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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CAATGTTGTGGCTGCAACTGATTTAACACTGATGGCATTGGCAGGAATAGGCCTGCGTCACGATAAGgtaaaagttttcccaggggtaatatgaaactctttttcattttaccttttgagtgttccatattagctactgatgcaaatcctggctgccatgttaactttgcacctttgaattcaactattgtgttctctttccatattctgacatatcatactccag

Basic information

species Oryza sativa
transcript LOC_Os05g39230.1
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g39230.2 (Oryza sativa), 5'ss of exon 6
lower sequence: AC197705.4_FGT011 (Zea mays), 5'ss of exon 7
CAATGTTGTGGCTGCAACTGATTTAACACTGATGGCATTGGCAGGAATAGGCCTGCGTCACGATAAGgtaaaagttttcccaggggtaatatgaaactctttttcattttaccttttgagtgttccatattagctactgatgcaaatcctggctgccatgt-taactttgcacctttgaattcaactattgtgttctct----ttccatattctgaca------tatcatactccag
|||||| || |||||||||||||| ||  ||||||||||||||||||||||||| ||   | | |||||||||       ||   |    || ||   || |   ||| |         |||   |  ||  | | ||||| ||| || |   |   |||  ||  |||||||| |  ||||    |||| |||| | |     ||  | |  |||||       ||||| || |||
CAATGTGGTTGCTGCAACTGATTTGACCATGATGGCATTGGCAGGAATAGGCCTTCGATGCAACAAGgtaaaa-------caaaag--gcattaagtactatcctattctg------aggtggctcccatgtgttgctgatacaagtcatta-tataatgcctatttttgcaccatcaaatt--ggtattctgttgtttgaaactctttgtgttgacaacttgacatcatgcttcag
















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|58602199|gb|CK012727.1|CK012727
EST:     CTGATTTAACACTGATGGCATTGGCAGGAATAGGCCTGCGTCACGATAAG                         AAATTAGGTTTTGCGTCTTGTGAACGAAGACCAGGTGCTACTGAAGGG
genomic: CTGATTTAACACTGATGGCATTGGCAGGAATAGGCCTGCGTCACGATAAGgtaaaagttt ... catactccagAAATTAGGTTTTGCGTCTTGTGAACGAAGACCAGGTGCTACTGAAGGG
EST: gi|8856717|gb|AU094035.1|AU094035
EST:     CTGATTTAACACTGATGGCATTGGCAGGAATAGGCCTGCGTCACGATAAG                         AAATTAGGTTTTGCGTCTTGTGAACGAAGACCAGGTGCTACTGAAGGGGTA
genomic: CTGATTTAACACTGATGGCATTGGCAGGAATAGGCCTGCGTCACGATAAGgtaaaagttt ... catactccagAAATTAGGTTTTGCGTCTTGTGAACGAAGACCAGGTGCTACTGAAGGGGTA
EST: gi|29689746|gb|CB686021.1|CB686021
EST:     CTGATTTAACACTGATGGCATTGGCAGGAATAGGCCTGCGTCACGATAAG                         AAATTAGGTTTTGCGTCTTGTGAACGAAGACCAGGTGCTACTGAAGGGGTA
genomic: CTGATTTAACACTGATGGCATTGGCAGGAATAGGCCTGCGTCACGATAAGgtaaaagttt ... catactccagAAATTAGGTTTTGCGTCTTGTGAACGAAGACCAGGTGCTACTGAAGGGGTA

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: 36 (upstream exon), 45 (downstream exon)
Score: 2

CAATGTTGTGGCTGCAACTGATTTAACACTGATGGCATTGGCAGGAATAGGCCTGCGTCACGATAAGgtaaaagttt ... catactccagAAATTAGGTTTTGCGTCTTGTGAACGAAGACCAGGTGCTACTGAAGGGGTAAATGTACTAATCGAAAAAGAAAACCAGGATGGACAATGGGCATATGGTA




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