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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tactgtttctatgcaaaactaacgtgttaacgtgtgcaatttgcatcaaagtttaccatttaccccacgcaacttatcaaaacgttgcgcgacctcgcagGCAACCACCTCTTGATCAATCTCGCAGGCGCCCGAAGCATTGGAGATATCTGGTCTCGCTTTATTTGGTCATGGATTCTACTTATCCTCGTGTAACTGTA

Basic information

species Oryza sativa
transcript LOC_Os03g13970.1
intron # 10
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|5055982|gb|AU075361.1|AU075361
EST:     GACAAGCCAGAAGATGAGAAGAAATAAATCAACTCCTTTGTGTCTTCCTT                         GCAACCACCTCTTGATCAATCTCGCAGGCGCCCGAAGCATTGGAGATATCT
genomic: GACAAGCCAGAAGATGAGAAGAAATAAATCAACTCCTTTGTGTCTTCCTTgtaagatttc ... gacctcgcagGCAACCACCTCTTGATCAATCTCGCAGGCGCCCGAAGCATTGGAGATATCT
EST: gi|33657882|gb|CF280496.1|CF280496
EST:     GACAAGCCAGAAGATGAGAAGAAATAAATCAACTCCTTTGTGTCTTCCTT                         GCAACCACCTCATGATCAATCTCGCAGGCGCCCGAAGCATTGGAGATATCT
genomic: GACAAGCCAGAAGATGAGAAGAAATAAATCAACTCCTTTGTGTCTTCCTTgtaagatttc ... gacctcgcagGCAACCACCTCTTGATCAATCTCGCAGGCGCCCGAAGCATTGGAGATATCT
EST: gi|88471377|gb|CI408648.1|CI408648
EST:     GACAAGCCAGAAGATGAGAAGAAATAAATCAACTCCTTTGTGTCTTCCTT                         GCAACCACCTCTTGATCAATCTCGCAGGCGCCCGAAGCATTGGAGATATCT
genomic: GACAAGCCAGAAGATGAGAAGAAATAAATCAACTCCTTTGTGTCTTCCTTgtaagatttc ... gacctcgcagGCAACCACCTCTTGATCAATCTCGCAGGCGCCCGAAGCATTGGAGATATCT
EST: gi|86491666|gb|CI134299.1|CI134299
EST:     GACAAGCCAGAAGATGAGAAGAAATAAATCAACTCCTTTGTGTCTTCCTT                         GCAACCACCTCTTGATCAATCTCGCAGGCGCCCGAAGCATTGGAGATATCT
genomic: GACAAGCCAGAAGATGAGAAGAAATAAATCAACTCCTTTGTGTCTTCCTTgtaagatttc ... gacctcgcagGCAACCACCTCTTGATCAATCTCGCAGGCGCCCGAAGCATTGGAGATATCT
EST: gi|86834663|gb|CI340780.1|CI340780
EST:     GACAAGCCAGAAGATGAGAAGAAATAAATCAACTCCTTTGTGTCTTCCTT                         GCAACCACCTCTTGATCAATCTCGCAGGCGCCCGAAGCATTGGAGATATCT
genomic: GACAAGCCAGAAGATGAGAAGAAATAAATCAACTCCTTTGTGTCTTCCTTgtaagatttc ... gacctcgcagGCAACCACCTCTTGATCAATCTCGCAGGCGCCCGAAGCATTGGAGATATCT
EST: gi|33801681|gb|CF326712.1|CF326712
EST:     GACAAGCCAGAAGATGAGAAGAAATAAATCAACTCCTTTGTGTCTTCCTT                         GCAACCACCTCTTGATCAATCTCGCAGGCGCCCGAAGCATTGGAGATATCT
genomic: GACAAGCCAGAAGATGAGAAGAAATAAATCAACTCCTTTGTGTCTTCCTTgtaagatttc ... gacctcgcagGCAACCACCTCTTGATCAATCTCGCAGGCGCCCGAAGCATTGGAGATATCT
EST: gi|88247152|gb|CI247001.1|CI247001
EST:     GACAAGCCAGAAGATGAGAAGAAATAAATCAACTCCTTTGTGTCTTCCTT                         GCAACCACCTCTTGATCAATCTCGCAGGCGCCCGAAGCATTGGAGATATCT
genomic: GACAAGCCAGAAGATGAGAAGAAATAAATCAACTCCTTTGTGTCTTCCTTgtaagatttc ... gacctcgcagGCAACCACCTCTTGATCAATCTCGCAGGCGCCCGAAGCATTGGAGATATCT
EST: gi|88840672|gb|CI080126.1|CI080126
EST:     GACAAGCCAGAAGATGAGAAGAAATAAATCAACTCCTTTGTGTCTTCCTT                         GCAACCACCTCTTGATCAATCTCGCAGGCGCCCGAAGCATTGGAGATATCT
genomic: GACAAGCCAGAAGATGAGAAGAAATAAATCAACTCCTTTGTGTCTTCCTTgtaagatttc ... gacctcgcagGCAACCACCTCTTGATCAATCTCGCAGGCGCCCGAAGCATTGGAGATATCT
EST: gi|88217668|gb|CI217517.1|CI217517
EST:     GACAAGCCAGAAGATGAGAAGAAATAAATCAACTCCTTTGTGTCTTCCTT                         GCAACCACCTCTTGATCAATCTCGCAGGCGCCCGAAGCATTGGAGATATCT
genomic: GACAAGCCAGAAGATGAGAAGAAATAAATCAACTCCTTTGTGTCTTCCTTgtaagatttc ... gacctcgcagGCAACCACCTCTTGATCAATCTCGCAGGCGCCCGAAGCATTGGAGATATCT
EST: gi|88971753|gb|CI388991.1|CI388991
EST:     GACAAGCCAGAAGATGAGAAGAAATAAATCAACTCCTTTGTGTCTTCCTT                         GCAACCACCTCTTGATCAATCTCGCAGGCGCCCGAAGCATTGGAGATATCT
genomic: GACAAGCCAGAAGATGAGAAGAAATAAATCAACTCCTTTGTGTCTTCCTTgtaagatttc ... gacctcgcagGCAACCACCTCTTGATCAATCTCGCAGGCGCCCGAAGCATTGGAGATATCT
EST: gi|44670518|gb|CR283952.1|CR283952
EST:     AACAAGCCAGAAGATGAGAAGAAATAAATCAACTCCTTTGTGTCTTCCTT                         GCAACCACCTCTTGATCAATCTCGCAGGCGCCCGAAGCATTGGAGATATCT
genomic: GACAAGCCAGAAGATGAGAAGAAATAAATCAACTCCTTTGTGTCTTCCTTgtaagatttc ... gacctcgcagGCAACCACCTCTTGATCAATCTCGCAGGCGCCCGAAGCATTGGAGATATCT
EST: gi|58675750|gb|CK064437.1|CK064437
EST:     AACAAGCCAGAAGATGAGAAGAAATAAATCAACTCCTTTGTGTCTTCCTT                         GCAACCACCTCTTGATCAATCTCGCAGGCGCCCGAAGCATTGGAGATATCT
genomic: GACAAGCCAGAAGATGAGAAGAAATAAATCAACTCCTTTGTGTCTTCCTTgtaagatttc ... gacctcgcagGCAACCACCTCTTGATCAATCTCGCAGGCGCCCGAAGCATTGGAGATATCT
EST: gi|29678148|gb|CB674423.1|CB674423
EST:     GACAAGCCAGAAGATGAGAAGAAATAAATCAACTCCTTTGTGTCTTCCTT                         GCAACCACCTCTTGATCAATCTCGCAGGCGCCCGAAGCATTGGAGATATCT
genomic: GACAAGCCAGAAGATGAGAAGAAATAAATCAACTCCTTTGTGTCTTCCTTgtaagatttc ... gacctcgcagGCAACCACCTCTTGATCAATCTCGCAGGCGCCCGAAGCATTGGAGATATCT
EST: gi|88411406|gb|CI518930.1|CI518930
EST:     GACAAGCCAGAAGATGAGAAGAAATAAATCAACTCCTTTGTGTCTTCCTT                         GCAACCACCTCTTGATCAATCTCGCAGGCGCCCGAAGCATTGGAGATATCT
genomic: GACAAGCCAGAAGATGAGAAGAAATAAATCAACTCCTTTGTGTCTTCCTTgtaagatttc ... gacctcgcagGCAACCACCTCTTGATCAATCTCGCAGGCGCCCGAAGCATTGGAGATATCT
EST: gi|88840095|gb|CI079549.1|CI079549
EST:     GACAAGCCAGAAGATGAGAAGAAATAAATCAACTCCTTTGTGTCTTCCTT                         GCAACCACCTCTTGATCAATCTCGCAGGCGCCCGAAGCATTGGAGATATCT
genomic: GACAAGCCAGAAGATGAGAAGAAATAAATCAACTCCTTTGTGTCTTCCTTgtaagatttc ... gacctcgcagGCAACCACCTCTTGATCAATCTCGCAGGCGCCCGAAGCATTGGAGATATCT
EST: gi|88841708|gb|CI080964.1|CI080964
EST:     GACAAGCCAGAAGATGAGAAGAAATAAATCAACTCCTTTGTGTCTTCCTT                         GCAACCACCTCTTGATCAATCTCGCAGGCGCCCGAAGCATTGGAGATATCT
genomic: GACAAGCCAGAAGATGAGAAGAAATAAATCAACTCCTTTGTGTCTTCCTTgtaagatttc ... gacctcgcagGCAACCACCTCTTGATCAATCTCGCAGGCGCCCGAAGCATTGGAGATATCT
EST: gi|86412758|gb|CI067163.1|CI067163
EST:     GACAAGCCAGAAGATGAGAAGAAATAAATCAACTCCTTTGTGTCTTCCTT                         GCAACCACCTCTTGATCAATCTCGCAGGCGCCCGAAGCATTGGAGATATCT
genomic: GACAAGCCAGAAGATGAGAAGAAATAAATCAACTCCTTTGTGTCTTCCTTgtaagatttc ... gacctcgcagGCAACCACCTCTTGATCAATCTCGCAGGCGCCCGAAGCATTGGAGATATCT
EST: gi|86537394|gb|CI177600.1|CI177600
EST:     GACAAGCCAGAAGATGAGAAGAAATAAATCAACTCCTTTGTGTCTTCCTT                         GCAACCACCTCTTGATCAATCTCGCAGGCGCCCGAAGCATTGGAGATATCT
genomic: GACAAGCCAGAAGATGAGAAGAAATAAATCAACTCCTTTGTGTCTTCCTTgtaagatttc ... gacctcgcagGCAACCACCTCTTGATCAATCTCGCAGGCGCCCGAAGCATTGGAGATATCT
EST: gi|89166075|gb|CI103165.1|CI103165
EST:     GACAAGCCAGAAGATGAGAAGAAATAAATCAACTCCTTTGTGTCTTCCTT                         GCAACCACCTCTTGATCAATCTCGCAGGCGCCCGAAGCATTGGAGATATCT
genomic: GACAAGCCAGAAGATGAGAAGAAATAAATCAACTCCTTTGTGTCTTCCTTgtaagatttc ... gacctcgcagGCAACCACCTCTTGATCAATCTCGCAGGCGCCCGAAGCATTGGAGATATCT
EST: gi|88217103|gb|CI216952.1|CI216952
EST:     GACAAGCCAGAAGATGAGAAGAAATAAATCAACTCCTTTGTGTCTTCCTT                         GCAACCACCTCTTGATCAATCTCGCAGGCGCCCGAAGCATTGGAGATATCT
genomic: GACAAGCCAGAAGATGAGAAGAAATAAATCAACTCCTTTGTGTCTTCCTTgtaagatttc ... gacctcgcagGCAACCACCTCTTGATCAATCTCGCAGGCGCCCGAAGCATTGGAGATATCT
EST: gi|88262482|gb|CI366256.1|CI366256
EST:     GACAAGCCAGAAGATGAGAAGAAATAAATCAACTCCTTTGTGTCTTCCTT                         GCAACCACCTCTTGATCAATCTCGCAGGCGCCCGAAGCATTGGAGATATCT
genomic: GACAAGCCAGAAGATGAGAAGAAATAAATCAACTCCTTTGTGTCTTCCTTgtaagatttc ... gacctcgcagGCAACCACCTCTTGATCAATCTCGCAGGCGCCCGAAGCATTGGAGATATCT
EST: gi|55409357|gb|CV721733.1|CV721733
EST:     ATCAACTCCTTTGTGTCTTCCTT                         GCAACCACCTATTGATCAATCTCGCAGGCGCCCGAAGCATTGGAGATATCT
genomic: ATCAACTCCTTTGTGTCTTCCTTgtaagatttc ... gacctcgcagGCAACCACCTCTTGATCAATCTCGCAGGCGCCCGAAGCATTGGAGATATCT
EST: gi|88830946|gb|CI079380.1|CI079380
EST:     GACAAGCCAGAAGATGAGAAGAAATAAATCAACTCCTTTGTGTCTTCCTT                         GCAACCACCTCTTGATCAATCTCGCAGGCGCCCGAAGCATTGGAGATATCT
genomic: GACAAGCCAGAAGATGAGAAGAAATAAATCAACTCCTTTGTGTCTTCCTTgtaagatttc ... gacctcgcagGCAACCACCTCTTGATCAATCTCGCAGGCGCCCGAAGCATTGGAGATATCT
EST: gi|86413292|gb|CI067697.1|CI067697
EST:     GACAAGCCAGAAGATGAGAAGAAATAAATCAACTCCTTTGTGTCTTCCTT                         GCAACCACCTCTTGATCAATCTCGCAGGCGCCCGAAGCATTGGAGATATCT
genomic: GACAAGCCAGAAGATGAGAAGAAATAAATCAACTCCTTTGTGTCTTCCTTgtaagatttc ... gacctcgcagGCAACCACCTCTTGATCAATCTCGCAGGCGCCCGAAGCATTGGAGATATCT
EST: gi|88258169|gb|CI360755.1|CI360755
EST:     GACAAGCCAGAAGATGAGAAGAAATAAATCAACTCCTTTGTGTCTTCCTT                         GCAACCACCTCTTGATCAATCTCGCAGGCGCCCGAAGCATTGGAGATATCT
genomic: GACAAGCCAGAAGATGAGAAGAAATAAATCAACTCCTTTGTGTCTTCCTTgtaagatttc ... gacctcgcagGCAACCACCTCTTGATCAATCTCGCAGGCGCCCGAAGCATTGGAGATATCT
EST: gi|88460344|gb|CI529419.1|CI529419
EST:     GACAAGCCAGAAGATGAGAAGAAATAAATCAACTCCTTTGTGTCTTCCTT                         GCAACCACCTCTTGATCAATCTCGCAGGCGCCCGAAGCATTGGAGATATCT
genomic: GACAAGCCAGAAGATGAGAAGAAATAAATCAACTCCTTTGTGTCTTCCTTgtaagatttc ... gacctcgcagGCAACCACCTCTTGATCAATCTCGCAGGCGCCCGAAGCATTGGAGATATCT
EST: gi|86428134|gb|CI073231.1|CI073231
EST:     GACAAGCCAGAAGATGAGAAGAAATAAATCAACTCCTTTGTGTCTTCCTT                         GCAACCACCTCTTGATCAATCTCGCAGGCGCCCGAAGCATTGGAGATATCT
genomic: GACAAGCCAGAAGATGAGAAGAAATAAATCAACTCCTTTGTGTCTTCCTTgtaagatttc ... gacctcgcagGCAACCACCTCTTGATCAATCTCGCAGGCGCCCGAAGCATTGGAGATATCT
EST: gi|88903289|gb|CI088827.1|CI088827
EST:     GACAAGCCAGAAGATGAGAAGAAATAAATCAACTCCTTTGTGTCTTCCTT                         GCAACCACCTCTTGATCAATCTCGCAGGCGCCCGAAGCATTGGAGATATCT
genomic: GACAAGCCAGAAGATGAGAAGAAATAAATCAACTCCTTTGTGTCTTCCTTgtaagatttc ... gacctcgcagGCAACCACCTCTTGATCAATCTCGCAGGCGCCCGAAGCATTGGAGATATCT
EST: gi|86486706|gb|CI129339.1|CI129339
EST:     GACAAGCCAGAAGATGAGAAGAAATAAATCAACTCCTTTGTGTCTTCCTT                         GCAACCACCTCTTGATCAATCTCGTC-G-CGCCCGAAGCATTGGAGATATC
genomic: GACAAGCCAGAAGATGAGAAGAAATAAATCAACTCCTTTGTGTCTTCCTTgtaagatttc ... gacctcgcagGCAACCACCTCTTGATCAATCTCG-CAGGCGCCCGAAGCATTGGAGATATC
EST: gi|86419054|gb|CI053855.1|CI053855
EST:     GACAAGCCAGAAGATGAGAAGAAATAAATCAACTCCTTTGTGTCTTCCTT                         GCAACCACCTCTTGATCAATCTCGCAGGCGCCCGAAGCATTGGAGATATCT
genomic: GACAAGCCAGAAGATGAGAAGAAATAAATCAACTCCTTTGTGTCTTCCTTgtaagatttc ... gacctcgcagGCAACCACCTCTTGATCAATCTCGCAGGCGCCCGAAGCATTGGAGATATCT
EST: gi|88828527|gb|CI073397.1|CI073397
EST:     GACAAGCCAGAAGATGAGAAGAAATAAATCAACTCCTTTGTGTCTTCCTT                         GCAACCACCTCTTGATCAATCTCGCAGGCGCCCGAAGCATTGGAGATATCT
genomic: GACAAGCCAGAAGATGAGAAGAAATAAATCAACTCCTTTGTGTCTTCCTTgtaagatttc ... gacctcgcagGCAACCACCTCTTGATCAATCTCGCAGGCGCCCGAAGCATTGGAGATATCT
EST: gi|88245959|gb|CI245808.1|CI245808
EST:     GACAAGCCAGAAGATGAGAAGAAATAAATCAACTCCTTTGTGTCTTCCTT                         GCAACCACCTCTTGATCAATCTCGCAGGCGCCCGAAGCATTGGAGATATCT
genomic: GACAAGCCAGAAGATGAGAAGAAATAAATCAACTCCTTTGTGTCTTCCTTgtaagatttc ... gacctcgcagGCAACCACCTCTTGATCAATCTCGCAGGCGCCCGAAGCATTGGAGATATCT
EST: gi|6449564|gb|AU081506.1|AU081506
EST:     GACAAGCCAGAAGATGAGAAGAAATAAATCAACTCCTTTGTGTCTTCCTT                         GCAACCACCTCTTGATCAATCTCGCAGGCGCCCGAAGCATTGGAGATATCT
genomic: GACAAGCCAGAAGATGAGAAGAAATAAATCAACTCCTTTGTGTCTTCCTTgtaagatttc ... gacctcgcagGCAACCACCTCTTGATCAATCTCGCAGGCGCCCGAAGCATTGGAGATATCT
EST: gi|88262261|gb|CI365837.1|CI365837
EST:     GACAAGCCAGAAGATGAGAAGAAATAAATCAACTCCTTTGTGTCTTCCTT                         GCAACCACCTCTTGATCAATCTCGCAGGCGCCCGAAGCATTGGAGATATCT
genomic: GACAAGCCAGAAGATGAGAAGAAATAAATCAACTCCTTTGTGTCTTCCTTgtaagatttc ... gacctcgcagGCAACCACCTCTTGATCAATCTCGCAGGCGCCCGAAGCATTGGAGATATCT
EST: gi|33654617|gb|CF277231.1|CF277231
EST:     GCCAAGCCAGAAGATGAGAAGAAATAAATCAACTCCTTTGTGTCTTCCTT                         GCAACCACCTCTTGATCAATCTCGCAGGCGCCCGAAGCATTGGAGATATCT
genomic: GACAAGCCAGAAGATGAGAAGAAATAAATCAACTCCTTTGTGTCTTCCTTgtaagatttc ... gacctcgcagGCAACCACCTCTTGATCAATCTCGCAGGCGCCCGAAGCATTGGAGATATCT

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: 74 (upstream exon), 73 (downstream exon)
Score: 53

CAAGAGAAGAAGGAAGACAAATCAGACAAGCCAGAAGATGAGAAGAAATAAATCAACTCCTTTGTGTCTTCCTTgtaagatttc ... gacctcgcagGCAACCACCTCTTGATCAATCTCGCAGGCGCCCGAAGCATTGGAGATATCTGGTCTCGCTTTATTTGGTCATGGATTCTACTTATCCTCGTGTAACTGTA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcaaagtttaccatttaccccacgcaacttatcaaaacgttgcgcgacctcgcagGCAACCACCTCTTGATCAATCTCGCAGGCGCCCGAAGCATTGGAGATATCTGGTCTCGCTTTATTTGGTCATGGATTCTACTTATCCTCGTGTAACTGTA
                            ttatcaaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tactgtttctatgcaaaactaacgtgttaacgtgtgcaatttgcatcaaagtttaccatttaccccacgcaacttatcaaaacgttgcgcgacctcgcagGCAACCACCTCTTGATCAATCTCGCAGGCGCCCGAAGCATTGGAGATATCTGGTCTCGCTTTATTTGGTCATGGATTCTACTTATCCTCGTGTAACTGTA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CATGGA
tactgtt
- - - - ctatgca
- - - - - - - -aaactaa
- - - - - - - - - - - - - - - cgtgtgc
- - - - - - - - - - - - - - - - - - - - - -catcaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -atcaaaa