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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCCAATGCCATCGTCACAGATGTCAGgtaaattataatttttttctcggtttgtttattttatgctagagtgctcctctaaagctagcgctttggacattcag

Basic information

species Oryza sativa
transcript LOC_Os12g01170.1
intron # 6
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|89187213|gb|CI047280.1|CI047280
EST:     GCCAATGCCATCGTCACAGATGTCAG                         ACCGAAGAGGGGGGTCTTCGGCTTCCAATGCAAGGAAGGATGAATACAACT
genomic: GCCAATGCCATCGTCACAGATGTCAGgtaaattata ... ggacattcagACCGAAGAGGGGGGTCTTCGGCTTCCAATGCAAGGAAGGATGAATACAACT
EST: gi|88544420|gb|CI472517.1|CI472517
EST:     GCCAATGCCATCGTCACAGATGTCAG                         ACCGAAGAGGGGGGTCTTCGGCTTCCAATGCAAGGAAGGATGAATACAACT
genomic: GCCAATGCCATCGTCACAGATGTCAGgtaaattata ... ggacattcagACCGAAGAGGGGGGTCTTCGGCTTCCAATGCAAGGAAGGATGAATACAACT
EST: gi|88531358|gb|CI459827.1|CI459827
EST:     GCCAATGCCATCGTCACAGATGTCAG                         ACCGAAGAGGGGGGTCTTCGGCTTCCAATGCAAGGAAGGATGAATACAACT
genomic: GCCAATGCCATCGTCACAGATGTCAGgtaaattata ... ggacattcagACCGAAGAGGGGGGTCTTCGGCTTCCAATGCAAGGAAGGATGAATACAACT
EST: gi|13165397|gb|AU174194.1|AU174194
EST:     GCCAATGCCATCGTCACAGATGTCAG                         ACCGAAGAGGGGGGTCTTCGGCTTCCAATGCAAGGAAGGATGAATACAACT
genomic: GCCAATGCCATCGTCACAGATGTCAGgtaaattata ... ggacattcagACCGAAGAGGGGGGTCTTCGGCTTCCAATGCAAGGAAGGATGAATACAACT
EST: gi|88217599|gb|CI217448.1|CI217448
EST:     GCCAATGCCATCGTCACAGATGTCAG                         ACCGAAGAGGGGGGTCTTCGGCTTCCAATGCAAGGAAGGATGAATACAACT
genomic: GCCAATGCCATCGTCACAGATGTCAGgtaaattata ... ggacattcagACCGAAGAGGGGGGTCTTCGGCTTCCAATGCAAGGAAGGATGAATACAACT
EST: gi|86500721|gb|CI143354.1|CI143354
EST:     GCCAATGCCATCGTCACAGATGTCAG                         ACCGAAGAGGGGGGTCTTCGGCTTCCAATGCAAGGAAGGATGAATACAACT
genomic: GCCAATGCCATCGTCACAGATGTCAGgtaaattata ... ggacattcagACCGAAGAGGGGGGTCTTCGGCTTCCAATGCAAGGAAGGATGAATACAACT
EST: gi|88846847|gb|CI005826.1|CI005826
EST:     GCCAATGCCATCGTCACAGATGTCAG                         ACCGAAGAGGGGGGTCTTCGGCTTCCAATGCAAGGAAGGATGAATACAACT
genomic: GCCAATGCCATCGTCACAGATGTCAGgtaaattata ... ggacattcagACCGAAGAGGGGGGTCTTCGGCTTCCAATGCAAGGAAGGATGAATACAACT
EST: gi|86503159|gb|CI145792.1|CI145792
EST:     GCCAATGCCATCGTCACAGATGTCAG                         ACCGAAGAGGGGGGTCTTCGGCTTCCAATGCAAGGAAGGATGAATACAACT
genomic: GCCAATGCCATCGTCACAGATGTCAGgtaaattata ... ggacattcagACCGAAGAGGGGGGTCTTCGGCTTCCAATGCAAGGAAGGATGAATACAACT
EST: gi|88441245|gb|CI538688.1|CI538688
EST:     GGGAAGGCCAATGCCATCGTCACAGATGTCAG                         ACCGAAGA-GGGGGTCTTCGGCTTCCAATGCAAGGAAGGATGAATACAACT
genomic: GGGAAGGCCAATGCCATCGTCACAGATGTCAGgtaaattata ... ggacattcagACCGAAGAGGGGGGTCTTCGGCTTCCAATGCAAGGAAGGATGAATACAACT
EST: gi|86524884|gb|CI165090.1|CI165090
EST:     GCCAATGCCATCGTCACAGATGTCAG                         ACCGAAGAGGGGGGTCTTCGGCTTCCAATGCAAGGAAGGATGAATACAACT
genomic: GCCAATGCCATCGTCACAGATGTCAGgtaaattata ... ggacattcagACCGAAGAGGGGGGTCTTCGGCTTCCAATGCAAGGAAGGATGAATACAACT
EST: gi|29678194|gb|CB674469.1|CB674469
EST:     GCCAATGCCATCGTCACAGATGTCAG                         ACCGAAGAGGGGGGTCTTCGGCTTCCAATGCAAGGAAGGATGAATACAACT
genomic: GCCAATGCCATCGTCACAGATGTCAGgtaaattata ... ggacattcagACCGAAGAGGGGGGTCTTCGGCTTCCAATGCAAGGAAGGATGAATACAACT
EST: gi|88542597|gb|CI471936.1|CI471936
EST:     GCCAATGCCATCGTCACAGATGTCAG                         ACCGAAGAGGGGGGTCTTCGGCTTCCAATGCAAGGAAGGATGAATACAACT
genomic: GCCAATGCCATCGTCACAGATGTCAGgtaaattata ... ggacattcagACCGAAGAGGGGGGTCTTCGGCTTCCAATGCAAGGAAGGATGAATACAACT
EST: gi|88382263|gb|CI521263.1|CI521263
EST:     TCACAGATGTCAG                         ACCGAAGAGGGGGGTCTTCGGCTTCCAATGCAAGGAAGGATGAATACAACT
genomic: TCACAGATGTCAGgtaaattata ... ggacattcagACCGAAGAGGGGGGTCTTCGGCTTCCAATGCAAGGAAGGATGAATACAACT
EST: gi|58693613|gb|CK082300.1|CK082300
EST:     GCCAATGCCATCGTCACAGATGTCAG                         ACCGAAGAGGGGGGTCTTCGGCTTCCAATGCAAGGAAGGATGAATACAACT
genomic: GCCAATGCCATCGTCACAGATGTCAGgtaaattata ... ggacattcagACCGAAGAGGGGGGTCTTCGGCTTCCAATGCAAGGAAGGATGAATACAACT
EST: gi|86525225|gb|CI165431.1|CI165431
EST:     GCCAATGCCATCGTCACAGATGTCAG                         ACCGAAGAGGGGGGTCTTCGGCTTCCAATGCAAGGAAGGATGAATACAACT
genomic: GCCAATGCCATCGTCACAGATGTCAGgtaaattata ... ggacattcagACCGAAGAGGGGGGTCTTCGGCTTCCAATGCAAGGAAGGATGAATACAACT
EST: gi|58680893|gb|CK069580.1|CK069580
EST:     AGGCCAATGCCATCGTCACAGATGTCAG                         ACCGAAGAGGGGGGTCTTCGGCTTCCAATGCAAGGAAGGATGAATACAACT
genomic: AGGCCAATGCCATCGTCACAGATGTCAGgtaaattata ... ggacattcagACCGAAGAGGGGGGTCTTCGGCTTCCAATGCAAGGAAGGATGAATACAACT
EST: gi|88976248|gb|CI024465.1|CI024465
EST:     GCCAATGCCATCGTCACAGATGTCAG                         ACCGAAGAGGGGGGTCTTCGGCTTCCAATGCAAGGAAGGATGAATACAACT
genomic: GCCAATGCCATCGTCACAGATGTCAGgtaaattata ... ggacattcagACCGAAGAGGGGGGTCTTCGGCTTCCAATGCAAGGAAGGATGAATACAACT
EST: gi|66914385|gb|CX101233.1|CX101233
EST:     GCCAATGCCATCGTCACAGATGTCAG                         ACCGAAGAGGGGGGTCTTCGGCTTCCAATGCAAGGAAGGATGAATACAACT
genomic: GCCAATGCCATCGTCACAGATGTCAGgtaaattata ... ggacattcagACCGAAGAGGGGGGTCTTCGGCTTCCAATGCAAGGAAGGATGAATACAACT
EST: gi|218486436|gb|FG966615.1|FG966615
EST:     GCCAATGCCATCGTCACAGATGTCAG                         ACCGAAGAGGGGGGTCTTCGGCTTCCAATGCAAGGAAGGATGAATACAACT
genomic: GCCAATGCCATCGTCACAGATGTCAGgtaaattata ... ggacattcagACCGAAGAGGGGGGTCTTCGGCTTCCAATGCAAGGAAGGATGAATACAACT
EST: gi|157651056|gb|EX450690.1|EX450690
EST:     GCCAATGCCATCGTCACAGATGTCAG                         ACCGAAGAGGGGGGTCTTCGGCTTCCAATGCAAGGAAGGATGAATACAACT
genomic: GCCAATGCCATCGTCACAGATGTCAGgtaaattata ... ggacattcagACCGAAGAGGGGGGTCTTCGGCTTCCAATGCAAGGAAGGATGAATACAACT
EST: gi|86261453|gb|CI017195.1|CI017195
EST:     GCCAATGCCATCGTCACAGATGTCAG                         ACCGAAGAGGGGGGTCTTCGGCTTCCAATGCAAGGAAGGATGAATACAACT
genomic: GCCAATGCCATCGTCACAGATGTCAGgtaaattata ... ggacattcagACCGAAGAGGGGGGTCTTCGGCTTCCAATGCAAGGAAGGATGAATACAACT
EST: gi|88530451|gb|CI458846.1|CI458846
EST:     GCCAATGCCATCGTCACAGATGTCAG                         ACCGAAGANNNNNNNTCTTCGGCTTCCAATGCAAGGAAGGATGAATACAAC
genomic: GCCAATGCCATCGTCACAGATGTCAGgtaaattata ... ggacattcagACCGAAGA-GGGGGGTCTTCGGCTTCCAATGCAAGGAAGGATGAATACAAC
EST: gi|29678195|gb|CB674470.1|CB674470
EST:     GCCAATGCCATCGTCACAGATGTCAG                         ACCGAAGAGGGGGGTCTTCGGCTTCCAATGCAAGGAAGGATGAATACAACT
genomic: GCCAATGCCATCGTCACAGATGTCAGgtaaattata ... ggacattcagACCGAAGAGGGGGGTCTTCGGCTTCCAATGCAAGGAAGGATGAATACAACT
EST: gi|86504868|gb|CI147501.1|CI147501
EST:     GCCAATGCCATCGTCACAGATGTCAG                         ACCGAAGAGGGGGTTCTTCGGCTTCCAATGCAAGGAAGGATGAATACAACT
genomic: GCCAATGCCATCGTCACAGATGTCAGgtaaattata ... ggacattcagACCGAAGAGGGGGGTCTTCGGCTTCCAATGCAAGGAAGGATGAATACAACT
EST: gi|58685986|gb|CK074673.1|CK074673
EST:     GCCAATGCCATCGTCACAGATGTCAG                         ACCGAAGAGGGGGGTCTTCGGCTTCCAATGCAAGGAAGGATGAATACAACT
genomic: GCCAATGCCATCGTCACAGATGTCAGgtaaattata ... ggacattcagACCGAAGAGGGGGGTCTTCGGCTTCCAATGCAAGGAAGGATGAATACAACT
EST: gi|86870305|gb|CI319411.1|CI319411
EST:     GCCAATGCCATCGTCACAGATGTCAG                         ACCGAAGAGGGGGGTCTTCGGCTTCCAATGCAAGGAAGGATGAATACAACT
genomic: GCCAATGCCATCGTCACAGATGTCAGgtaaattata ... ggacattcagACCGAAGAGGGGGGTCTTCGGCTTCCAATGCAAGGAAGGATGAATACAACT

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: 62 (upstream exon), 74 (downstream exon)
Score: 66

GCCAATGCCATCGTCACAGATGTCAGgtaaattata ... ggacattcagACCGAAGAGGGGGGTCTTCGGCTTCCAATGCAAGGAAGGATGAATACAACTGGAGATATGATGCTGATGATATCTCTGAAGAAGTGTTGCGAGCATCAAG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCCAATGCCATCGTCACAGATGTCAGgtaaattataatttttttctcggtttgtttattttatgctagagtgctcctctaaagctagcgctttggacattcag

- - - - - - - - CAGATG