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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCGCTTTCCTCCTATACAGTCGAAAGAACTGCCGTATTTGGAGTGTACAGTATCTATACTGACCGAATATGAAACTGCACTTAACCACCTTGACTGGGAGgtatgcaactacacattggttttagtcgttctttcactctcttctaataatcttgtggtactgcag

Basic information

species Oryza sativa
transcript LOC_Os10g42250.2
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os10g42250.2 (Oryza sativa), 5'ss of exon 3
lower sequence: Vv13s0101g00100.t01 (Vitis vinifera), 5'ss of exon 3
CCGCTTTCCTCCTATACAGTCGAAAGAACTGCCGTATTTGGAGTGTACAGTATCTATACTGACCGAATATGAAACTGCACTTAACCACCTTGACTGGGAGgtatgcaactacacattggttttagtcgttctttcactctcttctaataatcttgtggtactgcag-----------------------------------
 || || |||||||||||| | |||||| |||| ||  |||| |||||||| || || ||||| || ||||||||||  || ||| ||||||| |||||||||||    |   | ||| ||||| |  ||    | | |  | |   ||   |     || |  |                                    
TCGATTCCCTCCTATACAGGCTAAAGAATTGCCTTACCTGGAATGTACAGTTTCCATTCTGACTGATTATGAAACTGGGCTCAACTACCTTGATTGGGAGgtatgggtttgttccttg-ttttaatatttggaactcgcaatgcatgtaggttccatctattatactgtgttgatcagctgcctgatgaattatctcagcc
















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|2428016|gb|C72479.1|C72479
EST:     TATCTATACTGACCGAATATGAAACTGCACTTAACCANCTTGACTGGGAG                         GTGGGTAAGCATGGGTTAATTATTGAATTCA
genomic: TATCTATACTGACCGAATATGAAACTGCACTTAACCACCTTGACTGGGAGgtatgcaact ... ggtactgcagGTGGGTAAGCATGGGTTAATTATTGAATTCA
EST: gi|33680238|gb|CF308477.1|CF308477
EST:     TATCTATACTGACCGAATATGAAACTGCACTTAACCACCTTGACTGGGAG                         GTGGGTAAGCATGGGTTAATTATTGAATTCACTGATCCAGACTATAACATG
genomic: TATCTATACTGACCGAATATGAAACTGCACTTAACCACCTTGACTGGGAGgtatgcaact ... ggtactgcagGTGGGTAAGCATGGGTTAATTATTGAATTCACTGATCCAGACTATAACATG
EST: gi|44668540|gb|CR281974.1|CR281974
EST:     TATCTATACTGACCGAATATGAAACTGCACTTAACCACCTTGACTGGGAG                         GTGGGTAAGCATGGGTTAATTATTGAATTCACTGATCCAGACTATAACATG
genomic: TATCTATACTGACCGAATATGAAACTGCACTTAACCACCTTGACTGGGAGgtatgcaact ... ggtactgcagGTGGGTAAGCATGGGTTAATTATTGAATTCACTGATCCAGACTATAACATG
EST: gi|33814577|gb|CF333153.1|CF333153
EST:     TATCTATACTGACCGAATATGAAACTGCACTTAACCACCTTGACTGGGAG                         GTGGGTAAGCATGGGTTAATTATTGAATTCACTGATCCAGACTATAACATG
genomic: TATCTATACTGACCGAATATGAAACTGCACTTAACCACCTTGACTGGGAGgtatgcaact ... ggtactgcagGTGGGTAAGCATGGGTTAATTATTGAATTCACTGATCCAGACTATAACATG
EST: gi|55435942|gb|CV731108.1|CV731108
EST:     TATCTATACTGACCGAATATGAAACTGCACTTAACCACCTTGACTGGGAG                         GTGGGTAAGCATGGGTTAATTATTGAATTCACTGATCCAGACTATAAC
genomic: TATCTATACTGACCGAATATGAAACTGCACTTAACCACCTTGACTGGGAGgtatgcaact ... ggtactgcagGTGGGTAAGCATGGGTTAATTATTGAATTCACTGATCCAGACTATAAC
EST: gi|66931214|gb|CX118062.1|CX118062
EST:     TATCTATACTGACCGAATATGAAACTGCACTTAACCACCTTGACTGGGAG                         GTGGGTAAGCATGGGTTAATTATTGAATTCACTGATCCAGACTATAACATG
genomic: TATCTATACTGACCGAATATGAAACTGCACTTAACCACCTTGACTGGGAGgtatgcaact ... ggtactgcagGTGGGTAAGCATGGGTTAATTATTGAATTCACTGATCCAGACTATAACATG
EST: gi|58602145|gb|CK012673.1|CK012673
EST:     TATCTATACTGACCGAATATGAAACTGCACTTAACCACCTTGACTGGGAG                         GTGGGTAAGCATGGGTTAATTATTGAATTCACTGATCCAGACTATAACATG
genomic: TATCTATACTGACCGAATATGAAACTGCACTTAACCACCTTGACTGGGAGgtatgcaact ... ggtactgcagGTGGGTAAGCATGGGTTAATTATTGAATTCACTGATCCAGACTATAACATG
EST: gi|55415462|gb|CV727838.1|CV727838
EST:     TATCTATACTGACCGAATATGAAACTGCACTTAACCACCTTGACTGGGAG                         GTGGGTAAGCATGGGTTAATTATTGAATTCACTGATCCAGACTATAACATG
genomic: TATCTATACTGACCGAATATGAAACTGCACTTAACCACCTTGACTGGGAGgtatgcaact ... ggtactgcagGTGGGTAAGCATGGGTTAATTATTGAATTCACTGATCCAGACTATAACATG
EST: gi|218485154|gb|FG948395.1|FG948395
EST:     TATCTATACTGACCGAATATGAAACTGCACTTAACCACCTTGACTGGGAG                         GTGGGTAAGCATGGGTTAATTATTGAATTCACTGATCCAGACTATAACATG
genomic: TATCTATACTGACCGAATATGAAACTGCACTTAACCACCTTGACTGGGAGgtatgcaact ... ggtactgcagGTGGGTAAGCATGGGTTAATTATTGAATTCACTGATCCAGACTATAACATG
EST: gi|33812402|gb|CF332089.1|CF332089
EST:     TATCTATACTGACCGAATATGAAACTGCACTTAACCACCTTGACTGGGAG                         GTGGGTAAGCATGGGTTAATTATTGAATTCACTGATCCAGACTATAACATG
genomic: TATCTATACTGACCGAATATGAAACTGCACTTAACCACCTTGACTGGGAGgtatgcaact ... ggtactgcagGTGGGTAAGCATGGGTTAATTATTGAATTCACTGATCCAGACTATAACATG
EST: gi|58657144|gb|CK045824.1|CK045824
EST:     TATCTATACTGACCGAATATGAAACTGCACTTAACCACCTTGACTGGGAG                         GTGGGTAAGCATGGGTTAATTATTGAATTCACTGATCCAGACTATAACATG
genomic: TATCTATACTGACCGAATATGAAACTGCACTTAACCACCTTGACTGGGAGgtatgcaact ... ggtactgcagGTGGGTAAGCATGGGTTAATTATTGAATTCACTGATCCAGACTATAACATG

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: 65 (upstream exon), 56 (downstream exon)
Score: 48

CCGCTTTCCTCCTATACAGTCGAAAGAACTGCCGTATTTGGAGTGTACAGTATCTATACTGACCGAATATGAAACTGCACTTAACCACCTTGACTGGGAGgtatgcaact ... ggtactgcagGTGGGTAAGCATGGGTTAATTATTGAATTCACTGATCCAGACTATAACATGAGGCGCAGTGCAACTTATTTACCTGAGGTTGCTGCCCATGAAG




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