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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtgaacactcaccaatatttctttttttttccctcagtgtgtagttatgatggttaagataaaaggcactgcttgtacaattttgtgctaagtgatgactctcttaatgtttagCTGACAGGCTTATCAAAGAATTCCATCACTTTGAAGTGGGAAAGTGATAGTTGTTCTTCTGTTGAAATTTCTGGGCTTGATGTCGGGTGGGGACAG

Basic information

species Oryza sativa
transcript LOC_Os03g01750.7
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g01750.5 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM2G052546_T07 (Zea mays), 3'ss of exon 10
gtaagtgaacactcaccaatatttctttttttttccctcagtgtgtagttatgatggttaagataaa----aggcactgcttgtacaa---ttttgtgctaagtgatgactctcttaatgtttagCTGACAGGCTTATCAAAGAATTCCATCACTTTGAAGTGGGAAAGTGATAGTTGTTCTTCTGTTGAAATTTCTGGGCTTGATGTCGGGTGGGGACAG
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gtaagtgaatgcagaacta-atttct------------cagta-gtagttatgttggagaagatgaatacagatcatggcgagtcaaagattttcctactaagtgatggctgtcgtattatttagCTGACAGGATTATCCAAAAACACAATCACTTTGAAGTGGGAAGCTGATGGTTCTTCCTCTGTTGAAATTTCTGGGCTCGACATTGGCTGGGGTCAG
















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|25806922|gb|CA762883.1|CA762883
EST:     GAGCTTGCTTTCCAAAGTTGGAAGCCATTAAATTGGCTACTGCTGACATT                         CTGACAGGCTTATCAAAGAATTCCATCACT
genomic: GAGCTTGCTTTCCAAAGTTGGAAGCCATTAAATTGGCTACTGCTGACATTgtaagtgaac ... taatgtttagCTGACAGGCTTATCAAAGAATTCCATCACT
EST: gi|55828006|gb|AU065392.2|AU065392
EST:     GAGCTTGCTTTCCAAAGTTGGAAGCCATTAAATTGGCTACTGCTGACATT                         CTGACAGGCTTATCAAAGAATTCCATCACTTTGAAGTGGG
genomic: GAGCTTGCTTTCCAAAGTTGGAAGCCATTAAATTGGCTACTGCTGACATTgtaagtgaac ... taatgtttagCTGACAGGCTTATCAAAGAATTCCATCACTTTGAAGTGGG
EST: gi|428438|gb|D24587.1|D24587
EST:     GAGCTTGCTTTCCAAAGTTGGAAGCCATTAAATTGGCTACTGCTGACATT                         CTGACAGGCTTATCAAAGAATTCCATCACTTTGA
genomic: GAGCTTGCTTTCCAAAGTTGGAAGCCATTAAATTGGCTACTGCTGACATTgtaagtgaac ... taatgtttagCTGACAGGCTTATCAAAGAATTCCATCACTTTGA

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: 71 (upstream exon), 45 (downstream exon)
Score: 12

AGTAAACGAGCTTGCTTTCCAAAGTTGGAAGCCATTAAATTGGCTACTGCTGACATTgtaagtgaac ... taatgtttagCTGACAGGCTTATCAAAGAATTCCATCACTTTGAAGTGGGAAAGTGATAGTTGTTCTTCTGTTGAAATTTCTGGGCTTGATGTCGGGTGGGGACAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taaaaggcactgcttgtacaattttgtgctaagtgatgactctcttaatgtttagCTGACAGGCTTATCAAAGAATTCCATCACTTTGAAGTGGGAAAGTGATAGTTGTTCTTCTGTTGAAATTTCTGGGCTTGATGTCGGGTGGGGACAG
                                          tcttaat  putative branch site (score: 12)
 ctctctt  CT-rich tract
 ttaatgttta  TA-rich tract