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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagcccggagtgtatgccctacatcaatttataactgaattgatgtttactttgttcgcttcattcctatgtttcaacagCGTGGAGGAGTACTCATACAAAAATGGGGCAGATCTTCAGCTGCATCAACCGCCGTTTCCATCGTGGATGCTATTAGGTCCCTTGTAAATCCTACCCCAG

Basic information

species Oryza sativa
transcript LOC_Os08g44810.1
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os08g44810.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM2G129513_T01 (Zea mays), 3'ss of exon 9
-----------------------gtaagcccggagt-gtatgccctacatcaatttataactgaattgatgtttactttgttcgcttcattcctatgtttcaacagCGTGGAGGAGTACTCATACAAAAATGGGGCAGATCTTCAGCTGCATCAACCGCCGTTTCCATCGTGGATGCTATTAGGTCCCTTGTAAATCCTACCCCAG
                        || |   || || |  || |   |   || |||   |   | ||     || ||| |||      ||| ||| | | ||||||||||||| || ||||| ||||||||||||||||| ||||||||||| ||||| ||||| || |||||||||||||| ||||| |||| |||||||||||
gtatgtgcctctccctgtttgcaatatgtttggtgttgcctgtcactcgagaaattaagtcaagactgcaccataatttattc----tgttcatatatctaaacagCGTGGAGGTGTGCTCATCCAAAAATGGGGCAGATCATCAGCTGCATCGACCGCTGTTTCGATAGTGGATGCTATTAGATCCCTCGTAACTCCTACCCCAG
















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|29686260|gb|CB682535.1|CB682535
EST:     TTAAAGACACAAAGTGGTTAGAAGATGAATTCACCAAAACAGTTCAAAAG                         CGTGGAGGAGTACTCATACAAAAATGGGGCAGATCTTCAGCTGCATCAACC
genomic: TTAAAGACACAAAGTGGTTAGAAGATGAATTCACCAAAACAGTTCAAAAGgtaagcccgg ... gtttcaacagCGTGGAGGAGTACTCATACAAAAATGGGGCAGATCTTCAGCTGCATCAACC
EST: gi|38468692|gb|CF952823.1|CF952823
EST:     TTAAAGACACAAAGTGGTTAGAAGATGAATTCACCAAAACAGTTCAAAAG                         CGTGGAGGAGTACTCATACA
genomic: TTAAAGACACAAAGTGGTTAGAAGATGAATTCACCAAAACAGTTCAAAAGgtaagcccgg ... gtttcaacagCGTGGAGGAGTACTCATACA
EST: gi|86901993|gb|CI300232.1|CI300232
EST:     TTAAAGACACAAAGTGGTTAGAAGATGAATTCACCAAAACAGTTCAAAAG                         CGTGGAGGAGTACTCATACAAAAATGGGGCAGATCTTCAGCTGCATCAACC
genomic: TTAAAGACACAAAGTGGTTAGAAGATGAATTCACCAAAACAGTTCAAAAGgtaagcccgg ... gtttcaacagCGTGGAGGAGTACTCATACAAAAATGGGGCAGATCTTCAGCTGCATCAACC
EST: gi|3763525|gb|AU030277.1|AU030277
EST:     TTAAAGACACAAAGTGGTTAGAAGATGAATTCACCAAAACAGTTCAAAAG                         CGTGGAGGAGTACTCATACAAAAATGGGGCAGATCTTCAGCTGCATCAACC
genomic: TTAAAGACACAAAGTGGTTAGAAGATGAATTCACCAAAACAGTTCAAAAGgtaagcccgg ... gtttcaacagCGTGGAGGAGTACTCATACAAAAATGGGGCAGATCTTCAGCTGCATCAACC
EST: gi|29613418|gb|CB618431.1|CB618431
EST:     TTAAAGACACAAAGTGGTTAGAAGATGAATTCACCAAAACAGTTCAAAAG                         CGTGGAGGAGTACTCATACAAAAATGGGGCAGATCTTCAGCTGCATCAACC
genomic: TTAAAGACACAAAGTGGTTAGAAGATGAATTCACCAAAACAGTTCAAAAGgtaagcccgg ... gtttcaacagCGTGGAGGAGTACTCATACAAAAATGGGGCAGATCTTCAGCTGCATCAACC
EST: gi|29677718|gb|CB673993.1|CB673993
EST:     TTAAAGACACAAAGTGGTTAGAAGATGAATTCACCAAAACAGTTCAAAAG                         CGTGGAGGAGTACTCATACAAAAATGGGGCAGATCTTCAGCTGCATCAACC
genomic: TTAAAGACACAAAGTGGTTAGAAGATGAATTCACCAAAACAGTTCAAAAGgtaagcccgg ... gtttcaacagCGTGGAGGAGTACTCATACAAAAATGGGGCAGATCTTCAGCTGCATCAACC

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: 73 (upstream exon), 65 (downstream exon)
Score: 100

TCCTGATTTTTTGAATGCTAAAATTAACGGGAGACCAGTGAAAGAAGTCATTAAAGACACAAAGTGGTTAGAAGATGAATTCACCAAAACAGTTCAAAAGgtaagcccgg ... gtttcaacagCGTGGAGGAGTACTCATACAAAAATGGGGCAGATCTTCAGCTGCATCAACCGCCGTTTCCATCGTGGATGCTATTAGGTCCCTTGTAAATCCTACCCCAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aatttataactgaattgatgtttactttgttcgcttcattcctatgtttcaacagCGTGGAGGAGTACTCATACAAAAATGGGGCAGATCTTCAGCTGCATCAACCGCCGTTTCCATCGTGGATGCTATTAGGTCCCTTGTAAATCCTACCCCAG
                    tttacttt  TA-rich tract