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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ACACACCCTTCACAAACGTGTTTCTTATCATCAATTGATCTGCACACTCAATACTCCTACCAGgtaattatatgacagataataatgttttgtctcaaaataaatggtgtatcaatagaaagttcagctcttatcaatttataaaggatggtataatactttg...

Basic information

species Oryza sativa
transcript LOC_Os01g47262.1
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g47262.2 (Oryza sativa), 5'ss of exon 7
lower sequence: GLYMA01G03710.1 (Glycine max), 5'ss of exon 8
ACACACCCTTCACAAACGTGTTTCTTATCATCAATTGATCTGCACACTCAATACTCCTACCAGgtaattatatgacagataataatgttttgtctcaaaataaatggtgtatcaatagaaagttcagctcttatcaatttataaagga--tggtataatactttg
||||| ||||| ||||  |||||| | |||||  | ||||||||||||||||| ||||||||||| |||  ||   || |  |  |||| |  | ||   |   || |  |   ||      |||| || || |||| || ||| ||   | |  || ||  |  
ACACATCCTTCTCAAAGTTGTTTCATGTCATCGGTGGATCTGCACACTCAATATTCCTACCAGgtgattg-atccaagttttttttgttattacacacttttcttg-taaaagcatttttttttcaactattgtcaacttgtaacggcattagagtattatctcc
















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|44677600|gb|CR291034.1|CR291034
EST:     AAACGTGTTTCTTATCATCAATTGATCTGCACACTCAATACTCCTACCAG                         GTTGTGTTACCAGAGGCCGTTGCGATTGTGATTGCTCCCACTGATCCTACT
genomic: AAACGTGTTTCTTATCATCAATTGATCTGCACACTCAATACTCCTACCAGgtaattatat ... atttcttcagGTTATGTTACCAGAGGCCGTTGCGATTGTGATTGCTCCCACTGATCCTACT
EST: gi|218493474|gb|FG952533.1|FG952533
EST:     AAACGTGTTTCTTATCATCAATTGATCTGCACACTCAATACTCCTACCAG                         GTTATGTTACCAGAGGCCGTTGCGATTGTGATTGCTCCCACTGATCCTACT
genomic: AAACGTGTTTCTTATCATCAATTGATCTGCACACTCAATACTCCTACCAGgtaattatat ... atttcttcagGTTATGTTACCAGAGGCCGTTGCGATTGTGATTGCTCCCACTGATCCTACT
EST: gi|33658750|gb|CF281363.1|CF281363
EST:     AAACGTGTTTCTTATCATCAATTGATCTGCACACTCAATACTCCTACCAG                         GTTATGTTACCAGAGGCCGTTGCGATTGTGATTGCTCCCACTGATCCTACT
genomic: AAACGTGTTTCTTATCATCAATTGATCTGCACACTCAATACTCCTACCAGgtaattatat ... atttcttcagGTTATGTTACCAGAGGCCGTTGCGATTGTGATTGCTCCCACTGATCCTACT
EST: gi|29670555|gb|CB666830.1|CB666830
EST:     AAACGTGTTTCTTATCATCAATTGATCTGCACACTCAATACTCCTACCAG                         GTTATGTTACCAGAGGCCGTTGCGATTGTGATTGCTCCCACTGATCCTACT
genomic: AAACGTGTTTCTTATCATCAATTGATCTGCACACTCAATACTCCTACCAGgtaattatat ... atttcttcagGTTATGTTACCAGAGGCCGTTGCGATTGTGATTGCTCCCACTGATCCTACT
EST: gi|88226876|gb|CI224644.1|CI224644
EST:     AAACGTGTTTCTTATCATCAATTGATCTGCACACTCAATACTCCTACCAG                         GTTATGTTACCAGAGGCCGTTGCGATTGTGATTGCTCCCACTGATCCTACT
genomic: AAACGTGTTTCTTATCATCAATTGATCTGCACACTCAATACTCCTACCAGgtaattatat ... atttcttcagGTTATGTTACCAGAGGCCGTTGCGATTGTGATTGCTCCCACTGATCCTACT
EST: gi|86496637|gb|CI139270.1|CI139270
EST:     AAACGTGTTTCTTATCATCAATTGATCTGCACACTTAATACTCCTACCAG                         GTTATGTTACCAGAGGCCGTTGCGATTGTGATTGCTCCCACTGATCCTACT
genomic: AAACGTGTTTCTTATCATCAATTGATCTGCACACTCAATACTCCTACCAGgtaattatat ... atttcttcagGTTATGTTACCAGAGGCCGTTGCGATTGTGATTGCTCCCACTGATCCTACT

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: 63 (upstream exon), 53 (downstream exon)
Score: 152

ACACACCCTTCACAAACGTGTTTCTTATCATCAATTGATCTGCACACTCAATACTCCTACCAGgtaattatat ... atttcttcagGTTATGTTACCAGAGGCCGTTGCGATTGTGATTGCTCCCACTGATCCTACTAG




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