Sequence
atgc intronic sequence ATGC exonic sequencegtttgttgcttagctgaacattttcagtgttagttcatttctattacctacatgaatactgacacaattatttgtccagCCCCTATGGAGATCGATGAATACGATCTTGTTGATCCTGTTGATATCTTAACACCACTTGAGAAGTCTGGATTTTGGGATGGTGTG
Basic information
species | Oryza sativa |
transcript | LOC_Os01g60040.2 |
intron # | 7 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os01g60040.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G070126_T01 (Zea mays), 3'ss of exon 7
------gtttgttgcttagc---tgaacattttcagtgttagttcatttctattacctacatgaatactgacacaattat-ttgtccagCCCCTATGGAGATCGATGAATACGATCTTGTTGATCCTGTTGATATCTTAACACCACTTGAGAAGTCTGGATTTTGGGATGGTGTG
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gtgttcttctgaggattattatatggatattgctgttgatagtttgttcagactaatgatggaaatacttacataattctgctttgcagCCCCTGTGGAGATCGATGAATACGACCTTGTTGATCCTGTAGACATTTTAACCCCACTAGAAAAGTCTGGATTTTGGGACGGTGTG
upper sequence: LOC_Os01g60040.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G068755_T03 (Zea mays), 3'ss of exon 7
------------gtttgttgcttagctgaacattttcagtgttagttcatttctattacctacatgaatactgacacaattat-ttgtccagCCCCTATGGAGATCGATGAATACGATCTTGTTGATCCTGTTGATATCTTAACACCACTTGAGAAGTCTGGATTTTGGGATGGTGTG
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gtgtgttcttctgaggattatttatctggatattgctcttggtagtttgttcaaactaatgatggaaatacttatataattctactttgcagCCCCTGTGGAGATCGATGAATATGACCTTGTTGATCCTGTAGACATTTTAACCCCACTAGAAAAGTCTGGATTCTGGGACGGTGTG
upper sequence: LOC_Os01g60040.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GLYMA10G35140.1 (Glycine max), 3'ss of exon 7
---------------------------gtttgttgcttagctgaacattttcagtgttagttcatttctattacctacatgaatactgacacaattatttgtccagCCCCTATGGAGATCGATGAATACGATCTTGTTGATCCTGTTGATATCTTAACACCACTTGAGAAGTCTGGATTTTGGGATGGTGTG
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gtatctaagatttagtatctggagtatgtttttctttatatctgacatgttttgtctttccttggtagtactaatatactcatttttcaaatactttgattatcagCTCCTCAAGAAATCGACGAATATGAACTTGTTGATCCTGTTGATATATTGACTCCTTTGGAGAAGTCTGGATTTTGGGATGGAGTG
upper sequence: LOC_Os01g60040.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GLYMA20G32430.1 (Glycine max), 3'ss of exon 7
---------------------------gtttgttgcttagctgaacattttcagtgttagttcatttctattacctacatgaatactgacacaattatttgtc---cagCCCCTATGGAGATCGATGAATACGATCTTGTTGATCCTGTTGATATCTTAACACCACTTGAGAAGTCTGGATTTTGGGATGGTGTG
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gtatgtaagatttagtatctggagtatgtttttctttttctcagacatgttaacatgtctttcccttgtagtactaatattctcatttttcaaatactttgattatcagCTCCTCAAGAAATCGACGAATATGAACTTGTTGATCCTGTTGATATATTGATTCCTTTGGAGAAGTCAGGATTTTGGGATGGAGTT
upper sequence: LOC_Os01g60040.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GLYMA15G29520.1 (Glycine max), 3'ss of exon 4
---------------------------gtttgttgcttagctgaacattttcagtgttagttcatttctattacctacatgaatactgacacaattatttgtc---cagCCCCTATGGAGATCGATGAATACGATCTTGTTGATCCTGTTGATATCTTAACACCACTTGAGAAGTCTGGATTTTGGGATGGTGTG
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gtatgtaaaatttagtatctggagtatgtttttctttttctcagacatgctaacatgtctctcctttgtactactaatattctcatttttcaaatactttgattatcagCTCCTCAAGAAATCGATGAATATGAACTTGTTGATCCTGTTGATATATTGACTCCTTTAGAGAAGTCAGGATTTTGGGATGGAGTTMapped 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|86490173|gb|CI132806.1|CI132806EST: ATCCGAACAAGAAAAGGAACTTGAGGAGGAAGTTGTGCCAGAGGCAGCAGGCACTAACAATTCTGAAGAGGCAGTGCCAGAGG
genomic: ATCCGAACAAGAAAAGGAACTTGAGGAGGAAGTTGTGCCAGAGGCAGCAGGCACTAACAATTCTGAAGAGGCAGTGCCAGAGG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cagtgttagttcatttctattacctacatgaatactgacacaattatttgtccagCCCCTATGGAGATCGATGAATACGATCTTGTTGATCCTGTTGATATCTTAACACCACTTGAGAAGTCTGGATTTTGGGATGGTGTG
tactgac putative branch site (score: 1)
tttgtcc putative PPT
atttctatta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtttgttgcttagctgaacattttcagtgttagttcatttctattacctacatgaatactgacacaattatttgtccagCCCCTATGGAGATCGATGAATACGATCTTGTTGATCCTGTTGATATCTTAACACCACTTGAGAAGTCTGGATTTTGGGATGGTGTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT