Sequence
atgc intronic sequence ATGC exonic sequence...attattcagatttagattccattgaacaggcatatgtgagatttctggattcaagttgttgtcttcgtgacattcttcagagttctgaatctgtctgcagGACTCAGGAATGCAATGTTGACGGCTCTGAAGCCGTTCCAAAATGAACAGGGTGTAGGGATGTTCATAAATTCTTGTTTTGCACATTGCCAGAGTGAGCT
Basic information
species | Oryza sativa |
transcript | LOC_Os10g40290.1 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os10g40290.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GLYMA20G29930.2 (Glycine max), 3'ss of exon 10
----------------------------------------------------------------------------attattcagat-ttagattccattgaacaggcatatgtgagatttctggattcaag--ttgttgtcttcgtgacattcttcagagttctgaatctgtctg---cagGACTCAGGAATGCAATGTTGACGGCTCTGAAGCCGTTCCA---AAATGAACAGGGTGTAGGGATGTTCATAAATTCTTGTTTTGCACATTGCCAGAGTGAGCT
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gttcctatttcaagttttttggcagcagtttatggaatagctttcacccattctatctcagaagaagtctttagtgtttacaaacatgttagattttgagaatgaaatctgtagttagtacacgtgttcaaaactcatcatgatgtaaataagactcattttccttaatccactttattcagGTTTTAGGCTTGACATGCTTGGAGCTTTGAGACCGTTCTATATGAATTCAAGAAGAGGGGGGATGTTCATAAATTCATGTTTTGCTCATTGCCAGAGTGA---
upper sequence: LOC_Os10g40290.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GLYMA10G37890.1 (Glycine max), 3'ss of exon 10
----------------------------------------------------------------------------attattcagat-ttagattccattgaacaggcatatgtgagatttctggattcaagttgttgtcttcgtgacattcttcagagt------tctgaatctgtctg---cagGACTCAGGAATGCAATGTTGACGGCTCTGAAGCCGTTCCA---AAATGAACAGGGTGTAGGGATGTTCATAAATTCTTGTTTTGCACATTGCCAGAGTGAGCT
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gttcctatttcaacttttttctcagcagtttatggaatagctttcacccattctgtctcttaagaagtctttagtgtttgcaaacatgttagattttgtgaatgaagtctgt-tgtttactccacacttgttcaaaactcatcatgatgtaaataaaactgattttccttaatctactttattcagGTTTTAGGCTAGACATGCTTGGAGCTTTGAGACCGTTCTATATGAATTCAAGAAGAGGGGGGATGTTCATAAATTCATGTTTTGCTCATTGCCAAAGTGA--- atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tggattcaagttgttgtcttcgtgacattcttcagagttctgaatctgtctgcagGACTCAGGAATGCAATGTTGACGGCTCTGAAGCCGTTCCAAAATGAACAGGGTGTAGGGATGTTCATAAATTCTTGTTTTGCACATTGCCAGAGTGAGCT
tctgtct CT-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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
attattcagatttagattccattgaacaggcatatgtgagatttctggattcaagttgttgtcttcgtgacattcttcagagttctgaatctgtctgcagGACTCAGGAATGCAATGTTGACGGCTCTGAAGCCGTTCCAAAATGAACAGGGTGTAGGGATGTTCATAAATTCTTGTTTTGCACATTGCCAGAGTGAGCT
- - - - - - - - - - - - - caggcat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cattctt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ttctgaa