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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtccattcatagttcgcttgcctgtaacttgtttactcttttcttaattgtaggcactgagaacttcctttttttgattttttagGGATTCAACGATACCAGGCAAGAATACAACTATAACAATTCCTGGTTCATCTGACAG

Basic information

species Oryza sativa
transcript LOC_Os03g21990.1
intron # 5
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|44679480|gb|CR292914.1|CR292914
EST:     GGCAGCAGTACTGCTATTGTTCCTGCACCACATATGCTCCCCAAAGCACC                         GGATTCAACGATACCAGGCAAGAATACAACTATAACAATTCCTGGTTCATC
genomic: GGCAGCAGTACTGCTATTGTTCCTGCACCACATATGCTCCCCAAAGCACCgtaagtccat ... gattttttagGGATTCAACGATACCAGGCAAGAATACAACTATAACAATTCCTGGTTCATC
EST: gi|29643708|gb|CB648715.1|CB648715
EST:     GGCAGCAGTACTGCTATTGTTCCTGCACCACATATGCTCCCCAAAGCACC                         GGATTCAACGATACCAGGCAAGAATACAACTATAACAATTCCTGGTTCATC
genomic: GGCAGCAGTACTGCTATTGTTCCTGCACCACATATGCTCCCCAAAGCACCgtaagtccat ... gattttttagGGATTCAACGATACCAGGCAAGAATACAACTATAACAATTCCTGGTTCATC
EST: gi|58658761|gb|CK047441.1|CK047441
EST:     GGCAGCAGTACTGCTATTGTTCCTGCACCACATATGCTCCCCAAAGCACC                         GGATTCAACGATACCAGGCAAGAATACAACTATAACAATTCCTGGTTCATC
genomic: GGCAGCAGTACTGCTATTGTTCCTGCACCACATATGCTCCCCAAAGCACCgtaagtccat ... gattttttagGGATTCAACGATACCAGGCAAGAATACAACTATAACAATTCCTGGTTCATC
EST: gi|58593917|gb|CF992225.1|CF992225
EST:     GGCAGCAGTACTGCTATTGTTCCTGCACCACATATGCTCCCCAAAGCACC                         GGATTCAACGATACCAGGCAAGAATACAACTATTACAATTCCTGGTTCATC
genomic: GGCAGCAGTACTGCTATTGTTCCTGCACCACATATGCTCCCCAAAGCACCgtaagtccat ... gattttttagGGATTCAACGATACCAGGCAAGAATACAACTATAACAATTCCTGGTTCATC
EST: gi|58593323|gb|CF991631.1|CF991631
EST:     GGCAGCAGTACTGCTATTGTTCCTGCACCACATATGCTCCCCAAAGCACC                         GGATTCAACGATACCAGGCAAGAATACAACTATAACAATTCCTGGTTCATC
genomic: GGCAGCAGTACTGCTATTGTTCCTGCACCACATATGCTCCCCAAAGCACCgtaagtccat ... gattttttagGGATTCAACGATACCAGGCAAGAATACAACTATAACAATTCCTGGTTCATC
EST: gi|29679952|gb|CB676227.1|CB676227
EST:     GGCAGCAGTACTGCTATTGTTCCTGCACCACATATGCTCCCCAAAGCACC                         GGATTCAACGATACCAGGCAAGAATACAACTATAACAATTCCTGGTTCATC
genomic: GGCAGCAGTACTGCTATTGTTCCTGCACCACATATGCTCCCCAAAGCACCgtaagtccat ... gattttttagGGATTCAACGATACCAGGCAAGAATACAACTATAACAATTCCTGGTTCATC
EST: gi|27577849|gb|CB000544.1|CB000544
EST:     GGCAGCAGTACTGCTATTGTTCCTGCACCACATATGCTCCCCAAAGCACC                         GGATTCAACGATACCAGGCAAGAATACAACTATAACAATTCCTGGTTCATC
genomic: GGCAGCAGTACTGCTATTGTTCCTGCACCACATATGCTCCCCAAAGCACCgtaagtccat ... gattttttagGGATTCAACGATACCAGGCAAGAATACAACTATAACAATTCCTGGTTCATC
EST: gi|58689854|gb|CK078541.1|CK078541
EST:     GGCAGCAGTACTGCTATTGTTCCTGCACCACATATGCTCCCCAAAGCACC                         GGATTCAACGATACCAGGCAAGAATACAACTATAACAA
genomic: GGCAGCAGTACTGCTATTGTTCCTGCACCACATATGCTCCCCAAAGCACCgtaagtccat ... gattttttagGGATTCAACGATACCAGGCAAGAATACAACTATAACAA
EST: gi|27577027|gb|CA999721.1|CA999721
EST:     GGCAGCAGTACTGCTATTGTTCCTGCACCACATATGCTCCCCAAAGCACC                         GGATTCAACGATACCAGGCAAGAATACAACTATAACAATTCCTGGTTCATC
genomic: GGCAGCAGTACTGCTATTGTTCCTGCACCACATATGCTCCCCAAAGCACCgtaagtccat ... gattttttagGGATTCAACGATACCAGGCAAGAATACAACTATAACAATTCCTGGTTCATC
EST: gi|58671592|gb|CK060278.1|CK060278
EST:     GGCAGCAGTACTGCTATTGTTCCTGCACCACATATGCTCCCCAAAGCACC                         GGATTCAACGATACCAGGCAAGAATACAACTATAACAATTCCTGGTTCATC
genomic: GGCAGCAGTACTGCTATTGTTCCTGCACCACATATGCTCCCCAAAGCACCgtaagtccat ... gattttttagGGATTCAACGATACCAGGCAAGAATACAACTATAACAATTCCTGGTTCATC
EST: gi|58694088|gb|CK082775.1|CK082775
EST:     GGCAGCAGTACTGCTATTGTTCCTGCACCACATATGCTCCCCAAAGCACC                         GGATTCAACGATACCAGGCAAGAATACAACTATAACAATTCCTGGTTCATC
genomic: GGCAGCAGTACTGCTATTGTTCCTGCACCACATATGCTCCCCAAAGCACCgtaagtccat ... gattttttagGGATTCAACGATACCAGGCAAGAATACAACTATAACAATTCCTGGTTCATC
EST: gi|117225886|gb|CT848635.1|CT848635
EST:     GGCAGCAGTACTGCTATTGTTCCTGCACCACATATGCTCCCCAAAGCACC                         GGATTCAACGATACCAGGCAAGAATACAACTATAACAATTCCTGGTTCATC
genomic: GGCAGCAGTACTGCTATTGTTCCTGCACCACATATGCTCCCCAAAGCACCgtaagtccat ... gattttttagGGATTCAACGATACCAGGCAAGAATACAACTATAACAATTCCTGGTTCATC
EST: gi|58664642|gb|CK053328.1|CK053328
EST:     GGCAGCAGTACTGCTATTGTTCCTGCACCACATATGCTCCCCAAAGCACC                         GGATTCAACGATACCAGGCAAGAATACAACTATAACAATTCCTGGTTCATC
genomic: GGCAGCAGTACTGCTATTGTTCCTGCACCACATATGCTCCCCAAAGCACCgtaagtccat ... gattttttagGGATTCAACGATACCAGGCAAGAATACAACTATAACAATTCCTGGTTCATC
EST: gi|33653589|gb|CF276203.1|CF276203
EST:     GGCAGCAGTACTGCTATTGTTCCTGCACCACATATGCTCCCCAAAGCACC                         GGATTCAACGATACCAGGCAAGAATACAACTATAACAATTCCTGGTTCATC
genomic: GGCAGCAGTACTGCTATTGTTCCTGCACCACATATGCTCCCCAAAGCACCgtaagtccat ... gattttttagGGATTCAACGATACCAGGCAAGAATACAACTATAACAATTCCTGGTTCATC
EST: gi|58613176|gb|CK040888.1|CK040888
EST:     GGCAGCAGTACTGCTATTGTTCCTGCACCACATATGCTCCCCAAAGCACC                         GGATTCAACGATACCAGGCAAGAATACAACTATTACAATTCCTGGTTCATC
genomic: GGCAGCAGTACTGCTATTGTTCCTGCACCACATATGCTCCCCAAAGCACCgtaagtccat ... gattttttagGGATTCAACGATACCAGGCAAGAATACAACTATAACAATTCCTGGTTCATC

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: 75 (upstream exon), 57 (downstream exon)
Score: 61

GAACACAAGATGTCAAAGATGCTGATAACAAAGGCAGCAGTACTGCTATTGTTCCTGCACCACATATGCTCCCCAAAGCACCgtaagtccat ... gattttttagGGATTCAACGATACCAGGCAAGAATACAACTATAACAATTCCTGGTTCATCTGACAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtttactcttttcttaattgtaggcactgagaacttcctttttttgattttttagGGATTCAACGATACCAGGCAAGAATACAACTATAACAATTCCTGGTTCATCTGACAG
                                 cttcctttttttgatt  CT-rich tract
                                      tttttttgatttttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtccattcatagttcgcttgcctgtaacttgtttactcttttcttaattgtaggcactgagaacttcctttttttgattttttagGGATTCAACGATACCAGGCAAGAATACAACTATAACAATTCCTGGTTCATCTGACAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA