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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GATCACCATACGTGAAATCCGTGAACATCAGTGGTTCACAGTTGGTCTTCCGCGTTATTTAGCTGTGCCACCTCCTGACACTGCACAACAGGTTAAAAAGgtaacatgctgccattatgcatctaactatttaaagccgtattctgcttttgaaactttcagtgtttgatttgatcaatgtgagttttgtag

Basic information

species Oryza sativa
transcript LOC_Os05g45420.3
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g45420.3 (Oryza sativa), 5'ss of exon 6
lower sequence: GRMZM2G077278_T01 (Zea mays), 5'ss of exon 6
GATCACCATACGTGAAATCCGTGAACATCAGTGGTTCACAGTTGGTCTTCCGCGTTATTTAGCTGTGCCACCTCCTGACACTGCACAACAGGTTAAAAAGgtaacatgctgccattatgcatctaactatttaaagccgtat-tctgctt--ttgaaactttcag--tgtttgatttgatcaatgtga--gttttgtag--------------------------------------------------------
||| || |||||||||||||||||||||  ||||||||   |  | |||||||| ||||| |||||||| ||||| |||||||| ||||| |||||||||||   ||  |   ||| ||    || | | ||   | ||| | | || ||  || | ||||          || ||| ||  |||  |   ||  |||                                                         
GATTACAATACGTGAAATCCGTGAACATGTGTGGTTCAAGATCCGACTTCCGCGCTATTTGGCTGTGCCGCCTCCAGACACTGCTCAACAAGTTAAAAAGgt---ataattttattgtgtgcgtatcaacttggcgacgtgtatttgtttccttcagacttaagaatcccctgcttttatggatgacactattccgtaaaatactttgtcttttctacttcaggagatgatttgaaattgttttgaattttgtag

upper sequence: LOC_Os05g45420.3 (Oryza sativa), 5'ss of exon 6
lower sequence: GLYMA08G26180.1 (Glycine max), 5'ss of exon 6
GATCACCATACGTGAAATCCGTGAACATCAGTGGTTCACAGTTGGTCTTCCGCGTTATTTAGCTGTGCCACCTCCTGACACTGCACAACAGGTTAAAAAGgt--aacatgctgccattatgcatc--taactatttaaagccgtattctgcttttg---aaactttcagtgtttgatttgatcaatgtgagttttgtag----
 || ||||||| ||| |||||| |||| |  ||||||  || | | |||||||||||||||||||||||||| || || ||    |||||||  ||||||||  |   |  |  | || ||  |   |  ||  ||    || | ||  ||| ||    ||| | ||  || || ||  ||  ||||| ||||    |     
AATGACCATACCTGAGATCCGTCAACACCCATGGTTCCAAGCTCGACTTCCGCGTTATTTAGCTGTGCCACCACCAGATACAATGCAACAGGCCAAAAAGgtttatttttatatctttttgtgttattcccttcttccctccatttttcgctcttctgtaaattatctatggttcatgaga--aatgt-agttgaaaaatact
















Mapped 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|27577190|gb|CA999884.1|CA999884
EST:     CGCGTTATTTAGCTGTGCCACCTCCTGACACTGCACAACAGGTTAAAAAG                         CTCGACGATGAAACTCTGAATGATGTTATCAATATGGGGTTTGACAAGAAT
genomic: CGCGTTATTTAGCTGTGCCACCTCCTGACACTGCACAACAGGTTAAAAAGgtaacatgct ... agttttgtagCTCGACGATGAAACTCTGAATGATGTTATCAATATGGGGTTTGACAAGAAT
EST: gi|40488690|gb|BX899031.1|BX899031
EST:     CGCGTTATTTAGCTGTGCCACCTCCTGACACTGCACAACAGGTTAAAAAG                         CTCGATGATGAAACTCTGAATGATGTTATCAATATGGGGTTTGACAAGAAT
genomic: CGCGTTATTTAGCTGTGCCACCTCCTGACACTGCACAACAGGTTAAAAAGgtaacatgct ... agttttgtagCTCGACGATGAAACTCTGAATGATGTTATCAATATGGGGTTTGACAAGAAT
EST: gi|13420630|gb|AU174720.1|AU174720
EST:     CGCGTTATTTAGCTGTGCCACCTCCTGACACTGCACAACAGGTTAAAAAG                         CTCGACGATGAAACTCTGAATGATGTTATCAATATGGGGTTTGACAAGAAT
genomic: CGCGTTATTTAGCTGTGCCACCTCCTGACACTGCACAACAGGTTAAAAAGgtaacatgct ... agttttgtagCTCGACGATGAAACTCTGAATGATGTTATCAATATGGGGTTTGACAAGAAT
EST: gi|38481090|gb|CF965179.1|CF965179
EST:     GTTATTTAGCTGTGCCACCTCCTGACACTGCACAACAGTGTTAAAAAG                         CTCGACGATGAAACTCTGAATGATGTTATCAATATGTGGTGTTTGACAAG
genomic: GTTATTTAGCTGTGCCACCTCCTGACACTGCACAACAG-GTTAAAAAGgtaacatgct ... agttttgtagCTCGACGATGAAACTCTGAATGATGTTATCAATATG-GG-GTTTGACAAG
EST: gi|66924039|gb|CX110887.1|CX110887
EST:     CGCGTTATTTAGCTGTGCCACCTCCTGACACTGCACAACAGGTTAAAAAG                         CTCGACGATGAAACTCTGAATGATGTTATCAATATGGGGTTTGACAAGA
genomic: CGCGTTATTTAGCTGTGCCACCTCCTGACACTGCACAACAGGTTAAAAAGgtaacatgct ... agttttgtagCTCGACGATGAAACTCTGAATGATGTTATCAATATGGGGTTTGACAAGA
EST: gi|29680933|gb|CB677208.1|CB677208
EST:     CGCGTTATTTAGCTGTGCCACCTCCTGACACTGCACAACAGGTTAAAAAG                         CTCGACGATGAAACTCTGAATGATGTTATCAATATGG
genomic: CGCGTTATTTAGCTGTGCCACCTCCTGACACTGCACAACAGGTTAAAAAGgtaacatgct ... agttttgtagCTCGACGATGAAACTCTGAATGATGTTATCAATATGG

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: 67 (upstream exon), 73 (downstream exon)
Score: 40

GATCACCATACGTGAAATCCGTGAACATCAGTGGTTCACAGTTGGTCTTCCGCGTTATTTAGCTGTGCCACCTCCTGACACTGCACAACAGGTTAAAAAGgtaacatgct ... agttttgtagCTCGACGATGAAACTCTGAATGATGTTATCAATATGGGGTTTGACAAGAATCAGCTAATCGAATCACTTCACAAGAGACTGCAAAACGAG




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