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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtctgatcactctctctctctctctctctctctctctccaagtttaacaatcttaaagcaaaacaaatggcacatccagaccatatgggcaaaacatgaacaaaaatgtgtggttacctgcagGATCGGAATATCATGACAGATTTTGACATTTCCAAGGAAGCAGGGGGTTCCAACAGACCCATTAACAGAAATTATACAGCGGATGTCACCACCTCAGTGT

Basic information

species Oryza sativa
transcript LOC_Os06g07130.1
intron # 15
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g07130.1 (Oryza sativa), 3'ss of exon 15
lower sequence: GRMZM2G103033_T03 (Zea mays), 3'ss of exon 14
gtctgatcactctctctctctctctctctctctctctccaagtttaacaatcttaaagcaaaacaaatggcacatccagaccatatgggcaaaacatgaacaaaaatgtgtggttacctgcagGATCGGAATATCATGACAGATTTTGACATTTCCAAGGAAGCAGGGGGTTCCAACAGACCCATTAACAGAAATTATACAGCGGATGTCACCACCTCAGTGT
                                         |||| |     |   | |||   |||  |   ||  |   |||||     | || |       |||  ||   ||  ||||||| | |||||||| ||  || ||||||||| | |||||||||||||||||||  | | ||| ||||| ||  ||                          
-----------------------------------------gtttgatcccttcttaacaatg-aaaaagtttattta---catat-----atactt---ttttaattggttaataattgcagGACCAGAATATCAGGAAGGACTTTGACATTACTAAGGAAGCAGGGGGTTCCAGAAAAGCCACTAACATAACCTA--------------------------
















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|29626581|gb|CB631592.1|CB631592
EST:     TAGTTATAGAAAGTGGATCAGGAAGGCGTTTATTTAACATCGACATTCAG                         GATCGGAATATCATGACAGATTTTGACATTTCCAAGGAAGCAGGGGGTTCC
genomic: TAGTTATAGAAAGTGGATCAGGAAGGCGTTTATTTAACATCGACATTCAGgtctgatcac ... ttacctgcagGATCGGAATATCATGACAGATTTTGACATTTCCAAGGAAGCAGGGGGTTCC
EST: gi|286986|gb|D15792.1|D15792
EST:     TAGTTATAGAAAGTGGATCAGGAAGGCGTTTATTTAACATCGACATTCAG                         GATCGGAATATCATGACAGATTTTGACATTTCCAAGGAAGCAGGGGGTTCC
genomic: TAGTTATAGAAAGTGGATCAGGAAGGCGTTTATTTAACATCGACATTCAGgtctgatcac ... ttacctgcagGATCGGAATATCATGACAGATTTTGACATTTCCAAGGAAGCAGGGGGTTCC
EST: gi|29679066|gb|CB675341.1|CB675341
EST:     TAGTTATAGAAAGTGGATCAGGAAGGCGTTTATTTAACATCGACATTCAG                         GATCGGAATATCATGACAGATTTTGACATTTCCAAGGAAGCAGGGGGTTCC
genomic: TAGTTATAGAAAGTGGATCAGGAAGGCGTTTATTTAACATCGACATTCAGgtctgatcac ... ttacctgcagGATCGGAATATCATGACAGATTTTGACATTTCCAAGGAAGCAGGGGGTTCC
EST: gi|218501924|gb|FG968995.1|FG968995
EST:     TAGTTATAGAAAGTGGATCAGGAAGGCGTTTATTTAACATCGACATTCAG                         GATCGGAATATCATGACAGATTTTGACATTTCCAAGGAAGCAGGGGGTTCC
genomic: TAGTTATAGAAAGTGGATCAGGAAGGCGTTTATTTAACATCGACATTCAGgtctgatcac ... ttacctgcagGATCGGAATATCATGACAGATTTTGACATTTCCAAGGAAGCAGGGGGTTCC
EST: gi|29625290|gb|CB630301.1|CB630301
EST:     TAGTTATAGAAAGTGGATCAGGAAGGCGTTTATTTAACATCGACATTCAG                         GATCGGAATATCATGACAGATTTTGACATTTCCAAGGAAGCAGGGGGTTCC
genomic: TAGTTATAGAAAGTGGATCAGGAAGGCGTTTATTTAACATCGACATTCAGgtctgatcac ... ttacctgcagGATCGGAATATCATGACAGATTTTGACATTTCCAAGGAAGCAGGGGGTTCC

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: 46 (upstream exon), 73 (downstream exon)
Score: 15

GGTTGGCTTGCCTAGTGGGAAATATACAGTTCAACTCTTCTTTGCAGAGATAGTTATAGAAAGTGGATCAGGAAGGCGTTTATTTAACATCGACATTCAGgtctgatcac ... ttacctgcagGATCGGAATATCATGACAGATTTTGACATTTCCAAGGAAGCAGGGGGTTCCAACAGACCCATTAACAGAAATTATACAGCGGATGTCACCACCTCAGTGT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggcacatccagaccatatgggcaaaacatgaacaaaaatgtgtggttacctgcagGATCGGAATATCATGACAGATTTTGACATTTCCAAGGAAGCAGGGGGTTCCAACAGACCCATTAACAGAAATTATACAGCGGATGTCACCACCTCAGTGT
                              aacaaaaat  TA-rich tract