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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgattgattttccctcgattacacaattacatcgataaataatgagcatacatttggaccctaacatcttgtgtgtgatgtttgcagTTTGAGATCATTCAATTACTACTCAAGGAATGCAACAAGATTGAAGGTCATCAGCAGCAG

Basic information

species Oryza sativa
transcript LOC_Os12g02094.1
intron # 4
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|112786000|gb|EE591849.1|EE591849
EST:     ACCACATCATCGATGAAATTATGTCCAAACTGAAAGATCCTGATGCAGAG                         TTTGAGATCATTCAATTACTACTCAAGGAATGCACCAAGATTGAAGGTCAT
genomic: ACCACATCATCGATGAAATTATGTCCAAACTGAAAGATCCTGATGCAGAGgtgattgatt ... atgtttgcagTTTGAGATCATTCAATTACTACTCAAGGAATGCAACAAGATTGAAGGTCAT
EST: gi|33674097|gb|CF302336.1|CF302336
EST:     CATCATCGATGAAATTATGTCCAAACTGAAAGATCCTGATGCAGAG                         TTTGAGATCATTCAATTACTACTCAAGGAATGCAACAAGATTGAAGGTCAT
genomic: CATCATCGATGAAATTATGTCCAAACTGAAAGATCCTGATGCAGAGgtgattgatt ... atgtttgcagTTTGAGATCATTCAATTACTACTCAAGGAATGCAACAAGATTGAAGGTCAT
EST: gi|86875076|gb|CI322291.1|CI322291
EST:     ACCACATCATCGATGAAATTATGTCCAAACTGAAAGATCCTGATGCAGAG                         TTTGAGATCATTCAATTACTACTCAAGGAATGCAACAAGATTGAAGGTCAT
genomic: ACCACATCATCGATGAAATTATGTCCAAACTGAAAGATCCTGATGCAGAGgtgattgatt ... atgtttgcagTTTGAGATCATTCAATTACTACTCAAGGAATGCAACAAGATTGAAGGTCAT
EST: gi|33685698|gb|CF313937.1|CF313937
EST:     ACCACATCATCGATGAAATTATGTCCAAACTGAAAGATCCTGATGCAGAG                         TTTGAGATCATTCAATTACTACTCAAGGAATGCAACAAGATTGAAGGTCAT
genomic: ACCACATCATCGATGAAATTATGTCCAAACTGAAAGATCCTGATGCAGAGgtgattgatt ... atgtttgcagTTTGAGATCATTCAATTACTACTCAAGGAATGCAACAAGATTGAAGGTCAT
EST: gi|163920568|gb|EG714508.1|EG714508
EST:     ACCACATCATCGATGAAATTATGTCCAAACTGAAAGATCCTGATGCAGAG                         TTTGAGATCATTCAATTACTACTCAAGGAATGCAACAAGATTGAAGGTCAT
genomic: ACCACATCATCGATGAAATTATGTCCAAACTGAAAGATCCTGATGCAGAGgtgattgatt ... atgtttgcagTTTGAGATCATTCAATTACTACTCAAGGAATGCAACAAGATTGAAGGTCAT
EST: gi|88965963|gb|CI006739.1|CI006739
EST:     ACCACATCATCGATGAAATTATGTCCAAACTGAAAGATCCTGATGCAGAG                         TTTGAGATCATTCAATTACTACTCAAGGAATGCAACAAGATTGAAGGTCAT
genomic: ACCACATCATCGATGAAATTATGTCCAAACTGAAAGATCCTGATGCAGAGgtgattgatt ... atgtttgcagTTTGAGATCATTCAATTACTACTCAAGGAATGCAACAAGATTGAAGGTCAT
EST: gi|5803366|gb|AI978314.1|AI978314
EST:     GAAAGATCCTGATGCAGAG                         TTTGAGATCATTCAATTACTACTCAAGGAATGCAACAAGATTGAAGGTCAT
genomic: GAAAGATCCTGATGCAGAGgtgattgatt ... atgtttgcagTTTGAGATCATTCAATTACTACTCAAGGAATGCAACAAGATTGAAGGTCAT
EST: gi|86871914|gb|CI332086.1|CI332086
EST:     ATGAAATTATGTCCAAACTGAAAGATCCTGATGCAGAG                         TTTGAGATCATTCAATTACTACTCAAGGAATGCAACAAGATTGAAGGTCAT
genomic: ATGAAATTATGTCCAAACTGAAAGATCCTGATGCAGAGgtgattgatt ... atgtttgcagTTTGAGATCATTCAATTACTACTCAAGGAATGCAACAAGATTGAAGGTCAT
EST: gi|86871216|gb|CI328418.1|CI328418
EST:     ACCACATCATCGATGAAATTATGTCCAAACTGAAAGATCCTGATGCAGAG                         TTTGAGATCATTCAATTACTACTGCAAGGAATGCAACAAGATTGAAGGTCA
genomic: ACCACATCATCGATGAAATTATGTCCAAACTGAAAGATCCTGATGCAGAGgtgattgatt ... atgtttgcagTTTGAGATCATTCAATTACTACT-CAAGGAATGCAACAAGATTGAAGGTCA
EST: gi|88902054|gb|CI374662.1|CI374662
EST:     ACCACATCATCGATGAAATTATGTCCAAACTGAAAGATCCTGATGCAGAG                         TTTGAGATCATTCAATTACTACTCAAGGAATGCAACAAGATTGAAGGTCAT
genomic: ACCACATCATCGATGAAATTATGTCCAAACTGAAAGATCCTGATGCAGAGgtgattgatt ... atgtttgcagTTTGAGATCATTCAATTACTACTCAAGGAATGCAACAAGATTGAAGGTCAT
EST: gi|3759064|gb|C96763.1|C96763
EST:     ACCACATCATCGATGAAATTATGTCCAAACTGAAAGATCCTGATGCAGAG                         TTTGAGATCATTCAATTACTACTCAAGGAATGCAACAAGATTGAAGGTCAT
genomic: ACCACATCATCGATGAAATTATGTCCAAACTGAAAGATCCTGATGCAGAGgtgattgatt ... atgtttgcagTTTGAGATCATTCAATTACTACTCAAGGAATGCAACAAGATTGAAGGTCAT
EST: gi|86903545|gb|CI323028.1|CI323028
EST:     ACCACATCATCGATGAAATTATGTCCAAACTGAAAGATCCTGATGCAGAG                         TTTGAGATCATTCAATTACTACTCAAGGAATGCAACAAGATTGAAGGTCAT
genomic: ACCACATCATCGATGAAATTATGTCCAAACTGAAAGATCCTGATGCAGAGgtgattgatt ... atgtttgcagTTTGAGATCATTCAATTACTACTCAAGGAATGCAACAAGATTGAAGGTCAT
EST: gi|86873796|gb|CI341229.1|CI341229
EST:     AATTATGTCCAAACTGAAAGATCCTGATGCAGAG                         TTTGAGATCATTCAATTACTACTCAAGGAATGCAACAAGATTGAAGGTCAT
genomic: AATTATGTCCAAACTGAAAGATCCTGATGCAGAGgtgattgatt ... atgtttgcagTTTGAGATCATTCAATTACTACTCAAGGAATGCAACAAGATTGAAGGTCAT
EST: gi|88222925|gb|CI220671.1|CI220671
EST:     ACCACATCATCGATGAAATTATGTCCAAACTGAAAGATCCTGATGCAGAG                         TTTGAGATCATTCAATTACTACTCAAGGAATGCAACAAGATTGAAGGTCAT
genomic: ACCACATCATCGATGAAATTATGTCCAAACTGAAAGATCCTGATGCAGAGgtgattgatt ... atgtttgcagTTTGAGATCATTCAATTACTACTCAAGGAATGCAACAAGATTGAAGGTCAT

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: 71 (upstream exon), 62 (downstream exon)
Score: 133

CATGGCTCTTTTATCAGCTATGAAAAGTGAAAGCACATGCGTATTCTGCCACCACATCATCGATGAAATTATGTCCAAACTGAAAGATCCTGATGCAGAGgtgattgatt ... atgtttgcagTTTGAGATCATTCAATTACTACTCAAGGAATGCAACAAGATTGAAGGTCATCAGCAGCAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cgataaataatgagcatacatttggaccctaacatcttgtgtgtgatgtttgcagTTTGAGATCATTCAATTACTACTCAAGGAATGCAACAAGATTGAAGGTCATCAGCAGCAG
                          ccctaac  putative branch site (score: 133)
     aataatga  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgattgattttccctcgattacacaattacatcgataaataatgagcatacatttggaccctaacatcttgtgtgtgatgtttgcagTTTGAGATCATTCAATTACTACTCAAGGAATGCAACAAGATTGAAGGTCATCAGCAGCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG