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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCCTTCCAGTGCCCCAGATTTTGGGCAGGGTCGACAAGTCTTAGCTGTTTATCCTAGCACAACAGCACTATATAGAGCTACTGTTGCCTCTAATCGTAAGgtaacatcttaaaatctttcatgaatcctatgtaaatcttttaagtcttgacagtaatttgagtttctttctgtgttctagtcctgtcctgtccatatgt...

Basic information

species Oryza sativa
transcript LOC_Os12g19350.1
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os12g19350.1 (Oryza sativa), 5'ss of exon 7
lower sequence: GRMZM5G862959_T01 (Zea mays), 5'ss of exon 7
TCCTTCCAGTGCCCCAGATTTTGGGCAGGGTCGACAAGTCTTAGCTGTTTATCCTAGCACAACAGCACTATATAGAGCTACTGTTGCCTCTAATCGTAAGgtaacatcttaaaatctttcatgaatcctatgtaaatcttttaagtcttgacagtaatttgag-tttctttctgtgttctagtcctgtcctgtccatatgt------------------
             || ||||||||||||||||||||||| ||||||||||||||| ||||||||||| |||| |||||||| || || ||| ||||||||||||||||||||  |    ||| ||  | ||| | |  |    |||| | | | | ||   |  |||  || |||  |  | |   |   | |  ||   |                  
-------------CCGGATTTTGGGCAGGGTCGACAAGTTTTAGCTGTTTATCCTGGCACAACAGCATTATACAGAGCTACCGTAGCTTCTCATCGTAAGGTAACATCTTAAGgtgca-cattaaaacaatggatagtt----agtcataataatgatgcaaaattttcttgtgtacttcaatttcgaaat-ttgatgcattactgtcacgtttaactt

upper sequence: LOC_Os12g19350.1 (Oryza sativa), 5'ss of exon 7
lower sequence: GRMZM5G862959_T02 (Zea mays), 5'ss of exon 7
TCCTTCCAGTGCCCCAGATTTTGGGCAGGGTCGACAAGTCTTAGCTGTTTATCCTAGCACAACAGCACTATATAGAGCTACTGTTGCCTCTAATCGTAAGgtaacatcttaaaatctttcatgaatcctatgtaaatcttttaagtcttgacagtaatttgag-tttctttctgtgttctagtcctgtcctgtccatatgt-----
|||||| |||||||| ||||||||||||||||||||||| ||||||||||||||| ||||||||||| |||| |||||||| || || ||| ||||||||||||||||||||  |    ||| ||  | ||| | |  |    |||| | | | | ||   |  |||  || |||  |  | |   |   | |  ||   |     
TCCTTCGAGTGCCCCGGATTTTGGGCAGGGTCGACAAGTTTTAGCTGTTTATCCTGGCACAACAGCATTATACAGAGCTACCGTAGCTTCTCATCGTAAGgtaacatcttaaggtgca-cattaaaacaatggatagtt----agtcataataatgatgcaaaattttcttgtgtacttcaatttcgaaat-ttgatgcattactg
















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|58664363|gb|CK053049.1|CK053049
EST:     CAGCACTATATAGAGCTACTGTTGCCTCTAATCGTAAG                         AGGAAATCTGACGA
genomic: CAGCACTATATAGAGCTACTGTTGCCTCTAATCGTAAGgtaacatctt ... aacaatgcagAGGAAATCTGACGA
EST: gi|88519487|gb|CI447141.1|CI447141
EST:     ATCCTAGCACAACAGCACTATATAGAGCTACTGTTGCCTCTAATCGTAAG                         AGGAAATCTGACGA
genomic: ATCCTAGCACAACAGCACTATATAGAGCTACTGTTGCCTCTAATCGTAAGgtaacatctt ... aacaatgcagAGGAAATCTGACGA
EST: gi|29685642|gb|CB681917.1|CB681917
EST:     ATCCTAGCACAACAGCACTATATAGAGCTACTGTTGCCTCTAATCGTAAG                         AGGAAATCTGACGA
genomic: ATCCTAGCACAACAGCACTATATAGAGCTACTGTTGCCTCTAATCGTAAGgtaacatctt ... aacaatgcagAGGAAATCTGACGA
EST: gi|58695843|gb|CK084530.1|CK084530
EST:     ATCCTAGCACAACAGCACTATATAGAGCTACTGTTGCCTCTAATCGTAAG                         AGGAAATCTGACGA
genomic: ATCCTAGCACAACAGCACTATATAGAGCTACTGTTGCCTCTAATCGTAAGgtaacatctt ... aacaatgcagAGGAAATCTGACGA
EST: gi|88511815|gb|CI439321.1|CI439321
EST:     ATCCTAGCACAACAGCACTATATAGAGCTACTGTTGCCTCTAATCGTAAG                         AGGAAATCTGACGA
genomic: ATCCTAGCACAACAGCACTATATAGAGCTACTGTTGCCTCTAATCGTAAGgtaacatctt ... aacaatgcagAGGAAATCTGACGA
EST: gi|88902143|gb|CI374751.1|CI374751
EST:     ATCCTAGCACAACAGCACTATATAGAGCTACTGTTGCCTCTAATCGTAAG                         AGGAAATCTGACGA
genomic: ATCCTAGCACAACAGCACTATATAGAGCTACTGTTGCCTCTAATCGTAAGgtaacatctt ... aacaatgcagAGGAAATCTGACGA
EST: gi|88517931|gb|CI444820.1|CI444820
EST:     ATCCTAGCACAACAGCACTATATAGAGCTACTGTTGCCTCTAATCGTAAG                         AGGAAATCTGACGA
genomic: ATCCTAGCACAACAGCACTATATAGAGCTACTGTTGCCTCTAATCGTAAGgtaacatctt ... aacaatgcagAGGAAATCTGACGA
EST: gi|218496318|gb|FG954188.1|FG954188
EST:     ATCCTAGCACAACAGCACTATATAGAGCTACTGTTGCCTCTAATCGTAAG                         AGGAAATCTGACGA
genomic: ATCCTAGCACAACAGCACTATATAGAGCTACTGTTGCCTCTAATCGTAAGgtaacatctt ... aacaatgcagAGGAAATCTGACGA
EST: gi|3767294|gb|AU031404.1|AU031404
EST:     ATCCTAGCACAACAGCACTATATAGAGCTACTGTTGCCTCTAATCGTAAG                         AGGAAATCTGACGA
genomic: ATCCTAGCACAACAGCACTATATAGAGCTACTGTTGCCTCTAATCGTAAGgtaacatctt ... aacaatgcagAGGAAATCTGACGA
EST: gi|88473931|gb|CI411202.1|CI411202
EST:     ATCCTAGCACAACAGCACTATATAGAGCTACTGTTGCCTCTAATCGTAAG                         AGGAAATCTGACGA
genomic: ATCCTAGCACAACAGCACTATATAGAGCTACTGTTGCCTCTAATCGTAAGgtaacatctt ... aacaatgcagAGGAAATCTGACGA
EST: gi|15847274|gb|BI795550.1|BI795550
EST:     ATCCTAGCAC-ACAGCACTATATAGAGCTACTGTTGCCTCTAATCGTAAG                         AGGAAATCTGACGA
genomic: ATCCTAGCACAACAGCACTATATAGAGCTACTGTTGCCTCTAATCGTAAGgtaacatctt ... aacaatgcagAGGAAATCTGACGA
EST: gi|218491607|gb|FG958897.1|FG958897
EST:     ATCCTAGCACAACAGCACTATATAGAGCTACTGTTGCCTCTAATCGTAAG                         AGGAAATCTGACGA
genomic: ATCCTAGCACAACAGCACTATATAGAGCTACTGTTGCCTCTAATCGTAAGgtaacatctt ... aacaatgcagAGGAAATCTGACGA
EST: gi|86428812|gb|CI075493.1|CI075493
EST:     ATCCTAGCACAACAGCACTATATAGAGCTACTGTTGCCTCTAATCGTAAG                         AGGAAATCTGACGA
genomic: ATCCTAGCACAACAGCACTATATAGAGCTACTGTTGCCTCTAATCGTAAGgtaacatctt ... aacaatgcagAGGAAATCTGACGA
EST: gi|88284496|gb|CI405942.1|CI405942
EST:     ATCCTAGCACAACAGCACTATATAGAGCTACTGTTGCCTCTAATCGTAAG                         AGGAAATCTGACGA
genomic: ATCCTAGCACAACAGCACTATATAGAGCTACTGTTGCCTCTAATCGTAAGgtaacatctt ... aacaatgcagAGGAAATCTGACGA
EST: gi|88483496|gb|CI420767.1|CI420767
EST:     ATCCTAGCACAACAGCACTATATAGAGCTACTGTTGCCTCTAATCGTAAG                         AGGAAATCTGACGA
genomic: ATCCTAGCACAACAGCACTATATAGAGCTACTGTTGCCTCTAATCGTAAGgtaacatctt ... aacaatgcagAGGAAATCTGACGA
EST: gi|88974062|gb|CI002724.1|CI002724
EST:     ATCCTAGCACAACAGCACTATATAGAGCTACTGTTGCCTCTAATCGTAAG                         AGGAAATCTGACGA
genomic: ATCCTAGCACAACAGCACTATATAGAGCTACTGTTGCCTCTAATCGTAAGgtaacatctt ... aacaatgcagAGGAAATCTGACGA
EST: gi|29685641|gb|CB681916.1|CB681916
EST:     ATCCTAGCACAACAGCACTATATAGAGCTACTGTTGCCTCTAATCGTAAG                         AGGAAATCTGACGA
genomic: ATCCTAGCACAACAGCACTATATAGAGCTACTGTTGCCTCTAATCGTAAGgtaacatctt ... aacaatgcagAGGAAATCTGACGA
EST: gi|88839574|gb|CI005362.1|CI005362
EST:     ATCCTAGCACAACAGCACTATATAGAGCTACTGTTGCCTCTAATCGTAAG                         AGGAAATCTGACGA
genomic: ATCCTAGCACAACAGCACTATATAGAGCTACTGTTGCCTCTAATCGTAAGgtaacatctt ... aacaatgcagAGGAAATCTGACGA
EST: gi|109711804|gb|CI028974.1|CI028974
EST:     ATCCTAGCACAACAGCACTATATAGAGCTACTGTTGCCTCTAATCGTAAG                         AGGAAATCTGACGA
genomic: ATCCTAGCACAACAGCACTATATAGAGCTACTGTTGCCTCTAATCGTAAGgtaacatctt ... aacaatgcagAGGAAATCTGACGA

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: 73 (upstream exon), 75 (downstream exon)
Score: 24

TCCTTCCAGTGCCCCAGATTTTGGGCAGGGTCGACAAGTCTTAGCTGTTTATCCTAGCACAACAGCACTATATAGAGCTACTGTTGCCTCTAATCGTAAGgtaacatctt ... aacaatgcagAGGAAATCTGACGA




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TCCTTCCAGTGCCCCAGATTTTGGGCAGGGTCGACAAGTCTTAGCTGTTTATCCTAGCACAACAGCACTATATAGAGCTACTGTTGCCTCTAATCGTAAGgtaacatcttaaaatctttcatgaatcctatgtaaatcttttaagtcttgacagtaatttgagtttctttctgtgttctagtcctgtcctgtccatatgt

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCT