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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agctgtaacctagcaaaataactaattataaaacccgtctagatcatagagcacacttcttaaattttgagcacttatttcatggacttattttgtgtagGGTATATGGCTCTGTGAACATCGTGACAATGCTTCCTCCCGGAAAATTGTGATCACTCTCAATGGGGTCTAGATGAAGGTCTTCAAAGGCTGGGATGCAG

Basic information

species Oryza sativa
transcript LOC_Os02g09460.1
intron # 6
splice site 3'
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|88211486|gb|CI211126.1|CI211126
EST:     GATCCCTATAACTGATGGGCATCTCAATATGGGCACTTGGCAG                         GGTATATGGCTCTGTGAACATCGTGACAATGCTTCCTCCCGGAAAATTGTG
genomic: GATCCCTATAACTGATGGGCATCTCAATATGGGCACTTGGCAGgtaatagaaa ... ttttgtgtagGGTATATGGCTCTGTGAACATCGTGACAATGCTTCCTCCCGGAAAATTGTG
EST: gi|86485004|gb|CI127637.1|CI127637
EST:     GATCCCTATAACTGATGGGCATCTCAATATGGGCACTTGGCAG                         GGTATATGGCTCTGTGAACATCGTGACAATGCTTCCTCCCGGAAAATTGTG
genomic: GATCCCTATAACTGATGGGCATCTCAATATGGGCACTTGGCAGgtaatagaaa ... ttttgtgtagGGTATATGGCTCTGTGAACATCGTGACAATGCTTCCTCCCGGAAAATTGTG
EST: gi|88435892|gb|CI514031.1|CI514031
EST:     GATCCCTATAACTGATGGGCATCTCAATATGGGCACTTGGCAG                         GGTATATGGCTCTGTGAACATCGTGACAATGCTTCCTCCCGGAAAATTGTG
genomic: GATCCCTATAACTGATGGGCATCTCAATATGGGCACTTGGCAGgtaatagaaa ... ttttgtgtagGGTATATGGCTCTGTGAACATCGTGACAATGCTTCCTCCCGGAAAATTGTG
EST: gi|86528104|gb|CI168310.1|CI168310
EST:     GATCCCTATAACTGATGGGCATCTCAATATGGGCACTTGGCAG                         GGTATATGGCTCTGTGAACATCGTGACAATGCTTCCTCCCGGAAAATTGTG
genomic: GATCCCTATAACTGATGGGCATCTCAATATGGGCACTTGGCAGgtaatagaaa ... ttttgtgtagGGTATATGGCTCTGTGAACATCGTGACAATGCTTCCTCCCGGAAAATTGTG
EST: gi|88547724|gb|CI478044.1|CI478044
EST:     GATCCCTATAACTGATGGGCATCTCNATATGGGCACTTGGCAG                         GGTATATGGCTCTGTGAACATCGTGACAATGCTTCCTCCCGGAAAATTGTG
genomic: GATCCCTATAACTGATGGGCATCTCAATATGGGCACTTGGCAGgtaatagaaa ... ttttgtgtagGGTATATGGCTCTGTGAACATCGTGACAATGCTTCCTCCCGGAAAATTGTG
EST: gi|88293128|gb|CI512893.1|CI512893
EST:     GATCCCTATAACTGATGGGCATCTCAATATGGGCACTTGGCAG                         GGTATATGGCTCTGTGAACATCGTGACAATGCTTCCTCCCGGAAAATTGTG
genomic: GATCCCTATAACTGATGGGCATCTCAATATGGGCACTTGGCAGgtaatagaaa ... ttttgtgtagGGTATATGGCTCTGTGAACATCGTGACAATGCTTCCTCCCGGAAAATTGTG
EST: gi|9866191|gb|AU101941.1|AU101941
EST:     GATCCCTATAACTGATGGGCATCNCAATATGGGCNCTTGGCAG                         GGTATATGGCTCTGTGAACATCGTGACAATGCTTCCTCCCGGAAAATTGTG
genomic: GATCCCTATAACTGATGGGCATCTCAATATGGGCACTTGGCAGgtaatagaaa ... ttttgtgtagGGTATATGGCTCTGTGAACATCGTGACAATGCTTCCTCCCGGAAAATTGTG
EST: gi|86595369|gb|CI262607.1|CI262607
EST:     GATCCCTATAACTGATGGGCATCTCAATATGGGCACTTGGCAG                         GGTATATGGCTCTGTGAACATCGTGACAATGCTTCCTCCCGGAAAATTGTG
genomic: GATCCCTATAACTGATGGGCATCTCAATATGGGCACTTGGCAGgtaatagaaa ... ttttgtgtagGGTATATGGCTCTGTGAACATCGTGACAATGCTTCCTCCCGGAAAATTGTG
EST: gi|86834560|gb|CI344491.1|CI344491
EST:     GATCCCTATAACTGATGGGCATCTCAATATGGGCACTTGGCAG                         GGTATATGGCTCTGTGAACATCGTGACAATGCTTCCTCCCGGAAAATTGTG
genomic: GATCCCTATAACTGATGGGCATCTCAATATGGGCACTTGGCAGgtaatagaaa ... ttttgtgtagGGTATATGGCTCTGTGAACATCGTGACAATGCTTCCTCCCGGAAAATTGTG
EST: gi|40493973|gb|BX901795.1|BX901795
EST:     GATCCCTATAACTGATGGGCATCTCAATATGGGCACTTGGCAG                         GGTATATGGCTCTGTGAACATCGTGA
genomic: GATCCCTATAACTGATGGGCATCTCAATATGGGCACTTGGCAGgtaatagaaa ... ttttgtgtagGGTATATGGCTCTGTGAACATCGTGA
EST: gi|86414523|gb|CI068926.1|CI068926
EST:     GATCCCTATAACTGATGGGCATCTCAATATGGGCACTTGGCAG                         GGTATATGGCTCTGTGAACATCGTGACAATGCTTCCTCCCGGAAAATTGTG
genomic: GATCCCTATAACTGATGGGCATCTCAATATGGGCACTTGGCAGgtaatagaaa ... ttttgtgtagGGTATATGGCTCTGTGAACATCGTGACAATGCTTCCTCCCGGAAAATTGTG
EST: gi|88259596|gb|CI363889.1|CI363889
EST:     GATCCCTATAACTGATGGGCATCTCAATATGGGCACTTGGCAG                         GGTATATGGCTCTGTGAACATCGTGACAATGCTTCCTCCCGGAAAATTGTG
genomic: GATCCCTATAACTGATGGGCATCTCAATATGGGCACTTGGCAGgtaatagaaa ... ttttgtgtagGGTATATGGCTCTGTGAACATCGTGACAATGCTTCCTCCCGGAAAATTGTG
EST: gi|88216643|gb|CI214743.1|CI214743
EST:     GATCCCTATAACTGATGGGCATCTCAATATGGGCACTTGGCAG                         GGTATATGGCTCTGTGAACATCGTGACAATGCTTCCTCCCGGAAAATTGTG
genomic: GATCCCTATAACTGATGGGCATCTCAATATGGGCACTTGGCAGgtaatagaaa ... ttttgtgtagGGTATATGGCTCTGTGAACATCGTGACAATGCTTCCTCCCGGAAAATTGTG
EST: gi|88292048|gb|CI532640.1|CI532640
EST:     ATCCCTATGAGTGATGGGCATCTCAATATGGGCACTTGGCAGG                         GGTATATGGCTCTGTGAACATCGTGACAATGCTTCCTCCCGGAAAATTGT
genomic: ATCCCTATAACTGATGGGCATCTCAATATGGGCACTTGGCA-Ggtaatagaaa ... ttttgtgtagGGTATATGGCTCTGTGAACATCGTGACAATGCTTCCTCCCGGAAAATTGT
EST: gi|88244910|gb|CI242761.1|CI242761
EST:     GATCCCTATAACTGATGGGCATCTCAATATGGGCACTTGGCAG                         GGTATATGGCTCTGTGAACATCGTGACAATGCTTCCTCCCGGAAAATTGTG
genomic: GATCCCTATAACTGATGGGCATCTCAATATGGGCACTTGGCAGgtaatagaaa ... ttttgtgtagGGTATATGGCTCTGTGAACATCGTGACAATGCTTCCTCCCGGAAAATTGTG
EST: gi|88979867|gb|CI026167.1|CI026167
EST:     GATCCCTATAACTGATGGGCATCTCAATATGGGCACTTGGCAG                         GGTATATGGCTCTGTGAACATCGTGACAATGCTTCCTCCCGGAAAATTGTG
genomic: GATCCCTATAACTGATGGGCATCTCAATATGGGCACTTGGCAGgtaatagaaa ... ttttgtgtagGGTATATGGCTCTGTGAACATCGTGACAATGCTTCCTCCCGGAAAATTGTG
EST: gi|88239487|gb|CI239964.1|CI239964
EST:     GATCCCTATAACTGATGGGCATCTCAATATGGGCACTTGGCAG                         GGTATATGGCTCTGTGAACATCGTGACAATGCTTCCTCCCGGAAAATTGTG
genomic: GATCCCTATAACTGATGGGCATCTCAATATGGGCACTTGGCAGgtaatagaaa ... ttttgtgtagGGTATATGGCTCTGTGAACATCGTGACAATGCTTCCTCCCGGAAAATTGTG
EST: gi|88214348|gb|CI214197.1|CI214197
EST:     GATCCCTATAACTGATGGGCATCTCAATATGGGCACTTGGCAG                         GGTATATGGCTCTGTGAACATCGTGACAATGCTTCCTCCCGGAAAATTGTG
genomic: GATCCCTATAACTGATGGGCATCTCAATATGGGCACTTGGCAGgtaatagaaa ... ttttgtgtagGGTATATGGCTCTGTGAACATCGTGACAATGCTTCCTCCCGGAAAATTGTG
EST: gi|88526829|gb|CI454918.1|CI454918
EST:     GATCCCTATAACTGATGGGCATCTCAATATGGGCACTTGGCAG                         GGTATATGGCTCTGTGAACATCGTGACAATGCTTCCTCCCGGAAAATTGTG
genomic: GATCCCTATAACTGATGGGCATCTCAATATGGGCACTTGGCAGgtaatagaaa ... ttttgtgtagGGTATATGGCTCTGTGAACATCGTGACAATGCTTCCTCCCGGAAAATTGTG
EST: gi|86879801|gb|CI339929.1|CI339929
EST:     GATCCCTATAACTGATGGGCATCTCAATATGGGCACTTGGCAG                         GGTATATGGCTCTGTGAACATCGTGACAATGCTTCCTCCCGGAAAATTGTG
genomic: GATCCCTATAACTGATGGGCATCTCAATATGGGCACTTGGCAGgtaatagaaa ... ttttgtgtagGGTATATGGCTCTGTGAACATCGTGACAATGCTTCCTCCCGGAAAATTGTG
EST: gi|88319148|gb|CI513212.1|CI513212
EST:     GATCCCTATAACTGATGGGCATCTCAATATGGGCACTTGGCAG                         GGTATATGGCTCTGTGAACATCGTGACAATGCTTCCTCCCGGAAAATTGTG
genomic: GATCCCTATAACTGATGGGCATCTCAATATGGGCACTTGGCAGgtaatagaaa ... ttttgtgtagGGTATATGGCTCTGTGAACATCGTGACAATGCTTCCTCCCGGAAAATTGTG
EST: gi|86495983|gb|CI138616.1|CI138616
EST:     GATCCCTATAACTGATGGGCATCTCAATATGGGCACTTGGCAG                         GGTATATGGCTCTGTGAACATCGTGACAATGCTTCCTCCCGGAAAATTGTG
genomic: GATCCCTATAACTGATGGGCATCTCAATATGGGCACTTGGCAGgtaatagaaa ... ttttgtgtagGGTATATGGCTCTGTGAACATCGTGACAATGCTTCCTCCCGGAAAATTGTG
EST: gi|88243875|gb|CI242997.1|CI242997
EST:     GATCCCTATAACTGATGGGCATCTCAATATGGGCACTTGGCAG                         GGTATATGGCTCTGTGAACATCGTGACAATGCTTCCTCCCGGAAAATTGTG
genomic: GATCCCTATAACTGATGGGCATCTCAATATGGGCACTTGGCAGgtaatagaaa ... ttttgtgtagGGTATATGGCTCTGTGAACATCGTGACAATGCTTCCTCCCGGAAAATTGTG
EST: gi|58664625|gb|CK053311.1|CK053311
EST:     GATCCCTATAACTGATGGGCATCTCAATATGGGCACTTGGCAG                         GGTATATGGCTCTGTGAACATCGTGACAATGCTTCCTCCCGGAAAATTGTG
genomic: GATCCCTATAACTGATGGGCATCTCAATATGGGCACTTGGCAGgtaatagaaa ... ttttgtgtagGGTATATGGCTCTGTGAACATCGTGACAATGCTTCCTCCCGGAAAATTGTG
EST: gi|88543260|gb|CI473251.1|CI473251
EST:     GATCCCTATAACTGATGGGCATCTCAATATGGGCACTTGGCAG                         GGTATATGGCTCTGTGAACATCGTGACAATGCTTCCTCCCGGAAAATTGTG
genomic: GATCCCTATAACTGATGGGCATCTCAATATGGGCACTTGGCAGgtaatagaaa ... ttttgtgtagGGTATATGGCTCTGTGAACATCGTGACAATGCTTCCTCCCGGAAAATTGTG
EST: gi|86483406|gb|CI126039.1|CI126039
EST:     GATCCCTATAACTGATGGGCATCTCAATATGGGCACTTGGCAG                         GGTATATGGCTCTGTGAACATCGTGACAATGCTTCCTCCCGGAAAATTGTG
genomic: GATCCCTATAACTGATGGGCATCTCAATATGGGCACTTGGCAGgtaatagaaa ... ttttgtgtagGGTATATGGCTCTGTGAACATCGTGACAATGCTTCCTCCCGGAAAATTGTG
EST: gi|86835521|gb|CI347978.1|CI347978
EST:     GATCCCTATAACTGATTGACATCTCAATATGGGCACTTGGCAG                         GGTATATGGCTCTGTGAACATCGTGACAATGCTTCCTCCCGGAAAATTGTG
genomic: GATCCCTATAACTGATGGGCATCTCAATATGGGCACTTGGCAGgtaatagaaa ... ttttgtgtagGGTATATGGCTCTGTGAACATCGTGACAATGCTTCCTCCCGGAAAATTGTG
EST: gi|88213410|gb|CI213259.1|CI213259
EST:     GATCCCTATAACTGATGGGCATCTCAATATGGGCACTTGGCAG                         GGTATATGGCTCTGTGAACATCGTGACAATGCTTCCTCCCGGAAAATTGTG
genomic: GATCCCTATAACTGATGGGCATCTCAATATGGGCACTTGGCAGgtaatagaaa ... ttttgtgtagGGTATATGGCTCTGTGAACATCGTGACAATGCTTCCTCCCGGAAAATTGTG
EST: gi|55411794|gb|CV724170.1|CV724170
EST:     GATCCCTATAACTGATGGGCATCTCAATATGGGCACTTGGCAG                         GGTATATGGCTCTGTGAACATCGTGACAATGCTTCCTCCCGGAAAATTGTG
genomic: GATCCCTATAACTGATGGGCATCTCAATATGGGCACTTGGCAGgtaatagaaa ... ttttgtgtagGGTATATGGCTCTGTGAACATCGTGACAATGCTTCCTCCCGGAAAATTGTG

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: 61 (upstream exon), 70 (downstream exon)
Score: 20

GATCCCTATAACTGATGGGCATCTCAATATGGGCACTTGGCAGgtaatagaaa ... ttttgtgtagGGTATATGGCTCTGTGAACATCGTGACAATGCTTCCTCCCGGAAAATTGTGATCACTCTCAATGGGGTCTAGATGAAGGTCTTCAAAGGCTGGGATGCAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atagagcacacttcttaaattttgagcacttatttcatggacttattttgtgtagGGTATATGGCTCTGTGAACATCGTGACAATGCTTCCTCCCGGAAAATTGTGATCACTCTCAATGGGGTCTAGATGAAGGTCTTCAAAGGCTGGGATGCAG
                                         cttatttt  CT-rich tract
         acttcttaaatttt  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
agctgtaacctagcaaaataactaattataaaacccgtctagatcatagagcacacttcttaaattttgagcacttatttcatggacttattttgtgtagGGTATATGGCTCTGTGAACATCGTGACAATGCTTCCTCCCGGAAAATTGTGATCACTCTCAATGGGGTCTAGATGAAGGTCTTCAAAGGCTGGGATGCAG

agctgta
- - - - - - - aaaataa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tttcatg