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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CGAGACATACATGCAGCTTTTAGAGCCGGAATTACAACTTGATAAGCAGAAAAATGAGATGAAAAGAAAGGAAGCATGGCGTGTTTATGGTGCCCTGCTGgttagattacaagctttcaatgaatacatgttatctatttttatgcaccagcttcttacctgtggaatgtatttttcag

Basic information

species Oryza sativa
transcript LOC_Os01g32750.1
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g32750.1 (Oryza sativa), 5'ss of exon 10
lower sequence: GRMZM2G013908_T01 (Zea mays), 5'ss of exon 10
CGAGACATACATGCAGCTTTTAGAGCCGGAATTACAACTTGATAAGCAGAAAAATGAGATGAAAAGAAAGGAAGCATGGCGTGTTTATGGTGCCCTGCTGgttagattacaagctttcaatgaatacatg--ttatc-tatttttatgcaccagct----------------tcttacctgtggaatgtatttttcag-
 | |||||| ||||| ||| | ||||||||| | || ||||| ||||||||||| ||||||||||| |||||||| |||||||||||||||||| ||||||| || | |  || | ||| | |||| |    ||||| ||||||  | ||||| ||                ||||||| |||||||| ||||||    
TGTGACATATATGCAACTTCTGGAGCCGGAACTGCAGCTTGAGAAGCAGAAAAACGAGATGAAAAGGAAGGAAGCTTGGCGTGTTTATGGTGCCTTGCTGgtcagttca-gagttctcagtcaatataatatttatcgtattttggttcaccaactaatgccaggccaagtttcttaccagtggaatgcatttttttag

upper sequence: LOC_Os01g32750.1 (Oryza sativa), 5'ss of exon 10
lower sequence: Vv12s0059g00410.t01 (Vitis vinifera), 5'ss of exon 3
CGAGACATACATGCAGCTTTTAGAGCCGGAATTACAACTTGATAAGCAGAAAAATGAGATGAAAAGAAAGGAAGCATGGCGTGTTTATGGTGCCCTGCTGgttagattacaagctttcaatgaatac---atgttatctatttttatgcaccagcttcttacctgtggaatgtatttttcag------------------------------
 ||  ||||| | |  ||| | || || ||  | |  ||||| |||||||| |||||||| || ||  | |||||||||||||||||||| ||| |||||||  | ||    | ||  ||||  |     |||||||| | | | |     |      |    | |    || || |  |                                
TGAACCATACCTTCGACTTCTTGAACCTGAGATGCTCCTTGAGAAGCAGAAGAATGAGATAAAGAGGCATGAAGCATGGCGTGTTTATGGGGCCTTGCTGgtgcgttt---tgtttctaatgggtttgtaatgttatccagtatgagaagtcctaagatgggttatatgttgcatgtaacgagaacatgtttcttttattctttctttctag
















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|58693421|gb|CK082108.1|CK082108
EST:     AAAATGAGATGAAAAGAAAGGAAGCATGGCGTGTTTATGGTGCCCTGCTG                         TGTGCTGCAGGAAAATGCTTATATGATCGGCTCAAGTTGTTTCCTAATTTG
genomic: AAAATGAGATGAAAAGAAAGGAAGCATGGCGTGTTTATGGTGCCCTGCTGgttagattac ... tatttttcagTGTGCTGCAGGAAAATGCTTATATGATCGGCTCAAGTTGTTTCCTAATTTG
EST: gi|27548087|gb|CA766146.2|CA766146
EST:     AAAATGAGATGAAAAGAAAGGAAGCATGGCGTGTTTATGGTGCCCTGCTG                         TGTGCTGCAGGAAAATGCTTATATGATCGGCTCAAGTTGTTTCCTAATTTG
genomic: AAAATGAGATGAAAAGAAAGGAAGCATGGCGTGTTTATGGTGCCCTGCTGgttagattac ... tatttttcagTGTGCTGCAGGAAAATGCTTATATGATCGGCTCAAGTTGTTTCCTAATTTG
EST: gi|428421|gb|D24570.1|D24570
EST:     AAAATGAGATGAAAAGAAAGGAAGCATGGCGTGTTTATGGTGCCCTGCTG                         TGTGCTGCAGGAAAATGCTTATATGATCGGCTCAAGTTGTTTCCTAATTTG
genomic: AAAATGAGATGAAAAGAAAGGAAGCATGGCGTGTTTATGGTGCCCTGCTGgttagattac ... tatttttcagTGTGCTGCAGGAAAATGCTTATATGATCGGCTCAAGTTGTTTCCTAATTTG
EST: gi|29614713|gb|CB619726.1|CB619726
EST:     AAAATGAGATGAAAAGAAAGGAAGCATGGCGTGTTTATGGTGCCCTGCTG                         TGTGCTGCAGGAAAATGCTTATATGATCGGCTCAAGTTGTTTCCTAATTTG
genomic: AAAATGAGATGAAAAGAAAGGAAGCATGGCGTGTTTATGGTGCCCTGCTGgttagattac ... tatttttcagTGTGCTGCAGGAAAATGCTTATATGATCGGCTCAAGTTGTTTCCTAATTTG
EST: gi|29681489|gb|CB677764.1|CB677764
EST:     AAAATGAGATGAAAAGAAAGGAAGCATGGCGTGTTTATGGTGCCCTGCTG                         TGTGCTGCAGGAAAATGCTTATATGATCGGCTCAAGTTGTTTCCTAATTTG
genomic: AAAATGAGATGAAAAGAAAGGAAGCATGGCGTGTTTATGGTGCCCTGCTGgttagattac ... tatttttcagTGTGCTGCAGGAAAATGCTTATATGATCGGCTCAAGTTGTTTCCTAATTTG

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: 48 (upstream exon), 70 (downstream exon)
Score: 15

CGAGACATACATGCAGCTTTTAGAGCCGGAATTACAACTTGATAAGCAGAAAAATGAGATGAAAAGAAAGGAAGCATGGCGTGTTTATGGTGCCCTGCTGgttagattac ... tatttttcagTGTGCTGCAGGAAAATGCTTATATGATCGGCTCAAGTTGTTTCCTAATTTGCTTTCTCCATCAACACGGCCTCTTTTGAGGAGTAATAAGAGAGTCGTGA




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CGAGACATACATGCAGCTTTTAGAGCCGGAATTACAACTTGATAAGCAGAAAAATGAGATGAAAAGAAAGGAAGCATGGCGTGTTTATGGTGCCCTGCTGgttagattacaagctttcaatgaatacatgttatctatttttatgcaccagcttcttacctgtggaatgtatttttcag

- - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA