Sequence
atgc intronic sequence ATGC exonic sequence...taactgaattatagcatgcatttttattttctctttgacaatggttttgtcatatttcaaatgtcatttctaatctccatgcttgttttaatgcatcaagGGTTGAGGAGTATCACATAGATGGATTTCGATTTGACCTTGCAAGTGTTCTTTGTCGTGGACCAGATGGTTGTCCTCTTGATGCACCTCCACTCATCAAG
Basic information
species | Oryza sativa |
transcript | LOC_Os09g29404.1 |
intron # | 11 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os09g29404.3 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G150796_T03 (Zea mays), 3'ss of exon 11
-taactgaattatagcatgcatttttattttctctttgacaatggttttgtcatatttcaaatgtcatttctaatctccatgcttg-ttttaatgcatcaagGGTTGAGGAGTATCACATAGATGGATTTCGATTTGACCTTGCAAGTGTTCTTTGTCGTGGACCAGATGGTTGTCCTCTTGATGCACCTCCACTCATCAAG
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tgcagtaagatggataatgcattgcctagtcctattttact-tgatatcagtttcagttttgtgttgtttctgat-tgcatgagtgcttttgtttcttcaagGGTTAAGGAGTATCACATAGATGGATTTCGGTTTGACCTTGCGAGTGTTCTTTGTCGTGGACCAGATGGCAGTCCTCTTGATGCACCTCCACTTATTAAG
upper sequence: LOC_Os09g29404.3 (Oryza sativa), 3'ss of exon 1
lower sequence: GLYMA06G10540.1 (Glycine max), 3'ss of exon 9
-taactgaattatagcatgcatttttattttctctttgacaatggttttgtcatatttcaaatgtcatttctaatctccatgcttgttttaatgcatca-agGGTTGAGGAGTATCACATAGATGGATTTCGATTTGACCTTGCAAGTGTTCTTTGTCGTGGACCAGATGGTTGTCCTCTTGATGCACCTCCACTCATCAAG
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agtattaacatttataaactaactaagtcatcattttcttt-taagttcctaattattgaagcactattgtta-ttttaataatatttttactttattgtagGGTCACCGAATACCATGTGGATGGATTTCGATTTGATCTTGCAAGTGTCCTGTGTCGAGGAATTGATGGCTCCCCCCTCAATGCACCCCCACTTATTAGG
upper sequence: LOC_Os09g29404.3 (Oryza sativa), 3'ss of exon 1
lower sequence: Vv18s0001g06520.t01 (Vitis vinifera), 3'ss of exon 12
taactgaattatagcatgcatttttatttt----ctctttgacaatggttttgtcatatttca-aatgtcatttctaatctccatgcttgttt--taatgcatc-aagGGTTGAGGAGTATCACATAGATGGATTTCGATTTGACCTTGCAAGTGTTCTTTGTCGTGGACCAGATGGTTGTCCTCTTGATGCACCTCCACTCATCAAG
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--------ttgttgatggtatctttatgatgaaactactttgatatatatttgtattattggatagccactcttcacactgttattcttttctactaaccaactgaagGGTCATTGAGTATCATGTGGATGGATTTCGATTTGATCTGGCTAGCGTTCTTTGTCGAGGAACAGATGGTTCTCCACTTAATGCTCCCCCAATTATTAGG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttgtcatatttcaaatgtcatttctaatctccatgcttgttttaatgcatcaagGGTTGAGGAGTATCACATAGATGGATTTCGATTTGACCTTGCAAGTGTTCTTTGTCGTGGACCAGATGGTTGTCCTCTTGATGCACCTCCACTCATCAAG
atatttcaaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
taactgaattatagcatgcatttttattttctctttgacaatggttttgtcatatttcaaatgtcatttctaatctccatgcttgttttaatgcatcaagGGTTGAGGAGTATCACATAGATGGATTTCGATTTGACCTTGCAAGTGTTCTTTGTCGTGGACCAGATGGTTGTCCTCTTGATGCACCTCCACTCATCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG