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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGTGCAGCTAATCTCAAAATCTACTATGCTACGTGTTTCACTTTGATTGCTGGGATAATGGTTTTCGGTGGATTTCTTGCACCAATTgtaagttacactgtctagtccttgtcaccatttttatcattattgattccatcaatatccagtggatgtttaacaatttattgtacttttcttgcag

Basic information

species Oryza sativa
transcript LOC_Os02g43500.1
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g43500.1 (Oryza sativa), 5'ss of exon 4
lower sequence: Vv16s0013g00290.t01 (Vitis vinifera), 5'ss of exon 4
AGTGCAGCTAATCTCAAAATCTACTATGCTACGTGTTTCACTTTGATTGCTGGGATAATGGTTTTCGGTGGATTTCTTGCACCAATTgtaagttacactgtctagtccttgtcaccatttttatcattattgattccatcaatatccag--tggatgtttaacaatttattgtacttt--tcttgcag-----------------------------------------------------------------------------------
||| |||| ||||| ||| | || |||||||| |||||| || | ||||||||||| ||  |||| ||||| || |||||||||| |||||||||     || | |     | | ||   | |||| ||  | |||   |  | | | |  ||||||| |  ||| | || | | |    ||| | |                                                                                    
AGTTCAGCAAATCTGAAACTATATTATGCTACATGTTTCTCTCTTATTGCTGGGATCATCATTTTTGGTGGTTTACTTGCACCAACTgtaagtta--tcatccaatttggattatca---taatcagtaacgcttcttacttttttcgggttggatgtctt-caaataatgggaatagaatctggaaaaaaattctatgaaattagttttggttcttgttgagacataaacataaatcccagtttgtaaacatttttctttcttatctcag
















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|29661124|gb|CB657399.1|CB657399
EST:     TCACTTTGATTGCTGGGATAATGGTTTTCGGTGGATTTCTTGCACCAATT                         CTGGAACTTAAACTCGGTGTGGGAGGAACATCTTATGCAGACTTCATCCGC
genomic: TCACTTTGATTGCTGGGATAATGGTTTTCGGTGGATTTCTTGCACCAATTgtaagttaca ... tttcttgcagCTGGAACTTAAACTCGGTGTGGGAGGAACATCTTATGCAGACTTCATCCGC
EST: gi|218495170|gb|FG957512.1|FG957512
EST:     TCACTTTGATTGCTGGGATAATGGTTTTCGGTGGATTTCTTGCACCAATT                         CTGGAACTTAAACTCGGTGTGGGAGGAACATCTTATGCAGACTTCATCCGC
genomic: TCACTTTGATTGCTGGGATAATGGTTTTCGGTGGATTTCTTGCACCAATTgtaagttaca ... tttcttgcagCTGGAACTTAAACTCGGTGTGGGAGGAACATCTTATGCAGACTTCATCCGC
EST: gi|29619334|gb|CB624346.1|CB624346
EST:     TCACTTTGATTGCTGGGATAATGGTTTTCGGTGGATTTCTTGCACCAATT                         CTGGAACTTAAACTCGGTGTGGGAGGAACATCTTATGCAGACTTCATCCGC
genomic: TCACTTTGATTGCTGGGATAATGGTTTTCGGTGGATTTCTTGCACCAATTgtaagttaca ... tttcttgcagCTGGAACTTAAACTCGGTGTGGGAGGAACATCTTATGCAGACTTCATCCGC
EST: gi|58608739|gb|CK036772.1|CK036772
EST:     GGTGGATTTCTTGCACCAATT                         CTGGAACTTAAACTCGGTGTGGGAGGAACATCTTATGCGGACTTCATCCGC
genomic: GGTGGATTTCTTGCACCAATTgtaagttaca ... tttcttgcagCTGGAACTTAAACTCGGTGTGGGAGGAACATCTTATGCAGACTTCATCCGC
EST: gi|88468873|gb|CI696875.1|CI696875
EST:     GGATTTCTTGCACCAATT                         CTGGAACTTAAACTCGGTGTGGGAGGAACATCTTATGCAGACTTCATCCGC
genomic: GGATTTCTTGCACCAATTgtaagttaca ... tttcttgcagCTGGAACTTAAACTCGGTGTGGGAGGAACATCTTATGCAGACTTCATCCGC
EST: gi|29684684|gb|CB680959.1|CB680959
EST:     TCACTTTGATTGCTGGGATAATGGTTTTCGGTGGATTTCTTGCACCAATT                         CTGGAACTTAAACTCGGTGTGGGAGGAACATCTTATGCAGACTTCATCCGC
genomic: TCACTTTGATTGCTGGGATAATGGTTTTCGGTGGATTTCTTGCACCAATTgtaagttaca ... tttcttgcagCTGGAACTTAAACTCGGTGTGGGAGGAACATCTTATGCAGACTTCATCCGC
EST: gi|218483643|gb|FG955539.1|FG955539
EST:     TCACTTTGATTGCTGGGATAATGGTTTTCGGTGGATTTCTTGCACCAATT                         CTGGAACTTAAACTCGGTGTGGGAGGAACATCTTATGCAGACTTCATCCGC
genomic: TCACTTTGATTGCTGGGATAATGGTTTTCGGTGGATTTCTTGCACCAATTgtaagttaca ... tttcttgcagCTGGAACTTAAACTCGGTGTGGGAGGAACATCTTATGCAGACTTCATCCGC
EST: gi|29643098|gb|CB648105.1|CB648105
EST:     GCTGGGATAATGGTTTTCGGTGGATTTCTTGCACCAATT                         TTGGAACTTAAACTCGGTGTGGGAGGAACATCTTATGCAGACTTCATCCGC
genomic: GCTGGGATAATGGTTTTCGGTGGATTTCTTGCACCAATTgtaagttaca ... tttcttgcagCTGGAACTTAAACTCGGTGTGGGAGGAACATCTTATGCAGACTTCATCCGC
EST: gi|218491083|gb|FG953112.1|FG953112
EST:     TCACTTTGATTGCTGGGATAATGGTTTTCGGTGGATTTCTTGCACCAATT                         CTGGAACTTAAACTCGGTGTGGGAGGAACATCTTATGCAGACTTCATCCGC
genomic: TCACTTTGATTGCTGGGATAATGGTTTTCGGTGGATTTCTTGCACCAATTgtaagttaca ... tttcttgcagCTGGAACTTAAACTCGGTGTGGGAGGAACATCTTATGCAGACTTCATCCGC
EST: gi|29660129|gb|CB656404.1|CB656404
EST:     TCACTTTGATTGCTGGGATAATGGTTTTCGGTGGATTTCTTGCACCAATT                         CTGGAACTTAAACTCGGTGTGGGAGGAACATCTTATGCAGACTTCATCCGC
genomic: TCACTTTGATTGCTGGGATAATGGTTTTCGGTGGATTTCTTGCACCAATTgtaagttaca ... tttcttgcagCTGGAACTTAAACTCGGTGTGGGAGGAACATCTTATGCAGACTTCATCCGC
EST: gi|29661191|gb|CB657466.1|CB657466
EST:     TCACTTTGATTGCTGGGATAATGGTTTTCGGTGGATTTCTTGCACCAATT                         CTGGAACTTAAACTCGGTGTGGGAGGAACATCTTATGCAGACTTCATCCGC
genomic: TCACTTTGATTGCTGGGATAATGGTTTTCGGTGGATTTCTTGCACCAATTgtaagttaca ... tttcttgcagCTGGAACTTAAACTCGGTGTGGGAGGAACATCTTATGCAGACTTCATCCGC
EST: gi|29660498|gb|CB656773.1|CB656773
EST:     GATAATGGTTTTCGGTGGATTTCTTGCACCAATT                         CTGGAACTTAAACTCGGTGTGGGAGGAACATCTTATGCAGACTTCATCCGC
genomic: GATAATGGTTTTCGGTGGATTTCTTGCACCAATTgtaagttaca ... tttcttgcagCTGGAACTTAAACTCGGTGTGGGAGGAACATCTTATGCAGACTTCATCCGC
EST: gi|29660247|gb|CB656522.1|CB656522
EST:     TTTTCGGTGGATTTCTTGCACCAATT                         CTGGAACTTAAACTCGGGTGTGGGAGGAACATCTTATGCAGACTTCATCCG
genomic: TTTTCGGTGGATTTCTTGCACCAATTgtaagttaca ... tttcttgcagCTGGAACTTAAACTC-GGTGTGGGAGGAACATCTTATGCAGACTTCATCCG
EST: gi|38480918|gb|CF965007.1|CF965007
EST:     GCTGGGATAATGGTTTTC-GTGGATTTCTTGCACCAATT                         CTGGAACTTAAACTCGGTGTGGGAGGAACATCTTATGCAGACTTCATCCGC
genomic: GCTGGGATAATGGTTTTCGGTGGATTTCTTGCACCAATTgtaagttaca ... tttcttgcagCTGGAACTTAAACTCGGTGTGGGAGGAACATCTTATGCAGACTTCATCCGC
EST: gi|29667086|gb|CB663361.1|CB663361
EST:     TCACTTTGATTGCTGGGATAATGGTTTTCGGTGGATTTCTTGCACCAATT                         CTGGAACTTAAACTCGGTGTGGGAGGAACATCTTATGCAGACTTCATCCGC
genomic: TCACTTTGATTGCTGGGATAATGGTTTTCGGTGGATTTCTTGCACCAATTgtaagttaca ... tttcttgcagCTGGAACTTAAACTCGGTGTGGGAGGAACATCTTATGCAGACTTCATCCGC
EST: gi|29687907|gb|CB684182.1|CB684182
EST:     GGATAATGGTTTTTGGGGGATTTTCTTGCACCAATT                         CTGGAACTTAAACTCGGTGTGGGAGGAACATCTTATGCAGACTTCATCCGC
genomic: GGATAATGGTTTTCGGTGGA-TTTCTTGCACCAATTgtaagttaca ... tttcttgcagCTGGAACTTAAACTCGGTGTGGGAGGAACATCTTATGCAGACTTCATCCGC
EST: gi|29684442|gb|CB680717.1|CB680717
EST:     TCACTTTGATTGCTGGGATAATGGTTTTCGGTGGATTTTTTGCACCAATT                         CTGGAACTTAAACTCGGTGTGGGAGGAACATCTTATGCAGACTTCATCCGC
genomic: TCACTTTGATTGCTGGGATAATGGTTTTCGGTGGATTTCTTGCACCAATTgtaagttaca ... tttcttgcagCTGGAACTTAAACTCGGTGTGGGAGGAACATCTTATGCAGACTTCATCCGC

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: 66 (upstream exon), 74 (downstream exon)
Score: 92

AGTGCAGCTAATCTCAAAATCTACTATGCTACGTGTTTCACTTTGATTGCTGGGATAATGGTTTTCGGTGGATTTCTTGCACCAATTgtaagttaca ... tttcttgcagCTGGAACTTAAACTCGGTGTGGGAGGAACATCTTATGCAGACTTCATCCGCAGTGTCCATTTGCCGATGCAACTGAG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGTGCAGCTAATCTCAAAATCTACTATGCTACGTGTTTCACTTTGATTGCTGGGATAATGGTTTTCGGTGGATTTCTTGCACCAATTgtaagttacactgtctagtccttgtcaccatttttatcattattgattccatcaatatccagtggatgtttaacaatttattgtacttttcttgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA