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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gattattttcccaatcagcctattctttgtttgatcatatcggtttcaattcactctgcagtacttctatacatgcctgacatcttccctttttcatcagCTGATGTCATTACCGAAGCTTGATTGGTGGTCCAGGAGCATACTTGCAGTAACATTAG

Basic information

species Oryza sativa
transcript LOC_Os03g12370.4
intron # 2
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|88852467|gb|CI374235.1|CI374235
EST:     GCAGGATTGTCTGATGGAAGCACAATATAACTCCAACAATCCTCAATATG                         CTGATGTCATTACCGAAGCTTGATTGGTGGTCCAGGAGCATACTTCCAGTA
genomic: GCAGGATTGTCTGATGGAAGCACAATATAACTCCAACAATCCTCAATATGgtaatgacta ... ttttcatcagCTGATGTCATTACCGAAGCTTGATTGGTGGTCCAGGAGCATACTTGCAGTA
EST: gi|29667708|gb|CB663983.1|CB663983
EST:     GCAGGATTGTCTGATGGAAGCACAATATAACTCCAACAATCCTCAATATG                         CTGATGTCATTACCGAAGCTTGATTGGTGGTCCAGGAGCATACTTGCAGTA
genomic: GCAGGATTGTCTGATGGAAGCACAATATAACTCCAACAATCCTCAATATGgtaatgacta ... ttttcatcagCTGATGTCATTACCGAAGCTTGATTGGTGGTCCAGGAGCATACTTGCAGTA
EST: gi|88250928|gb|CI248779.1|CI248779
EST:     GCAGGATTGTCTGATGGAAGCACAATATAACTCCAACAATCCTCAATATG                         CTGATGTCATTACCGAAGCTTGATTGGTGGTCCAGGAGCATACTTGCAGTA
genomic: GCAGGATTGTCTGATGGAAGCACAATATAACTCCAACAATCCTCAATATGgtaatgacta ... ttttcatcagCTGATGTCATTACCGAAGCTTGATTGGTGGTCCAGGAGCATACTTGCAGTA
EST: gi|27554416|gb|CA998316.1|CA998316
EST:     GCAGGATTGTCTGATGGAAGCACAATATAACTCCAACAATCCTCAATATG                         CTGATGTCATTACCGAAGCTTGATTGGTGGTCCAGGAGCATACTTGCAGTA
genomic: GCAGGATTGTCTGATGGAAGCACAATATAACTCCAACAATCCTCAATATGgtaatgacta ... ttttcatcagCTGATGTCATTACCGAAGCTTGATTGGTGGTCCAGGAGCATACTTGCAGTA
EST: gi|89163938|gb|CI101026.1|CI101026
EST:     GCAGGATTGTCTGATGGAAGCACAATATAACTCCAACAATCCTCAATATG                         CTGATGTCATTACCGAAGCTTGATTGGTGGTCCAGGAGCATACTTGCAGTA
genomic: GCAGGATTGTCTGATGGAAGCACAATATAACTCCAACAATCCTCAATATGgtaatgacta ... ttttcatcagCTGATGTCATTACCGAAGCTTGATTGGTGGTCCAGGAGCATACTTGCAGTA
EST: gi|88508192|gb|CI435698.1|CI435698
EST:     GCAGGATTGTCTGATGGAAGCACAATATAACTCCAACAATCCTCAATATG                         CTGATGTCATTACCGAAGCTTGATTGGTGGTCCAGGAGCATACTTGCAGTA
genomic: GCAGGATTGTCTGATGGAAGCACAATATAACTCCAACAATCCTCAATATGgtaatgacta ... ttttcatcagCTGATGTCATTACCGAAGCTTGATTGGTGGTCCAGGAGCATACTTGCAGTA
EST: gi|87033388|gb|CI188012.1|CI188012
EST:     GCAGGATTGTCTGATGGAAGCACAATATAACTCCAACAATCCTCAATATG                         CTGATGTCATTACCGAAGCTTGATTGGTGGTCCAGGAGCATACTTGCAGTA
genomic: GCAGGATTGTCTGATGGAAGCACAATATAACTCCAACAATCCTCAATATGgtaatgacta ... ttttcatcagCTGATGTCATTACCGAAGCTTGATTGGTGGTCCAGGAGCATACTTGCAGTA
EST: gi|88245332|gb|CI245181.1|CI245181
EST:     GCAGGATTGTCTGATGGAAGCACAATATAACTCCAACAATCCTCAATATG                         CTGATGTCATTACCGAAGCTTGATTGGTGGTCCAGGAGCATACTTGCAGTA
genomic: GCAGGATTGTCTGATGGAAGCACAATATAACTCCAACAATCCTCAATATGgtaatgacta ... ttttcatcagCTGATGTCATTACCGAAGCTTGATTGGTGGTCCAGGAGCATACTTGCAGTA
EST: gi|12404781|gb|AU166382.1|AU166382
EST:     GCAGGATTGTCTGATGGAAGCNCAATATAACTCCAACAATCCTCAATATG                         CTGATGTCATTACCGAAGCTTGATTGGTGGTCCAGGAGCATACTTGCAGTA
genomic: GCAGGATTGTCTGATGGAAGCACAATATAACTCCAACAATCCTCAATATGgtaatgacta ... ttttcatcagCTGATGTCATTACCGAAGCTTGATTGGTGGTCCAGGAGCATACTTGCAGTA
EST: gi|86828647|gb|CI278720.1|CI278720
EST:     GCAGGATTGTCTGATGGAAGCACAATATAACTCCAACAATCCTCAATATG                         CTGATGTCATTACCGAAGCTTGATTGGTGGTCCAGGAGCATACTTGCAGTA
genomic: GCAGGATTGTCTGATGGAAGCACAATATAACTCCAACAATCCTCAATATGgtaatgacta ... ttttcatcagCTGATGTCATTACCGAAGCTTGATTGGTGGTCCAGGAGCATACTTGCAGTA
EST: gi|88961046|gb|CI096449.1|CI096449
EST:     GCAGGATTGTCTGATGGAAGCACAATATAACTCCAACAATCCTCAATATG                         CTGATGTCATTACCGAAGCTTGATTGGTGGTCCAGGAGCATACTTGCAGTA
genomic: GCAGGATTGTCTGATGGAAGCACAATATAACTCCAACAATCCTCAATATGgtaatgacta ... ttttcatcagCTGATGTCATTACCGAAGCTTGATTGGTGGTCCAGGAGCATACTTGCAGTA
EST: gi|29671629|gb|CB667904.1|CB667904
EST:     GCAGGATTGTCTGATGGAAGCACAATATAACTCCAACAATCCTCAATATG                         CTGATGTCATTACCGAAGCTTGATTGGTGGTCCAGGAGCATACTTGCAGTA
genomic: GCAGGATTGTCTGATGGAAGCACAATATAACTCCAACAATCCTCAATATGgtaatgacta ... ttttcatcagCTGATGTCATTACCGAAGCTTGATTGGTGGTCCAGGAGCATACTTGCAGTA
EST: gi|88366596|gb|CI556380.1|CI556380
EST:     GCAGGGTTGTCTGATGGAAGCACAATATAAGTCCAACAATCCTCAATATG                         GTGATGTCATTACCGAAGCTTGATTGGTGGTCCAGGAGCATACTTGCAGTA
genomic: GCAGGATTGTCTGATGGAAGCACAATATAACTCCAACAATCCTCAATATGgtaatgacta ... ttttcatcagCTGATGTCATTACCGAAGCTTGATTGGTGGTCCAGGAGCATACTTGCAGTA
EST: gi|89169618|gb|CI109977.1|CI109977
EST:     GCAGGATTGTCTGATGGAAGCACAATATAACTCCGACAATCCTCAATATG                         CTGATGTCATTACCGAAGCTTGATTGGTGGTCCAGGAGCATACTTGCAGTA
genomic: GCAGGATTGTCTGATGGAAGCACAATATAACTCCAACAATCCTCAATATGgtaatgacta ... ttttcatcagCTGATGTCATTACCGAAGCTTGATTGGTGGTCCAGGAGCATACTTGCAGTA
EST: gi|88996490|gb|CI259994.1|CI259994
EST:     GCAGGATTGTCTGATGGAAGCACAATATAACTCCAACAATCCTCAATATG                         CTGATGTCATTACCGAAGCTTGATTGGTGGTCCAGGAGCATACTTGCAGTA
genomic: GCAGGATTGTCTGATGGAAGCACAATATAACTCCAACAATCCTCAATATGgtaatgacta ... ttttcatcagCTGATGTCATTACCGAAGCTTGATTGGTGGTCCAGGAGCATACTTGCAGTA
EST: gi|86413300|gb|CI067705.1|CI067705
EST:     GCAGGATTGTCTGATGGAAGCACAATATAACTCCAACAATCCTCAATATG                         CTGATGTCATTACCGAAGCTTGATTGGTGGTCCAGGAGCATACTTGCAGTA
genomic: GCAGGATTGTCTGATGGAAGCACAATATAACTCCAACAATCCTCAATATGgtaatgacta ... ttttcatcagCTGATGTCATTACCGAAGCTTGATTGGTGGTCCAGGAGCATACTTGCAGTA
EST: gi|86594995|gb|CI258249.1|CI258249
EST:     GCAGGATTGTCTGATGGAAGCACAATATAACTCCAACAATCCTCAATATG                         CTGATGTCATTACCGAAGCTTGATTGGTGGTCCAGGAGCATACTTGCAGTA
genomic: GCAGGATTGTCTGATGGAAGCACAATATAACTCCAACAATCCTCAATATGgtaatgacta ... ttttcatcagCTGATGTCATTACCGAAGCTTGATTGGTGGTCCAGGAGCATACTTGCAGTA
EST: gi|88206077|gb|CI205926.1|CI205926
EST:     GCGGGATTGTCTGATGGAAGCACAATATAACTCCAACAATCCTCAATATG                         CTGATGTCATTACCGAAGCTTGATTGGTGGTCCAGGAGCATACTTGCAGTA
genomic: GCAGGATTGTCTGATGGAAGCACAATATAACTCCAACAATCCTCAATATGgtaatgacta ... ttttcatcagCTGATGTCATTACCGAAGCTTGATTGGTGGTCCAGGAGCATACTTGCAGTA
EST: gi|86431737|gb|CI085348.1|CI085348
EST:     GCAGGATTGTCTGATGGAAGCACAATATAACTCCAACAATCCTCAATATG                         CTGATGTCATTACCGAAGCTTGATTGGTGGTCCAGGAGCATACTTGCAGTA
genomic: GCAGGATTGTCTGATGGAAGCACAATATAACTCCAACAATCCTCAATATGgtaatgacta ... ttttcatcagCTGATGTCATTACCGAAGCTTGATTGGTGGTCCAGGAGCATACTTGCAGTA
EST: gi|86495289|gb|CI137922.1|CI137922
EST:     GCAGGATTGTCTGATGGAAGCACAATATAACTCCAACAATCCTCAATATG                         CTGATGTCATTACCGAAGCTTGATTGGTGGTCCAGGAGCATACTTGCAGTA
genomic: GCAGGATTGTCTGATGGAAGCACAATATAACTCCAACAATCCTCAATATGgtaatgacta ... ttttcatcagCTGATGTCATTACCGAAGCTTGATTGGTGGTCCAGGAGCATACTTGCAGTA
EST: gi|86825574|gb|CI361750.1|CI361750
EST:     TCAGGATTGTCTGATGTAAGCACAATATAACTCCAACAATCCTCAATATG                         CTGATGTCATTACCGAAGCTTGATTGGTGGTCCAGGATCATACTTGCAGTA
genomic: GCAGGATTGTCTGATGGAAGCACAATATAACTCCAACAATCCTCAATATGgtaatgacta ... ttttcatcagCTGATGTCATTACCGAAGCTTGATTGGTGGTCCAGGAGCATACTTGCAGTA
EST: gi|88968188|gb|CI098430.1|CI098430
EST:     GCAGGATTGTCTGATGGAAGCACAATATAACTCCAACAATCCTCAATATG                         CTGATGTCATTACCGAAGCTTGATTGGTGGTCCAGGAGCATACTTGCAGTA
genomic: GCAGGATTGTCTGATGGAAGCACAATATAACTCCAACAATCCTCAATATGgtaatgacta ... ttttcatcagCTGATGTCATTACCGAAGCTTGATTGGTGGTCCAGGAGCATACTTGCAGTA
EST: gi|86497061|gb|CI139694.1|CI139694
EST:     GCAGGATTGTCTGATGGAAGCACAATATAACTCCAACAATCCTCAATATG                         CTGATGTCATTACCGAAGCTTGATTGGTGGTCCAGGAGCATACTTGCAGTA
genomic: GCAGGATTGTCTGATGGAAGCACAATATAACTCCAACAATCCTCAATATGgtaatgacta ... ttttcatcagCTGATGTCATTACCGAAGCTTGATTGGTGGTCCAGGAGCATACTTGCAGTA
EST: gi|218482494|gb|FG954955.1|FG954955
EST:     GCAGGATTGTCTGATGGAAGCACAATATAACTCCAACAATCCTCAATATG                         CTGATGTCATTACCGAAGCTTGATTGGTGGTCCAGGAGCATACTTGCAGTA
genomic: GCAGGATTGTCTGATGGAAGCACAATATAACTCCAACAATCCTCAATATGgtaatgacta ... ttttcatcagCTGATGTCATTACCGAAGCTTGATTGGTGGTCCAGGAGCATACTTGCAGTA

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: 60 (upstream exon), 48 (downstream exon)
Score: 7

CAAATGGGCCCTCCTTTGAGTGTTCAAGATTATGATTTTCCGCAGTTAGAGCAGGATTGTCTGATGGAAGCACAATATAACTCCAACAATCCTCAATATGgtaatgacta ... ttttcatcagCTGATGTCATTACCGAAGCTTGATTGGTGGTCCAGGAGCATACTTGCAGTAACATTAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcaattcactctgcagtacttctatacatgcctgacatcttccctttttcatcagCTGATGTCATTACCGAAGCTTGATTGGTGGTCCAGGAGCATACTTGCAGTAACATTAG
                             gcctgac  putative branch site (score: 7)
                                   catcttccctttttca  CT-rich tract
                                            tttttcat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gattattttcccaatcagcctattctttgtttgatcatatcggtttcaattcactctgcagtacttctatacatgcctgacatcttccctttttcatcagCTGATGTCATTACCGAAGCTTGATTGGTGGTCCAGGAGCATACTTGCAGTAACATTAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA
- - - - - - - - - - - - - -tgtttga
- - - - - - - - - - - - - - - - - - - - - - - - - - -ctctgca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tacatgc