Sequence
atgc intronic sequence ATGC exonic sequencegtgagtactggacctgccatttcatttcattgtgatcagcagggcataaaccatttgaaataaaatttgcagTGCACTGAGGAAGCTCATCGTCCGGTAGACTGTGCCACTGTTTCAAAGTGGATCCTCAAGAACAGTGCGGAGTCTGAAAATATGAACTG
Basic information
species | Oryza sativa |
transcript | LOC_Os04g41470.2 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os04g41470.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM5G876621_T01 (Zea mays), 3'ss of exon 6
gtgagtactggacctg-ccatttcatttcattgtgatcagcagggcataaaccatttgaaataaaatttgcagTGCACTGAGGAAGCTCATCGTCCGGTAGACTGTGCCACTGTTTCAAAGTGGATCCTCAAGAACAGTGCGGAGTCTGAAAATATGAACTG
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gtgagtgctcaaactgattagttcatttttacataatcagcagaccatata----ttttattctttttttcagTGCACCGAGGAAGCTCATCGTCCAGTAGACTGTGCCACTGTTTCGAAGTGGATCCTCAAGAACAGTGCAGAGTCAGAGAATATGAATTG
upper sequence: LOC_Os04g41470.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G431691_T01 (Zea mays), 3'ss of exon 5
gtgagtactggacctg-ccatttcatttcattgtgatcagcagggcataaaccatttgaaataaaatttg--cagTGCACTGAGGAAGCTCATCGTCCGGTAGACTGTGCCACTGTTTCAAAGTGGATCCTCAAGAACAGTGCGGAGTCTGAAAATATGAACTG-----------
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gtgagtgttgaaactgattagttcatttttacataatcagcagtgagcaaaccatatattttcttcttttttcagTGCACCGAGGAAGCTCATCGTCCAGTAGATTGTGCCACTGTTTCGAAGTGGATCCTCAAGAACAGTGCGGAGTCAGAGAATATGAACTGGTATAGAAGGA
upper sequence: LOC_Os04g41470.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G006428_T01 (Zea mays), 3'ss of exon 6
gtgagtactggacctg-ccatttcatttcattgtgatcagcagggcataaaccatttgaaataaaatttg--cagTGCACTGAGGAAGCTCATCGTCCGGTAGACTGTGCCACTGTTTCAAAGTGGATCCTCAAGAACAGTGCGGAGTCTGAAAATATGAACTG
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gtgagtgctgaaactgattagttcatttttacataatctgcagtgagcagaccatatattttcttcttttttcagTGCACCGAGGAAGCTCATCGTCCAGTAGACTGTGCCACTGTTTCGAAGTGGATCCTCAAGAACAGTGCGGAGTCGGAGAATATGAACTG
upper sequence: LOC_Os04g41470.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G157933_T01 (Zea mays), 3'ss of exon 5
gtgagtactggacctg-ccatttcatttcattgtgatcagcagggcataaaccatttgaaataaaatttg--cagTGCACTGAGGAAGCTCATCGTCCGGTAGACTGTGCCACTGTTTCAAAGTGGATCCTCAAGAACAGTGCGGAGTCTGAAAATATGAACTG-----------
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gtgagtgctgaaactgattagttcatttttacataatcagcagtgagcagaccatatattttcttcttttttcagTGCACCGAGGAAGCTCATCGTCCAGTAGACTGTGCCACTGTTTCGAAGTGGATCCTCAAGAACAGTGTGGAGTCAGAGAATATGAACTGGTATAGAAGGA
upper sequence: LOC_Os04g41470.1 (Oryza sativa), 3'ss of exon 6
lower sequence: EFJ08409 (Selaginella moellendorffii), 3'ss of exon 6
gtgagtactggacctgccatttcatttcattgtgatcagcagggcataaaccatttgaaataaaatttgcagTGCACTGAGGAAGCTCATCGTCCGGTAGACTGTGCCACTGTTTCAAAGTGGATCCTCAAGAACAGTGCGGAGTCTGAAAATATGAACTG
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-------gtaaatgtttttttcttctttttgatgtcgcttgaggtttctgacgcttggttt----tctttagTGCTTAGAGGAAGCGCACCGACCGGTAGATTGTGAGACTGTTGCAAAGTGGATCCTCAAGAACAGCGCGGAGTCGGAAAACATGAACTG
upper sequence: LOC_Os04g41470.1 (Oryza sativa), 3'ss of exon 6
lower sequence: EFJ15174 (Selaginella moellendorffii), 3'ss of exon 6
gtgagtactggacctgccatttcatttcattgtgatcagcagggcataaaccatttgaaataaaatttgcagTGCACTGAGGAAGCTCATCGTCCGGTAGACTGTGCCACTGTTTCAAAGTGGATCCTCAAGAACAGTGCGGAGTCTGAAAATATGAACTG
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gtaaatgtt-----tttttcttctttttgatgtcgcc--tggggtttctgacgcttggttt----tctttagTGCTTAGAGGAAGCGCACCGACCGGTAGATTGTGAGACTGTTGCAAAGTGGATCCTCAAGAACAGCGCGGAGTCAGAAAACATGAACTGMapped 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|86901737|gb|CI310499.1|CI310499EST: GTGGTAGCTATGATGTGAACTGCAACTGTTCATACGGCTTTTGTTGGAAC TGCACTGAGGAAGCTCATCGTCCGGTAGACTGTGCCACTGTTTCAAAGTGG
genomic: GTGGTAGCTATGATGTGAACTGCAACTGTTCATACGGCTTTTGTTGGAACgtgagtactg ... aaatttgcagTGCACTGAGGAAGCTCATCGTCCGGTAGACTGTGCCACTGTTTCAAAGTGG
EST:
gi|29623493|gb|CB628504.1|CB628504EST: GTGGTAGCTATGATGTGAACTGCAACTGTTCATACGGCTTTTGTTGGAAC TGCACTGAGGAAGCTCATCGTCCGGTCGACTGTGCCACTGTTTCAAAGTGG
genomic: GTGGTAGCTATGATGTGAACTGCAACTGTTCATACGGCTTTTGTTGGAACgtgagtactg ... aaatttgcagTGCACTGAGGAAGCTCATCGTCCGGTAGACTGTGCCACTGTTTCAAAGTGG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.catttcatttcattgtgatcagcagggcataaaccatttgaaataaaatttgcagTGCACTGAGGAAGCTCATCGTCCGGTAGACTGTGCCACTGTTTCAAAGTGGATCCTCAAGAACAGTGCGGAGTCTGAAAATATGAACTG
ataaaccatttgaaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgagtactggacctgccatttcatttcattgtgatcagcagggcataaaccatttgaaataaaatttgcagTGCACTGAGGAAGCTCATCGTCCGGTAGACTGTGCCACTGTTTCAAAGTGGATCCTCAAGAACAGTGCGGAGTCTGAAAATATGAACTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC