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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagttctgacataaattgttggatgaaaaccaatataacaagttattaagttctgctccccacagtagcacaaggtcttttatgcacttagttattctttcttttgcaattttacttgtattccatgtacttttgatttgagttcggtgttattatcacgacatttaaattcttgtttcagGCCAAGGACTGGAAAAAGGCATTGCAGCTATTTGAGGAGATCAAGTCAATCAAATTAATGCCAACCGTTTCAATGATGAATGCTCTGATCACCGCATTGT

Basic information

species Oryza sativa
transcript LOC_Os10g10170.1
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os10g10170.2 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G018929_T02 (Zea mays), 3'ss of exon 3
gtaagttctgacataaattgttggatgaaaaccaatataacaagttattaagttctgctccccacagtagcacaaggtcttttatgcacttagttattctttcttttgcaattttacttgtattccatgtacttttgatttgagttcggtgttattatcacgacatttaaattcttgtttcagGCCAAGGACTGGAAAAAGGCATTGCAGCTATTTGAGGAGATCAAGTCAATCAAATTAATGCCAACCGTTTCAATGATGAATGCTCTGATCACCGCATTGT
                                                                              |||  |||         |||    || || | | |  |||  | ||  |   | | ||  ||| ||  |         |||| ||  |    | |  ||||||||||  | |||||||| |||||| |||||||||  |||||||||||||| |||||||| |  ||| | |||||||||||||||||| |||||||| |  |||
-------------------------------------------------------------------------tgttacttgcatgttacatcccatttcccctcttcctaatacactgatgttttac-caatattccttttagcac---------atcatgatttgaggactgctgtttcagGCGGACGACTGGAAGAAGGCACTGCAGCTATACGAGGAGATCAAGTCTATCAAATTGACCCCATCGGTTTCAATGATGAATGCTTTGATCACCTCTCTGT
















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|58691402|gb|CK080089.1|CK080089
EST:     ATCAAGTTGGAACCATTGCATACAGTTCATTAATGGGTGCTTGCTGCAAT                         GCCAAGGACTGGAAAAAGGCATTGCAGCTATTTGAGGAGATCAAGTCAATC
genomic: ATCAAGTTGGAACCATTGCATACAGTTCATTAATGGGTGCTTGCTGCAATgtaagttctg ... cttgtttcagGCCAAGGACTGGAAAAAGGCATTGCAGCTATTTGAGGAGATCAAGTCAATC
EST: gi|58695106|gb|CK083793.1|CK083793
EST:     ATCAAGTTGGAACCATTGCATACAGTTCATTAATGGGTGCTTGCTGCAAT                         GCCAAGGACTGGAAAAAGGCATTGCAGCTATTTGAGGAGATCAAGTCAATC
genomic: ATCAAGTTGGAACCATTGCATACAGTTCATTAATGGGTGCTTGCTGCAATgtaagttctg ... cttgtttcagGCCAAGGACTGGAAAAAGGCATTGCAGCTATTTGAGGAGATCAAGTCAATC

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: 74 (upstream exon), 64 (downstream exon)
Score: 13

GAGGGCTGATGCTGCCTTTGAGATAATGAAAGATGCAAGAGCAAAGGGATATCAAGTTGGAACCATTGCATACAGTTCATTAATGGGTGCTTGCTGCAATgtaagttctg ... cttgtttcagGCCAAGGACTGGAAAAAGGCATTGCAGCTATTTGAGGAGATCAAGTCAATCAAATTAATGCCAACCGTTTCAATGATGAATGCTCTGATCACCGCATTGT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtacttttgatttgagttcggtgttattatcacgacatttaaattcttgtttcagGCCAAGGACTGGAAAAAGGCATTGCAGCTATTTGAGGAGATCAAGTCAATCAAATTAATGCCAACCGTTTCAATGATGAATGCTCTGATCACCGCATTGT
    ttttgat  putative branch site (score: 13)
                                           ttcttgtttc  putative PPT
                                    atttaaattcttgttt  TA-rich tract