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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AAATGATGCTGGACTGGCGGCAGCTGAGTTGGCATTAGCAGTTGAGAAACACGTTTTGGAATCAGGATCAATTGATACTGTTGGGACAGTTGgtatgcttgatgaaattgattttattttctgttgaatatatcattctttcatgactgtgatgttttaatactccatagtaaattaggacatacatgtgcc...

Basic information

species Oryza sativa
transcript LOC_Os12g40550.1
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os12g40550.1 (Oryza sativa), 5'ss of exon 8
lower sequence: GRMZM2G130034_T01 (Zea mays), 5'ss of exon 8
AAATGATGCTGGACTGGCGGCAGCTGAGTTGGCATTAGCAGTTGAGAAACACGTTTTGGAATCAGGATCAATTGATACTGTTGGGACAGTTGgtatgcttgatgaaattgattttattttctg--ttgaatatatcattctttcatgactgtgatgttttaatactccatagtaaattaggacatacatgtgcc
|||||||||||||||||| |||||||| || ||||||||||| |||||||| ||  |||||||||||||||||||||| ||||| || ||||||||| || || ||    ||||   ||| |   |  ||| ||||||||  || ||  |||||  |  |||||     || || ||| |||| || || ||  
AAATGATGCTGGACTGGCAGCAGCTGAATTAGCATTAGCAGTCGAGAAACATGTCCTGGAATCAGGATCAATTGATACGGTTGGCACCGTTGgtatgttttataaaccatatttagctttttacataaaatctatcattccatcctgtttgtgacatcataatatcatgtaatacatttggac-taaatatgt-

upper sequence: LOC_Os12g40550.1 (Oryza sativa), 5'ss of exon 8
lower sequence: Vv05s0020g04900.t01 (Vitis vinifera), 5'ss of exon 8
AAATGATGCTGGACTGGCGGCAGCTGAGTTGGCATTAGCAGTTGAGAAACACGTTTTGGAATCAGGATCAATTGATACTGTTGGGACAGTTGgtatgcttgatgaaattgatttt--attttctgttgaatatatcattctttcatgactgtgatgttttaatactccatagtaaattaggacatacatgtgcc-
||||||||| ||| |||| || || ||||| ||| |||| ||||||||||| || || ||||| ||||| |||||||||||||| || || |||  |     |    || |||    || | |   || |   || ||  |||  | | |   ||  |  | |     ||| || |||   |  || ||||  | 
AAATGATGCAGGATTGGCAGCTGCAGAGTTAGCACTAGCTGTTGAGAAACATGTGTTAGAATCTGGATCTATTGATACTGTTGGTACTGTGGgtgagtcatgttttcttcattcctgatgtccaagtgcaggaat-atagtttggttattac-atactgaattttattata-tatattgatatttatatgtatct
















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|29639192|gb|CB644201.1|CB644201
EST:     TGAGAAACACGTTTTGGAATCAGGATCAATTGATACTGTTGGGACAGTTG                         GTATTCTGCAGCTACATCCAGGAGCAATCAATAGCATCCCAAGTAAATCGC
genomic: TGAGAAACACGTTTTGGAATCAGGATCAATTGATACTGTTGGGACAGTTGgtatgcttga ... tcttcttcagGTATTCTGCAGCTACATCCAGGAGCAATCAATAGCATCCCAAGTAAATCGC
EST: gi|29676280|gb|CB672555.1|CB672555
EST:     GAATCAGGATCAATTGATACTGTTGGGACAGTTG                         GTATTTTGCAGCTACATCCAGGAGCAATCAATAGCATCCCAAGTAAATCGC
genomic: GAATCAGGATCAATTGATACTGTTGGGACAGTTGgtatgcttga ... tcttcttcagGTATTCTGCAGCTACATCCAGGAGCAATCAATAGCATCCCAAGTAAATCGC
EST: gi|2311967|gb|C28122.1|C28122
EST:     GAGAAACACGTTTTGGAATCAGGATCAATTGATACTGTTGGGACAGTTG                         GTATTCTGCAGCTACATCCAGGAGCAATCAATAGCATCCCAAGTAAATCGC
genomic: GAGAAACACGTTTTGGAATCAGGATCAATTGATACTGTTGGGACAGTTGgtatgcttga ... tcttcttcagGTATTCTGCAGCTACATCCAGGAGCAATCAATAGCATCCCAAGTAAATCGC
EST: gi|29665068|gb|CB661343.1|CB661343
EST:     TGAGAAACACGTTTTGGAATCAGGATCAATTGATACTGTTGGGACAGTTG                         GTATTCTGCAGCTACATCCAGGAGCAATCAATAGCATCCCAAGTAAATCGC
genomic: TGAGAAACACGTTTTGGAATCAGGATCAATTGATACTGTTGGGACAGTTGgtatgcttga ... tcttcttcagGTATTCTGCAGCTACATCCAGGAGCAATCAATAGCATCCCAAGTAAATCGC
EST: gi|38471018|gb|CF955149.1|CF955149
EST:     TGAGAAACACGTTTTGGAATCAGGATCAATTGATACTGTTGGGACAGTTG                         GTATATCTGCAGCTACATCCAGGAGCAATCAATAGCATCCCAAGTAAATCG
genomic: TGAGAAACACGTTTTGGAATCAGGATCAATTGATACTGTTGGGACAGTTGgtatgcttga ... tcttcttcagGTAT-TCTGCAGCTACATCCAGGAGCAATCAATAGCATCCCAAGTAAATCG
EST: gi|29625973|gb|CB630984.1|CB630984
EST:     TGAGAAACACGTTTTGGAATCAGGATCAATTGATACTGTTGGGACAGTTG                         GTATTCTGCAGCTACATCCAGGAGCAATCAATAGCATCCCAAGTAAATCGC
genomic: TGAGAAACACGTTTTGGAATCAGGATCAATTGATACTGTTGGGACAGTTGgtatgcttga ... tcttcttcagGTATTCTGCAGCTACATCCAGGAGCAATCAATAGCATCCCAAGTAAATCGC
EST: gi|27578088|gb|CB000783.1|CB000783
EST:     TGAGAAACACGTTTTGGAATCAGGATCAATTGATACTGTTGGGACAGTTG                         GTATTCTGCAGCTACATCCAGGAGCAATCAATAGCATCCCAAGTAAATCGC
genomic: TGAGAAACACGTTTTGGAATCAGGATCAATTGATACTGTTGGGACAGTTGgtatgcttga ... tcttcttcagGTATTCTGCAGCTACATCCAGGAGCAATCAATAGCATCCCAAGTAAATCGC
EST: gi|58682834|gb|CK071521.1|CK071521
EST:     TGAGAAACACGTTTTGGAATCAGGATCAATTGATACTGTTGGGACAGTTG                         GTATTCTGCAGCTACATCCAGGAGCAATCAATAGCATCCCAAGTAAATCGC
genomic: TGAGAAACACGTTTTGGAATCAGGATCAATTGATACTGTTGGGACAGTTGgtatgcttga ... tcttcttcagGTATTCTGCAGCTACATCCAGGAGCAATCAATAGCATCCCAAGTAAATCGC

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), 48 (downstream exon)
Score: 17

AAATGATGCTGGACTGGCGGCAGCTGAGTTGGCATTAGCAGTTGAGAAACACGTTTTGGAATCAGGATCAATTGATACTGTTGGGACAGTTGgtatgcttga ... tcttcttcagGTATTCTGCAGCTACATCCAGGAGCAATCAATAGCATCCCAAGTAAATCGCATGTGGAAATTG




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