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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaatcctattcactttgtggtttgcatggttattgatgctgatgtaaacttagctcaaattttgtttgaattttcagGTCCAGGATCTTACTCATTTACCATTTGCTGCTAGAGAGTTAATGATCATAAAGATTGCTGTAAACACCACAGCCCGCAGGGCTATCCTAGATATTGCTG

Basic information

species Oryza sativa
transcript LOC_Os11g14950.1
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os11g14950.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM2G077215_T01 (Zea mays), 3'ss of exon 9
gtaaatcctattcactttgtggtttgcatggttattgatgctgatgtaaacttagctcaaa-ttttgtttgaattttcagGTCCAGGATCTTACTCATTTACCATTTGCTGCTAGAGAGTTAATGATCATAAAGATTGCTGTAAACACCACAGCCCGCAGGGCTATCCTAGATATTGCTG
|||||   |||| || |||  |||| |||| || ||       ||  ||     ||| ||| |||| ||||  || |||||| |||||| |||| || |||||||||||||||||||||||||||||||||||| | || | |||  | ||||| || |||| | || ||||||||||| 
gtaaa---tattaacattgcagtttccatgattgtt-------atagaagtcacgctgaaagttttttttggtttctcagGTTCAGGATTTTACCCACTTACCATTTGCTGCTAGAGAGTTAATGATCATAAAGGTCGCGGCAAATGCTACAGCTCGAAGGGATGTCTTAGATATTGCTC
















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|29637024|gb|CB642033.1|CB642033
EST:     CTATTGCCAAGCTAGTACACCAACTGTATAAGCTCATTGATGTTTATGAG                         GTCCAGGATCTTACTCATTTACCA
genomic: CTATTGCCAAGCTAGTACACCAACTGTATAAGCTCATTGATGTTTATGAGgtaaatccta ... gaattttcagGTCCAGGATCTTACTCATTTACCA
EST: gi|29637025|gb|CB642034.1|CB642034
EST:     CTATTGCCAAGCTAGTACACCAACTGTATAAGCTCATTGATGTTTATGAG                         GTCCAGGATCTTACTCATTTACCATTTGCTGCTAGAGAGTTAATGATCATA
genomic: CTATTGCCAAGCTAGTACACCAACTGTATAAGCTCATTGATGTTTATGAGgtaaatccta ... gaattttcagGTCCAGGATCTTACTCATTTACCATTTGCTGCTAGAGAGTTAATGATCATA
EST: gi|218496146|gb|FG946660.1|FG946660
EST:     CTATTGCCAAGCTAGTACACCAACTGTATAAGCTCATTGATGTTTATGAG                         GTCCAGGATCTTACTCATTTACCATTTGCTGCTAGAGAGTTAATGATCATA
genomic: CTATTGCCAAGCTAGTACACCAACTGTATAAGCTCATTGATGTTTATGAGgtaaatccta ... gaattttcagGTCCAGGATCTTACTCATTTACCATTTGCTGCTAGAGAGTTAATGATCATA
EST: gi|29642738|gb|CB647745.1|CB647745
EST:     CTATTGCCAAGCTAGTACACCAACTGTATAAGCTCATTGATGTTTATGAG                         GTCCAGGATCTTACTCATTTACCATTTGCTGCTAGAGAGTTAATGATCATA
genomic: CTATTGCCAAGCTAGTACACCAACTGTATAAGCTCATTGATGTTTATGAGgtaaatccta ... gaattttcagGTCCAGGATCTTACTCATTTACCATTTGCTGCTAGAGAGTTAATGATCATA

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: 69 (upstream exon), 73 (downstream exon)
Score: 19

AAAAGAAGGCACTTCTCGGATCACTACTGTTGTCCCTGGAACTGATGAGTCTATTGCCAAGCTAGTACACCAACTGTATAAGCTCATTGATGTTTATGAGgtaaatccta ... gaattttcagGTCCAGGATCTTACTCATTTACCATTTGCTGCTAGAGAGTTAATGATCATAAAGATTGCTGTAAACACCACAGCCCGCAGGGCTATCCTAGATATTGCTG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgcatggttattgatgctgatgtaaacttagctcaaattttgtttgaattttcagGTCCAGGATCTTACTCATTTACCATTTGCTGCTAGAGAGTTAATGATCATAAAGATTGCTGTAAACACCACAGCCCGCAGGGCTATCCTAGATATTGCTG
              tgctgat  putative branch site (score: 19)
                                                ttttc  putative PPT
                                  aaattttgtttgaatt  TA-rich tract