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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtgatctttcataaatatttaggatcattcttgattattttccagctcctagaattttgtgtttctttcaggttgatctttcatagacatttaggatcattcttgattattttaccagctccttgaatttcttgtttctttcagGCCCACATTGAGCAGTGGATTGACTTTTCAGCCACAGAGGTTGATGCTAATACTGGAAAATGGCTCTTCCCACGTCTTGGATTTGCTCCTTATGTTGCTG

Basic information

species Oryza sativa
transcript LOC_Os02g12800.2
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g12800.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G134582_T01 (Zea mays), 3'ss of exon 5
gtgagtgatctttcataaatatttaggatcattcttgattattttccagctcctagaattttgtgtttctttcaggttgatctttcatagacatttaggatcattcttgatta--ttttaccagctccttgaatttcttgtttctttcagGCCCACATTGAGCAGTGGATTGACTTTTCAGCCACAGAGGTTGATGCTAATACTGGAAAATGGCTCTTCCCACGTCTTGGATTTGCTCCTTATGTTGCTG
                                                |    |    ||   | ||| | | |   | || |   ||   | |  | |    |  ||| |||  | || |   || ||||||  |   | || ||||||||||| |||||||| |||||||||||| | || |||||| ||||||| || | |||||| ||| | | ||||||  | || |||  |||  ||| || ||
------------------------------------------------gtgagtgatgttcaatatttttattaaaatcatttaatattttcttgcatgccattgtttgcttagatgtttctgtctgcttgaacctgc-gcttgtttcagGCCCATATTGAGCAATGGATTGACTTTGCTGCAACAGAGATTGATGCAAACATTGGAAAGTGGTTGTACCCACGGATGGGGTTTTATCCCCATGCTGGTG

upper sequence: LOC_Os02g12800.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G029559_T02 (Zea mays), 3'ss of exon 5
gtgagtgatctttcataaatatttaggatcattcttgattattttccagctcctagaattttgtgtttctttcaggttgatctttcatagacatttaggatcattcttgattattttaccagctccttgaatttcttgtttctttcagGCCCACATTGAGCAGTGGATTGACTTTTCAGCCACAGAGGTTGATGCTAATACTGGAAAATGGCTCTTCCCACGTCTTGGATTTGCTCCTTATGTTGCTG
                                                |    ||   ||   | |||| ||||  || || ||  ||     | | | ||  || |   |   | |  | |  | ||  |     || || ||||||||||| |||||||||||||| |||||| | || |||||||||||||| |  | |||||| ||| | | ||||||| | || |||  ||| |||| |||||
------------------------------------------------gtgagtaatgttcaatatttcattcaaattaattttatatt----tcttgaatttttttgcttagatgtttctgtccgtttgaacctgtgcttgtttcagGCCCATATTGAGCAGTGGATGGACTTTGCTGCGACAGAGGTTGATGCCAGCATTGGAAAGTGGTTGTACCCACGTATGGGGTTTTATCCCTATGCTGCTG
















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|58652699|gb|CK041379.1|CK041379
EST:     CTCGCTCGAAGTCTGACAACCCACTCTATGGGTCTTCACTGATTGAATAT                         GCCCACATTGAGCAGTGGATTGACTTTTCAGCCACAGAGGTTGATGCTAAT
genomic: CTCGCTCGAAGTCTGACAACCCACTCTATGGGTCTTCACTGATTGAATATgtgagtgatc ... tttctttcagGCCCACATTGAGCAGTGGATTGACTTTTCAGCCACAGAGGTTGATGCTAAT
EST: gi|58663459|gb|CK052145.1|CK052145
EST:     CTCGCTCGAAGTCTGACAACCCACTCTATGGGTCTTCACTGATTGAATAT                         GCCCACATTGAGCAGTGGATTGACTTTTCAGCCACAGAGGTTGATGCTAAT
genomic: CTCGCTCGAAGTCTGACAACCCACTCTATGGGTCTTCACTGATTGAATATgtgagtgatc ... tttctttcagGCCCACATTGAGCAGTGGATTGACTTTTCAGCCACAGAGGTTGATGCTAAT
EST: gi|58691659|gb|CK080346.1|CK080346
EST:     CCACTCTATGGGTCTTCACTGATTGAATAT                         GCCCACATTGAGCAGTGGATTGACTTTTCAGCCACAGAGGTTGATGCTAAT
genomic: CCACTCTATGGGTCTTCACTGATTGAATATgtgagtgatc ... tttctttcagGCCCACATTGAGCAGTGGATTGACTTTTCAGCCACAGAGGTTGATGCTAAT
EST: gi|58663492|gb|CK052178.1|CK052178
EST:     CTCGCTCGAAGTCTGACAACCCACTCTATGGGTCTTCACTGATTGAATAT                         GCCCACATTGAGCAGTGGATTGACTTTTCAGCCACAGAGGTTGATGCTAAT
genomic: CTCGCTCGAAGTCTGACAACCCACTCTATGGGTCTTCACTGATTGAATATgtgagtgatc ... tttctttcagGCCCACATTGAGCAGTGGATTGACTTTTCAGCCACAGAGGTTGATGCTAAT
EST: gi|14571342|gb|BI118710.1|BI118710
EST:     CTCGCTCGAAGTCTGACAACCCACTCTATGGGTCTTCACTGATTGAATAT                         GCCCACATTGAGCAGTGGATTGACTTTTCAGCCACAGAGGTCGATGCTAAT
genomic: CTCGCTCGAAGTCTGACAACCCACTCTATGGGTCTTCACTGATTGAATATgtgagtgatc ... tttctttcagGCCCACATTGAGCAGTGGATTGACTTTTCAGCCACAGAGGTTGATGCTAAT
EST: gi|88991494|gb|CI034829.1|CI034829
EST:     CTCGCTCGAAGTCTGACAACCCACTCTATGGGTCTTCACTGATTGAATAT                         GCCCACATTGAGCAGTGGATTGACTTTTCAGCCACAGAGGTTGATGCTAAT
genomic: CTCGCTCGAAGTCTGACAACCCACTCTATGGGTCTTCACTGATTGAATATgtgagtgatc ... tttctttcagGCCCACATTGAGCAGTGGATTGACTTTTCAGCCACAGAGGTTGATGCTAAT
EST: gi|58652610|gb|CK041290.1|CK041290
EST:     CTCGCTCGAAGTCTGACAACCCACTCTATGGGTCTTCACTGATTGAATAT                         GCCCACATTGAGCAGTGGATTGACTTTTCAGCCACAGAGGTTGATGCTAAT
genomic: CTCGCTCGAAGTCTGACAACCCACTCTATGGGTCTTCACTGATTGAATATgtgagtgatc ... tttctttcagGCCCACATTGAGCAGTGGATTGACTTTTCAGCCACAGAGGTTGATGCTAAT
EST: gi|58599056|gb|CK009584.1|CK009584
EST:     CTCGCTCGAAGTCTGACAACCCACTCTATGGGTCTTCACTGATTGAATAT                         GCCCACATTGAGCAGTGGATTGACTTTTCAGCCACAGAGGTTGATGCTAAT
genomic: CTCGCTCGAAGTCTGACAACCCACTCTATGGGTCTTCACTGATTGAATATgtgagtgatc ... tttctttcagGCCCACATTGAGCAGTGGATTGACTTTTCAGCCACAGAGGTTGATGCTAAT
EST: gi|33795619|gb|CF323679.1|CF323679
EST:     CTCGCTCGAAGTCTGACAACCCACTCTATGGGTCTTCACTGATTGAATAT                         GCCCACATTGAGCAGTGGATTGACTTTTCAGCCACAGAGGTTGATGCTAAT
genomic: CTCGCTCGAAGTCTGACAACCCACTCTATGGGTCTTCACTGATTGAATATgtgagtgatc ... tttctttcagGCCCACATTGAGCAGTGGATTGACTTTTCAGCCACAGAGGTTGATGCTAAT
EST: gi|33797146|gb|CF324438.1|CF324438
EST:     CTCGCTCGAAGTCTGACAACCCACTCTATGGGTCTTCACTGATTGAATAT                         GCCCACATTGAGCAGTGGATTGACTTTTCAGCCACAGAGGTTGATGCTAAT
genomic: CTCGCTCGAAGTCTGACAACCCACTCTATGGGTCTTCACTGATTGAATATgtgagtgatc ... tttctttcagGCCCACATTGAGCAGTGGATTGACTTTTCAGCCACAGAGGTTGATGCTAAT
EST: gi|58656426|gb|CK045106.1|CK045106
EST:     CTCGCTCGAAGTCTGACAACCCACTCTATGGGTCTTCACTGATTGAATAT                         GCCCACATTGAGCAGTGGATTGACTTTTCAGCCACAGAGGTTGATGCTAAT
genomic: CTCGCTCGAAGTCTGACAACCCACTCTATGGGTCTTCACTGATTGAATATgtgagtgatc ... tttctttcagGCCCACATTGAGCAGTGGATTGACTTTTCAGCCACAGAGGTTGATGCTAAT
EST: gi|29678878|gb|CB675153.1|CB675153
EST:     CTCGCTCGAAGTCTGACAACCCACTCTATGGGTCTTCACTGATTGAATAT                         GCCCACATTGAGCAGTGGATTGACTTTTCAGCCACAGAGGTTGATGCTAAT
genomic: CTCGCTCGAAGTCTGACAACCCACTCTATGGGTCTTCACTGATTGAATATgtgagtgatc ... tttctttcagGCCCACATTGAGCAGTGGATTGACTTTTCAGCCACAGAGGTTGATGCTAAT

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: 53 (upstream exon), 71 (downstream exon)
Score: 51

TTACTCGCTCGAAGTCTGACAACCCACTCTATGGGTCTTCACTGATTGAATATgtgagtgatc ... tttctttcagGCCCACATTGAGCAGTGGATTGACTTTTCAGCCACAGAGGTTGATGCTAATACTGGAAAATGGCTCTTCCCACGTCTTGGATTTGCTCCTTATGTTGCTG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttaggatcattcttgattattttaccagctccttgaatttcttgtttctttcagGCCCACATTGAGCAGTGGATTGACTTTTCAGCCACAGAGGTTGATGCTAATACTGGAAAATGGCTCTTCCCACGTCTTGGATTTGCTCCTTATGTTGCTG
           tcttgat  putative branch site (score: 51)
                                      tttcttgtttctttc  putative PPT
         attcttgattatttta  TA-rich tract