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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gttttgtactaatgaaaaatcaaatacctgtgattatttctccacatatgtattttttaactctatctggaatatgcatactgatgatttttcatatcagGCCATGTCTCATCCCCTGCCACTTCTGGTTCTGATCATGTGAACAAGCCTATTCCTGGACCGAGAATGCCGGATGGGACAAGGGGCTTTACAATGGGGCG

Basic information

species Oryza sativa
transcript LOC_Os01g55170.1
intron # 9
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|29643681|gb|CB648688.1|CB648688
EST:     ATATAAATCTCAAGGAAGAGGTCAGATTCAGCAAAATACAAGTGGGCAAG                         GCCATGTCTCATCCCCTGCCACTTCTGGTTCTGATCATGTGAACAAGCCTA
genomic: ATATAAATCTCAAGGAAGAGGTCAGATTCAGCAAAATACAAGTGGGCAAGgtaaactgtt ... ttcatatcagGCCATGTCTCATCCCCTGCCACTTCTGGTTCTGATCATGTGAACAAGCCTA
EST: gi|88663817|gb|CI486993.1|CI486993
EST:     ATATAAATCTCAAGGAAGAGGTCAGATTCAGCAAAATACAAGTGGGCAAG                         GCCATGTCTCATCCCCTGCCACTTCTGGTTCTGATCATGTGAACAAGCCTA
genomic: ATATAAATCTCAAGGAAGAGGTCAGATTCAGCAAAATACAAGTGGGCAAGgtaaactgtt ... ttcatatcagGCCATGTCTCATCCCCTGCCACTTCTGGTTCTGATCATGTGAACAAGCCTA
EST: gi|88278052|gb|CI398854.1|CI398854
EST:     CAAGTGGGCAAG                         GCCATGTCTCATCCCCTGCCACTTCTGGTTCTGATCATGTGAACAAGCCTA
genomic: CAAGTGGGCAAGgtaaactgtt ... ttcatatcagGCCATGTCTCATCCCCTGCCACTTCTGGTTCTGATCATGTGAACAAGCCTA
EST: gi|109712028|gb|CI029198.1|CI029198
EST:     ATATAAATCTCAAGGAAGAGGTCAGATTCAGCAAAATACAAGTGGGCAAG                         GCCATGTCTCATCCCCTGCCACTTCTGGTTCTGATCATGTGAACAAGCCTA
genomic: ATATAAATCTCAAGGAAGAGGTCAGATTCAGCAAAATACAAGTGGGCAAGgtaaactgtt ... ttcatatcagGCCATGTCTCATCCCCTGCCACTTCTGGTTCTGATCATGTGAACAAGCCTA
EST: gi|218505277|gb|FG951207.1|FG951207
EST:     ATATAAATCTCAAGGAAGAGGTCAGATTCAGCAAAATACAAGTGGGCAAC                         GCCATGTCTCATCCCCTGCCACTTCTGGTTCTGATCATGTGAACCAGCCTA
genomic: ATATAAATCTCAAGGAAGAGGTCAGATTCAGCAAAATACAAGTGGGCAAGgtaaactgtt ... ttcatatcagGCCATGTCTCATCCCCTGCCACTTCTGGTTCTGATCATGTGAACAAGCCTA
EST: gi|33794161|gb|CF322971.1|CF322971
EST:     ATATAAATCTCAAGGAAGAGGTCAGATTCAGCAAAATACAAGTGGGCAAG                         GCCATGTCTCATCCCCTGCCACTTCTGGTTCTGATCATGTGAACAAGCCTA
genomic: ATATAAATCTCAAGGAAGAGGTCAGATTCAGCAAAATACAAGTGGGCAAGgtaaactgtt ... ttcatatcagGCCATGTCTCATCCCCTGCCACTTCTGGTTCTGATCATGTGAACAAGCCTA
EST: gi|29673355|gb|CB669630.1|CB669630
EST:     ATATAAATCTCAAGGAAGAGGTCAGATTCAGCAAAATACAAGTGGGCAAG                         GCCATGTCTCATCCCCTGCCACTTCTGGTTCTGATCATGTGAACAAGCCTA
genomic: ATATAAATCTCAAGGAAGAGGTCAGATTCAGCAAAATACAAGTGGGCAAGgtaaactgtt ... ttcatatcagGCCATGTCTCATCCCCTGCCACTTCTGGTTCTGATCATGTGAACAAGCCTA
EST: gi|86898803|gb|CI296092.1|CI296092
EST:     ATATAAATCTCAAGGAAGAGGTCAGATTCAGCAAAATACAAGTGGGCAAG                         GCCATGTCTCATCCCCTGCCACTTCTGGTTCTGATCATGTG
genomic: ATATAAATCTCAAGGAAGAGGTCAGATTCAGCAAAATACAAGTGGGCAAGgtaaactgtt ... ttcatatcagGCCATGTCTCATCCCCTGCCACTTCTGGTTCTGATCATGTG
EST: gi|88977082|gb|CI024819.1|CI024819
EST:     ATATAAATCTCAAGGAAGAGGTCAGATTCAGCAAAATACAAGTGGGCAAG                         GCCATGTCTCATCCCCTGCCACTTCTGGTTCTGATCATGTGAACAAGCCTA
genomic: ATATAAATCTCAAGGAAGAGGTCAGATTCAGCAAAATACAAGTGGGCAAGgtaaactgtt ... ttcatatcagGCCATGTCTCATCCCCTGCCACTTCTGGTTCTGATCATGTGAACAAGCCTA
EST: gi|29682355|gb|CB678630.1|CB678630
EST:     ATATAAATCTCAAGGAAGAGGTCAGATTCAGCAAAATACAAGTGGGCAAG                         GCCATGTCTCATCCCCTGCCACTTCTGGTTCTGATCATGTGAACAAGCCTA
genomic: ATATAAATCTCAAGGAAGAGGTCAGATTCAGCAAAATACAAGTGGGCAAGgtaaactgtt ... ttcatatcagGCCATGTCTCATCCCCTGCCACTTCTGGTTCTGATCATGTGAACAAGCCTA
EST: gi|88419290|gb|CI513711.1|CI513711
EST:     GAGGTCAGATTCAGCGGAATACAAGTGGGCAAG                         GCCATGTCTCATCCCCTGCCACTTCTGGTTCTGATCATGTGGACAAGCCTA
genomic: GAGGTCAGATTCAGCAAAATACAAGTGGGCAAGgtaaactgtt ... ttcatatcagGCCATGTCTCATCCCCTGCCACTTCTGGTTCTGATCATGTGAACAAGCCTA
EST: gi|29640595|gb|CB645604.1|CB645604
EST:     ATATAAATCTCAAGGAAGAGGTCAGATTCAGCAAAATACAAGTGGGCAAG                         GCCATGTCTCATCCCCTGCCACTTCTGGTTCTGATCATGTGAACAAGCCTA
genomic: ATATAAATCTCAAGGAAGAGGTCAGATTCAGCAAAATACAAGTGGGCAAGgtaaactgtt ... ttcatatcagGCCATGTCTCATCCCCTGCCACTTCTGGTTCTGATCATGTGAACAAGCCTA
EST: gi|88478103|gb|CI415374.1|CI415374
EST:     CTCAAGGAAGAGGTCAGATTCAGCAAAATACAAGTGGGCAAG                         GCCATGTCTCATCCCCTGCCACTTCTGGTTCTGATCATGTGAACAAGCCTA
genomic: CTCAAGGAAGAGGTCAGATTCAGCAAAATACAAGTGGGCAAGgtaaactgtt ... ttcatatcagGCCATGTCTCATCCCCTGCCACTTCTGGTTCTGATCATGTGAACAAGCCTA
EST: gi|88661682|gb|CI458201.1|CI458201
EST:     ATATAAATCTCAAGGAAGAGGTCAGATTCAGCAAAATACAAGTGGGCAAG                         GCCATGTCTCATCCCCTGCCACTTCTGGTTCTGATCATGTGAACAAGCCTA
genomic: ATATAAATCTCAAGGAAGAGGTCAGATTCAGCAAAATACAAGTGGGCAAGgtaaactgtt ... ttcatatcagGCCATGTCTCATCCCCTGCCACTTCTGGTTCTGATCATGTGAACAAGCCTA
EST: gi|38480080|gb|CF964169.1|CF964169
EST:     ATATAAATCTCAAGGAAGAGGTCAGATTCAGCAAAATACAAGTGGGCAAG                         GCCATGTCTCATCCCCTGCCACTTCTGGTTCTGATCATGTGAACAAGCCTA
genomic: ATATAAATCTCAAGGAAGAGGTCAGATTCAGCAAAATACAAGTGGGCAAGgtaaactgtt ... ttcatatcagGCCATGTCTCATCCCCTGCCACTTCTGGTTCTGATCATGTGAACAAGCCTA
EST: gi|88303892|gb|CI512966.1|CI512966
EST:     AGGTCAGATTCAGCAGAATACAAGTGGGCAAG                         GCCATGTCTCATCCCCTGCCACTTCTGGTTCTGATCATGTGAACAAGCCTA
genomic: AGGTCAGATTCAGCAAAATACAAGTGGGCAAGgtaaactgtt ... ttcatatcagGCCATGTCTCATCCCCTGCCACTTCTGGTTCTGATCATGTGAACAAGCCTA
EST: gi|7378454|gb|AU088725.1|AU088725
EST:     ATATAAATCTCAAGGAAGAGGTCAGATTCAGCAAAATACAAGTGGGCAAG                         GCCATGTCTCATCCCCTGCCACTTCTGGTTCTGATCATGTGAACAAGCCTA
genomic: ATATAAATCTCAAGGAAGAGGTCAGATTCAGCAAAATACAAGTGGGCAAGgtaaactgtt ... ttcatatcagGCCATGTCTCATCCCCTGCCACTTCTGGTTCTGATCATGTGAACAAGCCTA
EST: gi|567971|gb|D38805.1|D38805
EST:     --ATAAATCTCAAGGAAGAGGTCAGATTCAGCAAAATACAAGTGGGCAAG                         GCCATGTCTCATCCCCTGCCACTTCTGGTTCTGATCATGTGAACAAGCCTA
genomic: ATATAAATCTCAAGGAAGAGGTCAGATTCAGCAAAATACAAGTGGGCAAGgtaaactgtt ... ttcatatcagGCCATGTCTCATCCCCTGCCACTTCTGGTTCTGATCATGTGAACAAGCCTA
EST: gi|86511851|gb|CI154484.1|CI154484
EST:     ATATAAATCTCAAGGAAGAGGTCAGATTCAGCAAAATACAAGTGGGCAAG                         GCCATGTCTCATCCCCTGCCACTTCTGGTTCTGATCATGTGAACAAGCCTA
genomic: ATATAAATCTCAAGGAAGAGGTCAGATTCAGCAAAATACAAGTGGGCAAGgtaaactgtt ... ttcatatcagGCCATGTCTCATCCCCTGCCACTTCTGGTTCTGATCATGTGAACAAGCCTA
EST: gi|58686024|gb|CK074711.1|CK074711
EST:     ATATAAATCTCAAGGAAGAGGTCAGATTCAGCAAAATACAAGTGGGCAAG                         GCCATGTCTCATCCCCTGCCACTTCTGGTTCTGATCATGTGAACAAGCCTA
genomic: ATATAAATCTCAAGGAAGAGGTCAGATTCAGCAAAATACAAGTGGGCAAGgtaaactgtt ... ttcatatcagGCCATGTCTCATCCCCTGCCACTTCTGGTTCTGATCATGTGAACAAGCCTA
EST: gi|88662889|gb|CI474929.1|CI474929
EST:     ATATAAATGTCAAGGGAGAGTTCAGATTCAGCAAAATACAAGTGGGCAAG                         GCCATGTCTCATCCCCTGCCACTTCTGGTTCTGATCATGTGAACAAGCCTA
genomic: ATATAAATCTCAAGGAAGAGGTCAGATTCAGCAAAATACAAGTGGGCAAGgtaaactgtt ... ttcatatcagGCCATGTCTCATCCCCTGCCACTTCTGGTTCTGATCATGTGAACAAGCCTA
EST: gi|58687646|gb|CK076333.1|CK076333
EST:     ATATAAATCTCAAGGAAGAGGTCAGATTCAGCAAAATACAAGTGGGCAAG                         GCCATGTCTCATCCCCTGCCACTTCTGGTTCTGATCATGTGAACAAGCCTA
genomic: ATATAAATCTCAAGGAAGAGGTCAGATTCAGCAAAATACAAGTGGGCAAGgtaaactgtt ... ttcatatcagGCCATGTCTCATCCCCTGCCACTTCTGGTTCTGATCATGTGAACAAGCCTA

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: 73 (upstream exon), 74 (downstream exon)
Score: 24

GACATGCACCAACACCAAAAAGTAAATGCTAAAGGAGGACGAAAAGGTCGATATAAATCTCAAGGAAGAGGTCAGATTCAGCAAAATACAAGTGGGCAAGgtaaactgtt ... ttcatatcagGCCATGTCTCATCCCCTGCCACTTCTGGTTCTGATCATGTGAACAAGCCTATTCCTGGACCGAGAATGCCGGATGGGACAAGGGGCTTTACAATGGGGCG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atatgtattttttaactctatctggaatatgcatactgatgatttttcatatcagGCCATGTCTCATCCCCTGCCACTTCTGGTTCTGATCATGTGAACAAGCCTATTCCTGGACCGAGAATGCCGGATGGGACAAGGGGCTTTACAATGGGGCG
                                 tactgat  putative branch site (score: 24)
 tttttcat  putative PPT
 tattttttaactctat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttttgtactaatgaaaaatcaaatacctgtgattatttctccacatatgtattttttaactctatctggaatatgcatactgatgatttttcatatcagGCCATGTCTCATCCCCTGCCACTTCTGGTTCTGATCATGTGAACAAGCCTATTCCTGGACCGAGAATGCCGGATGGGACAAGGGGCTTTACAATGGGGCG

- - - - - - - - aaatcaa
- - - - - - - - - - - - - cctgtga
- - - - - - - - - - - - - - - - - - - -ctccaca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgcatac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gatgatt