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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacgtgttaaaaaaattacactgaatagtatgctgtaaaacgtgcactcatgcaatctcttgtttttttcctttctgtataaataaatgtgtgcccattctgcagtatgacatagaactgttctcatgcagtctcctttttttcccccttgtttccagATCCCCCTTATCGTATTGACAGCATACCTCAAAAGTAAATTCAGAGATACAATG

Basic information

species Oryza sativa
transcript LOC_Os05g10810.1
intron # 14
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g10810.1 (Oryza sativa), 3'ss of exon 14
lower sequence: GRMZM2G130749_T02 (Zea mays), 3'ss of exon 13
gtacgtgttaaaaaaattacactgaatagtatgctgtaaaacgtgcactcatgcaatctcttgtttttttcctttctgtataaataaatgtgtgcccattctgcagtatgacatagaactgttctcatgcagtctcctttttttcccccttgtttccagATCCCCCTTATCGTATTGACAGCATACCTCAAAAGTAAATTCAGAGATACAATG
                                                       | |    |        | |    |||   |  |||| |     || |    ||  ||| | ||||||||| |  |  | |   || ||| || ||| || |||||| ||||| ||| |||||||| |||||||||||| ||||||||| || ||||||
-------------------------------------------------------accagaaggcaacagtcatctaatatggttccatgtatttatgttgtctccta-aacagaaaactgttctgacaccatat---ttcttttcctctttttaccagATTCCCCTCATCATATTGACATCATACCTCAAAAATAAATTCAGTGACACAATG
















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|29664361|gb|CB660636.1|CB660636
EST:     TTCCCTGCCGCATTCTCAAGTTCTGGGCATTCTTAGGAATAATGCTACAG                         ATCCCCCTTATCGTATTGACAGCATACCTCAAAAGTAAATTCAGAGATACA
genomic: TTCCCTGCCGCATTCTCAAGTTCTGGGCATTCTTAGGAATAATGCTACAGgtacgtgtta ... ttgtttccagATCCCCCTTATCGTATTGACAGCATACCTCAAAAGTAAATTCAGAGATACA
EST: gi|29615462|gb|CB620474.1|CB620474
EST:     TTCCCTGCCGCATTCTCAAGTTCTGGGCATTCTTAGGAATAATGCTACAG                         ATCCCCCTTATCGTATTGACAGCATACCTCAAAAGTAAATTCAGAGATACA
genomic: TTCCCTGCCGCATTCTCAAGTTCTGGGCATTCTTAGGAATAATGCTACAGgtacgtgtta ... ttgtttccagATCCCCCTTATCGTATTGACAGCATACCTCAAAAGTAAATTCAGAGATACA
EST: gi|29664325|gb|CB660600.1|CB660600
EST:     TTCCCTGCCGCATTCTCAAGTTCTGGGCATTCTTAGGAATAATGCTACAG                         ATCCCCCTTATCGTATTGACAGCATACCTCAAAAGTAAATTCAGAGATACA
genomic: TTCCCTGCCGCATTCTCAAGTTCTGGGCATTCTTAGGAATAATGCTACAGgtacgtgtta ... ttgtttccagATCCCCCTTATCGTATTGACAGCATACCTCAAAAGTAAATTCAGAGATACA
EST: gi|25803480|gb|CA759449.1|CA759449
EST:     TTCCCTGCCGCATTCTCAAGTTCTGGGCATTCTTAGGAATAATGCTACAG                         ATCCCCCTTATCGTATTGACAGCATACCTCAAAAGTAAATTCAGAGATACA
genomic: TTCCCTGCCGCATTCTCAAGTTCTGGGCATTCTTAGGAATAATGCTACAGgtacgtgtta ... ttgtttccagATCCCCCTTATCGTATTGACAGCATACCTCAAAAGTAAATTCAGAGATACA
EST: gi|88521128|gb|CI448787.1|CI448787
EST:     TTCCCTGCCGCATTCTCAAGTTCTGGGCATTCTTAGGAATAATGCTACAG                         ATCCCCCTTATCGTATTGACAGCATACCTCAAAAGTAAATTCAGAGATACA
genomic: TTCCCTGCCGCATTCTCAAGTTCTGGGCATTCTTAGGAATAATGCTACAGgtacgtgtta ... ttgtttccagATCCCCCTTATCGTATTGACAGCATACCTCAAAAGTAAATTCAGAGATACA
EST: gi|29641508|gb|CB646515.1|CB646515
EST:     TTCCCTGCCGCATTCTCAAGTTCTGGGCATTCTTAGGAATAATGCTACAG                         ATCCCCCTTATCGTATTGACAGCATACCTCAAAAGTAAATTCAGAGATACA
genomic: TTCCCTGCCGCATTCTCAAGTTCTGGGCATTCTTAGGAATAATGCTACAGgtacgtgtta ... ttgtttccagATCCCCCTTATCGTATTGACAGCATACCTCAAAAGTAAATTCAGAGATACA
EST: gi|29634262|gb|CB639271.1|CB639271
EST:     TTCCCTGCCGCATTCTCAAGTTCTGGGCATTCTTAGGAATAATGCTACAG                         ATCCCCCTTATCGTATTGACAGCATACCTCAAAAGTAAATTCAGAGATACA
genomic: TTCCCTGCCGCATTCTCAAGTTCTGGGCATTCTTAGGAATAATGCTACAGgtacgtgtta ... ttgtttccagATCCCCCTTATCGTATTGACAGCATACCTCAAAAGTAAATTCAGAGATACA
EST: gi|29664324|gb|CB660599.1|CB660599
EST:     TTCCCTGCCGCATTCTCAAGTTCTGGGCATTCTTAGGAATAATGCTACAG                         ATCCCCCTTATCGTATTGACAGCATACCTCAAAAGTAAATTCAGAGATACA
genomic: TTCCCTGCCGCATTCTCAAGTTCTGGGCATTCTTAGGAATAATGCTACAGgtacgtgtta ... ttgtttccagATCCCCCTTATCGTATTGACAGCATACCTCAAAAGTAAATTCAGAGATACA
EST: gi|29664362|gb|CB660637.1|CB660637
EST:     TTCCCTGCCGCATTCTCAAGTTCTGGGCATTCTTAGGAATAATGCTACAG                         ATCCCCCTTATCGTATTGACAGCATACCTCAAAAGTAAATTCAGAGATACA
genomic: TTCCCTGCCGCATTCTCAAGTTCTGGGCATTCTTAGGAATAATGCTACAGgtacgtgtta ... ttgtttccagATCCCCCTTATCGTATTGACAGCATACCTCAAAAGTAAATTCAGAGATACA
EST: gi|29646484|gb|CB651491.1|CB651491
EST:     TTCCCTGCCGCATTCTCAAGTTCTGGGCATTCTTAGGAATAATGCTACAG                         ATCCCCCTTATCGTATTGACAGCATACCTCAAAAGTAAATTCAGAGATACA
genomic: TTCCCTGCCGCATTCTCAAGTTCTGGGCATTCTTAGGAATAATGCTACAGgtacgtgtta ... ttgtttccagATCCCCCTTATCGTATTGACAGCATACCTCAAAAGTAAATTCAGAGATACA
EST: gi|88477472|gb|CI414743.1|CI414743
EST:     CAAGTTCTGGGCATTCTTAGGGATAATG-TAGCAG                         ATCCCCCTTATCGGTATTGACAGCATACCTCAAAAGTAAATTCAGAGATA
genomic: CAAGTTCTGGGCATTCTTAGGAATAATGCTA-CAGgtacgtgtta ... ttgtttccagATCCCCCTTATC-GTATTGACAGCATACCTCAAAAGTAAATTCAGAGATA
EST: gi|88520579|gb|CI448233.1|CI448233
EST:     TTCCCTGCCGCATTCTCAAGTTCTGGGCATTCTTAGGAATAATGCTACAG                         ATCCCCCTTATCGTATTGACAGCATACCTCAAAAGTAAATTCAGAGATACA
genomic: TTCCCTGCCGCATTCTCAAGTTCTGGGCATTCTTAGGAATAATGCTACAGgtacgtgtta ... ttgtttccagATCCCCCTTATCGTATTGACAGCATACCTCAAAAGTAAATTCAGAGATACA
EST: gi|29614065|gb|CB619078.1|CB619078
EST:     TTCCCTGCCGCATTCTCAAGTTCTGGGCATTCTTAGGAATAATGCTACAG                         ATCCCCCTTATCGTATTGACAGCATACCTCAAAAGTAAATTCAGAGATACA
genomic: TTCCCTGCCGCATTCTCAAGTTCTGGGCATTCTTAGGAATAATGCTACAGgtacgtgtta ... ttgtttccagATCCCCCTTATCGTATTGACAGCATACCTCAAAAGTAAATTCAGAGATACA
EST: gi|66928227|gb|CX115075.1|CX115075
EST:     TTCCCTGCCGCATTCTCAAGTTCTGGGCATTCTTAGGAATAATGCTACAG                         ATCCCCCTTATCGTATTGACAGCATACCTCAAAAGTAAATTCAGAGATACA
genomic: TTCCCTGCCGCATTCTCAAGTTCTGGGCATTCTTAGGAATAATGCTACAGgtacgtgtta ... ttgtttccagATCCCCCTTATCGTATTGACAGCATACCTCAAAAGTAAATTCAGAGATACA
EST: gi|29615460|gb|CB620472.1|CB620472
EST:     TTCCCTGCCGCATTCTCAAGTTCTGGGCATTCTTAGGAATAATGCTACAG                         ATCCCCCTTATCGTATTGACAGCATACCTCAAAAGTAAATTCAGAGATACA
genomic: TTCCCTGCCGCATTCTCAAGTTCTGGGCATTCTTAGGAATAATGCTACAGgtacgtgtta ... ttgtttccagATCCCCCTTATCGTATTGACAGCATACCTCAAAAGTAAATTCAGAGATACA

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: 63 (upstream exon), 54 (downstream exon)
Score: 49

ATATGTGTCGCTGTTCCCTGCCGCATTCTCAAGTTCTGGGCATTCTTAGGAATAATGCTACAGgtacgtgtta ... ttgtttccagATCCCCCTTATCGTATTGACAGCATACCTCAAAAGTAAATTCAGAGATACAATG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agtatgacatagaactgttctcatgcagtctcctttttttcccccttgtttccagATCCCCCTTATCGTATTGACAGCATACCTCAAAAGTAAATTCAGAGATACAATG
                 ttctcatgcagtctcc  CT-rich tract
                                 ttttttt  TA-rich tract