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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tggatcattgagtggcatactggcatgatttcgggacaatcacattatgaggtttggtctgcattactgaatttcttctgtccctgcattgctgatgcagTTTGTGGAGCACCAAAGAGAAGGTTCAAGCCGTACGAGCCTAAGGTGGCCAAGAACGCCAACGCCACCGATGCCCGCAAGGCTAGGAAGGAGCAGCTGAA

Basic information

species Oryza sativa
transcript LOC_Os11g32500.1
intron # 2
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|27576865|gb|CA999559.1|CA999559
EST:     CAGCGACAGGACCCCCTTCGACAAGCTTCCCGACAAGTACTTCTGCCCCG                         TTTGTGGAGCACCAAAGAGAAGGTTCAAGCCGTACGAGCCTAAGGTGGCCA
genomic: CAGCGACAGGACCCCCTTCGACAAGCTTCCCGACAAGTACTTCTGCCCCGgtaagaacag ... gctgatgcagTTTGTGGAGCACCAAAGAGAAGGTTCAAGCCGTACGAGCCTAAGGTGGCCA
EST: gi|38477358|gb|CF961491.1|CF961491
EST:     CAGCGACAGGACCCCCTTCGACAAGCTTCCCGACAAGTACTTCTGCCCCG                         TTTGTGGAGCACCAAAGAGAAGGTTCAAGCCGTACGAGCCTAAGGTGGCCA
genomic: CAGCGACAGGACCCCCTTCGACAAGCTTCCCGACAAGTACTTCTGCCCCGgtaagaacag ... gctgatgcagTTTGTGGAGCACCAAAGAGAAGGTTCAAGCCGTACGAGCCTAAGGTGGCCA
EST: gi|86599734|gb|CI253719.1|CI253719
EST:     AGCGGACAGGACCCCCTTCGACAAGCTTCCCGACAAGTACTTCTGCCCCG                         TTTGTGGAGCACCAAAGAGAAGGTTCAAGCCGTACGAGCCTAAGGTGGCCA
genomic: AGC-GACAGGACCCCCTTCGACAAGCTTCCCGACAAGTACTTCTGCCCCGgtaagaacag ... gctgatgcagTTTGTGGAGCACCAAAGAGAAGGTTCAAGCCGTACGAGCCTAAGGTGGCCA
EST: gi|15854402|gb|BI807198.1|BI807198
EST:     CAGCGACAGGACCCCCTTCGACAAGCTTCCCGACAAGTACTTCTGCCCCG                         TTTGTGGAGCACCAAAGAGAAGGTTCAAGCCGTACGAGCCTAAGGTGGCCA
genomic: CAGCGACAGGACCCCCTTCGACAAGCTTCCCGACAAGTACTTCTGCCCCGgtaagaacag ... gctgatgcagTTTGTGGAGCACCAAAGAGAAGGTTCAAGCCGTACGAGCCTAAGGTGGCCA
EST: gi|27576230|gb|CA998924.1|CA998924
EST:     CAGCGACAGGACCCCCTTCGACAAGCTTCCCGACAAGTACTTCTGCCCCG                         TTTGTGGAGCACCAAAGAGAATGTTCAAGCCGTACGAGCCTAAGGTGGCCT
genomic: CAGCGACAGGACCCCCTTCGACAAGCTTCCCGACAAGTACTTCTGCCCCGgtaagaacag ... gctgatgcagTTTGTGGAGCACCAAAGAGAAGGTTCAAGCCGTACGAGCCTAAGGTGGCCA
EST: gi|88987923|gb|CI017986.1|CI017986
EST:     TTCCCGACAAGTACTTCTGCCCCG                         TTTGTGGAGCACCAAAGAGAAGGTTCAAGCCGTACGAGCCTAAGGTGGCCA
genomic: TTCCCGACAAGTACTTCTGCCCCGgtaagaacag ... gctgatgcagTTTGTGGAGCACCAAAGAGAAGGTTCAAGCCGTACGAGCCTAAGGTGGCCA
EST: gi|87016907|gb|CI284241.1|CI284241
EST:     CAGCGACAGGACCCCCTTCGACAAGCTTCCCGACAAGTACTTCTGCCCCG                         TTTGTGGAGCACCAAAGAGAAGGTTCAAGCCGTACGAGCCTAAGGTGGCCA
genomic: CAGCGACAGGACCCCCTTCGACAAGCTTCCCGACAAGTACTTCTGCCCCGgtaagaacag ... gctgatgcagTTTGTGGAGCACCAAAGAGAAGGTTCAAGCCGTACGAGCCTAAGGTGGCCA
EST: gi|86261567|gb|CI017309.1|CI017309
EST:     CAGCGACAGGACCCCCTTCGACAAGCTTCCCGACAAGTACTTCTGCCCCG                         TTTGTGGAGCACCAAAGAGAAGGTTCAAGCCGTACGAGCCTAAGGTGGCCA
genomic: CAGCGACAGGACCCCCTTCGACAAGCTTCCCGACAAGTACTTCTGCCCCGgtaagaacag ... gctgatgcagTTTGTGGAGCACCAAAGAGAAGGTTCAAGCCGTACGAGCCTAAGGTGGCCA
EST: gi|38480409|gb|CF964498.1|CF964498
EST:     CAGCGACAGGACCCCCTTCGACAAGCTTCCCGACAAGTACTTCTGCCCCG                         TTTGTGGAGCACCAAAGAGAAGGTTCAAGCCGTACGAGCCTAAGGTGGCCA
genomic: CAGCGACAGGACCCCCTTCGACAAGCTTCCCGACAAGTACTTCTGCCCCGgtaagaacag ... gctgatgcagTTTGTGGAGCACCAAAGAGAAGGTTCAAGCCGTACGAGCCTAAGGTGGCCA

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: 59 (upstream exon), 59 (downstream exon)
Score: 38

GTACATCTACAGCGACAGGACCCCCTTCGACAAGCTTCCCGACAAGTACTTCTGCCCCGgtaagaacag ... gctgatgcagTTTGTGGAGCACCAAAGAGAAGGTTCAAGCCGTACGAGCCTAAGGTGGCCAAGAACGCCAACGCCACCGATGCCCGCAAGGCTAGGAAGGAGCAGCTGAA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatgaggtttggtctgcattactgaatttcttctgtccctgcattgctgatgcagTTTGTGGAGCACCAAAGAGAAGGTTCAAGCCGTACGAGCCTAAGGTGGCCAAGAACGCCAACGCCACCGATGCCCGCAAGGCTAGGAAGGAGCAGCTGAA
                                            tgctgat  putative branch site (score: 38)
                        aatttctt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tggatcattgagtggcatactggcatgatttcgggacaatcacattatgaggtttggtctgcattactgaatttcttctgtccctgcattgctgatgcagTTTGTGGAGCACCAAAGAGAAGGTTCAAGCCGTACGAGCCTAAGGTGGCCAAGAACGCCAACGCCACCGATGCCCGCAAGGCTAGGAAGGAGCAGCTGAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGA
- - - - - - -ggcatac
- - - - - - - - - - -ggcatga
- - - - - - - - - - - - - - - - - -acaatca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -tctgcat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tactgaa