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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCATCTGCTGGCATGACTCCCCCAGGTTTACTTGGTACCTCGAGTTTTGGAGTCCTTCCACAGCAACCTCAGCAGCTGTACCAGTCACCTGCACCTCCAAgtatttccatatctcagcataatctctgaaattgtgctctttattagtatttcttatctgtgtgctaatttgtggttcaacttcag

Basic information

species Oryza sativa
transcript LOC_Os02g11820.1
intron # 12
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|86827321|gb|CI270968.1|CI270968
EST:     AGTCCTTCCACAGCAACCTCAGCAGCTGTACCAGTCACCTGCACCTCCAA                         ATCATTACATGATGCAGCAAGTTCCAAACATGTCTGAGCAGTTACCTAATA
genomic: AGTCCTTCCACAGCAACCTCAGCAGCTGTACCAGTCACCTGCACCTCCAAgtatttccat ... tcaacttcagATCATTACATGATGCAGCAAGTTCCAAACATGTCTGAGCAGTTACCTAATA
EST: gi|88236936|gb|CI234787.1|CI234787
EST:     TGTACCAGTCACCTGCACCTCCAA                         ATCATTACATGATGCAGCAAGTTCCAAACATGTCTGAGCAGTTACCTAATA
genomic: TGTACCAGTCACCTGCACCTCCAAgtatttccat ... tcaacttcagATCATTACATGATGCAGCAAGTTCCAAACATGTCTGAGCAGTTACCTAATA
EST: gi|86482102|gb|CI124735.1|CI124735
EST:     CCAGTCACCTGCACCTCCGA                         ATCATTACATGATGCAGCAAGTTCCAAACATGTCTGAGCAGTTACCTAATA
genomic: CCAGTCACCTGCACCTCCAAgtatttccat ... tcaacttcagATCATTACATGATGCAGCAAGTTCCAAACATGTCTGAGCAGTTACCTAATA
EST: gi|87037946|gb|CI192568.1|CI192568
EST:     AGTCCTTCCACAGCAACCTCAGCAGCTGTACCAGTCACCTGCACCTCCAA                         ATCATTACATGATGCAGCAAGTTCCAAACATGTCTGAGCAGTTACCTAATA
genomic: AGTCCTTCCACAGCAACCTCAGCAGCTGTACCAGTCACCTGCACCTCCAAgtatttccat ... tcaacttcagATCATTACATGATGCAGCAAGTTCCAAACATGTCTGAGCAGTTACCTAATA
EST: gi|86437635|gb|CI119357.1|CI119357
EST:     AGTCCTTCCACAGCAACCTCAGCAGCTGTACCAGTCACCTGCACCTCCAA                         ATCATTACATGATGCAGCAAGTTCCAAACATGTCTGAGCAGTTACCTAATA
genomic: AGTCCTTCCACAGCAACCTCAGCAGCTGTACCAGTCACCTGCACCTCCAAgtatttccat ... tcaacttcagATCATTACATGATGCAGCAAGTTCCAAACATGTCTGAGCAGTTACCTAATA
EST: gi|87035950|gb|CI190572.1|CI190572
EST:     AGTCCTTCCACAGCAACCTCAGCAGCTGTACCAGTCACCTGCACCTCCAA                         ATCATTACATGATGCAGCAAGTTCCAAACATGTCTGAGCAGTTATCTAATA
genomic: AGTCCTTCCACAGCAACCTCAGCAGCTGTACCAGTCACCTGCACCTCCAAgtatttccat ... tcaacttcagATCATTACATGATGCAGCAAGTTCCAAACATGTCTGAGCAGTTACCTAATA
EST: gi|58674115|gb|CK062801.1|CK062801
EST:     AGTCCTTCCACAGCAACCTCAGCAGCTGTACCAGTCACCTGCACCTCCAA                         ATCATTACATGATGCAGCAAGTTCCAAACATGTCTGAGCAGTTACCTAATA
genomic: AGTCCTTCCACAGCAACCTCAGCAGCTGTACCAGTCACCTGCACCTCCAAgtatttccat ... tcaacttcagATCATTACATGATGCAGCAAGTTCCAAACATGTCTGAGCAGTTACCTAATA
EST: gi|87038360|gb|CI192982.1|CI192982
EST:     AGTCCTTCCACAGCAACCTCAGCAGCTGTACCAGTCACCTGCACCTCCAA                         ATCATTACATGATGCAGCAAGTTCCAAACATGTCTGAGCAGTTACCTAATA
genomic: AGTCCTTCCACAGCAACCTCAGCAGCTGTACCAGTCACCTGCACCTCCAAgtatttccat ... tcaacttcagATCATTACATGATGCAGCAAGTTCCAAACATGTCTGAGCAGTTACCTAATA
EST: gi|3766575|gb|AU030685.1|AU030685
EST:     AGCCCTTCCACAGCAACCTCAGCAGCTGTACCAGTCACCTGCACCTCCAA                         ATCATTACATGATGCAGCAAGTTCCAAACATGTCTGAGCANTTACCTAATA
genomic: AGTCCTTCCACAGCAACCTCAGCAGCTGTACCAGTCACCTGCACCTCCAAgtatttccat ... tcaacttcagATCATTACATGATGCAGCAAGTTCCAAACATGTCTGAGCAGTTACCTAATA
EST: gi|86477959|gb|CI120592.1|CI120592
EST:     AGTCCTTCCACAGCAACTTCAGCAGCTGTACCAGTCACCTGCACCTCCAA                         ATCATTACATGATGCAGCAAGTTCCAAACATGTCTGAGCAGTTACCTAATA
genomic: AGTCCTTCCACAGCAACCTCAGCAGCTGTACCAGTCACCTGCACCTCCAAgtatttccat ... tcaacttcagATCATTACATGATGCAGCAAGTTCCAAACATGTCTGAGCAGTTACCTAATA
EST: gi|88834377|gb|CI077660.1|CI077660
EST:     AGTCCTTCCACAGCAACCTCAGCAGCTGTACCAGTCACCTGCACCTCCAA                         ATCATTACATGATGCAGCAAGTTCCAAACATGTCTGAGCAGTTACCTAATA
genomic: AGTCCTTCCACAGCAACCTCAGCAGCTGTACCAGTCACCTGCACCTCCAAgtatttccat ... tcaacttcagATCATTACATGATGCAGCAAGTTCCAAACATGTCTGAGCAGTTACCTAATA
EST: gi|86513692|gb|CI156325.1|CI156325
EST:     AGTCCTTCCACAGCAACCTCAGCAGCTGTACCAGTCACCTGCACCTCCAA                         ATCATTACATGATGCAGCAAGTTCCAAACATGTCTGAGCAGTTACCTAATA
genomic: AGTCCTTCCACAGCAACCTCAGCAGCTGTACCAGTCACCTGCACCTCCAAgtatttccat ... tcaacttcagATCATTACATGATGCAGCAAGTTCCAAACATGTCTGAGCAGTTACCTAATA
EST: gi|86855869|gb|CI271088.1|CI271088
EST:     AGTCCTTCCACAGCAACCTCAGCAGCTGTACCAGTCACCTGCACCTCCAA                         ATCATTACATGATGCAGCAAGTTCCAAACATGTCTGAGCAGTTACCTAATA
genomic: AGTCCTTCCACAGCAACCTCAGCAGCTGTACCAGTCACCTGCACCTCCAAgtatttccat ... tcaacttcagATCATTACATGATGCAGCAAGTTCCAAACATGTCTGAGCAGTTACCTAATA
EST: gi|86437244|gb|CI118966.1|CI118966
EST:     GTCCTTCCACAGCAACCTCAGCAGCTGTACCAGTCACCTGCACCTCCAA                         ATCATTACATGATGCAGCAAGTTCCAAACATGTCTGAGCAGTTACCTAATA
genomic: GTCCTTCCACAGCAACCTCAGCAGCTGTACCAGTCACCTGCACCTCCAAgtatttccat ... tcaacttcagATCATTACATGATGCAGCAAGTTCCAAACATGTCTGAGCAGTTACCTAATA
EST: gi|86481992|gb|CI124625.1|CI124625
EST:     GCAGCTGTACCAGTCACCTGCACCTCCAA                         ATCATTACATGATGCAGCAAGTTCCAAACATGTCTGAGCAGTTACCTAATA
genomic: GCAGCTGTACCAGTCACCTGCACCTCCAAgtatttccat ... tcaacttcagATCATTACATGATGCAGCAAGTTCCAAACATGTCTGAGCAGTTACCTAATA
EST: gi|86436745|gb|CI118467.1|CI118467
EST:     AGTCCTTCCACAGCAACCTCAGCAGCTGTACCAGTCACCTGCACCTCCAA                         ATCATTACATGATGCAGCAAGTTCCAAACATGTCTGAGCAGTTACCTAATA
genomic: AGTCCTTCCACAGCAACCTCAGCAGCTGTACCAGTCACCTGCACCTCCAAgtatttccat ... tcaacttcagATCATTACATGATGCAGCAAGTTCCAAACATGTCTGAGCAGTTACCTAATA
EST: gi|29674781|gb|CB671056.1|CB671056
EST:     AGTCCTTCCACAGCAACCTCAGCAGCTGTACCAGTCACCTGCACCTCCAA                         ATCATTACATGATGCAGCAAGTTCCAAACATGTCTGAGCAGTTACCTAATA
genomic: AGTCCTTCCACAGCAACCTCAGCAGCTGTACCAGTCACCTGCACCTCCAAgtatttccat ... tcaacttcagATCATTACATGATGCAGCAAGTTCCAAACATGTCTGAGCAGTTACCTAATA
EST: gi|87023322|gb|CI272150.1|CI272150
EST:     CCACAGCAACCTCAGCAGCTGTACCAGTCACCTGCACCTCCAA                         ATCATTACATGATGCAGCAAGTTCCAAACATGTCTGAGCAGTTACCTAATA
genomic: CCACAGCAACCTCAGCAGCTGTACCAGTCACCTGCACCTCCAAgtatttccat ... tcaacttcagATCATTACATGATGCAGCAAGTTCCAAACATGTCTGAGCAGTTACCTAATA
EST: gi|87016249|gb|CI271660.1|CI271660
EST:     AGTCCTTCCACAGCAACCTCAGCAGCTGTACCAGTCACCTGCACCTCCAA                         ATCATTACATGATGCAGCAAGTTCCAAACATGTCTGAGCAGTTACCTAATA
genomic: AGTCCTTCCACAGCAACCTCAGCAGCTGTACCAGTCACCTGCACCTCCAAgtatttccat ... tcaacttcagATCATTACATGATGCAGCAAGTTCCAAACATGTCTGAGCAGTTACCTAATA
EST: gi|86478599|gb|CI121232.1|CI121232
EST:     CAGCAACCTCAGCAGCTGTACCAGTCACCTGCACCTCCAA                         ATCATTACATGATGCAGCAAGTTCCAAACATGTCTGAGCAGTTACCTAATA
genomic: CAGCAACCTCAGCAGCTGTACCAGTCACCTGCACCTCCAAgtatttccat ... tcaacttcagATCATTACATGATGCAGCAAGTTCCAAACATGTCTGAGCAGTTACCTAATA
EST: gi|86497710|gb|CI140343.1|CI140343
EST:     AGCAACCTCAGCAGCTGTACCAGTCACCTGCACCTCCAA                         ATCATTACATGATGCAGCAAGTTCCAAACATGTCTGAGCAGTTACCTAATA
genomic: AGCAACCTCAGCAGCTGTACCAGTCACCTGCACCTCCAAgtatttccat ... tcaacttcagATCATTACATGATGCAGCAAGTTCCAAACATGTCTGAGCAGTTACCTAATA
EST: gi|87038839|gb|CI193461.1|CI193461
EST:     AGTCCTTCCACAGCAACCTCAGCAGCTGTACCAGTCACCTGCACCTCCAA                         ATCATTACATGATGCAGCAAGTTCCAAACATGTCTGAGCAGTTACCTAATA
genomic: AGTCCTTCCACAGCAACCTCAGCAGCTGTACCAGTCACCTGCACCTCCAAgtatttccat ... tcaacttcagATCATTACATGATGCAGCAAGTTCCAAACATGTCTGAGCAGTTACCTAATA
EST: gi|87016434|gb|CI273644.1|CI273644
EST:     AGTCCTTCCACAGCAACCTCAGCAGCTGTACCAGTCACCTGCACCTCCAA                         ATCATTACATGATGCAGCAAGTTCCAAACATGTCTGAGCAGTTACCTAATA
genomic: AGTCCTTCCACAGCAACCTCAGCAGCTGTACCAGTCACCTGCACCTCCAAgtatttccat ... tcaacttcagATCATTACATGATGCAGCAAGTTCCAAACATGTCTGAGCAGTTACCTAATA
EST: gi|87021407|gb|CI274014.1|CI274014
EST:     AGTCCTTCCACAGCAACCTCAGCAGCTGTACCAGTCACCTGCACCTCCAA                         ATCATTACATGATGCAGCAAGTTCCAAACATGTCTGAGCAGTTACCTAATA
genomic: AGTCCTTCCACAGCAACCTCAGCAGCTGTACCAGTCACCTGCACCTCCAAgtatttccat ... tcaacttcagATCATTACATGATGCAGCAAGTTCCAAACATGTCTGAGCAGTTACCTAATA

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: 74 (upstream exon), 64 (downstream exon)
Score: 30

GCATCTGCTGGCATGACTCCCCCAGGTTTACTTGGTACCTCGAGTTTTGGAGTCCTTCCACAGCAACCTCAGCAGCTGTACCAGTCACCTGCACCTCCAAgtatttccat ... tcaacttcagATCATTACATGATGCAGCAAGTTCCAAACATGTCTGAGCAGTTACCTAATACCATGCTTCCAAT




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCATCTGCTGGCATGACTCCCCCAGGTTTACTTGGTACCTCGAGTTTTGGAGTCCTTCCACAGCAACCTCAGCAGCTGTACCAGTCACCTGCACCTCCAAgtatttccatatctcagcataatctctgaaattgtgctctttattagtatttcttatctgtgtgctaatttgtggttcaacttcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG