGCTCCATAATgtgagattca ... gtttttacagCCTTCTGTGGCAACTACAGACACGAGCTGTGAGTCTGTGGTTACAAGTGGT
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
TGCGATGAACAAGCTGTTGATGGAGGAGAATGACAGGCTGCAGAAGCAGGTGTCCCGCCTCGTTTACGAGAACGGGTACATGCGGCAGCAGCTCCATAATgtgagattcatcatctttgctaatctcatcagacataactcatgatatgcaagtgtttgcctcagaggcatgatctgagtctgagttctacaatggcaag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTC