Sequence
atgc intronic sequence ATGC exonic sequence...aactactgggagtggggacaattgtttctcagcataactattttaacatatttcttttcatgtttgctgtcatcctgagttgccgagatacattttgtagGCATATTTCCCTCCAATTTCTCAGCCAGAAGGTCGTCCTTTGACAATTCAAGACGCAAAAGGCAAAGAATGGCATTTTCAGTTCAGATTCTGGCCAAATA
Basic information
species | Oryza sativa |
transcript | LOC_Os07g48200.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os07g48200.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G158162_T03 (Zea mays), 3'ss of exon 5
aactactgggagtggggacaattgtttct-cagcataactattttaacatatttcttttcatgtt--tgctgtcatcctgagttgccgagatacattttgtagGCATATTTCCCTCCAATTTCTCAGCCAGAAGGTCGTCCTTTGACAATTCAAGACGCAAAAGGCAAAGAATGGCATTTTCAGTTCAGATTCTGGCCAAATA
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---ttctgttcacgaaatttattgctagtgcaggaagcgtttctgtatgcattattttccctattgtttctgtcatcctgagttaacaaggttctctgtgtagGCATATTTTCCCCCAATTTCTCAACCAGAAGGACGCCCCTTGACAATTCAAGATGCAAGAGGAAAAGAATGGCATTTTCAGTTTAGGTTTTGGCCAAATA
upper sequence: LOC_Os07g48200.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G172621_T01 (Zea mays), 3'ss of exon 5
--aactactgggagtggggacaattgtttctca-gcataactattttaacatatttcttttcatgtttgctgtcatcctgagttgccgagatacattttgtagGCATATTTCCCTCCAATTTCTCAGCCAGAAGGTCGTCCTTTGACAATTCAAGACGCAAAAGGCAAAGAATGGCATTTTCAGTTCAGATTCTGGCCAAATA
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tctactgctcgtgttcatgaaacttattgctagtgcaggaagctgcttctgtatgcattcttttttccactgt--ttctgacatcctgag-ttctctgtgtagGCATATTTCCCCCCAATTTCCCAACCGGAAGGTCGCCCCTTGACAATTCAAGATGCAAGAGGAAAAGAATGGCATTTTCAGTTTAGGTTTTGGCCAAATA
upper sequence: LOC_Os07g48200.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA01G32810.1 (Glycine max), 3'ss of exon 10
-------------------------aactactgggagtggggacaattgtttctcagcataactattttaaca-----tatttcttttcatgtttgctgtcatcctgagttgccgagata------cattttgtagGCATATTTCCCTCCAATTTCTCAGCCAGAAGGTCGTCCTTTGACAATTCAAGACGCAAAAGGCAAAGAATGGCATTTTCAGTTCAGATTCTGGCCAAATA
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gtaatttatcttaactcatctgttgaactggcatttactgttgtcattttatattaac-taacaattctagtaaaagttgtttttcttgatgagtctggtaatttgttaaaactgaaagaggagaccattgtgcagGCATATTTCCCTCCAATCTCTCAACCAGAGGGCCTTCCTTTACGAATCCAAGATGTGAAAGGAAAAGAATGGATGTTTCAATTTAGATTTTGGCCAAATA
upper sequence: LOC_Os07g48200.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA03G04330.1 (Glycine max), 3'ss of exon 7
-------------------------aactactgggagtggggacaattgtttctcagcataactattttaaca-----tatttcttttcatgtttgctgtcatcctgagttgccgagatac------attttgtagGCATATTTCCCTCCAATTTCTCAGCCAGAAGGTCGTCCTTTGACAATTCAAGACGCAAAAGGCAAAGAATGGCATTTTCAGTTCAGATTCTGGCCAAATA
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gtaatttatcctaactcatctgttgaactggcctttactgttgtcattttatattaac-taacaattctagtaaaagttatttttcttgacgagtctggtaatttgttaaaactgaaagacgagagcattgtgcagGCATATTTCCCTCCAATCTCTCAACCAGAGGGCCTTCCTTTACGAATCCAAGATGTGAAAGGAAAAGAATGGATGTTTCAGTTTAGATTTTGGCCAAATAMapped 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|58671720|gb|CK060406.1|CK060406EST: GTGATGCAGGCCGCATAGGGCGCCTTGTTCTACCAAAAGCCTGTGCAGAG GCATATTTCCCTCCAATTTCTCAGCCAGAAGGTCGTCCTTTGACAATTCAA
genomic: GTGATGCAGGCCGCATAGGGCGCCTTGTTCTACCAAAAGCCTGTGCGGAGgtattttttt ... cattttgtagGCATATTTCCCTCCAATTTCTCAGCCAGAAGGTCGTCCTTTGACAATTCAA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.acatatttcttttcatgtttgctgtcatcctgagttgccgagatacattttgtagGCATATTTCCCTCCAATTTCTCAGCCAGAAGGTCGTCCTTTGACAATTCAAGACGCAAAAGGCAAAGAATGGCATTTTCAGTTCAGATTCTGGCCAAATA
ttttaac putative branch site (score: 2)
atacatttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
aactactgggagtggggacaattgtttctcagcataactattttaacatatttcttttcatgtttgctgtcatcctgagttgccgagatacattttgtagGCATATTTCCCTCCAATTTCTCAGCCAGAAGGTCGTCCTTTGACAATTCAAGACGCAAAAGGCAAAGAATGGCATTTTCAGTTCAGATTCTGGCCAAATA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- ctactgg
- - - - - - - - - - - tgtttct
- - - - - - - - - - - - - - - agcataa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gctgtca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gttgccg