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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGGCGCGATGGCGTCCCTCTCCATCTCTGCGCCGGGGGCGGCGAGCACCAGCAGCTTCTGGGGCCACCCGCTCTCCACCTTCGCCGCCGCGCCGGCTGGGgtttgtgccgactcccaaccctgattctcatttttcgcattcctttatgtttgctctgctcttatgattcgctggaaaagtagaaatgccagcttgcact...

Basic information

species Oryza sativa
transcript LOC_Os06g46930.1
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g46930.1 (Oryza sativa), 5'ss of exon 1
lower sequence: GRMZM2G463913_T01 (Zea mays), 5'ss of exon 1
GGGCGCGATGGCGTCCCTCTCCATCTCTGCGCCGGG------GGCGGCGAGCACCAGCAGCTTCTGGGGCCACCCGCTCTCCACCTTCGCCGCCGCGCCGGCTGGGgtttgtgccgactcccaaccctgattctcatttttcgcattcctttatgtttgctctgctcttatgattcgctggaaaagtagaaatgccagcttgcact---
       |||||||| ||||||||||| ||||  ||      | ||||||||| |||||||||||||||| ||| |||| |||||| | ||||  ||| | ||||||| ||| ||  || || |      ||| | || | |  ||   ||  |   |  |  |    | |  |  | || || | |  |      || ||        
------CATGGCGTCGCTCTCCATCTCCGCGCTAGGCGCGGCGACGGCGAGCAGCAGCAGCTTCTGGGGCAACCGGCTCGCCACCTACTCCGCGCCGCAGCCTGGGgtctgttcctgcttcccaattccgttc-cgttctgctgatggtttggtagataataagtagctgt--tctggtgaaagattttactctggagtttctggatag
















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:     TCAGCTTCTGGGGCCACCCGCTCTCCACCCTCGCCGCCGCGCCGGCTGGG                         GTTAAATTTATGATCAAGACATGCCCAATTCAAATGAGG
genomic: GCAGCTTCTGGGGCCACCCGCTCTCCACCTTCGCCGCCGCGCCGGCTGGGgtttgtgccg ... ttatatgcagGTTAAATTTATGATCAAGACATGCCCAATTCAAATGAGG
EST: gi|88330769|gb|CI636777.1|CI636777
EST:     GCAGCTTCTGGGGCCACCCGCTCTCCACCTTCGCCGCCGCGCCGGCTGGG                         GTTAAATTTATGATCAAGACATGCCCAATTCAAATGAGG
genomic: GCAGCTTCTGGGGCCACCCGCTCTCCACCTTCGCCGCCGCGCCGGCTGGGgtttgtgccg ... ttatatgcagGTTAAATTTATGATCAAGACATGCCCAATTCAAATGAGG
EST: gi|33815049|gb|CF333389.1|CF333389
EST:     GCAGCTTCTGGGGCCACCCGCTCTCCACCTTCGCCGCCGCGCCGGCTGGG                         GTTAAATTTATGATCAAGACATGCCCAATTCAAATGAGG
genomic: GCAGCTTCTGGGGCCACCCGCTCTCCACCTTCGCCGCCGCGCCGGCTGGGgtttgtgccg ... ttatatgcagGTTAAATTTATGATCAAGACATGCCCAATTCAAATGAGG
EST: gi|38474567|gb|CF958700.1|CF958700
EST:     GCAGCTTCTGGGGCCACCCGCTCTCCACCTTCGCCGCCGCGCCGGCTGGG                         GTTAAATTTATGATCAAGACATGCCCAATTCAAATGAGG
genomic: GCAGCTTCTGGGGCCACCCGCTCTCCACCTTCGCCGCCGCGCCGGCTGGGgtttgtgccg ... ttatatgcagGTTAAATTTATGATCAAGACATGCCCAATTCAAATGAGG
EST: gi|55412137|gb|CV724513.1|CV724513
EST:     GCAGCTTCTGGGGCCACCCGCTCTCCACCTTCGCCGCCGCGCCGGCTGGG                         GTTAAATTTATGATCAAGACATGCCCAATTCAAATGGGG
genomic: GCAGCTTCTGGGGCCACCCGCTCTCCACCTTCGCCGCCGCGCCGGCTGGGgtttgtgccg ... ttatatgcagGTTAAATTTATGATCAAGACATGCCCAATTCAAATGAGG
EST: gi|58594789|gb|CF993097.1|CF993097
EST:     GCAGCTTCTGGGGCCACCCGCTCTCCACCTTCGCCGCCGCGCCGGCTGGG                         GTTAAATTTATGATCAAGACATGCCCAATTCAAATGAGG
genomic: GCAGCTTCTGGGGCCACCCGCTCTCCACCTTCGCCGCCGCGCCGGCTGGGgtttgtgccg ... ttatatgcagGTTAAATTTATGATCAAGACATGCCCAATTCAAATGAGG
EST: gi|88352549|gb|CI654374.1|CI654374
EST:     GCAGCTTCTGGGGCCACCCGCTCTCCACCTTCGCCGCCGCGCCGGCTGGG                         GTTAAATTTATGATCAAGACATGCCCAATTCAAATGAGG
genomic: GCAGCTTCTGGGGCCACCCGCTCTCCACCTTCGCCGCCGCGCCGGCTGGGgtttgtgccg ... ttatatgcagGTTAAATTTATGATCAAGACATGCCCAATTCAAATGAGG
EST: gi|56157658|gb|C25003.2|C25003
EST:     GCAGCTTCTGGGGCCACCCGCTCTCCACCTTCGCCGCCGCGCCGGCTGGG                         GTTAAATTTATGATCAAGACATGCCCAATTCAAATGAGG
genomic: GCAGCTTCTGGGGCCACCCGCTCTCCACCTTCGCCGCCGCGCCGGCTGGGgtttgtgccg ... ttatatgcagGTTAAATTTATGATCAAGACATGCCCAATTCAAATGAGG
EST: gi|88414886|gb|CI601718.1|CI601718
EST:     GCAGCTTCTGGGGCCACCCGCTCTCCACCTTCGCCGCCGCGCCGGCTGGG                         GTTAAATTTATGATCAAGACATGCCCAATTCAAATGAGG
genomic: GCAGCTTCTGGGGCCACCCGCTCTCCACCTTCGCCGCCGCGCCGGCTGGGgtttgtgccg ... ttatatgcagGTTAAATTTATGATCAAGACATGCCCAATTCAAATGAGG
EST: gi|33801796|gb|CF326771.1|CF326771
EST:     GCAGCTTCTGGGGCCACCCGCTCTCCACCTTCGCCGCCGCGCCGGCTGGG                         GTTAAATTTATGATCAAGACATGCCCAATTCAAATGAGG
genomic: GCAGCTTCTGGGGCCACCCGCTCTCCACCTTCGCCGCCGCGCCGGCTGGGgtttgtgccg ... ttatatgcagGTTAAATTTATGATCAAGACATGCCCAATTCAAATGAGG
EST: gi|86830951|gb|CI295472.1|CI295472
EST:     GCAGCTTCTGGGGCCACCCGCTCTCCACCTTCGCCGCCGCGCCGGCTGGG                         GTTAAATTTATGATCAAGACATGCCCAATTCAAATGAGG
genomic: GCAGCTTCTGGGGCCACCCGCTCTCCACCTTCGCCGCCGCGCCGGCTGGGgtttgtgccg ... ttatatgcagGTTAAATTTATGATCAAGACATGCCCAATTCAAATGAGG
EST: gi|38477056|gb|CF961189.1|CF961189
EST:     GCAGCTTCTGGGGCCACCCGCTCTCCACCTTCGCCGCCGCGCCGGCTGGG                         GTTAAATTTATGATCAAGACATGCCCAATTCAAATGAGG
genomic: GCAGCTTCTGGGGCCACCCGCTCTCCACCTTCGCCGCCGCGCCGGCTGGGgtttgtgccg ... ttatatgcagGTTAAATTTATGATCAAGACATGCCCAATTCAAATGAGG
EST: gi|3763301|gb|AU030053.1|AU030053
EST:     GCAGCTTCTGGGGCCACCCGCTCTCCACCTTCGCCGCCGCGCCGGCTGGG                         GTTAAATTTATGATCAAGACATGCCCAATTCAAATGAGG
genomic: GCAGCTTCTGGGGCCACCCGCTCTCCACCTTCGCCGCCGCGCCGGCTGGGgtttgtgccg ... ttatatgcagGTTAAATTTATGATCAAGACATGCCCAATTCAAATGAGG
EST: gi|88572695|gb|CI664266.1|CI664266
EST:     GCAGCTTCTGGGGCCACCCGCTCTCCACCTTCGCCGCCGCGCCGGCTGGG                         GTTAAATTTATGATCAAGACATGCCCAATTCAAATGAGG
genomic: GCAGCTTCTGGGGCCACCCGCTCTCCACCTTCGCCGCCGCGCCGGCTGGGgtttgtgccg ... ttatatgcagGTTAAATTTATGATCAAGACATGCCCAATTCAAATGAGG
EST: gi|55413199|gb|CV725575.1|CV725575
EST:     TCTTCTTCTGGGGCCACCCGCTCTCCACCTTCGCCGCCGCGCCGGCTGGG                         GTTAAATTTATGATCAAGACATGCCCAATTCAAATGAGG
genomic: GCAGCTTCTGGGGCCACCCGCTCTCCACCTTCGCCGCCGCGCCGGCTGGGgtttgtgccg ... ttatatgcagGTTAAATTTATGATCAAGACATGCCCAATTCAAATGAGG
EST: gi|88370230|gb|CI585235.1|CI585235
EST:     GCAGCTTCTGGGGCCACCCGCTCTCCACCTTCGCCGCCGCGCCGGCTGGG                         GTTAAATTTATGATCAAGACATGCCCAATTCAAATGAGG
genomic: GCAGCTTCTGGGGCCACCCGCTCTCCACCTTCGCCGCCGCGCCGGCTGGGgtttgtgccg ... ttatatgcagGTTAAATTTATGATCAAGACATGCCCAATTCAAATGAGG
EST: gi|163920604|gb|EG710655.1|EG710655
EST:     GCAGCTTCTGGGGCCACCCGCTCTCCACCTTCGCCGCCGCGCCGGCTGGG                         GTTAAATTTATGATCAAGACATGCCCAATTCAAATGAGG
genomic: GCAGCTTCTGGGGCCACCCGCTCTCCACCTTCGCCGCCGCGCCGGCTGGGgtttgtgccg ... ttatatgcagGTTAAATTTATGATCAAGACATGCCCAATTCAAATGAGG
EST: gi|88312960|gb|CI592244.1|CI592244
EST:     GCAGCTTCTGGGGCCACCCGCTCTCCACCTTCGCCGCCGCGCCGGCTGGG                         GTTAAATTTATGATCAAGACATGCCCAATTCAAATGAGG
genomic: GCAGCTTCTGGGGCCACCCGCTCTCCACCTTCGCCGCCGCGCCGGCTGGGgtttgtgccg ... ttatatgcagGTTAAATTTATGATCAAGACATGCCCAATTCAAATGAGG
EST: gi|88348216|gb|CI637677.1|CI637677
EST:     GCAGCTTCTGGGGCCACCCGCTCTCCACCTTCGCCGCCGCGCCGGCTGGG                         GTTAAATTTATGATCAAGACATGCCCAATTCAAATGAGG
genomic: GCAGCTTCTGGGGCCACCCGCTCTCCACCTTCGCCGCCGCGCCGGCTGGGgtttgtgccg ... ttatatgcagGTTAAATTTATGATCAAGACATGCCCAATTCAAATGAGG

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), 67 (downstream exon)
Score: 47

GGGCGCGATGGCGTCCCTCTCCATCTCTGCGCCGGGGGCGGCGAGCACCAGCAGCTTCTGGGGCCACCCGCTCTCCACCTTCGCCGCCGCGCCGGCTGGGgtttgtgccg ... ttatatgcagGTTAAATTTATGATCAAGACATGCCCAATTCAAATGAGG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGGCGCGATGGCGTCCCTCTCCATCTCTGCGCCGGGGGCGGCGAGCACCAGCAGCTTCTGGGGCCACCCGCTCTCCACCTTCGCCGCCGCGCCGGCTGGGgtttgtgccgactcccaaccctgattctcatttttcgcattcctttatgtttgctctgctcttatgattcgctggaaaagtagaaatgccagcttgcact

- - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ccaaccc