Sequence
atgc intronic sequence ATGC exonic sequencegtgatgttctgttctaactgaaatgcctcagatggactcagtttgacatgtgaaggtatacaatttagttaaaagtaaaaaaaatcattgttatctgtgttcagGTTGATGAAGAACCTGCGATCAGGACAAACACTACAATTCTTCTTGGAAATATTGCAAACTACATGAATGATGGG
Basic information
species | Oryza sativa |
transcript | LOC_Os01g60440.1 |
intron # | 13 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os01g60440.1 (Oryza sativa), 3'ss of exon 13
lower sequence: GRMZM2G098078_T02 (Zea mays), 3'ss of exon 13
gtgatgttctgttctaactgaaatgcctcagatggactcagtttgacatgtgaaggtatacaatttagttaaaagtaaaaaaaatcattgttatctgtgttcagGTTGATGAAGAACCTGCGATCAGGACAAACACTACAATTCTTCTTGGAAATATTGCAAACTACATGAATGATGGG
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--------------------------gtgaagttcactt--ttggatttgaaaaggtttatactgcagtta----tgataga---cactgctttctgtga-cagGTGGATGAAGAACCTGGAATCAGGACGAACACTACAATTCTTCTTGGCAATATTGCAAGCTACATGAATGATGGG
upper sequence: LOC_Os01g60440.1 (Oryza sativa), 3'ss of exon 13
lower sequence: AC218972.3_FGT001 (Zea mays), 3'ss of exon 13
-------------------------------gtgatgttctgttctaactgaaatgcct------cagatggactcagttt---gacatgtgaaggtatacaatttagttaaaagtaaaaaa--aatcattgttatctgtgttcagGTTGATGAAGAACCTGCGATCAGGACAAACACTACAATTCTTCTTGGAAATATTGCAAACTACATGAATGATGGG
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gtccgttattgcagttatctcagcgtacaatctcaggatctctcttaaaatatctctctaagctacaggtgaaattcatttttggattttaaaaggtttatactgcagttatg-gtagacaactagacactgctttatgtga-cagGTGGACGAAGAACCTGGTATCAGGACAAACACAACAATTCTTCTTGGCAATATTGCAGGCTACATGAACGATGGG
upper sequence: LOC_Os01g60440.1 (Oryza sativa), 3'ss of exon 13
lower sequence: GRMZM2G098078_T01 (Zea mays), 3'ss of exon 13
gtgatgttctgttctaactgaaatgcctcagatggactcagtttgacatgtgaaggtatacaatttagttaaaagtaaaaaaaatcattgttatctgtgttcagGTTGATGAAGAACCTGCGATCAGGACAAACACTACAATTCTTCTTGGAAATATTGCAAACTACATGAATGATGGG-------------------------
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--------------------------gtgaagttcactt--ttggatttgaaaaggtttatactgcagtta----tgataga---cactgctttctgtga-cagGTGGATGAAGAACCTGGAATCAGGACGAACACTACAATTCTTCTTGGCAATATTGCAAGCTACATGAATGATGGGGTCTGTCTCAAAGATGCAACTATTG
upper sequence: LOC_Os01g60440.1 (Oryza sativa), 3'ss of exon 13
lower sequence: EFJ18677 (Selaginella moellendorffii), 3'ss of exon 11
gtgatgttctgttctaactgaaatgcctcagatggactcagtttgacatgtgaaggtatacaatttagttaaaagtaaaaaaaatcattgttatctgtgttcagGTTGATGAAGAACCTGCGATCAGGACAAACACTACAATTCTTCTTGGAAATATTGCAAACTACATGAATGATGGG
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-------------------------------------------------gttcctttttctcttcttttttcttatagtctgattcttatatgacgcatttcagGTTGACGAAGAACCTGCGATACGAACGAACACTACAATTTTACTGGGAAACATTGCCGGCCTTCTTAACGACTCTMapped 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|29623603|gb|CB628614.1|CB628614EST: CTCAGCGTACGATTTCAGGATCTCTCTTGAAGTATCTATCTAAGCTCCAG GTTGATGAAGAACCTGCGATCAGGACAAACACTACAATTCTTCTTGGAAAT
genomic: CTCAGCGTACGATTTCAGGATCTCTCTTGAAGTATCTATCTAAGCTCCAGgtgatgttct ... ctgtgttcagGTTGATGAAGAACCTGCGATCAGGACAAACACTACAATTCTTCTTGGAAAT
EST:
gi|701421|gb|D47712.1|D47712EST: CTCAGCGTACGATTTCAGGATCTCTCTTGAAGTATCTATCTAAGCTGCAG GTTGATGAAGAACCTGCGATCAGGACAAACACTACAATTCTTCTTGGAAAT
genomic: CTCAGCGTACGATTTCAGGATCTCTCTTGAAGTATCTATCTAAGCTCCAGgtgatgttct ... ctgtgttcagGTTGATGAAGAACCTGCGATCAGGACAAACACTACAATTCTTCTTGGAAAT
EST:
gi|109974420|gb|DT806899.1|DT806899EST: GATTTCAGGATCTCTCTTGAAGTATCTATCTAAGCTCCAG GTTGATGAAGAACCTGCGATCAGGACAAACACTACAAGTCTTCTTGGAAAT
genomic: GATTTCAGGATCTCTCTTGAAGTATCTATCTAAGCTCCAGgtgatgttct ... ctgtgttcagGTTGATGAAGAACCTGCGATCAGGACAAACACTACAATTCTTCTTGGAAAT
EST:
gi|701323|gb|D47614.1|D47614EST: CTCAGCGTACGATTTCAGGATCTCTCTTGAAGTATCTATCTAAGCTCCAG GTTGATGAAGAACCTGCGATCAGGACAAACACTACAATTCTTCTTGGAAAT
genomic: CTCAGCGTACGATTTCAGGATCTCTCTTGAAGTATCTATCTAAGCTCCAGgtgatgttct ... ctgtgttcagGTTGATGAAGAACCTGCGATCAGGACAAACACTACAATTCTTCTTGGAAAT
EST:
gi|55411921|gb|CV724297.1|CV724297EST: AGCGTACGATGTCAGGATCTCTCTTGAAGTATCTATCTAAGCTCCAG GTTGATGAAGAACCTGCGATCAGGACAAACACTACAATTCTTCTTGGAAAC
genomic: AGCGTACGATTTCAGGATCTCTCTTGAAGTATCTATCTAAGCTCCAGgtgatgttct ... ctgtgttcagGTTGATGAAGAACCTGCGATCAGGACAAACACTACAATTCTTCTTGGAAAT
RNA-Seq data
ATGC Supported by RNA-Seq exonic block that spans over the splice site
atgs Truncated intron sequence
Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.
Found data for 1 RNA-Seqlibrary.
Block sizes:
73 (upstream exon),
74 (downstream exon)
Score:
46TTATCTCAGCGTACGATTTCAGGATCTCTCTTGAAGTATCTATCTAAGCTCCAGgtgatgttct ... ctgtgttcagGTTGATGAAGAACCTGCGATCAGGACAAACACTACAATTCTTCTTGGAAATATTGCAAACTACATGAATGATGGG
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atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gtgaaggtatacaatttagttaaaagtaaaaaaaatcattgttatctgtgttcagGTTGATGAAGAACCTGCGATCAGGACAAACACTACAATTCTTCTTGGAAATATTGCAAACTACATGAATGATGGG
tatacaatttagttaa TA-rich tract