Sequence
atgc intronic sequence ATGC exonic sequencegtcagtgttattgaacattatccatcttgctattttctgcagcaattctaagctagttattctgttaattgattctggatttctgatgtgattgttacaaacaaaattcagAGCAACAGAAGAACAATAATGGACGATCCTTTCATCCGTAATTATATTGAGGACCTATTGAAGAACATCAGAACTCAAGTTCTGCTCAAGCTTATTAAGC
Basic information
species | Oryza sativa |
transcript | LOC_Os01g17180.2 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os01g17180.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM2G132804_T01 (Zea mays), 3'ss of exon 9
gtcagtgttattgaacattatccatcttgctattttctgcagcaattctaagctagttattctgttaattgattctggattt-ctgatgtgattgttacaaacaaaatt---cagAGCAACAGAAGAACAATAATGGACGATCCTTTCATCCGTAATTATATTGAGGACCTATTGAAGAACATCAGAACTCAAGTTCTGCTCAAGCTTATTAAGC
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----------------------------------gtcagcgtctatttct--tcagaaattttatctcttaattttccatgtactaatgcaagtgttatcaacttctttttgcagAGTAATAGAAGAACAATAATGGATGATCCTTTTATCCGTAACTATATTGAGGATCTGTTGAAGAACATCAGAACCCAAGTGCTGCTCAAGCTTATTAAAC
upper sequence: LOC_Os01g17180.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM2G079196_T01 (Zea mays), 3'ss of exon 9
gtcagtgttattgaacattatccatcttgctattttctgcagcaattctaagctagttattctgttaattgattctggatttctgatgtgattgttacaaacaaaatt-----cagAGCAACAGAAGAACAATAATGGACGATCCTTTCATCCGTAATTATATTGAGGACCTATTGAAGAACATCAGAACTCAAGTTCTGCTCAAGCTTATTAAGC
||| || | |||| |||| |||| | ||| || | || || || | | || | || ||| | ||||| ||| || ||||| || |||||||||||||||||||||||||| |||||||| |||||||||||| ||||||||||||||||||| ||||| ||||||||||||||||| |
---gttgtcgtttacgcttat-----atgctctttttgttatttattt--agtt--tttttttgcttttcattttctatgtactaatgcaagtgttatcaactttttttttggcagAGTAATAGAAGAACAATAATGGACGATCCTTTTATCCGTAACTATATTGAGGACTTATTGAAGAACATCAGAACCCAAGTGCTGCTCAAGCTTATTAAAC
upper sequence: LOC_Os01g17180.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GLYMA19G30100.1 (Glycine max), 3'ss of exon 9
gtcagtgttattgaacattatccatcttgctattttctgcagcaattc-----taagctagttattctgttaattgattctggatttct---gatgtgattgttacaaacaaaatt--cagAGCAACAGAAGAACAATAATGGACGATCCTTTCATCCGTAATTATATTGAGGACCTATTGAAGAACATCAGAACTCAAGTTCTGCTCAAGCTTATTAAGC
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-gtacttttattgagtctagcaagagaatatgtctgctgcactaatttgaccataaagtatttctcctattt-ttcatccaatatttgtcggaatttgattttgggtaatttactttccagAGTAACAGAAGAACCATCATGGATGATCCATTTATCAGAAACTACATTGAGGATCTGCTAAAGAACATCAGAACTCAAGTCTTGCTGAAGCTCATCAAAC
upper sequence: LOC_Os01g17180.1 (Oryza sativa), 3'ss of exon 9
lower sequence: PP1S90_192V6.1 (Physcomitrella patens), 3'ss of exon 9
-----------------------------------------------------------------------gtcagtgttattgaacattatccatcttgcta--ttttctgcagcaattctaagctagttattctgttaattgattctggatttctgatgtgattgttacaaacaaaattcagAGCAACAGAAGAACAATAATGGACGATCCTTTCATCCGTAATTATATTGAGGACCTATTGAAGAACATCAGAACTCAAGTTCTGCTCAAGCTTATTAAGC
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gtactgccacttcagcaagttttggggactgatcataatatcgacgcgaaatttttaatcatcagagataaaattttgcagtcgaacttgttctgtggtgaaaaacatgttcttgagatcgcatgcgtacctcaaagtacacttattctatctctggcttatgctcgttttttc----atatagAGCAACAGAAAGACAATAATGGACGATCCCTTCATAAGGAATTACATTGAAGATCTGCTTAGCAAAATCCGCACACAAGTGTTGCTGAAGCTCATCAAGC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttattctgttaattgattctggatttctgatgtgattgttacaaacaaaattcagAGCAACAGAAGAACAATAATGGACGATCCTTTCATCCGTAATTATATTGAGGACCTATTGAAGAACATCAGAACTCAAGTTCTGCTCAAGCTTATTAAGC
ttctgat putative branch site (score: 3)
ttacaaacaaaatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtcagtgttattgaacattatccatcttgctattttctgcagcaattctaagctagttattctgttaattgattctggatttctgatgtgattgttacaaacaaaattcagAGCAACAGAAGAACAATAATGGACGATCCTTTCATCCGTAATTATATTGAGGACCTATTGAAGAACATCAGAACTCAAGTTCTGCTCAAGCTTATTAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT