Sequence
atgc intronic sequence ATGC exonic sequencegtaaaggcttctgttgtccaaaggaatgatcattatttttccatttgtgtttggtcatttgttggtaaatactagctttgtcatccagaagagagaagcctatttcttgcttctgcagtattttttttttatcttgaacttagtaaattatgattggtgcagACCTAGAGCTATACTGGACATCATAAAATCAGGTGAGAATTTTAGGATCTCCACAACAACAAGGATGCCAGAGCAAGGAACATGTGAACGTTGTGGCTAC
Basic information
species | Oryza sativa |
transcript | LOC_Os01g41565.1 |
intron # | 8 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os01g41565.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G402242_T01 (Zea mays), 3'ss of exon 7
gtaaaggcttctgttgtccaaaggaatgatcattatttttccatttgtgtttggtcatttgttggtaaatactagctttgtcatccagaagagagaagcctatttcttgcttctgcagtattttttttttatcttgaacttagtaaattatgattggtgcagACCTAGAGCTATACTGGACATCATAAAATCAGGTGAGAATTTTAGGATCTCCACAACAACAAGGATGCCAGAGCAAGGAACATGTGAACGTTGTGGCTAC
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----------------------------------------------------------------gtaaatactgaattttc--tccatat---atatattcaatggatgtgtgcat-gttctttttcagCAGCCTTGGCTCAGTAGACGATGAATGTTGCAGGCCTAGAGCTATACTAGACATCATAAAATCCGGTGAAAATTTCAGAATCTCCACAACAACAAGGATG---------------------------------
upper sequence: LOC_Os01g41565.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G402242_T02 (Zea mays), 3'ss of exon 7
gtaaaggcttctgttgtccaaaggaatgatcattatttttccatttgtgtttggtcatttgttggtaaatactagctttgtcatccagaagagagaagcctatttcttgcttctgcagtattttttttttatcttgaacttagtaaattatgattggtgcagACCTAGAGCTATACTGGACATCATAAAATCAGGTGAGAATTTTAGGATCTCCACAACAACAAGGATGCCAGAGCAAGGAACATGTGAACGTTGTGGCTAC
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---------------------ggttttgctcgtgaatttattaa--agatttagaaagaatgaggtaaatactgaattttc--tccatat---atatattcaatggatgtgtgcat-gttctttttcagCAGCCTTGGCTCAGTAGACGATGAATGTTGCAGGCCTAGAGCTATACTAGACATCATAAAATCCGGTGAAAATTTCAGAATCTCCACAACAACAAGGATG---------------------------------
upper sequence: LOC_Os01g41565.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G402242_T03 (Zea mays), 3'ss of exon 8
gtaaaggcttctgttgtccaaaggaatgatcattatttttccatttgtgtttggtcatttgttggtaaatactagctttgtcatccagaagagagaagcctatttcttgcttctgcagtattttttttttatcttgaacttagtaaattatgattggtgcagACCTAGAGCTATACTGGACATCATAAAATCAGGTGAGAATTTTAGGATCTCCACAACAACAAGGATGCCAGAGCAAGGAACATGTGAACGTTGTGGCTAC
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----------------------------------------------------------------gtaaatactgaattttc--tccatat---atatattcaatggatgtgtgcat-gttctttttcagcagccttggctcagtagacgatgaatgttgcagGCCTAGAGCTATACTAGACATCATAAAATCCGGTGAAAATTTCAGAATCTCCACAACAACAAGGATGCCAGAGCAAGGAACGTGTGAACGATGTGGCTAC
upper sequence: LOC_Os01g41565.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GLYMA04G00350.1 (Glycine max), 3'ss of exon 2
gtaaaggcttctgttgtccaaaggaatgatcattatttttccatttgtgtttggtcatttgttggtaaatactagctttgtcatccagaagagagaagcctatttcttgcttctgcagtattttttttttatct--tgaactta-gtaaattatgattggtgcagACCTAGAGCTATACTGGACATCATAAAATCAGGTGAGAATTTTAGGATCTCCACAACAACAAGGATGCCAGAGCAAGGAACATGTGAACGTTGTGGCTAC
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---------------------------------------------------------------------------------------gtgctgattatccaatttgcttgctttcttgtactcgctcacaaattgctgtgcttatgtttattata--caatgcagACCTAGGGCCATTCTGGACATCATCAAATCAGGGGAGAATTTCAGGATTTCTACTAGTACCAAGATGCCAGAGCAGGGAACATGCGAACGCTGCGGTTAT
upper sequence: LOC_Os01g41565.1 (Oryza sativa), 3'ss of exon 8
lower sequence: Vv18s0001g00440.t01 (Vitis vinifera), 3'ss of exon 8
gtaaaggcttctgttgtccaaaggaatgatcattatttttccatttgtgtttggtcatttgttggtaaatactagctttgtcatccagaagagagaagcctatttcttgcttctgcagtattttttttttatcttga-acttagtaaattatgattggtgcagACCTAGAGCTATACTGGACATCATAAAATCAGGTGAGAATTTTAGGATCTCCACAACAACAAGGATGCCAGAGCAAGGAACATGTGAACGTTGTGGCTAC
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------------gttgttgcctttgacactatttcagcagtgattggcatcacatagttcatgaaataatgctgttttcctgcttttgtaga-------ctttcacttgatgctgtcag---ctattttcattttgacacctttccggttg-gttcattgtagGCCCAGAGCTATACTTGACATCATCAGATCAGGTGAAAAGTTTAGGATATCCACTTCTGCAAAAATGCCAGAGCAGGGAACATGTGAACGGTGTGGTTAT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgcttctgcagtattttttttttatcttgaacttagtaaattatgattggtgcagACCTAGAGCTATACTGGACATCATAAAATCAGGTGAGAATTTTAGGATCTCCACAACAACAAGGATGCCAGAGCAAGGAACATGTGAACGTTGTGGCTAC
tattttttttttatct 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaaaggcttctgttgtccaaaggaatgatcattatttttccatttgtgtttggtcatttgttggtaaatactagctttgtcatccagaagagagaagcctatttcttgcttctgcagtattttttttttatcttgaacttagtaaattatgattggtgcagACCTAGAGCTATACTGGACATCATAAAATCAGGTGAGAATTTTAGGATCTCCACAACAACAAGGATGCCAGAGCAAGGAACATGTGAACGTTGTGGCTAC
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