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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtagcattcctattcatctttcttctatattgcaaatttcaataaacatgatgggtgcactgttatttttcagGTATTGATAAAATAGTTGGTTTTGCTTTGAGTCATCAACTTAAGCACTCTACAATTCCAGACCCTTCGAGTGATGTTCGTTTCACTCTATCTAGTGAAAG

Basic information

species Oryza sativa
transcript LOC_Os03g22420.2
intron # 18
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g22420.2 (Oryza sativa), 3'ss of exon 18
lower sequence: GRMZM2G042074_T02 (Zea mays), 3'ss of exon 13
gtgagtagcattcctattcatctttcttctatattgcaaatttcaataaacatgatgggtgcactgttatttttcagGTATTGATAAAATAGTTGGTTTTGCTTTGAGTCATCAACTTAAGCACTCTACAATTCCAGACCC---TTCGAGTGATGTTCGTTTCACTCTATCTAGTGAAAG
||||||  ||||| ||| ||| ||  |   | ||   |   ||     |   | || | | || ||||||||| ||||||||||||||||| |||||||||||||||| |||||||||||| ||| ||||| |||||||||   || |||| |||| |  ||   |||||| || ||   
gtgagtgccattcatatccattttaatgtaagatcata---tttgcccagtgtcattgatacattgttatttt-cagGTATTGATAAAATAATTGGTTTTGCTTTGAGCCATCAACTTAAGAACTGTACAAATCCAGACCCCCCTTTGAGTAATGTGCAGTTTGTTCTATCCAGCGA---
















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|58605943|gb|CK033976.1|CK033976
EST:     CAGTGATCTTGAAACAGTATGTGTTAAGGATCGTCTCCTAACAAACGAAT                         GTATTGATAAAATAGTTGGTTTTGCTTTGAGTCATCAACTTAAGCACTCTA
genomic: CAGTGATCTTGAAACAGTATGTGTTAAGGATCGTCTCCTAACAAACGAATgtgagtagca ... tatttttcagGTATTGATAAAATAGTTGGTTTTGCTTTGAGTCATCAACTTAAGCACTCTA
EST: gi|58688470|gb|CK077157.1|CK077157
EST:     TCCTAACAAACGAAT                         GTATTGATAAAATAGTTGGTTTTGCTTTGAGTCATCAACTTAAGCACTCTA
genomic: TCCTAACAAACGAATgtgagtagca ... tatttttcagGTATTGATAAAATAGTTGGTTTTGCTTTGAGTCATCAACTTAAGCACTCTA
EST: gi|29635827|gb|CB640836.1|CB640836
EST:     GAAACAGTATGTGTTAAGGATCGTCTCCTAACAAACGAAT                         GTATTGATAAAATAGTTGGTTTTGCTTTGAGTCATCAACTTAAGCACTCTA
genomic: GAAACAGTATGTGTTAAGGATCGTCTCCTAACAAACGAATgtgagtagca ... tatttttcagGTATTGATAAAATAGTTGGTTTTGCTTTGAGTCATCAACTTAAGCACTCTA

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), 73 (downstream exon)
Score: 45

TTTCTATTAAAGATGGGCTTGGAAAGCAGTGATCTTGAAACAGTATGTGTTAAGGATCGTCTCCTAACAAACGAATgtgagtagca ... tatttttcagGTATTGATAAAATAGTTGGTTTTGCTTTGAGTCATCAACTTAAGCACTCTACAATTCCAGACCCTTCGAGTGATGTTCGTTTCACTCTATCTAGTGAAAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttcttctatattgcaaatttcaataaacatgatgggtgcactgttatttttcagGTATTGATAAAATAGTTGGTTTTGCTTTGAGTCATCAACTTAAGCACTCTACAATTCCAGACCCTTCGAGTGATGTTCGTTTCACTCTATCTAGTGAAAG
                                            ttatttttc  CT-rich tract
       tatattgcaaatttca  TA-rich tract