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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ACTAGCTACCCTTCTTCATATGGTTCGACACACTCACATAAACAATTGACAGGCGGACCTGTGAATATTGAGCAATCATCTATGAGCAGTATGAGTGAAGgtatatgaatttcttttcttcaccttttttttagccattcttcctggccagtgattttctatctattaaaacaaaaatatcttccccttcttgtggcctg...

Basic information

species Oryza sativa
transcript 13113.m00220
intron # 7
splice site 5'
intron type U2

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|58586932|gb|CF985240.1|CF985240
EST:     AGGCGGACCTGTGAATATTGAGCAATCATCTATGAGCAGTATGAGTGAAG                         ATGGAACTAGAAACATGTCCAACGGGAGCCAAGCAGCAAGATATGCAGCCA
genomic: AGGCGGACCTGTGAATATTGAGCAATCATCTATGAGCAGTATGAGTGAAGgtatatgaat ... tattatgcagATGGAACTAGAAACATGTCCAACGGGAGCCAAGCAGCAAGATATGCAGCCA
EST: gi|58604357|gb|CK014885.1|CK014885
EST:     AGGCGGACCTGTGAATATTGAGCAATCATCTATGAGCAGTATGAGTGAAG                         ATGGAACTAGAAACATGTCCAACGGGAGCCAAGCAGCAAGATATGCAGCCA
genomic: AGGCGGACCTGTGAATATTGAGCAATCATCTATGAGCAGTATGAGTGAAGgtatatgaat ... tattatgcagATGGAACTAGAAACATGTCCAACGGGAGCCAAGCAGCAAGATATGCAGCCA
EST: gi|218499567|gb|FG966235.1|FG966235
EST:     TGAGCAATCATCTATGAGCAGTATGAGTGAAG                         ATGGAACTAGAAACATGTCCAACGGGAGCCTAGCAGCAAGATATGCAGCCA
genomic: TGAGCAATCATCTATGAGCAGTATGAGTGAAGgtatatgaat ... tattatgcagATGGAACTAGAAACATGTCCAACGGGAGCCAAGCAGCAAGATATGCAGCCA
EST: gi|218496784|gb|FG956411.1|FG956411
EST:     AGGCGGACCTGTGAATATTGAGCAATCATCTATGAGCAGTATGAGTGAAG                         ATGGAACTAGAAACATGTCCAACGGGAGCCAAGCAGCAAGATATGCAGCCA
genomic: AGGCGGACCTGTGAATATTGAGCAATCATCTATGAGCAGTATGAGTGAAGgtatatgaat ... tattatgcagATGGAACTAGAAACATGTCCAACGGGAGCCAAGCAGCAAGATATGCAGCCA
EST: gi|66917992|gb|CX104840.1|CX104840
EST:     AGGCGGACCTGTGAATATTGAGCAATCATCTATGAGCAGTATGAGTGAAG                         ATGGAACTAGAAACATGTCCAACGGGAGCCAAGCAGCAAGATATGCAGCCA
genomic: AGGCGGACCTGTGAATATTGAGCAATCATCTATGAGCAGTATGAGTGAAGgtatatgaat ... tattatgcagATGGAACTAGAAACATGTCCAACGGGAGCCAAGCAGCAAGATATGCAGCCA
EST: gi|116875181|gb|EC365689.1|EC365689
EST:     AGGCGGACCTGTGAATATTGAGCAATCATCTATGAGCAGTATGAGTGAAG                         ATGGAACTAGAAACATGTCCAACGGGAGCCTAGCAGCAAGATATGCAGCCA
genomic: AGGCGGACCTGTGAATATTGAGCAATCATCTATGAGCAGTATGAGTGAAGgtatatgaat ... tattatgcagATGGAACTAGAAACATGTCCAACGGGAGCCAAGCAGCAAGATATGCAGCCA

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), 71 (downstream exon)
Score: 46

ACTAGCTACCCTTCTTCATATGGTTCGACACACTCACATAAACAATTGACAGGCGGACCTGTGAATATTGAGCAATCATCTATGAGCAGTATGAGTGAAGgtatatgaat ... tattatgcagATGGAACTAGAAACATGTCCAACGGGAGCCAAGCAGCAAGATATGCAGCCAATCCTCAGGACATCTCACAAAGTATCACCATGCCATATGACATGAGTTC




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ACTAGCTACCCTTCTTCATATGGTTCGACACACTCACATAAACAATTGACAGGCGGACCTGTGAATATTGAGCAATCATCTATGAGCAGTATGAGTGAAGgtatatgaatttcttttcttcaccttttttttagccattcttcctggccagtgattttctatctattaaaacaaaaatatcttccccttcttgtggcctg

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCAG