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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTCCATCGACCAACTTGCTTACTGTATCAACAGTTTCAGAGATGCTGCCTTGTCCAAAGATCCGAAGTTTGATCACATTGAGATGGAGGAGAAACAGAAGgtattcaatgcatcaactacaaaattagcacaatatcttttctctatacactgattgcaatgctagttcacgaactacgttctgctagtgaatggtaaca...

Basic information

species Oryza sativa
transcript LOC_Os01g08560.1
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g08560.2 (Oryza sativa), 5'ss of exon 8
lower sequence: GLYMA13G43630.2 (Glycine max), 5'ss of exon 8
TTCCATCGACCAACTTGCTTACTGTATCAACAGTTTCAGAGATGCTGCCTTGTCCAAAGATCCGAAGTTTGATCACATTGAGATGGAGGAGAAACAGAAGgtattcaatgcatcaactacaaaattagcacaatatcttttctctatacactgattgcaatgctagttcacgaactacgttctgctagtgaatggtaaca-
    || || |||||||| || ||||| || ||||  ||||| |||||  |||| || ||||| ||||||||||||||||| ||  | |||||||| ||||||        ||    |||     |       ||||  || | | |   ||| |||| ||  ||| | |   | ||  ||| | |  |   || || || 
AGTAATTGATCAACTTGCCTATTGTATAAATAGTTATAGAGAAGCTGCAATGTCAAATGATCCCAAGTTTGATCACATTGACATCAATGAGAAACAAAAGgta--------attggttactgctctgattatgtatcacttttttttc--ctggttgccat-ttagctga--gattattttccgttt-tatttgttatcag
















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|58677519|gb|CK066206.1|CK066206
EST:     TGTCCAAAGATCCGAAGTTTGATCACATTGAGATGGAGGAGAAACAGAAG                         GTGATTAACCAGTGTTCCGAAGCAGAAGTCTGGCTGAGAGAGAAAATACAG
genomic: TGTCCAAAGATCCGAAGTTTGATCACATTGAGATGGAGGAGAAACAGAAGgtattcaatg ... tcacatgcagGTGATTAACCAGTGTTCCGAAGCAGAAGTCTGGCTGAGAGAGAAAATACAG
EST: gi|86436862|gb|CI118584.1|CI118584
EST:     GGTCCAAAGATCCGAAGTTTGATCACATTGAGATGGAGGAGAAACAGAAG                         GTGATTAACCAGTGTTCCGAAGCAGTAGTCTGGCTGAGAGAGAAAATACAG
genomic: TGTCCAAAGATCCGAAGTTTGATCACATTGAGATGGAGGAGAAACAGAAGgtattcaatg ... tcacatgcagGTGATTAACCAGTGTTCCGAAGCAGAAGTCTGGCTGAGAGAGAAAATACAG
EST: gi|27921378|gb|CB097186.1|CB097186
EST:     TGTCCAAAGATCCGAAGTTTGATCACATTGAGATGGAGGAGAAACAGAAG                         GTGATTAACCAGTGTTCCGAAGCAGAAGTCTGGCTGAGAGAGAAAATACAG
genomic: TGTCCAAAGATCCGAAGTTTGATCACATTGAGATGGAGGAGAAACAGAAGgtattcaatg ... tcacatgcagGTGATTAACCAGTGTTCCGAAGCAGAAGTCTGGCTGAGAGAGAAAATACAG
EST: gi|58683636|gb|CK072323.1|CK072323
EST:     TGTCCAAAGATCCGAAGTTTGATCACATTGAGATGGAGGAGAAACAGAAG                         GTGATTAACCAGTGTTCCGAAGCAGAAGTCTGGCTGAGAGAGAAAATACAG
genomic: TGTCCAAAGATCCGAAGTTTGATCACATTGAGATGGAGGAGAAACAGAAGgtattcaatg ... tcacatgcagGTGATTAACCAGTGTTCCGAAGCAGAAGTCTGGCTGAGAGAGAAAATACAG
EST: gi|29678339|gb|CB674614.1|CB674614
EST:     TGTCCAAAGATCCGAAGTTTGATCACATTGAGATGGAGGAGAAACAGAAG                         GTGATTAACCAGTGTTCCGAAGCAGAAGTCTGGCTGAGAGAGAAAATACAG
genomic: TGTCCAAAGATCCGAAGTTTGATCACATTGAGATGGAGGAGAAACAGAAGgtattcaatg ... tcacatgcagGTGATTAACCAGTGTTCCGAAGCAGAAGTCTGGCTGAGAGAGAAAATACAG
EST: gi|29680266|gb|CB676541.1|CB676541
EST:     TGTCCAAAGATCCGAAGTTTGATCACATTGAGATGGAGGAGAAACAGAAG                         GTGATTAACCAGTGTTCCGAAGCAGAAGTCTGGCTGAGAGAGAAAATACAG
genomic: TGTCCAAAGATCCGAAGTTTGATCACATTGAGATGGAGGAGAAACAGAAGgtattcaatg ... tcacatgcagGTGATTAACCAGTGTTCCGAAGCAGAAGTCTGGCTGAGAGAGAAAATACAG
EST: gi|218478821|gb|FG953668.1|FG953668
EST:     TGTCCAAAGATCCGAAGTTTGATCACATTGAGATGGAGGAGAAACAGAAG                         GTGATTAACCAGTGTTCCGAAGCAGAAGTCTGGCTGAGAGAGAAAATACAG
genomic: TGTCCAAAGATCCGAAGTTTGATCACATTGAGATGGAGGAGAAACAGAAGgtattcaatg ... tcacatgcagGTGATTAACCAGTGTTCCGAAGCAGAAGTCTGGCTGAGAGAGAAAATACAG
EST: gi|87021150|gb|CI271957.1|CI271957
EST:     TGTCCAAAGATCCGAAGTTTGATCACATTGAGATGGAGGAGAAACAGAAG                         GTGATTAACCAGTGTTCCGAAGCAGAAGTCTGGCTGAGAGAGTAAATACAG
genomic: TGTCCAAAGATCCGAAGTTTGATCACATTGAGATGGAGGAGAAACAGAAGgtattcaatg ... tcacatgcagGTGATTAACCAGTGTTCCGAAGCAGAAGTCTGGCTGAGAGAGAAAATACAG
EST: gi|29619081|gb|CB624093.1|CB624093
EST:     ATTGAGATGGAGGAGAAACAGAAG                         GTGATTAACCAGTGTTCCGAAGCAGAAGTCTGGCTGAGAGAGAAAATACAG
genomic: ATTGAGATGGAGGAGAAACAGAAGgtattcaatg ... tcacatgcagGTGATTAACCAGTGTTCCGAAGCAGAAGTCTGGCTGAGAGAGAAAATACAG
EST: gi|87023343|gb|CI272171.1|CI272171
EST:     TGTCCAAAGATCCGAAGTTTGATCACATTGAGATGGAGGAGACACAGAAG                         GTGATTAACCAGTGTTCCGAAGCAGAAGTCTGGCTGAGAGAGAAAATACAG
genomic: TGTCCAAAGATCCGAAGTTTGATCACATTGAGATGGAGGAGAAACAGAAGgtattcaatg ... tcacatgcagGTGATTAACCAGTGTTCCGAAGCAGAAGTCTGGCTGAGAGAGAAAATACAG
EST: gi|86479448|gb|CI122081.1|CI122081
EST:     TGTCCAAAGATCCGAAGTTTGATCACATTGAGATGGAGGAGAAACAGAAG                         GTGATTAACCAGTGTTCCGAAGCAGAAGTCTGGCTGAGAGAGAAAATACGG
genomic: TGTCCAAAGATCCGAAGTTTGATCACATTGAGATGGAGGAGAAACAGAAGgtattcaatg ... tcacatgcagGTGATTAACCAGTGTTCCGAAGCAGAAGTCTGGCTGAGAGAGAAAATACAG
EST: gi|27553959|gb|CA997859.1|CA997859
EST:     TGTCCAAAGATCCGAAGTTTGATCACATTGAGATGGAGGAGAAACAGAAG                         GTGATTAACCAGTGTTCCGAAGCAGAAGTCTGGCTGAGAGAGAAAATACAG
genomic: TGTCCAAAGATCCGAAGTTTGATCACATTGAGATGGAGGAGAAACAGAAGgtattcaatg ... tcacatgcagGTGATTAACCAGTGTTCCGAAGCAGAAGTCTGGCTGAGAGAGAAAATACAG
EST: gi|218497201|gb|FG952163.1|FG952163
EST:     TGTCCAAAGATCCGAAGTTTGATCACATTGAGATGGAGGAGAAACAGAAG                         G-GATTAACCAGTGTTCCGAAGCAGAAGTCTGGCTGAGAGAGAAAATACAG
genomic: TGTCCAAAGATCCGAAGTTTGATCACATTGAGATGGAGGAGAAACAGAAGgtattcaatg ... tcacatgcagGTGATTAACCAGTGTTCCGAAGCAGAAGTCTGGCTGAGAGAGAAAATACAG
EST: gi|58600907|gb|CK011435.1|CK011435
EST:     GTCCAAAGATCCGAAGTTTGATCACATTGAGATGGAGGAGAAACAGAAG                         GTGATTAACCAGTGTTCCGAAGCAGAAGTCTGGCTGAGAGAGAAAATACAG
genomic: GTCCAAAGATCCGAAGTTTGATCACATTGAGATGGAGGAGAAACAGAAGgtattcaatg ... tcacatgcagGTGATTAACCAGTGTTCCGAAGCAGAAGTCTGGCTGAGAGAGAAAATACAG
EST: gi|86829544|gb|CI286738.1|CI286738
EST:     TGTCCAAAGATCCGAAGTTTGATCACATTGAGATGGAGGAGAAACAGAAG                         GTGATTAACCAGTGTTCCGAAGCAGAAGTCTGGCTGAGAGAGAAAATACAG
genomic: TGTCCAAAGATCCGAAGTTTGATCACATTGAGATGGAGGAGAAACAGAAGgtattcaatg ... tcacatgcagGTGATTAACCAGTGTTCCGAAGCAGAAGTCTGGCTGAGAGAGAAAATACAG

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: 72 (upstream exon), 74 (downstream exon)
Score: 93

TTCCATCGACCAACTTGCTTACTGTATCAACAGTTTCAGAGATGCTGCCTTGTCCAAAGATCCGAAGTTTGATCACATTGAGATGGAGGAGAAACAGAAGgtattcaatg ... tcacatgcagGTGATTAACCAGTGTTCCGAAGCAGAAGTCTGGCTGAGAGAGAAAATACAGCAGCAAGATGCTCTGCCGAAGCATGCTAACCCTGTCCTACTCTCTTCTG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTCCATCGACCAACTTGCTTACTGTATCAACAGTTTCAGAGATGCTGCCTTGTCCAAAGATCCGAAGTTTGATCACATTGAGATGGAGGAGAAACAGAAGgtattcaatgcatcaactacaaaattagcacaatatcttttctctatacactgattgcaatgctagttcacgaactacgttctgctagtgaatggtaaca

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA