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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttttcccttaattaatgcttccttttctttgggataaattactatttcagtatttatccatcttatttgatgttcttgctcctcttgccagGAAAAGAGCCAGATGTAGCAGCATGGCGG

Basic information

species Oryza sativa
transcript LOC_Os12g40880.2
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os12g40880.1 (Oryza sativa), 3'ss of exon 10
lower sequence: GRMZM2G035338_T02 (Zea mays), 3'ss of exon 10
gttttcccttaattaatgcttccttttctttgggataaattactatttcagtatttatccatcttatttgatgttcttgctcctcttgccagGAAAAGAGCCAGATGTAGCAGCATGGCGG
|||| | || | | ||||| | | | | ||| || ||| | | ||| | |||||| ||||||||||||||||||||||||||||| ||
-------------gtctgctctaatccattcacattccagcactatattatttatgtcacatattcattgtttgttttgtttctcttgtcagGAAAAGAGCCAGATGTAGCAGCATGGAGG
















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|88555903|gb|CI486193.1|CI486193
EST:     TGACATTGATGTCTCCATGCAAAGAGTGCTCCAGAGACATGTCGCCACAG                         GAAAAGAGCCAGATGTAGCAGCATGGCGG
genomic: TGACATTGATGTCTCCATGCAAAGAGTGCTCCAGAGACATGTCGCCACAGgttttccctt ... ctcttgccagGAAAAGAGCCAGATGTAGCAGCATGGCGG
EST: gi|88972880|gb|CI019499.1|CI019499
EST:     TGACATTGATGTCTCCATGCAAAGAGTGCTCCAGAGACATGTCGCCACAG                         GAAAAGAGCCAGATGTAGCAGCATGGCGG
genomic: TGACATTGATGTCTCCATGCAAAGAGTGCTCCAGAGACATGTCGCCACAGgttttccctt ... ctcttgccagGAAAAGAGCCAGATGTAGCAGCATGGCGG
EST: gi|12622959|gb|AU173172.1|AU173172
EST:     TGACATTGATGTCTCCATGCAAAGAGTGCTCCAGAGACATGTCGCCACAG                         GAAAAGAGCCAGATGTAGCAGCATGGCGG
genomic: TGACATTGATGTCTCCATGCAAAGAGTGCTCCAGAGACATGTCGCCACAGgttttccctt ... ctcttgccagGAAAAGAGCCAGATGTAGCAGCATGGCGG
EST: gi|88519788|gb|CI447442.1|CI447442
EST:     TGACATTGATGTCTCCATGCAAAGAGTGCTCCAGAGACATGTCGCCACAG                         GAAAAGAGCCAGATGTAGCAGCATGGGCGG
genomic: TGACATTGATGTCTCCATGCAAAGAGTGCTCCAGAGACATGTCGCCACAGgttttccctt ... ctcttgccagGAAAAGAGCCAGATGTAGCAGCAT-GGCGG
EST: gi|88967316|gb|CI002498.1|CI002498
EST:     TGACATTGATGTCTCCATGCAAAGAGTGCTCCAGAGACATGTCGCCACAG                         GAAAAGAGCCAGATGTAGCAGCATGGCGG
genomic: TGACATTGATGTCTCCATGCAAAGAGTGCTCCAGAGACATGTCGCCACAGgttttccctt ... ctcttgccagGAAAAGAGCCAGATGTAGCAGCATGGCGG
EST: gi|88457129|gb|CI531728.1|CI531728
EST:     CATGCAAAGAGTGCTCCAGAGACATGTCGCCACAG                         GAAAAGAGCCAGATGTAGCAGCATGGCGG
genomic: CATGCAAAGAGTGCTCCAGAGACATGTCGCCACAGgttttccctt ... ctcttgccagGAAAAGAGCCAGATGTAGCAGCATGGCGG
EST: gi|88484850|gb|CI422121.1|CI422121
EST:     TGACATTGATGTCTCCATGCAAAGAGTGCTCCAGAGACATGTCGCCACAG                         GAAAAGAGCCAGATGTAGCAGCATGGCGG
genomic: TGACATTGATGTCTCCATGCAAAGAGTGCTCCAGAGACATGTCGCCACAGgttttccctt ... ctcttgccagGAAAAGAGCCAGATGTAGCAGCATGGCGG
EST: gi|13895854|gb|AU068162.2|AU068162
EST:     TGACATTGATGTCTCCATGCAAAGAGTGCTCCAGAGACATGTCGCCACAG                         GAAAAGAGCCAGATGTAGCAGCATGGCGG
genomic: TGACATTGATGTCTCCATGCAAAGAGTGCTCCAGAGACATGTCGCCACAGgttttccctt ... ctcttgccagGAAAAGAGCCAGATGTAGCAGCATGGCGG
EST: gi|88554268|gb|CI484437.1|CI484437
EST:     TGACATTGATGTCTCCATGCAAAGAGTGCTCCAGAGACATGTCGCCACA-                         GAGAAAGAGCCAGATGTAGCAGCATGGCGG
genomic: TGACATTGATGTCTCCATGCAAAGAGTGCTCCAGAGACATGTCGCCACAGgttttccctt ... ctcttgccagGA-AAAGAGCCAGATGTAGCAGCATGGCGG
EST: gi|88530957|gb|CI459391.1|CI459391
EST:     TGACATTGATGTCTCCATGCAAAGAGTGCTCCAGAGACATGTCGCCACAG                         GAAAAGAGCCAGATGTAGCAGCATGGCGG
genomic: TGACATTGATGTCTCCATGCAAAGAGTGCTCCAGAGACATGTCGCCACAGgttttccctt ... ctcttgccagGAAAAGAGCCAGATGTAGCAGCATGGCGG
EST: gi|88522664|gb|CI449421.1|CI449421
EST:     TGACATTGATGTCTCCATGCAAAGAGTGCTCCAGAGACATGTCGCCACAG                         GAAAAGAGCCAGATGTAGCAGCATGGCGG
genomic: TGACATTGATGTCTCCATGCAAAGAGTGCTCCAGAGACATGTCGCCACAGgttttccctt ... ctcttgccagGAAAAGAGCCAGATGTAGCAGCATGGCGG
EST: gi|88554994|gb|CI485212.1|CI485212
EST:     TGACATTGATGTCTCCATGCAAAGAGTGCTCCAGAGACATGTCGCCACAG                         GAAAAGAGCCAGATGTAGCAGCATGGCGG
genomic: TGACATTGATGTCTCCATGCAAAGAGTGCTCCAGAGACATGTCGCCACAGgttttccctt ... ctcttgccagGAAAAGAGCCAGATGTAGCAGCATGGCGG
EST: gi|89194890|gb|CI003354.1|CI003354
EST:     TGACATTGATGTCTCCATGCAAAGAGTGCTCCAGAGACATGTCGCCACAG                         GAAAAGAGCCAGATGTAGCAGCATGGCGG
genomic: TGACATTGATGTCTCCATGCAAAGAGTGCTCCAGAGACATGTCGCCACAGgttttccctt ... ctcttgccagGAAAAGAGCCAGATGTAGCAGCATGGCGG
EST: gi|88524459|gb|CI450372.1|CI450372
EST:     TGACATTGATGTCTCCATGCAAAGAGTGCTCCAGAGACATGTCGCCACAG                         GAAAAGAGCCAGATGTAGCAGCATGGCGG
genomic: TGACATTGATGTCTCCATGCAAAGAGTGCTCCAGAGACATGTCGCCACAGgttttccctt ... ctcttgccagGAAAAGAGCCAGATGTAGCAGCATGGCGG
EST: gi|88526128|gb|CI452507.1|CI452507
EST:     TGACATTGATGTCTCCATGCAAAGAGTGCTCCAGAGACATGTCGCCACAG                         GAAAAGAGCCAGATGTAGCAGCATGGCGG
genomic: TGACATTGATGTCTCCATGCAAAGAGTGCTCCAGAGACATGTCGCCACAGgttttccctt ... ctcttgccagGAAAAGAGCCAGATGTAGCAGCATGGCGG
EST: gi|88559654|gb|CI490251.1|CI490251
EST:     TGACATTGATGTCTCCATGCAAAGAGTGCTCCAGAGACATGTCGCCACAG                         GAAAAGAGCCAGATGTAGCAGCATGGCGG
genomic: TGACATTGATGTCTCCATGCAAAGAGTGCTCCAGAGACATGTCGCCACAGgttttccctt ... ctcttgccagGAAAAGAGCCAGATGTAGCAGCATGGCGG

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), 29 (downstream exon)
Score: 15

GTTTATCGATATTGACATTGATGTCTCCATGCAAAGAGTGCTCCAGAGACATGTCGCCACAGgttttccctt ... ctcttgccagGAAAAGAGCCAGATGTAGCAGCATGGCGG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aattactatttcagtatttatccatcttatttgatgttcttgctcctcttgccagGAAAAGAGCCAGATGTAGCAGCATGGCGG
                            atttgat  putative branch site (score: 15)
 ttcttgctcctcttgc  CT-rich tract
 tatttcagtatttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttttcccttaattaatgcttccttttctttgggataaattactatttcagtatttatccatcttatttgatgttcttgctcctcttgccagGAAAAGAGCCAGATGTAGCAGCATGGCGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG