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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgcaagacagttctagataacaacatttcacactccgatgttacaagctacactccagctattaatgcttatatttttgttcatttaccaattccttcagATCCTAGAACCCTCCAAGGAACTTGCGATGCAACTCATGGAATTAGGTCAACAACACTCTCCGACAAGGAAGCTGGGCGTGGACATGCTGAGAGAGCGGG

Basic information

species Oryza sativa
transcript LOC_Os10g26140.3
intron # 11
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|86502356|gb|CI144989.1|CI144989
EST:     TGGCCCGCAGCAACCGTTATCCTGAAATAGCCTTGTTTGTATCCAACAAG                         ATCCTAGAACCCTCCAAGGAACTTGCGATGCAACTCATGGAATTAGGTCAA
genomic: TGGCCCGCAGCAACCGTTATCCTGAAATAGCCTTGTTTGTATCCAACAAGgtcagtatgt ... attccttcagATCCTAGAACCCTCCAAGGAACTTGCGATGCAACTCATGGAATTAGGTCAA
EST: gi|89186084|gb|CI047953.1|CI047953
EST:     TGGCCCGCAGCAACCGTTATCCTGAAATAGCCTTGTTTGTATCCNACAAG                         ATCCTAGAACCCTCCAAGGAACTTGCGATGCAACTCATGGAATTAGGTCAA
genomic: TGGCCCGCAGCAACCGTTATCCTGAAATAGCCTTGTTTGTATCCAACAAGgtcagtatgt ... attccttcagATCCTAGAACCCTCCAAGGAACTTGCGATGCAACTCATGGAATTAGGTCAA
EST: gi|86477411|gb|CI120044.1|CI120044
EST:     TGGCCCGCAGCAACCGTTATCCTGAAATAGCCTTGTTTGTATCCAACAAG                         ATCCTAGAACCCTCCAAGGAACTTGCGATGCAACTCATGGAATTAGGTCAA
genomic: TGGCCCGCAGCAACCGTTATCCTGAAATAGCCTTGTTTGTATCCAACAAGgtcagtatgt ... attccttcagATCCTAGAACCCTCCAAGGAACTTGCGATGCAACTCATGGAATTAGGTCAA
EST: gi|94362431|gb|CI052426.1|CI052426
EST:     TGGCCCGCAGCAACCGTTATCCTGAAATAGCCTTGTTTGTATCCAACAAG                         ATCCTAGAACCCTCCAAGGAACTTGCGATGCAACTCATGGAATTAGGTCAA
genomic: TGGCCCGCAGCAACCGTTATCCTGAAATAGCCTTGTTTGTATCCAACAAGgtcagtatgt ... attccttcagATCCTAGAACCCTCCAAGGAACTTGCGATGCAACTCATGGAATTAGGTCAA
EST: gi|89192800|gb|CI050098.1|CI050098
EST:     TGGCCCGCAGCAACCGTTATCCTGAAATAGCCTTGTTTGTATCCAACAAG                         ATCCTAGAACCCTCCAAGGAACTTGCGATGCAACTCATGGAATTAGGTCAA
genomic: TGGCCCGCAGCAACCGTTATCCTGAAATAGCCTTGTTTGTATCCAACAAGgtcagtatgt ... attccttcagATCCTAGAACCCTCCAAGGAACTTGCGATGCAACTCATGGAATTAGGTCAA
EST: gi|86482162|gb|CI124795.1|CI124795
EST:     TGGCCCGCAGCAACCGTTATCCTGAAATAGCCTTGTTTGTATCCAACAAG                         ATCCTAGAACCCTCCAAGGAACTTGCGATGCAACTCATGGAATTAGGTCAA
genomic: TGGCCCGCAGCAACCGTTATCCTGAAATAGCCTTGTTTGTATCCAACAAGgtcagtatgt ... attccttcagATCCTAGAACCCTCCAAGGAACTTGCGATGCAACTCATGGAATTAGGTCAA
EST: gi|86884727|gb|CI313106.1|CI313106
EST:     CAGCAACCGTTATCCTGAAATAGCCTTGTTTGTATCCAACAAG                         ATCCTAGAACCCTCCAAGGAAC-TGCGATGCAACTCATGG-ATTAGGTCAA
genomic: CAGCAACCGTTATCCTGAAATAGCCTTGTTTGTATCCAACAAGgtcagtatgt ... attccttcagATCCTAGAACCCTCCAAGGAACTTGCGATGCAACTCATGGAATTAGGTCAA
EST: gi|86827328|gb|CI270972.1|CI270972
EST:     TGGCCCGCAGCAACCGTTATCCTGAAATAGCCTTGTTTGTATCCAACAAG                         ATCCTAGAACCCTCCAAGGAACTTGCGATGCAACTCATGGAATTAGGTCAA
genomic: TGGCCCGCAGCAACCGTTATCCTGAAATAGCCTTGTTTGTATCCAACAAGgtcagtatgt ... attccttcagATCCTAGAACCCTCCAAGGAACTTGCGATGCAACTCATGGAATTAGGTCAA
EST: gi|29621826|gb|CB626837.1|CB626837
EST:     TGGCCCGCAGCAACCGTTATCCTGAAATAGCCTTGTTTGTATCCAACAAG                         ATCCTAGAACCCTCCAAGGAACTTGCGATGCAACTCATGGAATTAGGTCGA
genomic: TGGCCCGCAGCAACCGTTATCCTGAAATAGCCTTGTTTGTATCCAACAAGgtcagtatgt ... attccttcagATCCTAGAACCCTCCAAGGAACTTGCGATGCAACTCATGGAATTAGGTCAA
EST: gi|87016317|gb|CI271728.1|CI271728
EST:     TGGCCCGCAGCAACCGTTATCCTGAAATAGCNTTGTTTGTATCCAACAAG                         ATCCTAGAACCCTCCAAGGAACTTGCGATGCAACTCATGGAATTAGGTCAA
genomic: TGGCCCGCAGCAACCGTTATCCTGAAATAGCCTTGTTTGTATCCAACAAGgtcagtatgt ... attccttcagATCCTAGAACCCTCCAAGGAACTTGCGATGCAACTCATGGAATTAGGTCAA
EST: gi|16578849|gb|BI812944.1|BI812944
EST:     TGTTTGTATCC-ACAAG                         ATCCTAGAACCCTCCAAGGAACTTGCGATGCAACTCATGGAATTAGGTCGA
genomic: TGTTTGTATCCAACAAGgtcagtatgt ... attccttcagATCCTAGAACCCTCCAAGGAACTTGCGATGCAACTCATGGAATTAGGTCAA
EST: gi|29634117|gb|CB639126.1|CB639126
EST:     CCCGCAGCAACCGTTATCCTGAAATAGCCTTGTTTGTATCCAACAAG                         ATCCTAGAACCCTCCAAGGAACTTGCGATGCAACTCATGGAATTAGGTCAA
genomic: CCCGCAGCAACCGTTATCCTGAAATAGCCTTGTTTGTATCCAACAAGgtcagtatgt ... attccttcagATCCTAGAACCCTCCAAGGAACTTGCGATGCAACTCATGGAATTAGGTCAA
EST: gi|86478805|gb|CI121438.1|CI121438
EST:     TGGCCCGCAGCAACCGTTATCCTGAAATAGCCTTGTTTGTATCCAACAAG                         ATCCTAGAACCCTCCAAGGAACTTGCGATGCAACTCATGGAATTAGGTCAA
genomic: TGGCCCGCAGCAACCGTTATCCTGAAATAGCCTTGTTTGTATCCAACAAGgtcagtatgt ... attccttcagATCCTAGAACCCTCCAAGGAACTTGCGATGCAACTCATGGAATTAGGTCAA
EST: gi|86431426|gb|CI085037.1|CI085037
EST:     GGCCCGCAGCAACCGTTATCCTGAAATAGCCTTGTTTGTATCCAACAAG                         ATCCTAGAACCCTCCAAGGAACTTGCGATGCAACTCATGGAATTAGGTCAA
genomic: GGCCCGCAGCAACCGTTATCCTGAAATAGCCTTGTTTGTATCCAACAAGgtcagtatgt ... attccttcagATCCTAGAACCCTCCAAGGAACTTGCGATGCAACTCATGGAATTAGGTCAA
EST: gi|86437670|gb|CI119590.1|CI119590
EST:     GGCCCGCAGGCAACCGTTATCCTGAAATAGCCTTGTTTGTATCCAACAAG                         ATCCTAGAACCCTCCAAGGAACTTGCGATGCAACTCATGGAATTAGGTCAA
genomic: GGCCCGCA-GCAACCGTTATCCTGAAATAGCCTTGTTTGTATCCAACAAGgtcagtatgt ... attccttcagATCCTAGAACCCTCCAAGGAACTTGCGATGCAACTCATGGAATTAGGTCAA
EST: gi|286811|gb|D15618.1|D15618
EST:     TGGCCCGCAGCAACCGTTATCCTGAAATAGCCTTGTTTGTATCCAACAAG                         ATCCTAGAACCCTCCAAGGAACTTGCGATGCAACTCATGGAATTAGGTCAA
genomic: TGGCCCGCAGCAACCGTTATCCTGAAATAGCCTTGTTTGTATCCAACAAGgtcagtatgt ... attccttcagATCCTAGAACCCTCCAAGGAACTTGCGATGCAACTCATGGAATTAGGTCAA
EST: gi|87016228|gb|CI271639.1|CI271639
EST:     TGGCCCGCAGCAACCGTTATCCTGAAATAGCCTTGTTTGTATCCAACAAG                         ATCCTAGAACCCTCCAAGGAACTTGCGATGCAACTCATGGAATTAGGTCAA
genomic: TGGCCCGCAGCAACCGTTATCCTGAAATAGCCTTGTTTGTATCCAACAAGgtcagtatgt ... attccttcagATCCTAGAACCCTCCAAGGAACTTGCGATGCAACTCATGGAATTAGGTCAA
EST: gi|29630282|gb|CB635291.1|CB635291
EST:     TGGCCCGCAGCAACCGTTATCCTGAAATAGCCTTGTTTGTATCCAACAAG                         ATCCTAGAACCCTCCAAGGAACTTGCGATGCAACTCATGGAATTAGGTCGA
genomic: TGGCCCGCAGCAACCGTTATCCTGAAATAGCCTTGTTTGTATCCAACAAGgtcagtatgt ... attccttcagATCCTAGAACCCTCCAAGGAACTTGCGATGCAACTCATGGAATTAGGTCAA
EST: gi|29669543|gb|CB665818.1|CB665818
EST:     TGGCCCGCAGCAACCGTTATCCTGAAATAGCCTTGTTTGTATCCAACAAG                         ATCCTAGAACCCTCCAAGGAACTTGCGATGCAACTCATGGAATTAGGTCAA
genomic: TGGCCCGCAGCAACCGTTATCCTGAAATAGCCTTGTTTGTATCCAACAAGgtcagtatgt ... attccttcagATCCTAGAACCCTCCAAGGAACTTGCGATGCAACTCATGGAATTAGGTCAA
EST: gi|86481413|gb|CI124046.1|CI124046
EST:     CCGTTATCCTGAAATAGCCTTGTTTGTATCCAACAAG                         ATCCTAGAACCCTCCAAGGAACTTGCGATGCAACTCATGGAATTAGGTCAA
genomic: CCGTTATCCTGAAATAGCCTTGTTTGTATCCAACAAGgtcagtatgt ... attccttcagATCCTAGAACCCTCCAAGGAACTTGCGATGCAACTCATGGAATTAGGTCAA
EST: gi|89195851|gb|CI007270.1|CI007270
EST:     GCAGCAACCGTTATCCTGAAATAGCCTTGGTTTGTATCCAACAAG                         ATCCTAGAACCCTCCAAGGAACTTGCGATGCAACTCATGGAATTAGGTCAA
genomic: GCAGCAACCGTTATCCTGAAATAGCCTT-GTTTGTATCCAACAAGgtcagtatgt ... attccttcagATCCTAGAACCCTCCAAGGAACTTGCGATGCAACTCATGGAATTAGGTCAA
EST: gi|86437949|gb|CI119869.1|CI119869
EST:     TGGCCCGCAGCAGCCGTTATCCTGAAATAGCCTTGTTTGTATCCAACAAG                         ATCCTAGAACCCTCCAAGGAACTTGCGATGCAACTCATGGAATTAGGTCAA
genomic: TGGCCCGCAGCAACCGTTATCCTGAAATAGCCTTGTTTGTATCCAACAAGgtcagtatgt ... attccttcagATCCTAGAACCCTCCAAGGAACTTGCGATGCAACTCATGGAATTAGGTCAA

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: 46 (upstream exon), 62 (downstream exon)
Score: 14

AGCTGGGTTGAAGGCTCCTCCTAACCTTTTTGTGATGATGACAACACTGCTGGCCCGCAGCAACCGTTATCCTGAAATAGCCTTGTTTGTATCCAACAAGgtcagtatgt ... attccttcagATCCTAGAACCCTCCAAGGAACTTGCGATGCAACTCATGGAATTAGGTCAACAACACTCTCCGACAAGGAAGCTGGGCGTGGACATGCTGAGAGAGCGGG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agctacactccagctattaatgcttatatttttgttcatttaccaattccttcagATCCTAGAACCCTCCAAGGAACTTGCGATGCAACTCATGGAATTAGGTCAACAACACTCTCCGACAAGGAAGCTGGGCGTGGACATGCTGAGAGAGCGGG
              tattaat  putative branch site (score: 14)
                                              ttccttc  putative PPT
              tattaatgcttatatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgcaagacagttctagataacaacatttcacactccgatgttacaagctacactccagctattaatgcttatatttttgttcatttaccaattccttcagATCCTAGAACCCTCCAAGGAACTTGCGATGCAACTCATGGAATTAGGTCAACAACACTCTCCGACAAGGAAGCTGGGCGTGGACATGCTGAGAGAGCGGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
tgcaaga
- - - - - - - - - aacaaca
- - - - - - - - - - - - - ttcacac
- - - - - - - - - - - - - - - - - - - - - - -agctaca
- - - - - - - - - - - - - - - - - - - - - - - - - - ctccagc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aatgctt