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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTACGAAGGGCAGCGTGACATGCTGTACAACCAAACATATAACCTTGACCAAGTTGCTTTTGCATCAGAGGGACTTAAAGATGCTCAGCAAACGgtatatagctatagtatactcaagaagttttatttccatgatgttttacatcctgattcccaaacttatgatacaagtgttttcatttgggcag

Basic information

species Oryza sativa
transcript LOC_Os05g01250.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g01250.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G092468_T02 (Zea mays), 5'ss of exon 3
GTACGAAGGGCAGCGTGACATGCTGTACAACCAAACATATAACCTTGACCAAGTTGCTTTTGCATCAGAGGGACTTAAAGATGCTCAGCAAACGgtatatagctatagtatactcaagaagttttatttccatgatgttttacatcctgattcccaaacttatgatacaagtgttttcatttgggcag
|||||||||||||||||||||||| ||||||||||||||||||||||||||||||||||||||  |||||||||||||||||||||||||||| |||||   | | ||| |||   ||||        |  |  || | || |  | |   | | | | |  |      |   || ||||| || |||
GTACGAAGGGCAGCGTGACATGCTCTACAACCAAACATATAACCTTGACCAAGTTGCTTTTGCGGCAGAGGGACTTAAAGATGCTCAGCAAACTgtatacctccagagt-tacctgagaaaac---cctttaatatttcttgccactttccttctagaatcctagccttacgcttctcatt-ggacag

upper sequence: LOC_Os05g01250.1 (Oryza sativa), 5'ss of exon 3
lower sequence: Vv08s0007g02300.t01 (Vitis vinifera), 5'ss of exon 3
GTACGAAGGGCAGCGTGACATGCTGTACAACCAAACATATAACCTTGACCAAGTTGCTTTTGCATCAGAGGGACTTAAAGATGCTCAGCAAACGgtatatagctatagtatactcaagaagttttatttccatgatgttttacatcctgattcccaaacttatgatacaagtgttttcatttgggcag-------
||| ||||| |||||||||||||| |||||||||||||  ||||||||||||||| | |||||  | || ||| ||||||||||||||||||| |||  |      |   |  | | || | || |     |  |   |||   |    ||      |  ||| | |    |     |||||   |||       
GTATGAAGGACAGCGTGACATGCTTTACAACCAAACATTCAACCTTGACCAAGTTTCATTTGCGGCTGAAGGAATTAAAGATGCTCAGCAAACTgtaagtgtgctaatcgttgtgatgatgattcacacatacaagtatttgtgtatgtatatatgtatctat-agatggttccccccattttttcaggtggtgc
















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|88578356|gb|CI687279.1|CI687279
EST:     TTGACCAAGTTGCTTCTGCATCAGAGGGACTTAAAGATGCTCAGCAAACG                         ATGACTGGAATGAAGGCAGGCAATAAAGAGCTGAAAGGAATGATGAAAACT
genomic: TTGACCAAGTTGCTTTTGCATCAGAGGGACTTAAAGATGCTCAGCAAACGgtatatagct ... atttgggcagATGACTGCAATGAAGGCAGCCAATAAAGAGCTGAAAGGAATGATGAAAACT
EST: gi|33655394|gb|CF278008.1|CF278008
EST:     TTGACCAAGTTGCTTTTGCATCAGAGGGACTTAAAGATGCTCAGCAAACG                         ATGACTGCAATGAAGGCAGCCAATAAAGAGCTGAAAGGAATGATGAAAACT
genomic: TTGACCAAGTTGCTTTTGCATCAGAGGGACTTAAAGATGCTCAGCAAACGgtatatagct ... atttgggcagATGACTGCAATGAAGGCAGCCAATAAAGAGCTGAAAGGAATGATGAAAACT
EST: gi|27576216|gb|CA998910.1|CA998910
EST:     TTGACCAAGTTGCTTTTGCATCAGAGGGACTTAAAGATGCTCAGCAAACG                         ATGACTGCAATGAAGGCAGCCAATAAAGAGCTGAAAGGAATGATGAAAACT
genomic: TTGACCAAGTTGCTTTTGCATCAGAGGGACTTAAAGATGCTCAGCAAACGgtatatagct ... atttgggcagATGACTGCAATGAAGGCAGCCAATAAAGAGCTGAAAGGAATGATGAAAACT
EST: gi|5003511|gb|AU068660.1|AU068660
EST:     TTGACCAAGTTGCTTTTGCATCAGAGGGACTTAAAGATGCTCAGCAAACG                         ATGACTGCAATGAAGGCAGCCAATAAAGAGCTGAAAGGAATGATGAAAACT
genomic: TTGACCAAGTTGCTTTTGCATCAGAGGGACTTAAAGATGCTCAGCAAACGgtatatagct ... atttgggcagATGACTGCAATGAAGGCAGCCAATAAAGAGCTGAAAGGAATGATGAAAACT
EST: gi|88406674|gb|CI603868.1|CI603868
EST:     TTGACCAAGTTGCTTTTGCATCAGAGGGACTTAAAGATGCTCAGCAAACG                         ATGACTGCAATGAAGGCAGCCAATAAAGAGCTGAAAGGAATGATGAAAACT
genomic: TTGACCAAGTTGCTTTTGCATCAGAGGGACTTAAAGATGCTCAGCAAACGgtatatagct ... atttgggcagATGACTGCAATGAAGGCAGCCAATAAAGAGCTGAAAGGAATGATGAAAACT
EST: gi|88327316|gb|CI645093.1|CI645093
EST:     TTGACCAAGTTGCTTTTGCATCAGAGGGACTTAAAGATGCTCAGCAAACG                         ATGACTGCAATGAAGGCAGCCAATAAAGAGC
genomic: TTGACCAAGTTGCTTTTGCATCAGAGGGACTTAAAGATGCTCAGCAAACGgtatatagct ... atttgggcagATGACTGCAATGAAGGCAGCCAATAAAGAGC
EST: gi|33662787|gb|CF293754.1|CF293754
EST:     TTGACCAAGTTGCTTTTGCATCAGAGGGACTTAAAGATGCTCAGCAAACG                         ATGACTGCAATGAAGGCAGCCAATAAAGAGCTGAAAGGAATGATGAAAACT
genomic: TTGACCAAGTTGCTTTTGCATCAGAGGGACTTAAAGATGCTCAGCAAACGgtatatagct ... atttgggcagATGACTGCAATGAAGGCAGCCAATAAAGAGCTGAAAGGAATGATGAAAACT
EST: gi|38483033|gb|CF966835.1|CF966835
EST:     TTGACCAAGTTGCTTTTGCATCAGAGGGACTTAAAGATGCTCAGCAAACG                         ATGACTGCAATGAAGGCAGCCAATAAAGAGCTGAAAGGAATGATGAAAACT
genomic: TTGACCAAGTTGCTTTTGCATCAGAGGGACTTAAAGATGCTCAGCAAACGgtatatagct ... atttgggcagATGACTGCAATGAAGGCAGCCAATAAAGAGCTGAAAGGAATGATGAAAACT
EST: gi|88331043|gb|CI638451.1|CI638451
EST:     TTGACCAAGTTGCTTTTGCATCAGAGGGACTTAAAGATGCTCAGCAAACG                         ATGACTGCAATGAAGGCAGCCAATAAAGAGCTGA
genomic: TTGACCAAGTTGCTTTTGCATCAGAGGGACTTAAAGATGCTCAGCAAACGgtatatagct ... atttgggcagATGACTGCAATGAAGGCAGCCAATAAAGAGCTGA
EST: gi|5003512|gb|AU068661.1|AU068661
EST:     TTGACCAAGTTGCTTTTGCATCAGAGGGACTTAAAGATGCTCAGCAAACG                         ATGACTGCAATGAAGGCAGCCAATAAAGAGCTGAAAGGAATGATGAAAACT
genomic: TTGACCAAGTTGCTTTTGCATCAGAGGGACTTAAAGATGCTCAGCAAACGgtatatagct ... atttgggcagATGACTGCAATGAAGGCAGCCAATAAAGAGCTGAAAGGAATGATGAAAACT
EST: gi|27576887|gb|CA999581.1|CA999581
EST:     TTGACCAAGTTGCTTTTGCATCAGAGGGACTTAAAGATGCTCAGCAAACG                         ATGACTGCAATGAAGGCAGCCAATAAAGAGCTGAAAGGAATGATGAAAACT
genomic: TTGACCAAGTTGCTTTTGCATCAGAGGGACTTAAAGATGCTCAGCAAACGgtatatagct ... atttgggcagATGACTGCAATGAAGGCAGCCAATAAAGAGCTGAAAGGAATGATGAAAACT
EST: gi|33823135|gb|CF337370.1|CF337370
EST:     TTGACCAAGTTGCTTTTGCATCAGAGGGACTTAAAGATGCTCAGCAAACG                         ATGACTGCAATGAAGGCAGCCAATAAAGAGCTGAAAGGAATGATGAAAACT
genomic: TTGACCAAGTTGCTTTTGCATCAGAGGGACTTAAAGATGCTCAGCAAACGgtatatagct ... atttgggcagATGACTGCAATGAAGGCAGCCAATAAAGAGCTGAAAGGAATGATGAAAACT
EST: gi|117224782|gb|CT845909.1|CT845909
EST:     TTGACCAAGTTGCTTTTGCATCAGAGGGACTTAAAGATGCTCAGCAAACG                         ATGACTGCAATGAAGGCAGCCAATAAAGAGCTGAAAGGAATGATGAAAACT
genomic: TTGACCAAGTTGCTTTTGCATCAGAGGGACTTAAAGATGCTCAGCAAACGgtatatagct ... atttgggcagATGACTGCAATGAAGGCAGCCAATAAAGAGCTGAAAGGAATGATGAAAACT
EST: gi|218491828|gb|FG966677.1|FG966677
EST:     TTGACCAAGTTGCTTTTGCATCAGAGGGACTTAAAGATGCTCAGCAAACG                         ATGACTGCAATGAAGGCAGCCAATAAAGAGCTGAAAGGAATGATGAAAACT
genomic: TTGACCAAGTTGCTTTTGCATCAGAGGGACTTAAAGATGCTCAGCAAACGgtatatagct ... atttgggcagATGACTGCAATGAAGGCAGCCAATAAAGAGCTGAAAGGAATGATGAAAACT
EST: gi|27577821|gb|CB000516.1|CB000516
EST:     TTGACCAAGTTGCTTTTGCATCAGAGGGACTTAAAGATGCTCAGCAAACG                         ATGACTGCAATGAAGGCAGCCAATAAAGAGCTGAAAGGAATGATGAAAACT
genomic: TTGACCAAGTTGCTTTTGCATCAGAGGGACTTAAAGATGCTCAGCAAACGgtatatagct ... atttgggcagATGACTGCAATGAAGGCAGCCAATAAAGAGCTGAAAGGAATGATGAAAACT

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: 64 (upstream exon), 40 (downstream exon)
Score: 11

GTACGAAGGGCAGCGTGACATGCTGTACAACCAAACATATAACCTTGACCAAGTTGCTTTTGCATCAGAGGGACTTAAAGATGCTCAGCAAACGgtatatagct ... atttgggcagATGACTGCAATGAAGGCAGCCAATAAAGAGCTGAAAGGAATGATGAAAACTGTCAAGCTTGAAGATATAGAT




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTACGAAGGGCAGCGTGACATGCTGTACAACCAAACATATAACCTTGACCAAGTTGCTTTTGCATCAGAGGGACTTAAAGATGCTCAGCAAACGgtatatagctatagtatactcaagaagttttatttccatgatgttttacatcctgattcccaaacttatgatacaagtgttttcatttgggcag

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