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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaggcagtaaactcttttcatgtttttaaattcttgtttgtatgaaaaattcacatttacatattcataattctgttcttcaaaagGTCAGAAATGCAACAGAAATGCTACTGAATGTGACTTCAGGCCCTGCCTCCATAGTTCAG

Basic information

species Oryza sativa
transcript LOC_Os11g42510.1
intron # 4
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|29614602|gb|CB619615.1|CB619615
EST:     GGCGACTTGGTTGGTTGGCCTTCTGTGACCCCAATGGTGCACTCAAGCAT                         GTCAGAAATGCAACAGAAATGCTACTGAATGTGACTTCAGGCCCTGCGTCC
genomic: GGCGACTTGGTTGGTTGGCCTTCTGTGACCCCAATGGTGCACTCAAGCATgtaaggcagt ... tcttcaaaagGTCAGAAATGCAACAGAAATGCTACTGAATGTGACTTCAGGCCCTGCCTCC
EST: gi|29636664|gb|CB641673.1|CB641673
EST:     GGCGACTTGGTTGGTTGGCCTTCTGTGACCCCAATGGTGCACTCAAGCAT                         GTCAGAAATGCAACAGAAATGCTACTGAATGTGACTTCAGGCCCTGCCTCC
genomic: GGCGACTTGGTTGGTTGGCCTTCTGTGACCCCAATGGTGCACTCAAGCATgtaaggcagt ... tcttcaaaagGTCAGAAATGCAACAGAAATGCTACTGAATGTGACTTCAGGCCCTGCCTCC
EST: gi|29673666|gb|CB669941.1|CB669941
EST:     GGCGACTTGGTTGGTTGGCCTTCTGTGACCCCAATGGTGCACTCAAGCA-                         -T---AAATGCAACAGAAATGCTACTGAATGTGACTTCAGGCCCTGCCTCC
genomic: GGCGACTTGGTTGGTTGGCCTTCTGTGACCCCAATGGTGCACTCAAGCATgtaaggcagt ... tcttcaaaagGTCAGAAATGCAACAGAAATGCTACTGAATGTGACTTCAGGCCCTGCCTCC
EST: gi|29636535|gb|CB641544.1|CB641544
EST:     GGCGACTTGGTTGGTTGGCCTTCTGTGACCCCAATGGTGCACTCAAGCAT                         GTCAGAAATGCAACAGAAATGCTACTGAATGTGACTTCAGGCCCTGCCTCC
genomic: GGCGACTTGGTTGGTTGGCCTTCTGTGACCCCAATGGTGCACTCAAGCATgtaaggcagt ... tcttcaaaagGTCAGAAATGCAACAGAAATGCTACTGAATGTGACTTCAGGCCCTGCCTCC
EST: gi|29636663|gb|CB641672.1|CB641672
EST:     GGCGACTTGGTTGGTTGGCCTTCTGTGACCCCAATGGTGCACTCAAGCAT                         GTCAGAAATGCAACAGAAATGCTACTGAATGTGACTTCAGGCCCTGCCTCC
genomic: GGCGACTTGGTTGGTTGGCCTTCTGTGACCCCAATGGTGCACTCAAGCATgtaaggcagt ... tcttcaaaagGTCAGAAATGCAACAGAAATGCTACTGAATGTGACTTCAGGCCCTGCCTCC
EST: gi|29670359|gb|CB666634.1|CB666634
EST:     GGCGACTTGGTTGGTTGGCCTTCTGTGACCCCAATGGTGCACTCAAGCAT                         GTCAGAAATGCAACAGAAATGCTACTGAATGTGACTTCAGGCCCTGCCTCC
genomic: GGCGACTTGGTTGGTTGGCCTTCTGTGACCCCAATGGTGCACTCAAGCATgtaaggcagt ... tcttcaaaagGTCAGAAATGCAACAGAAATGCTACTGAATGTGACTTCAGGCCCTGCCTCC
EST: gi|29668799|gb|CB665074.1|CB665074
EST:     GGCGACTTGGTTGGTTGGCCTTCTGTGACCCCAATGGTGCACTCAAGCAT                         GTCAGAAATGCAACAGAAATGCTACTGAATGTGACTTCAGGCCCTGCCTCC
genomic: GGCGACTTGGTTGGTTGGCCTTCTGTGACCCCAATGGTGCACTCAAGCATgtaaggcagt ... tcttcaaaagGTCAGAAATGCAACAGAAATGCTACTGAATGTGACTTCAGGCCCTGCCTCC
EST: gi|58595127|gb|CF993435.1|CF993435
EST:     GGCGACTTGGTTGGTTGGCCGTCTGTGACCCCAATGGTGCACTCAAGCAT                         GTCAGAAATGCAACAGAAATGCTACTGAATGTGACTTCAGGCCCTGCCTCC
genomic: GGCGACTTGGTTGGTTGGCCTTCTGTGACCCCAATGGTGCACTCAAGCATgtaaggcagt ... tcttcaaaagGTCAGAAATGCAACAGAAATGCTACTGAATGTGACTTCAGGCCCTGCCTCC

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: 60 (upstream exon), 70 (downstream exon)
Score: 10

ACCAGTAATCACCATTGGAGCACTATCAAAGAAATTCATGCTGCCAGGATGGCGACTTGGTTGGTTGGCCTTCTGTGACCCCAATGGTGCACTCAAGCATgtaaggcagt ... tcttcaaaagGTCAGAAATGCAACAGAAATGCTACTGAATGTGACTTCAGGCCCTGCCTCCATAGTTCAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcttgtttgtatgaaaaattcacatttacatattcataattctgttcttcaaaagGTCAGAAATGCAACAGAAATGCTACTGAATGTGACTTCAGGCCCTGCCTCCATAGTTCAG
                                       ttctgttcttc  CT-rich tract
             aaaaattcacatttac  TA-rich tract