Sequence
atgc intronic sequence ATGC exonic sequencegtgagttatcaatctccgaatacatgcttgttttttattcttgcaactggcctagctgttccaattcaatccatattttttgaaaaaaaaaatattcatgccgtgtttgttgttagGTAGCATTCTTCAGGCAGTTCTTTGGGTCCGTCACCAAGGTGGACTACCTGACCATGCGGCAAGGCTTCATCAAT
Basic information
species | Oryza sativa |
transcript | LOC_Os06g29110.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os06g29110.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G032219_T02 (Zea mays), 3'ss of exon 6
gtgagttatcaatctccgaatacatgcttgttttttattcttgcaactggcctagctgttccaattcaatccatatttt---ttgaaaaaaaaaatattcatgccgtgtttgttgttagGTAGCATTCTTCAGGCAGTTCTTTGGGTCCGTCACCAAGGTGGACTACCTGACCATGCGGCAAGGCTTCATCAAT
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gtgagtactc---cgacggatcgccagctctttgcagcctgttcctatcgttaagtttctccgcctcgttttatagcctaggctctctgaacactccccctcccccggcccgctgc-agGTGGCGTTCTTCAGGCAGTTCTTCGCGTCCGTGACCAAGGTGGATTACCTGACCATGCGGCAGGGGTTCATCAAC
upper sequence: LOC_Os06g29110.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA04G01730.1 (Glycine max), 3'ss of exon 6
gtgagttatcaatctccgaatacatgcttgttttttattcttgcaactggcctagctgttccaattcaatccatattttttgaaaaaaaaaat-attcatgccgtgtttgttgttagGTAGCATTCTTCAGGCAGTTCTTTGGGTCCGTCACCAAGGTGGACTACCTGACCATGCGGCAAGGCTTCATCAAT
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-------gtgagtttc---atccat---tgttcctcaggaataaaatgaaaaaaaatatat-aatttatacaataattaacaataaaccattttaactatttgcctttttttgatagGTGGCATTCTTCAGGCAATTTTTCGGGTCTGTCACTAAGGTGGATTACATGACCATGCGGCACGGATTTATTAAC
upper sequence: LOC_Os06g29110.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA06G01820.1 (Glycine max), 3'ss of exon 6
gtgagttatcaatctccgaatacatgcttgttttttattcttgcaactggcctagctgttccaattcaatccatattttttgaaaaaaaaaatattcatgccgtgtttgttgttagGTAGCATTCTTCAGGCAGTTCTTTGGGTCCGTCACCAAGGTGGACTACCTGACCATGCGGCAAGGCTTCATCAAT
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gtgagt--ttcatccattgttcctcaggaataatttaaatgaaaaacaaaa-taaataccataattta---tgcaattaacaattaataaaccctttatttgggttttttgggtagGTGGCATTCTTCAGGCAATTCTTCGGTTCTGTCAGTAAGGTGGATTACATGACCATGCGGCACGGATTTATTAAC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.caattcaatccatattttttgaaaaaaaaaatattcatgccgtgtttgttgttagGTAGCATTCTTCAGGCAGTTCTTTGGGTCCGTCACCAAGGTGGACTACCTGACCATGCGGCAAGGCTTCATCAAT
aatccatattttttga 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgagttatcaatctccgaatacatgcttgttttttattcttgcaactggcctagctgttccaattcaatccatattttttgaaaaaaaaaatattcatgccgtgtttgttgttagGTAGCATTCTTCAGGCAGTTCTTTGGGTCCGTCACCAAGGTGGACTACCTGACCATGCGGCAAGGCTTCATCAAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA