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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtttcaattcttttttggtctgcagcttgctatttactcaaatgtctgaaatttccctttttccaatgcagCTTAAGCGATGGGAGAGGAAGAAGTGTAAACCAAACAGTCTTCCTGTCCTGCACAAGATGCATGTTAGGATTGGCGATACAGTACAAGTCATTGCAGGCC

Basic information

species Oryza sativa
transcript LOC_Os06g46930.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g46930.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G463913_T01 (Zea mays), 3'ss of exon 2
gtaagtttcaattcttttttggtctgcagcttgcta-----tttactcaaatgtctgaaatttcc--------ctttttccaatgcagCTTAAGCGATGGGAGAGGAAGAAGTGTAAACCAAACAGTCTTCCTGTCCTGCACAAGATGCATGTTAGGATTGGCGATACAGTACAAGTCATTGCAGGCC
|| |||   ||   | ||| |  |      ||| ||     ||||  |||   | |||||| |||        |  |||||| ||||||||||| |||||||| | ||||||||||||||||||||||||||||| ||||||||||||||||||||||| || || || ||||| || ||||||||||
gtgagtaaaaaaaatctttagtccaaatatttgataccttttttatccaataatgtgaaatgtcctaaaacttcactttccactgcagCTTAAGAGATGGGAGCGAAAGAAGTGTAAACCAAACAGTCTTCCTGTGCTGCACAAGATGCATGTTAGGATCGGGGACACGGTACAGGTTATTGCAGGCC

upper sequence: LOC_Os06g46930.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA12G34400.2 (Glycine max), 3'ss of exon 2
-----------------------gtaagtttcaattcttttttggtctgcagcttgctatttactcaaatgtctgaaatttccc-tttttccaatg-cagCTTAAGCGATGGGAGAGGAAGAAGTGTAAACCAAACAGTCTTCCTGTCCTGCACAAGATGCATGTTAGGATTGGCGATACAGTACAAGTCATTGCAGGCC
                         |   ||  | ||   | |  | || |||| ||  |    |    |||   | |||| |  ||| |||  || |||||||| ||||||||| ||||| ||||||||||||||||||||||| || ||||||| ||||||||||   |||| ||||| || ||||||||  | || |
ttatattgcaaaacagtatctagacatagttatactcaaatatattatgtagctagccttaatgttttgtgtaatatattttctgtttctcctctggcagCTTAAACGATGGGAGCGGAAGGAGTGTAAACCAAACAGTCTTCCTATCTTGCACAAAATGCATGTTAAACTTGGAGATACGGTGCAAGTCATATCTGGAC

upper sequence: LOC_Os06g46930.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA13G36150.1 (Glycine max), 3'ss of exon 2
--------------------------gta-agtttcaattcttttttggtctgcagcttgctatttactcaaatgtctgaaatttccctttttccaatgcagCTTAAGCGATGGGAGAGGAAGAAGTGTAAACCAAACAGTCTTCCTGTCCTGCACAAGATGCATGTTAGGATTGGCGATACAGTACAAGTCATTGCAGGCC
                          | | ||||  | |     | |  | || |||| ||   ||| |    ||| | | ||||   || | |    ||||||||| ||||||||  ||||| |||||||||||||||| |||||| || ||||||| ||||||||||   |||| ||||| || ||||||||  | || |
tttatattgcaaaacagcatatctaggcatagttatactcaaaatatattatgtagctagcc--ttaatgttttgtgtaatattttgtttctcctctggcagCTTAAACGATGGGAACGGAAGGAGTGTAAACCAAACAGCCTTCCTATCTTGCACAAAATGCATGTTAAACTTGGAGATACGGTGCAAGTCATATCTGGAC

upper sequence: LOC_Os06g46930.1 (Oryza sativa), 3'ss of exon 2
lower sequence: Vv19s0014g04970.t01 (Vitis vinifera), 3'ss of exon 2
---------------gtaagtt--tcaattcttttttggtctgcagcttgctatttact--------caaatgtctgaaatttccctttttccaatgcagCTTAAGCGATGGGAGAGGAAGAAGTGTAAACCAAACAGTCTTCCTGTCCTGCACAAGATGCATGTTAGGATTGGCGATACAGTACAAGTCATTGCAGGCC
                 || |   | | ||  ||  || ||   | | ||   | |  |        ||| ||  |  | |||  ||||  |  ||||||||||||||||||||| ||||| | || ||||| ||||| ||||| || || || || |||||||||| | | || ||||||||  || | ||  | ||  
ctgtctgagcaacgcaaaaatccatgagttacttgatgatcatgaacatggcttctcttaaaaataccaagtggttttactttgtctttacctcatgcagCTTAAGCGATGGGAGCGGAAGGAATGCAAACCCAACAGCCTTCCGGTGCTACATAAAATGCATGTTAAGGTGGGAGATACAGTGAAAATAATATCTGGTA

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|55412128|gb|CV724504.1|CV724504
EST:     GTTAAATTTATGATCAAGACATGCCCAATTCAAATGAGG                         CTTAAGCGATGGGAGAGGAAGAAGTGTAAACCAAACAGTCTTCCTGTCCTG
genomic: GTTAAATTTATGATCAAGACATGCCCAATTCAAATGAGGgtaagtttca ... tccaatgcagCTTAAGCGATGGGAGAGGAAGAAGTGTAAACCAAACAGTCTTCCTGTCCTG
EST: gi|88330769|gb|CI636777.1|CI636777
EST:     GTTAAATTTATGATCAAGACATGCCCAATTCAAATGAGG                         CTTAAGCGATGGGAGAGGAAGAAGTGTAAACCACACAGTCTTCCTGTCCTG
genomic: GTTAAATTTATGATCAAGACATGCCCAATTCAAATGAGGgtaagtttca ... tccaatgcagCTTAAGCGATGGGAGAGGAAGAAGTGTAAACCAAACAGTCTTCCTGTCCTG
EST: gi|33815049|gb|CF333389.1|CF333389
EST:     GTTAAATTTATGATCAAGACATGCCCAATTCAAATGAGG                         CTTAAGCGATGGGAGAGGAAGAAGTGTAAACCAAACAGTCTTCCTGTCCTG
genomic: GTTAAATTTATGATCAAGACATGCCCAATTCAAATGAGGgtaagtttca ... tccaatgcagCTTAAGCGATGGGAGAGGAAGAAGTGTAAACCAAACAGTCTTCCTGTCCTG
EST: gi|38474567|gb|CF958700.1|CF958700
EST:     GTTAAATTTATGATCAAGACATGCCCAATTCAAATGAGG                         CTTAAGCGATGGGAGAGGAAGAAGTGTAAACCAAACAGTCTTCCTGTCCTG
genomic: GTTAAATTTATGATCAAGACATGCCCAATTCAAATGAGGgtaagtttca ... tccaatgcagCTTAAGCGATGGGAGAGGAAGAAGTGTAAACCAAACAGTCTTCCTGTCCTG
EST: gi|55412137|gb|CV724513.1|CV724513
EST:     GTTAAATTTATGATCAAGACATGCCCAATTCAAATGGGG                         CTTAAGCGATGGGAGAGGAAGAAGTGTAAACCAAACAGTCTTCCTGTCCTG
genomic: GTTAAATTTATGATCAAGACATGCCCAATTCAAATGAGGgtaagtttca ... tccaatgcagCTTAAGCGATGGGAGAGGAAGAAGTGTAAACCAAACAGTCTTCCTGTCCTG
EST: gi|58594789|gb|CF993097.1|CF993097
EST:     GTTAAATTTATGATCAAGACATGCCCAATTCAAATGAGG                         CTTAAGCGAGGGGAGAGGAAGAAGTGTAAACCAAACAGTCTTCCTGTCCTG
genomic: GTTAAATTTATGATCAAGACATGCCCAATTCAAATGAGGgtaagtttca ... tccaatgcagCTTAAGCGATGGGAGAGGAAGAAGTGTAAACCAAACAGTCTTCCTGTCCTG
EST: gi|88352549|gb|CI654374.1|CI654374
EST:     GTTAAATTTATGATCAAGACATGCCCAATTCAAATGAGG                         CTTAAGCGATGGGAGAGGAAGAAGTGTAAACCAAACAGTCTTCCTGTCCTG
genomic: GTTAAATTTATGATCAAGACATGCCCAATTCAAATGAGGgtaagtttca ... tccaatgcagCTTAAGCGATGGGAGAGGAAGAAGTGTAAACCAAACAGTCTTCCTGTCCTG
EST: gi|56157658|gb|C25003.2|C25003
EST:     GTTAAATTTATGATCAAGACATGCCCAATTCAAATGAGG                         CTTAAGCGATGGGAGAGGAAGAAGTGTAAACCAAACAGTCTTCCTGTCCTG
genomic: GTTAAATTTATGATCAAGACATGCCCAATTCAAATGAGGgtaagtttca ... tccaatgcagCTTAAGCGATGGGAGAGGAAGAAGTGTAAACCAAACAGTCTTCCTGTCCTG
EST: gi|88414886|gb|CI601718.1|CI601718
EST:     GTTAAATTTATGATCAAGACATGCCCAATTCAAATGAGG                         CTTAAGCGATGGGAGAGGAAGAAGTGTAAACCAAACAGTCTTCCTGTCCTG
genomic: GTTAAATTTATGATCAAGACATGCCCAATTCAAATGAGGgtaagtttca ... tccaatgcagCTTAAGCGATGGGAGAGGAAGAAGTGTAAACCAAACAGTCTTCCTGTCCTG
EST: gi|33801796|gb|CF326771.1|CF326771
EST:     GTTAAATTTATGATCAAGACATGCCCAATTCAAATGAGG                         CTTAAGCGATGGGAGAGGAAGAAGTGTAAACCAAACAGTCTTCCTGTCCTG
genomic: GTTAAATTTATGATCAAGACATGCCCAATTCAAATGAGGgtaagtttca ... tccaatgcagCTTAAGCGATGGGAGAGGAAGAAGTGTAAACCAAACAGTCTTCCTGTCCTG
EST: gi|86830951|gb|CI295472.1|CI295472
EST:     GTTAAATTTATGATCAAGACATGCCCAATTCAAATGAGG                         CTTAAGCGATGGGAGAGGAAGAAGTGTAAACCAAACAGTCTTCCTGTCCTG
genomic: GTTAAATTTATGATCAAGACATGCCCAATTCAAATGAGGgtaagtttca ... tccaatgcagCTTAAGCGATGGGAGAGGAAGAAGTGTAAACCAAACAGTCTTCCTGTCCTG
EST: gi|38477056|gb|CF961189.1|CF961189
EST:     GTTAAATTTATGATCAAGACATGCCCAATTCAAATGAGG                         CTTAAGCGATGGGAGAGGAAGAAGTGTAAACCAAACAGTCTTCCTGTCCTG
genomic: GTTAAATTTATGATCAAGACATGCCCAATTCAAATGAGGgtaagtttca ... tccaatgcagCTTAAGCGATGGGAGAGGAAGAAGTGTAAACCAAACAGTCTTCCTGTCCTG
EST: gi|3763301|gb|AU030053.1|AU030053
EST:     GTTAAATTTATGATCAAGACATGCCCAATTCAAATGAGG                         CTTAAGCGATGGGAGAGGAAGAAGTGTAAACCAAACAGTCTTCCTGTCCTG
genomic: GTTAAATTTATGATCAAGACATGCCCAATTCAAATGAGGgtaagtttca ... tccaatgcagCTTAAGCGATGGGAGAGGAAGAAGTGTAAACCAAACAGTCTTCCTGTCCTG
EST: gi|88572695|gb|CI664266.1|CI664266
EST:     GTTAAATTTATGATCAAGACATGCCCAATTCAAATGAGG                         CTTAAGCGATGGGAGAGGAAGAAGTGTAAACCAAACAGTCTTCCTGTCCTG
genomic: GTTAAATTTATGATCAAGACATGCCCAATTCAAATGAGGgtaagtttca ... tccaatgcagCTTAAGCGATGGGAGAGGAAGAAGTGTAAACCAAACAGTCTTCCTGTCCTG
EST: gi|55413199|gb|CV725575.1|CV725575
EST:     GTTAAATTTATGATCAAGACATGCCCAATTCAAATGAGG                         CTTAAGCGATGGGAGAGGAAGAAGTGTAAACCAAACAGTCTTCCTGTCCTG
genomic: GTTAAATTTATGATCAAGACATGCCCAATTCAAATGAGGgtaagtttca ... tccaatgcagCTTAAGCGATGGGAGAGGAAGAAGTGTAAACCAAACAGTCTTCCTGTCCTG
EST: gi|88370230|gb|CI585235.1|CI585235
EST:     GTTAAATTTATGATCAAGACATGCCCAATTCAAATGAGG                         CTTAAGCGATGGGAGAGGAAGAAGTGTAAACCAAACAGTCTTCCTGTCCTG
genomic: GTTAAATTTATGATCAAGACATGCCCAATTCAAATGAGGgtaagtttca ... tccaatgcagCTTAAGCGATGGGAGAGGAAGAAGTGTAAACCAAACAGTCTTCCTGTCCTG
EST: gi|163920604|gb|EG710655.1|EG710655
EST:     GTTAAATTTATGATCAAGACATGCCCAATTCAAATGAGG                         CTTAAGCGATGGGAGAGGAAGAAGTGTAAACCAAACAGTCTTCCTGTCCTG
genomic: GTTAAATTTATGATCAAGACATGCCCAATTCAAATGAGGgtaagtttca ... tccaatgcagCTTAAGCGATGGGAGAGGAAGAAGTGTAAACCAAACAGTCTTCCTGTCCTG
EST: gi|88312960|gb|CI592244.1|CI592244
EST:     GTTAAATTTATGATCAAGACATGCCCAATTCAAATGAGG                         CTTAAGCGATGGGAGAGGAAGAAGTGTAAACCAAACAGTCTTCCTGTCCTG
genomic: GTTAAATTTATGATCAAGACATGCCCAATTCAAATGAGGgtaagtttca ... tccaatgcagCTTAAGCGATGGGAGAGGAAGAAGTGTAAACCAAACAGTCTTCCTGTCCTG
EST: gi|88348216|gb|CI637677.1|CI637677
EST:     GTTAAATTTATGATCAAGACATGCCCAATTCAAATGAGG                         CTTAAGCGATGGGAGAGGAAGAAGTGTAAACCAAACAGTCTTCCTGTCCTG
genomic: GTTAAATTTATGATCAAGACATGCCCAATTCAAATGAGGgtaagtttca ... tccaatgcagCTTAAGCGATGGGAGAGGAAGAAGTGTAAACCAAACAGTCTTCCTGTCCTG

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: 75 (upstream exon), 39 (downstream exon)
Score: 26

GTTAAATTTATGATCAAGACATGCCCAATTCAAATGAGGgtaagtttca ... tccaatgcagCTTAAGCGATGGGAGAGGAAGAAGTGTAAACCAAACAGTCTTCCTGTCCTGCACAAGATGCATGTTAGGATTGGCGATACAGTACAAGTCATTGCAGGCC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggtctgcagcttgctatttactcaaatgtctgaaatttccctttttccaatgcagCTTAAGCGATGGGAGAGGAAGAAGTGTAAACCAAACAGTCTTCCTGTCCTGCACAAGATGCATGTTAGGATTGGCGATACAGTACAAGTCATTGCAGGCC
                                   tttccctttttccaat  CT-rich tract
              tatttact  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtttcaattcttttttggtctgcagcttgctatttactcaaatgtctgaaatttccctttttccaatgcagCTTAAGCGATGGGAGAGGAAGAAGTGTAAACCAAACAGTCTTCCTGTCCTGCACAAGATGCATGTTAGGATTGGCGATACAGTACAAGTCATTGCAGGCC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG