Sequence
atgc intronic sequence ATGC exonic sequencegtatactttgttcttctacctatttgaccttttagcctttttaacgtcttctttttacccggtttagctgattatgattcaacaattttatgttatctttctaatccttctacaatctctgctagGTTTCATCCCGTTCTCCAAAGGAAGGTTCCTATTTCAAGCAGCTGCCCAAGTCCAGTGCTATTAAGGTGATTGATTTTGGCAGCACAACATATGACCAGC
Basic information
species | Oryza sativa |
transcript | LOC_Os12g27520.1 |
intron # | 7 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os12g27520.4 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G063792_T05 (Zea mays), 3'ss of exon 4
gtatactttgttcttctacctatttgaccttttagcctttttaacgtcttctttttacccggtttagctgattatgattcaacaattttatgttatctttctaatccttctacaatctctgctagGTTTCATCCCGTTCTCCAAAGGAAGGTTCCTATTTCAAGCAGCTGCCCAAGTCCAGTGCTATTAAGGTGATTGATTTTGGCAGCACAACATATGACCAGC
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-----------------acctacccaagatttaccttgtgctatgcttgttcttttattgtgtattggtagcgggggtagaaaaat---atggta-----ctgatcctcttttttcatttgccagGTCTCATCCCAATCCCCAAAGGAGGGGTCCTATTACAAGCAGTTGCCCAAGTCTAGTGCTATCAAGGTGATTGATTTCGGTAGCACTACTTATGATCAAC
upper sequence: LOC_Os12g27520.4 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G063792_T04 (Zea mays), 3'ss of exon 7
gtatactttgttcttctac--ctatttgacct-tttagcctttttaacgtcttctttttacccggtttagctgattatgattcaacaattttatgttatctttctaatccttctacaatctctgctagGTTTCATCCCGTTCTCCAAAGGAAGGTTCCTATTTCAAGCAGCTGCCCAAGTCCAGTGCTATTAAGGTGATTGATTTTGGCAGCACAACATATGACCAGC
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gtatatcttgttcttttatatttaattcacctacccaagatttaccttgtgctatgcttgttcttttattgtgtattggtagcgggggtagaaaaatatggtactgatcctcttttttcatttgccagGTCTCATCCCAATCCCCAAAGGAGGGGTCCTATTACAAGCAGTTGCCCAAGTCTAGTGCTATCAAGGTGATTGATTTCGGTAGCACTACTTATGATCAAC
upper sequence: LOC_Os12g27520.4 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G179308_T03 (Zea mays), 3'ss of exon 6
gtatactttgttcttctacctatttgacct-tttagcctttttaacgtcttctttttacccggtttagctgattatgattcaacaattttatgttatctttctaatccttctacaatc-tctgctagGTTTCATCCCGTTCTCCAAAGGAAGGTTCCTATTTCAAGCAGCTGCCCAAGTCCAGTGCTATTAAGGTGATTGATTTTGGCAGCACAACATATGACCAGC
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gtatattttgttcttttatttacatcacctacccaagatttaccttgccctgtgcttgttgatttctgttg-taataggttagtgaatattgaatatggtactgatcctctttttttcatttgctagGTTTCATCCCGATCCCCAAAGGAGGGATCCTATTACAAGCGGGTGCCCAAGTCTAGTGCTATCAAGGTGATTGATTTTGGTAGCACTACCTATGATCAAC
upper sequence: LOC_Os12g27520.4 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G179308_T04 (Zea mays), 3'ss of exon 3
gtatactttgttcttctacctatttgaccttttagcctttttaacgtcttctttttacccggtttagctgattatgattcaacaattttatgttatctttctaatccttctacaatc-tctgctagGTTTCATCCCGTTCTCCAAAGGAAGGTTCCTATTTCAAGCAGCTGCCCAAGTCCAGTGCTATTAAGGTGATTGATTTTGGCAGCACAACATATGACCAGC
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-----------------acctacccaagattt--acctt------gccctgtgcttgttgatttctgttg-taataggttagtgaatattgaatatggtactgatcctctttttttcatttgctagGTTTCATCCCGATCCCCAAAGGAGGGATCCTATTACAAGCGGGTGCCCAAGTCTAGTGCTATCAAGGTGATTGATTTTGGTAGCACTACCTATGATCAAC
upper sequence: LOC_Os12g27520.4 (Oryza sativa), 3'ss of exon 7
lower sequence: GLYMA06G18530.1 (Glycine max), 3'ss of exon 6
gtatactttgttcttctacctatttgaccttttagcctttttaacgtcttctttttacccggtttagctgattatgattcaacaattttatgttatctttctaatccttctacaatctctgctagGTTTCATCCCGTTCTCCAAAGGAAGGTTCCTATTTCAAGCAGCTGCCCAAGTCCAGTGCTATTAAGGTGATTGATTTTGGCAGCACAACATATGACCAGC------
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-----------------aggaaagtaagaacaccaagtggctgaaattgctatgctattaggt----cagatacagaaatgagatcactgacatccattgctgattgttt----atatttaacagAGTACAACCAGATCACCAA------GTTCCTTTTTCAAGAGAGTGCCCAAGTCAAGTGCTATAAAAGTTATTGATTTTGGCAGCACTACATATGAACGAGAAGATC
upper sequence: LOC_Os12g27520.4 (Oryza sativa), 3'ss of exon 7
lower sequence: GLYMA17G13440.1 (Glycine max), 3'ss of exon 6
gtatactttgttcttctacctatttgaccttttagcctttttaacgtcttctttttacccggtttagctgattatgattcaacaattttatgttatctttctaatccttctacaatctctgctagGTTTCATCCCGTTCTCCAAAGGAAGGTTCCTATTTCAAGCAGCTGCCCAAGTCCAGTGCTATTAAGGTGATTGATTTTGGCAGCACAACATATGACCAGC------
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----------------------gttggacctggaggataaaaaatgaaaccaagta--tggaactacccttttctagctttagcatcgattgatcaatcattgacattcattttatttttac-agAGTTCATCTAGATCACCAA------GTTCCTATTTCAAGAGAGTTCCCAAATCAAGTGCTATAAAGGTTATTGATTTTGGCAGCACCACTTATGAGCGAGAAGATC
upper sequence: LOC_Os12g27520.4 (Oryza sativa), 3'ss of exon 7
lower sequence: GLYMA05G02740.1 (Glycine max), 3'ss of exon 6
gtatactttgttcttctacctatttgaccttttagcctttttaacgtcttctttttacccggtttagctgattatgattcaacaattttatgttatctttctaatccttctacaatctctgctagGTTTCATCCCGTTCTCCAAAGGAAGGTTCCTATTTCAAGCAGCTGCCCAAGTCCAGTGCTATTAAGGTGATTGATTTTGGCAGCACAACATATGACCAGC------
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------gtcgtacctggatgaataaaaatgaaactgagtatggaagtacccttttctatc--tttagc--att--gattgatcaatcat-tgacatccattttat--ttttaca----------gAGTTCATCTAGATCATCAT------GTTCCTATTTCAAGAGAGTTCCCAAATCAAGTGCTATAAAGGTTATTGATTTTGGCAGCACCACTTATGAGCGAGAAGATC
upper sequence: LOC_Os12g27520.4 (Oryza sativa), 3'ss of exon 7
lower sequence: GLYMA04G36360.1 (Glycine max), 3'ss of exon 6
gtatactttgttcttctacctatttgaccttttagcctttttaacgtcttctttttacccggtttagctgattatgattcaacaattttatgttatctttctaatccttcta--caatctctgctagGTTTCATCCCGTTCTCCAAAGGAAGGTTCCTATTTCAAGCAGCTGCCCAAGTCCAGTGCTATTAAGGTGATTGATTTTGGCAGCACAACATATGACCAGC------
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------------------------ggaaaagtaagaacaccaagtggctgaaattg--ctatgctattaggtca-gatacagaaatgtgatcactgacatccattgcttattgtttatatttaacagAGTACAACCAGATCACCAA------GCTCCTTTTTCAAGAGAGTGCCCAAGTCAAGTGCTATAAAAGTTATTGATTTTGGCAGCACTACATATGAACGAGAAGATC
upper sequence: LOC_Os12g27520.4 (Oryza sativa), 3'ss of exon 7
lower sequence: AT4G24740.1 (Arabidopsis thaliana), 3'ss of exon 7
gtatactttgttcttctacctatttgaccttttagcctttttaacgtcttctttttacccg-gtttagc-tgattatgattcaacaattttatgttatctttctaatccttctacaatctctgctagGTTTCATCCCGTTCTCCAAAGGAAGGTTCCTATTTCAAGCAGCTGCCCAAGTCCAGTGCTATTAAGGTGATTGATTTTGGCAGCACAACATATGACCAGC------
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-----------------------------------------gtatatctcgaatgcaactgtgtgtgaccttaatgtggc-caactatttaag--tgctgaaggaatttggttgtgtttcctgatgcagGG-GTCCCGATTACAAAGGGATGTATGCTAT---AAAAGAGTGCCTAAATCAAGTGCAATAAAGGTGATTGATTTTGGTAGCACAACTTATGAGCGCCAGGACC
upper sequence: LOC_Os12g27520.4 (Oryza sativa), 3'ss of exon 7
lower sequence: Vv17s0000g09500.t01 (Vitis vinifera), 3'ss of exon 7
gtatactttgttcttctacctatttgaccttttagcctttttaacgtcttctttttacccggtttagctgattatgattcaacaattttatgttatctttctaatccttctacaat-ctctgctagGTTTCATCCCGTTCTCCAAAGGAAGGTTCCTATTTCAAGCAGCTGCCCAAGTCCAGTGCTATTAAGGTGATTGATTTTGGCAGCACAACATATGACCAGC
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------------gtactccagatgttaacttgatgtgtattaagtggcatatggttttgctttattattctttctgcatctacaatgccct--tgttattgtaacatatatttgttgcattttcagGTTTCATCCCGTTCACCCAAGGATGGTTCTTACTTTAAGAGAGTACCAAAATCAAGTGCTATTAAAGTGATTGATTTTGGAAGCACAACATATGAGCGAC
upper sequence: LOC_Os12g27520.4 (Oryza sativa), 3'ss of exon 7
lower sequence: Vv01s0137g00580.t01 (Vitis vinifera), 3'ss of exon 7
----gtatactt-tgttcttctacctatttgaccttttagcctttttaacgtcttcttttt----acccggtt-tagctgattatgattcaacaattttatgttatctttcta-----------atccttctacaatctctgct---------agGTTTCATCCCGTTCTCCAAAGGAAGGTTCCTATTTCAAGCAGCTGCCCAAGTCCAGTGCTATTAAGGTGATTGATTTTGGCAGCACAACATATGACCAGC
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gtatatctacttctgttctggtagcttttcaatttgtttgcacttctgttgttctttcaatcaagaccttattgttgatattcaggcttttccttttccctgttccctttccatatcagttattatctggtcataatgtttctttctaattgcagGTTACCACACGGTCACCAAAAGATGGAATATGTTATAAGAAGTTGCCAAGATCAAGTGCTATTAAGGTGATTGATTTTGGTAGCACAGCTTTTGAGTGTCMapped EST sequences
Showing partial alignments of ESTs and genomic sequences. See full alignments
ATGC EST sequence
ATGC genomic sequence (exon)
ATGC genomic sequence (truncated intron)
EST:
gi|86900381|gb|CI296424.1|CI296424EST: AGAACATTCTTCTTGTTTCTCCAGAGTACATTAAAGTGCCCGATTACAAA GTTTCATCCCGTTCTCCAAAGGAAGGTTCCTATTTCAAGCAGCTGCCCAAG
genomic: AGAACATTCTTCTTGTTTCTCCAGAGTACATTAAAGTGCCCGATTACAAAgtatactttg ... tctctgctagGTTTCATCCCGTTCTCCAAAGGAAGGTTCCTATTTCAAGCAGCTGCCCAAG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.attatgattcaacaattttatgttatctttctaatccttctacaatctctgctagGTTTCATCCCGTTCTCCAAAGGAAGGTTCCTATTTCAAGCAGCTGCCCAAGTCCAGTGCTATTAAGGTGATTGATTTTGGCAGCACAACATATGACCAGC
ttctaat putative branch site (score: 2)
tctctgct putative PPT
aattttatgttatctt TA-rich tract