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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cttcaacagatgatactttgttgttgcagtttgctcctctgtatcagcttagagacatgatttgcatgccatggactgatgacggtttcgaaatttgcagGAAACAATGAATGGGGCCGTATGACATTGAACCAAACATTTACTATAG

Basic information

species Oryza sativa
transcript LOC_Os02g52420.1
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g52420.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM2G101438_T02 (Zea mays), 3'ss of exon 8
-----------------------------cttcaacagatgatactttgttgttgcagtttgctc----ctctgtatcagcttagagacatgatttgcatgccatggac-tgatgacggtttcgaaatttgcagGAAACAATGAATGGGGCCGTATGACATTGAACCAAACATTTACTATAG
                              || |  |  || |   |||   |  | | |  |||     ||||  |   ||  |   ||| ||| | |||  ||     ||   | |  |||||||||||||||||||||||||||||| |||||||  ||||| ||||||||||||||||
gtgagttccccactttaacgaaaacatctttttattaattgctgtcttgcc-tcccggctatctcaaggttctggttgcactctgcaccat-attaggatgtgatatctgtgccaatgacttcgaaatttgcagGAAACAATGAATGGGGACGTATGATGTTGAATCAAACATTTACTATAG
















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|88663432|gb|CI482070.1|CI482070
EST:     TCATGGGGTTGGACAAGTGTTTCATGCTGAACCTGTGGTGCTTCATTTCC                         GAAACAATGAATGGGGCCGTATGACATTGAACCAAACATTTACTATAG
genomic: TCATGGGGTTGGACAAGTGTTTCATGCTGAACCTGTGGTGCTTCATTTCCgtgagtcctt ... aaatttgcagGAAACAATGAATGGGGCCGTATGACATTGAACCAAACATTTACTATAG
EST: gi|88662360|gb|CI467473.1|CI467473
EST:     TCATGGGGTTGGACAAGTGTTTCATGCTGAACCTGTGGTGCTTCATTTCC                         GAAACAATGAATGGGGCCGTATGACATTGAACCAAACATTTACTATAG
genomic: TCATGGGGTTGGACAAGTGTTTCATGCTGAACCTGTGGTGCTTCATTTCCgtgagtcctt ... aaatttgcagGAAACAATGAATGGGGCCGTATGACATTGAACCAAACATTTACTATAG
EST: gi|88662872|gb|CI474688.1|CI474688
EST:     TCATGGGGTTGGACAAGTGTTTCATGCTGAACCTGTGGTGCTTCATTTCC                         GAAACAATGAATGGGGCCGTATGACATTGAACCAAACATTTACTATAG
genomic: TCATGGGGTTGGACAAGTGTTTCATGCTGAACCTGTGGTGCTTCATTTCCgtgagtcctt ... aaatttgcagGAAACAATGAATGGGGCCGTATGACATTGAACCAAACATTTACTATAG
EST: gi|313084050|gb|HO213833.1|HO213833
EST:     TCATGGGGTTGGACAAGTGTTTCATGCTGAACCTGTGGTGCTTCATTTCC                         GAAACAATGAATGGGGCCGTATGACATTGAACCAAACATTTACTATAG
genomic: TCATGGGGTTGGACAAGTGTTTCATGCTGAACCTGTGGTGCTTCATTTCCgtgagtcctt ... aaatttgcagGAAACAATGAATGGGGCCGTATGACATTGAACCAAACATTTACTATAG
EST: gi|88661931|gb|CI462321.1|CI462321
EST:     GGGGTTGGACAAGTGTTTCATGCTGAACCTGTGGTGCTTCATTTCC                         GAAACAATGAATGGGGCCGTATGACATTGAACCAAACATTTACTATAG
genomic: GGGGTTGGACAAGTGTTTCATGCTGAACCTGTGGTGCTTCATTTCCgtgagtcctt ... aaatttgcagGAAACAATGAATGGGGCCGTATGACATTGAACCAAACATTTACTATAG
EST: gi|86841002|gb|CI335146.1|CI335146
EST:     TCATGGGGTTGGACAAGTGTTTCATGCTGAACCTGTGGTGCTTCATTTCC                         GAAACAATGAATGGGGCCGTATGACATTGAACCAAACATTTACTATAG
genomic: TCATGGGGTTGGACAAGTGTTTCATGCTGAACCTGTGGTGCTTCATTTCCgtgagtcctt ... aaatttgcagGAAACAATGAATGGGGCCGTATGACATTGAACCAAACATTTACTATAG
EST: gi|86492814|gb|CI135447.1|CI135447
EST:     TCATGGGGTTGGACAAGTGTTTCATGCTGAACCTGTGGTGCTTCATTTCC                         GAAACAATGAATGGGGCCGTATGACATTGAACCCAACATTTACTATAG
genomic: TCATGGGGTTGGACAAGTGTTTCATGCTGAACCTGTGGTGCTTCATTTCCgtgagtcctt ... aaatttgcagGAAACAATGAATGGGGCCGTATGACATTGAACCAAACATTTACTATAG
EST: gi|88662988|gb|CI476281.1|CI476281
EST:     TCATGGGGTTGGACAAGTGTTTCATGCTGAACCTGTGGTGCTTCATTTCC                         GAAACAATGAATGGGGCCGTATGACATTGAACCANACATTTACTATAG
genomic: TCATGGGGTTGGACAAGTGTTTCATGCTGAACCTGTGGTGCTTCATTTCCgtgagtcctt ... aaatttgcagGAAACAATGAATGGGGCCGTATGACATTGAACCAAACATTTACTATAG

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: 58 (upstream exon), 67 (downstream exon)
Score: 11

GGACCATGCAGATAAATTCAAGTTTGGTGTAGTTCGACAGTTCGTCGGTCATGGGGTTGGACAAGTGTTTCATGCTGAACCTGTGGTGCTTCATTTCCgtgagtcctt ... aaatttgcagGAAACAATGAATGGGGCCGTATGACATTGAACCAAACATTTACTATAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agcttagagacatgatttgcatgccatggactgatgacggtttcgaaatttgcagGAAACAATGAATGGGGCCGTATGACATTGAACCAAACATTTACTATAG
                            gactgat  putative branch site (score: 11)
                                             aaattt  TA-rich tract