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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagcaacaccgttctataacatactttattctgaagccaaaacttttgattttaattctttttttcttttgcagTTTTCTGTGACGGAGCACTTTAGAGAAGCAATTGGCTATCCCAGGCCTCCGCCTGGTGTATATTTCTTCTATGAATTTTCTCCAATTAAG

Basic information

species Oryza sativa
transcript LOC_Os03g20520.1
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|218482003|gb|FG956575.1|FG956575
EST:     TTCCCACAATCTATACCGACATTAGAGGACGGAAAATCAACTCAAATCAG                         TTTTCTGTGACGGAGCACTTTAGAGAAGCAATTGGCTATCCCAGGCCTCCG
genomic: TTCCCACAATCTATACCGACATTAGAGGACGGAAAATCAACTCAAATCAGgtaagcaaca ... tcttttgcagTTTTCTGTGACGGAGCACTTTAGAGAAGCAATTGGCTATCCCAGGCCTCCG
EST: gi|218492797|gb|FG953626.1|FG953626
EST:     TTCCCACAATCTATACCGACATTAGAGGACGGAAAATCAACTCAAATCAG                         TTTTCTGTGACGGAGCACTTTAGAGAAGCAATTGGCTATCCCAGGCCTCCG
genomic: TTCCCACAATCTATACCGACATTAGAGGACGGAAAATCAACTCAAATCAGgtaagcaaca ... tcttttgcagTTTTCTGTGACGGAGCACTTTAGAGAAGCAATTGGCTATCCCAGGCCTCCG
EST: gi|218505492|gb|FG958279.1|FG958279
EST:     TTCCCACAATCTATACCGACATTAGAGGACGGAAAATCAACTCAAATCAG                         TTTTCTGTGACGGAGCACTTTAGAGAAGCAATTGGCTATCCCAGGCCTCCG
genomic: TTCCCACAATCTATACCGACATTAGAGGACGGAAAATCAACTCAAATCAGgtaagcaaca ... tcttttgcagTTTTCTGTGACGGAGCACTTTAGAGAAGCAATTGGCTATCCCAGGCCTCCG
EST: gi|25803052|gb|CA759013.1|CA759013
EST:     TTCCCACAATCTATACCGACATTAGAGGACGGAAGATCAACTCAAATCAG                         TTTTCTGTGACGGAGCACTTTAGAGAAGCAATTGGCTATCCCAGGCCTCCG
genomic: TTCCCACAATCTATACCGACATTAGAGGACGGAAAATCAACTCAAATCAGgtaagcaaca ... tcttttgcagTTTTCTGTGACGGAGCACTTTAGAGAAGCAATTGGCTATCCCAGGCCTCCG
EST: gi|88847669|gb|CI018360.1|CI018360
EST:     TATACCGACATTAGAGGACGGAAAATCAACTCAAATCAG                         TTTTCTGTGACGGAGCACTTTAGAGAAGCAATTGGCTATCCCAGGCCTCCG
genomic: TATACCGACATTAGAGGACGGAAAATCAACTCAAATCAGgtaagcaaca ... tcttttgcagTTTTCTGTGACGGAGCACTTTAGAGAAGCAATTGGCTATCCCAGGCCTCCG
EST: gi|88989740|gb|CI107427.1|CI107427
EST:     TTCCCACAATCTATACCGACATTAGAGGACGGAAAATCAACTCAAATCAG                         TTTTCTGTGACGGAGCACTTTAGAGAAGCAATTGGCTATCCCAGGCCTCCG
genomic: TTCCCACAATCTATACCGACATTAGAGGACGGAAAATCAACTCAAATCAGgtaagcaaca ... tcttttgcagTTTTCTGTGACGGAGCACTTTAGAGAAGCAATTGGCTATCCCAGGCCTCCG
EST: gi|8859147|gb|AU096465.1|AU096465
EST:     TTCCCACAATCTATACCGACATTAGAGGACGGAAAATCAACTCAAATCAG                         TTTTCTGTGACGGAGCACTTTAGAGAAGCAATTGGCTATCCCAGGCCTCCG
genomic: TTCCCACAATCTATACCGACATTAGAGGACGGAAAATCAACTCAAATCAGgtaagcaaca ... tcttttgcagTTTTCTGTGACGGAGCACTTTAGAGAAGCAATTGGCTATCCCAGGCCTCCG
EST: gi|701663|gb|D47954.1|D47954
EST:     TTCCCACAATCTATACCGACATTAGAGGACGGAAAATCAACTCAAATCAG                         TTTTCTGTGACGGAGCACTTTAGAGAAGCAATTGGCTATCCCAGGCCTCCG
genomic: TTCCCACAATCTATACCGACATTAGAGGACGGAAAATCAACTCAAATCAGgtaagcaaca ... tcttttgcagTTTTCTGTGACGGAGCACTTTAGAGAAGCAATTGGCTATCCCAGGCCTCCG
EST: gi|89181360|gb|CI112866.1|CI112866
EST:     CATTAGAGGACGGAAAATCAACTCAAATCAG                         TTTTCTGTGACGGAGCACTTTAGAGAAGCAATTGGCTATCCCAGGCCTCCG
genomic: CATTAGAGGACGGAAAATCAACTCAAATCAGgtaagcaaca ... tcttttgcagTTTTCTGTGACGGAGCACTTTAGAGAAGCAATTGGCTATCCCAGGCCTCCG
EST: gi|86429502|gb|CI076183.1|CI076183
EST:     GAAAATCAACTCAAATCAG                         TTTTCTGTGACGGAGCACTTNAGAGAAGCAATTGGCTATCCCAGGCCTCCG
genomic: GAAAATCAACTCAAATCAGgtaagcaaca ... tcttttgcagTTTTCTGTGACGGAGCACTTTAGAGAAGCAATTGGCTATCCCAGGCCTCCG
EST: gi|29657637|gb|CB653912.1|CB653912
EST:     TTCCCACAATCTATACCGACATTAGAGGACGGAAAATCAACTCAAATCAG                         TTTTCTGTGACGGAGCACTTTAGAGAAGCAATTGGCTATCCCAGGCCTCCG
genomic: TTCCCACAATCTATACCGACATTAGAGGACGGAAAATCAACTCAAATCAGgtaagcaaca ... tcttttgcagTTTTCTGTGACGGAGCACTTTAGAGAAGCAATTGGCTATCCCAGGCCTCCG
EST: gi|58690521|gb|CK079208.1|CK079208
EST:     TTCCCACGATCTATACCGACATTAGAGGACGGAAAATCAACTCAAATCAG                         TTTTCTGTGACGGAGCACTTTAGAGAAGCAATTGGCTATCCCAGGCCTCCG
genomic: TTCCCACAATCTATACCGACATTAGAGGACGGAAAATCAACTCAAATCAGgtaagcaaca ... tcttttgcagTTTTCTGTGACGGAGCACTTTAGAGAAGCAATTGGCTATCCCAGGCCTCCG

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), 74 (downstream exon)
Score: 28

GTTGTTCCCACAATCTATACCGACATTAGAGGACGGAAAATCAACTCAAATCAGgtaagcaaca ... tcttttgcagTTTTCTGTGACGGAGCACTTTAGAGAAGCAATTGGCTATCCCAGGCCTCCGCCTGGTGTATATTTCTTCTATGAATTTTCTCCAATTAAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

catactttattctgaagccaaaacttttgattttaattctttttttcttttgcagTTTTCTGTGACGGAGCACTTTAGAGAAGCAATTGGCTATCCCAGGCCTCCGCCTGGTGTATATTTCTTCTATGAATTTTCTCCAATTAAG
                              ttttaat  putative branch site (score: 28)
                       cttttgattttaattc  CT-rich tract
                   aaaacttttgatttta  TA-rich tract