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 5'  3'   		2  
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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gcatgttccaacttcatgtttgtgaccaaaagaaaataacatcagcaagagaagttcatctgtgtaatttcttgccattgatgttgaccttccattgcagATAACTTGAGCACCATTACCACTGCCGGATTTGATGGTCCTGCTGCAAAGTCTGCCAAAAGAAAGAGAAAGAACCAATTCAGGGGCATCCGCCAGCGCCC

Basic information

species Oryza sativa
transcript LOC_Os02g54160.1
intron # 1
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|29645004|gb|CB650011.1|CB650011
EST:     TGACGTCGTCGAGATCAAGCCGGCCGCCTTCAAGAGGGCCCTCTCCAGAG                         ATAACTTGAGCACCATTACCACTGCCGGATTTGATGGTCCTGCTGCAAAGT
genomic: TGACGTCGTCGAGATCAAGCCGGCCGCCTTCAAGAGGGCCCTCTCCAGAGgtatgggcgt ... tccattgcagATAACTTGAGCACCATTACCACTGCCGGATTTGATGGTCCTGCTGCAAAGT
EST: gi|86596415|gb|CI284726.1|CI284726
EST:     TGACGTCGTCGAGATCAAGCCGGCCGCCTTCAAGAGGGCCCTCTCCAGAG                         ATAACTTGAGCACCATTACCACTGCCGGATTTGATGGTCCTGCTGCAAAGT
genomic: TGACGTCGTCGAGATCAAGCCGGCCGCCTTCAAGAGGGCCCTCTCCAGAGgtatgggcgt ... tccattgcagATAACTTGAGCACCATTACCACTGCCGGATTTGATGGTCCTGCTGCAAAGT
EST: gi|117233268|gb|CT848068.1|CT848068
EST:     TGACGTCGTCGAGATCAAGCCGGCCGCCTTCAAGAGGGCCCTCTCCAGAG                         ATAACTTGAGCACCATTACCACTGCCGGATTTGATGGTCCTGCTGCAAAGT
genomic: TGACGTCGTCGAGATCAAGCCGGCCGCCTTCAAGAGGGCCCTCTCCAGAGgtatgggcgt ... tccattgcagATAACTTGAGCACCATTACCACTGCCGGATTTGATGGTCCTGCTGCAAAGT
EST: gi|88693407|gb|CI736982.1|CI736982
EST:     TGACGTCGTCCAGATCAAGCCGGCCGCCTTCAAGAGGGCCCTCTCCAGAG                         ATAACTTGAGCACC
genomic: TGACGTCGTCGAGATCAAGCCGGCCGCCTTCAAGAGGGCCCTCTCCAGAGgtatgggcgt ... tccattgcagATAACTTGAGCACC
EST: gi|86821804|gb|CI309258.1|CI309258
EST:     TAACGTCGTCGAGATCAAGCCGGCCGCCTTCAAGAGGGCCCTCTCCAGAG                         ATAACTTGAGCACCATTACCACTGCCGGATTTGATGGTCCTGCTGCAAAGT
genomic: TGACGTCGTCGAGATCAAGCCGGCCGCCTTCAAGAGGGCCCTCTCCAGAGgtatgggcgt ... tccattgcagATAACTTGAGCACCATTACCACTGCCGGATTTGATGGTCCTGCTGCAAAGT
EST: gi|32948116|gb|BP184688.1|BP184688
EST:     TGACGTCGTCGAGATCAAGCCGGCCGCCTTCAAGAGGGCCCTCTCCAGAG                         ATAACTTGAGCACCATTACCACTGCCGGATTTGATGGTCCTGCTGCAAAGT
genomic: TGACGTCGTCGAGATCAAGCCGGCCGCCTTCAAGAGGGCCCTCTCCAGAGgtatgggcgt ... tccattgcagATAACTTGAGCACCATTACCACTGCCGGATTTGATGGTCCTGCTGCAAAGT
EST: gi|58674295|gb|CK062981.1|CK062981
EST:     TGACGTCGTCGAGATCAAGCCGGCCGCCTTCAAGAGGGCCCTCTCCAGAG                         ATAACTTGAGCACCATTACCACTGCCGGATTTGATGGTCCTGCTGCAAAGT
genomic: TGACGTCGTCGAGATCAAGCCGGCCGCCTTCAAGAGGGCCCTCTCCAGAGgtatgggcgt ... tccattgcagATAACTTGAGCACCATTACCACTGCCGGATTTGATGGTCCTGCTGCAAAGT
EST: gi|33793450|gb|CF322606.1|CF322606
EST:     TGACGTCGTCGAGATCAAGCCGGCCGCCTTCAAGAGGGCCCTCTCCAGAG                         ATAACTTGAGCACCATTACCACTGCCGGATTTGATGGTCCTGCTGCAAAGT
genomic: TGACGTCGTCGAGATCAAGCCGGCCGCCTTCAAGAGGGCCCTCTCCAGAGgtatgggcgt ... tccattgcagATAACTTGAGCACCATTACCACTGCCGGATTTGATGGTCCTGCTGCAAAGT
EST: gi|32948209|gb|BP184781.1|BP184781
EST:     TGACGTCGTCGAGATCAAGCCGGCCGCCTTCAAGAGGGCCCTCTCCAGAG                         ATAACTTGAGCACCATTACCACTGCCGGATTTGATGGTCCTGCTGCAAAGT
genomic: TGACGTCGTCGAGATCAAGCCGGCCGCCTTCAAGAGGGCCCTCTCCAGAGgtatgggcgt ... tccattgcagATAACTTGAGCACCATTACCACTGCCGGATTTGATGGTCCTGCTGCAAAGT
EST: gi|86894551|gb|CI308276.1|CI308276
EST:     TGACGTCGTCGAGATCAAGCCGGCCGCCTTCAAGAGGGCCCTCTCCAGAG                         ATAACTTGAGCACCATTACCACTGCCGGATTTGATGGTCCTGCTGCAAAGT
genomic: TGACGTCGTCGAGATCAAGCCGGCCGCCTTCAAGAGGGCCCTCTCCAGAGgtatgggcgt ... tccattgcagATAACTTGAGCACCATTACCACTGCCGGATTTGATGGTCCTGCTGCAAAGT
EST: gi|86832027|gb|CI305253.1|CI305253
EST:     GACGTCGTCGAGATCAAGCCGGCCGCCTTCAAGAGGGCCCTCTCCAGAAG                         ATA-CTTGAGCACCATTACCACTGCCGGATTTGATGGTCCTGC
genomic: GACGTCGTCGAGATCAAGCCGGCCGCCTTCAAGAGGGCCCTCTCCAGA-Ggtatgggcgt ... tccattgcagATAACTTGAGCACCATTACCACTGCCGGATTTGATGGTCCTGC
EST: gi|58605921|gb|CK033954.1|CK033954
EST:     TGACGTCGTCGAGATCAAGCCGGCCGCCTTCAAGAGGGCCCTCTCCAGAG                         ATAACTTGAGCACCATTACCACTGCCGGATTTGATGGTCCTGCTGCAAAGT
genomic: TGACGTCGTCGAGATCAAGCCGGCCGCCTTCAAGAGGGCCCTCTCCAGAGgtatgggcgt ... tccattgcagATAACTTGAGCACCATTACCACTGCCGGATTTGATGGTCCTGCTGCAAAGT
EST: gi|58656429|gb|CK045109.1|CK045109
EST:     TGACGTCGTCGAGATCAAGCCGGCCGCCTTCAAGAGGGCCCTCTCCAGAG                         ATAACTTGAGCACCATTACCA
genomic: TGACGTCGTCGAGATCAAGCCGGCCGCCTTCAAGAGGGCCCTCTCCAGAGgtatgggcgt ... tccattgcagATAACTTGAGCACCATTACCA
EST: gi|5607520|gb|AU076169.1|AU076169
EST:     TGACGTCGTCGAGATCAAGCCGGCCGCCTTCAAGAGGGCCCTCTCCAGAG                         ATAACTTGAGCACCATTACCACTGCCGGATTTGATGGTCCTGCTGCAAAGT
genomic: TGACGTCGTCGAGATCAAGCCGGCCGCCTTCAAGAGGGCCCTCTCCAGAGgtatgggcgt ... tccattgcagATAACTTGAGCACCATTACCACTGCCGGATTTGATGGTCCTGCTGCAAAGT
EST: gi|218485284|gb|FG954067.1|FG954067
EST:     TGACGTCGTCGAGATCAAGCCGGCCGCCTTCAAGAGGGCCCTCTCCAGAG                         ATAACTTGAGCACCATTACCACTGCCGGATTAGATGGTCCTGCTGCAAAGT
genomic: TGACGTCGTCGAGATCAAGCCGGCCGCCTTCAAGAGGGCCCTCTCCAGAGgtatgggcgt ... tccattgcagATAACTTGAGCACCATTACCACTGCCGGATTTGATGGTCCTGCTGCAAAGT
EST: gi|29658013|gb|CB654288.1|CB654288
EST:     TGACGTCGTCAAGATCAAGCCGGCCGCCTTCAAGAGGGCCCTCTCCAGAG                         ATAACTTGAGCACCATTACCACTGCCGGATTTGATGGTCCTGCTGCAAAGT
genomic: TGACGTCGTCGAGATCAAGCCGGCCGCCTTCAAGAGGGCCCTCTCCAGAGgtatgggcgt ... tccattgcagATAACTTGAGCACCATTACCACTGCCGGATTTGATGGTCCTGCTGCAAAGT
EST: gi|58612428|gb|CK040140.1|CK040140
EST:     TGACGTCGTCGAGATCAAGCCGGCCGCCTTCAAGAGGGCCCTCTCCAGAG                         ATAACTTGAGCACCATTACCACTGCCGGATTTGATGGTCCTGCTGCAAAGT
genomic: TGACGTCGTCGAGATCAAGCCGGCCGCCTTCAAGAGGGCCCTCTCCAGAGgtatgggcgt ... tccattgcagATAACTTGAGCACCATTACCACTGCCGGATTTGATGGTCCTGCTGCAAAGT
EST: gi|86904502|gb|CI308712.1|CI308712
EST:     TGACGTCGTCGAGATCAAGCCGGCCGCCTTCAAGAGGGCCCTCTCCAGAG                         ATAACTTGAGCACCATTACCACTGCCGGATTTGATGGTCCTGC
genomic: TGACGTCGTCGAGATCAAGCCGGCCGCCTTCAAGAGGGCCCTCTCCAGAGgtatgggcgt ... tccattgcagATAACTTGAGCACCATTACCACTGCCGGATTTGATGGTCCTGC
EST: gi|88719990|gb|CI745289.1|CI745289
EST:     GACGTCGTCGAGATCAAGCCGGCCCGC-TTCAAGAGGGCCCTCTCCAGAG                         ATAACTTGAGCACCATTAC
genomic: GACGTCGTCGAGATCAAGCCGGCC-GCCTTCAAGAGGGCCCTCTCCAGAGgtatgggcgt ... tccattgcagATAACTTGAGCACCATTAC
EST: gi|58653655|gb|CK042335.1|CK042335
EST:     TGACGTCGTCGAGATCAAGCCGGCCGCCTTCAAGAGGGCCCTCTCCAGAG                         ATAACTTGAGCACCATTACCACTGCCGGATTTGATGGTCCTGCTGCAAAGT
genomic: TGACGTCGTCGAGATCAAGCCGGCCGCCTTCAAGAGGGCCCTCTCCAGAGgtatgggcgt ... tccattgcagATAACTTGAGCACCATTACCACTGCCGGATTTGATGGTCCTGCTGCAAAGT
EST: gi|58687099|gb|CK075786.1|CK075786
EST:     TGACGTCGTCGAGATCAAGCCGGCCGCCTTCAAGAGGGCCCTCTCCAGAG                         ATAACTTGAGCACCATTACCACTGCCGGATTTGATGGTCCTGCTGCAAAGT
genomic: TGACGTCGTCGAGATCAAGCCGGCCGCCTTCAAGAGGGCCCTCTCCAGAGgtatgggcgt ... tccattgcagATAACTTGAGCACCATTACCACTGCCGGATTTGATGGTCCTGCTGCAAAGT
EST: gi|58602298|gb|CK012826.1|CK012826
EST:     TGACGTCGTCGAGATCAAGCCGGCCGCCTTCAAGAGGGCCCTCTCCAGAG                         ATAACTTGAGCACCATTACCACTGCCGGATTTGATGGTCCTGCTGCAAAGT
genomic: TGACGTCGTCGAGATCAAGCCGGCCGCCTTCAAGAGGGCCCTCTCCAGAGgtatgggcgt ... tccattgcagATAACTTGAGCACCATTACCACTGCCGGATTTGATGGTCCTGCTGCAAAGT
EST: gi|86821954|gb|CI309338.1|CI309338
EST:     TGACGTCGTCGAGATCAAGCCGGCCGCCCTCAAGAGGGCCCTCTCCAGAG                         ATAACTTGAGCACCATTACCACTGCCGGATTTGATGGTCCTGCTGCAAAGT
genomic: TGACGTCGTCGAGATCAAGCCGGCCGCCTTCAAGAGGGCCCTCTCCAGAGgtatgggcgt ... tccattgcagATAACTTGAGCACCATTACCACTGCCGGATTTGATGGTCCTGCTGCAAAGT
EST: gi|29657849|gb|CB654124.1|CB654124
EST:     TGACGTCGTCGAGATCAAGCCGGCCGCCTTCAAGAGGGCCCTCTCCAGAG                         ATAACTTGAGCACCATTACCACTGCCGGATTTGATGGTCCTGCTGCAAAGT
genomic: TGACGTCGTCGAGATCAAGCCGGCCGCCTTCAAGAGGGCCCTCTCCAGAGgtatgggcgt ... tccattgcagATAACTTGAGCACCATTACCACTGCCGGATTTGATGGTCCTGCTGCAAAGT
EST: gi|58664448|gb|CK053134.1|CK053134
EST:     TGACGTCGTCGAGATCAAGCCGGCCGCCTTCAAGAGGGCCCTCTCCAGAG                         ATAACTTGAGCACCATTACCACTGCCGGATTTGATGGTCCTGCTGCAAAGT
genomic: TGACGTCGTCGAGATCAAGCCGGCCGCCTTCAAGAGGGCCCTCTCCAGAGgtatgggcgt ... tccattgcagATAACTTGAGCACCATTACCACTGCCGGATTTGATGGTCCTGCTGCAAAGT
EST: gi|29680038|gb|CB676313.1|CB676313
EST:     TGACGTCGTCGAGATCAAGCCGGCCGCCTTCAAGAGGGCCCTCTCCAGAG                         ATAACTTGAGCACCATTACCACTGCCGGATTTGATGGTCCTGCTGCAAAGT
genomic: TGACGTCGTCGAGATCAAGCCGGCCGCCTTCAAGAGGGCCCTCTCCAGAGgtatgggcgt ... tccattgcagATAACTTGAGCACCATTACCACTGCCGGATTTGATGGTCCTGCTGCAAAGT
EST: gi|58593811|gb|CF992119.1|CF992119
EST:     TGACGTCGTCGAGATCAAGCCGGCCG-CTTCAAGAGGGCCCTCTCCAGAG                         ATAACTTGAGCACCATTACCACTGCCGGATTTGATGGTCCTGCTGCAAAGT
genomic: TGACGTCGTCGAGATCAAGCCGGCCGCCTTCAAGAGGGCCCTCTCCAGAGgtatgggcgt ... tccattgcagATAACTTGAGCACCATTACCACTGCCGGATTTGATGGTCCTGCTGCAAAGT
EST: gi|58653135|gb|CK041815.1|CK041815
EST:     TGACGTCGTCGAGATCAAGCCGGCCGCCTTCAAGAGGGCCCTCTCCAGAG                         ATAACTTGAGCACCATTACCACTGCCGGATTTGATGGTCCTGCTGCAAAGT
genomic: TGACGTCGTCGAGATCAAGCCGGCCGCCTTCAAGAGGGCCCTCTCCAGAGgtatgggcgt ... tccattgcagATAACTTGAGCACCATTACCACTGCCGGATTTGATGGTCCTGCTGCAAAGT
EST: gi|58613246|gb|CK040958.1|CK040958
EST:     TGACGTCGTCGAGATCAAGCCGGCCGCCTTCAAGAGGGCCCTCTCCAGAG                         ATAACTTGAGCACCATTACCACTGCCGGATTTGATGGTCCTGCTGCAAAGT
genomic: TGACGTCGTCGAGATCAAGCCGGCCGCCTTCAAGAGGGCCCTCTCCAGAGgtatgggcgt ... tccattgcagATAACTTGAGCACCATTACCACTGCCGGATTTGATGGTCCTGCTGCAAAGT
EST: gi|88412971|gb|CI578822.1|CI578822
EST:     TTACGTCGTCGAGATCAAGCCGGCCGCCTTCAAGAGGGCCCTCTACAGAG                         GTAACTTGAGCACCATTACCACTGGGGGATTTG
genomic: TGACGTCGTCGAGATCAAGCCGGCCGCCTTCAAGAGGGCCCTCTCCAGAGgtatgggcgt ... tccattgcagATAACTTGAGCACCATTACCACTGCCGGATTTG
EST: gi|86901728|gb|CI310490.1|CI310490
EST:     TGACGTCGTCGAGATCAAGCCGGCCGCCTTCAAGAGGGCCCTCTCCAGAG                         ATAACTTGAGCACCATTACCACTGCCGGATTTGATGGTCCTGCTGCAAAGT
genomic: TGACGTCGTCGAGATCAAGCCGGCCGCCTTCAAGAGGGCCCTCTCCAGAGgtatgggcgt ... tccattgcagATAACTTGAGCACCATTACCACTGCCGGATTTGATGGTCCTGCTGCAAAGT
EST: gi|86826088|gb|CI310975.1|CI310975
EST:     TGACGTCGTCGAGATCAAGCCGGCCGCCTTCAAGAGGGCCCTCTCCAGAG                         ATAACTTGAGCACCATTACCACTGCCGGATTTGATGGTCCTGC
genomic: TGACGTCGTCGAGATCAAGCCGGCCGCCTTCAAGAGGGCCCTCTCCAGAGgtatgggcgt ... tccattgcagATAACTTGAGCACCATTACCACTGCCGGATTTGATGGTCCTGC

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), 75 (downstream exon)
Score: 201

GAGGTGGACTCCGGGGACTCGGATTTGGAGCTCGGGGAGGAGGACGACGATGACGTCGTCGAGATCAAGCCGGCCGCCTTCAAGAGGGCCCTCTCCAGAGgtatgggcgt ... tccattgcagATAACTTGAGCACCATTACCACTGCCGGATTTGATGGTCCTGCTGCAAAGTCTGCCAAAAGAAAGAGAAAGAACCAATTCAGGGGCATCCGCCAGCGCCC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

caagagaagttcatctgtgtaatttcttgccattgatgttgaccttccattgcagATAACTTGAGCACCATTACCACTGCCGGATTTGATGGTCCTGCTGCAAAGTCTGCCAAAAGAAAGAGAAAGAACCAATTCAGGGGCATCCGCCAGCGCCC
                                    tgttgac  putative branch site (score: 201)
                                          ccttccatt  CT-rich tract
                   taatttctt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gcatgttccaacttcatgtttgtgaccaaaagaaaataacatcagcaagagaagttcatctgtgtaatttcttgccattgatgttgaccttccattgcagATAACTTGAGCACCATTACCACTGCCGGATTTGATGGTCCTGCTGCAAAGTCTGCCAAAAGAAAGAGAAAGAACCAATTCAGGGGCATCCGCCAGCGCCC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC