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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtataggccgaatatatatttgattcgatagtatttttcctttgacaatttggatgcaatgtcttgcagGGTGGCACTTTCACTGTGTCAAACTTGGGAGGCCCTTTTGGAATTAAGCAATTCTGTGCCATCGTAAATCCTCCACAATCAGCAATTTTGGCTATTGGCT

Basic information

species Oryza sativa
transcript LOC_Os06g01630.5
intron # 17
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g01630.5 (Oryza sativa), 3'ss of exon 17
lower sequence: AT1G54220.2 (Arabidopsis thaliana), 3'ss of exon 16
gtataggccgaatatatatttgattcgatagtatttttcctttgacaatttggatgcaatgtc----ttgcagGGTGGCACTTTCACTGTGTCAAACTTGGGAGGCCCTTTTGGAATTAAGCAATTCTGTGCCATCGTAAATCCTCCACAATCAGCAATTTTGGCTATTGGCT
   |  |   | |   ||| | | ||  || |  | |   |  |  ||  ||     ||| ||    |  ||||| || || || ||||| || ||||||||||| |||||||| || ||||||||||||||  |||| ||||| || ||| | || ||| | ||  |||| |
--gtgagagaattcattatcttactcactaatcatatctttcagtaaacatgctaataatctcgttttctcagGGAGGAACATTTACTGTCTCTAACTTGGGAGGACCTTTTGGCATCAAGCAATTCTGTGCAGTCGTTAATCCACCTCAAGCCGCCATTCTAGCAGTTGGAT

upper sequence: LOC_Os06g01630.5 (Oryza sativa), 3'ss of exon 17
lower sequence: Vv09s0002g01800.t01 (Vitis vinifera), 3'ss of exon 17
-----------gtataggccgaatatatatttgat------tcgatagtatttttcctttgacaatttggatgcaatgtcttgcagGGTGGCACTTTCACTGTGTCAAACTTGGGAGGCCCTTTTGGAATTAAGCAATTCTGTGCCATCGTAAATCCTCCACAATCAGCAATTTTGGCTATTGGCT
           || |       ||   |  |||        ||| |||  |||  | | ||| || | |  |       ||||||||| || || || |||||||| ||  ||||||| || ||||| || |||||||||||||||||| | |||||||| || ||||  ||| | || ||||| |
gtaaaaattatgtttcaatgttattagttgttggcaagtgatcgctagggtttaacatatgaaaactggcttcgtcctccttgcagGGAGGGACATTTACTGTGTCTAATCTGGGAGGACCCTTTGGTATCAAGCAATTCTGTGCCATCATCAATCCTCCTCAGTCAGGCATTCTAGCCATTGGGT

upper sequence: LOC_Os06g01630.5 (Oryza sativa), 3'ss of exon 17
lower sequence: Vv11s0016g01870.t01 (Vitis vinifera), 3'ss of exon 16
-----------------gtataggccg--aatatatatttgattcgatagtatttttcctttgacaatttggatgcaatgtct-tgcagGGTGGCACTTTCACTGTGTCAAACTTGGGAGGCCCTTTTGGAATTAAGCAATTCTGTGCCATCGTAAATCCTCCACAATCAGCAATTTTGGCTATTGGCT
                   || ||||   |||  ||  ||||||  ||  |  | ||        | ||      ||   | | ||||||| ||||| || ||||| || ||||||||||| || |||||| | || ||||| ||||||||  | |||||||| ||||| |  ||  | ||  |||| |
gtaactgcattaccttctaattggccatcaatggatggttgattgtatcatggtcttttaaatgaacttcatgatcatcatatatgcagGGAGGCACCTTTACTGTTTCGAACTTGGGAGGACCATTTGGAGTCAAACAATTTTGTGCCATAATCAATCCTCCCCAATCCGGCATCCTCGCAGTTGGGT

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|25803971|gb|CA759932.1|CA759932
EST:     AACTGGCTTAGAGAGCAAGGGACACCAGCCTTAAGCCAGAGGATTATGTG                         GGTGGCACTTTCCCTGTGTCAAACTTGGGAGGCCCTTTTGGAATTAAGCAA
genomic: AACTGGCTCAGAGAGCAAGGGACAACAGCCTTAAGCCAGAGGATTATGAGgtataggccg ... tgtcttgcagGGTGGCACTTTCACTGTGTCAAACTTGGGAGGCCCTTTTGGAATTAAGCAA
EST: gi|38477221|gb|CF961354.1|CF961354
EST:     AACTGGCTCAGAGAGCAAGGGACAACAGCCTTAAGCCAGAGGATTATGAG                         GGTGGCACTTTCACTGTGTCAAACTTGGGAGGCCCTTTTGGAATTAAGCAA
genomic: AACTGGCTCAGAGAGCAAGGGACAACAGCCTTAAGCCAGAGGATTATGAGgtataggccg ... tgtcttgcagGGTGGCACTTTCACTGTGTCAAACTTGGGAGGCCCTTTTGGAATTAAGCAA
EST: gi|58585940|gb|CF984248.1|CF984248
EST:     AACTGGCTCAGAGAGCAAGGGACAACAGACTTAAGCCAGAGGATTATGAG                         GGTGGCACTTTCACTGTGTCAAACTTGGGAGGCCCTTTTGGAATTAAGCAA
genomic: AACTGGCTCAGAGAGCAAGGGACAACAGCCTTAAGCCAGAGGATTATGAGgtataggccg ... tgtcttgcagGGTGGCACTTTCACTGTGTCAAACTTGGGAGGCCCTTTTGGAATTAAGCAA
EST: gi|24468761|gb|CA305710.1|CA305710
EST:     ACTTGGCTCAGAGAGCAAGGGACAACAGACTTAAGCCAGAGGATTATGAG                         GGTGGCACTTTCACTGTGTCAAACTTGGGAGGCCCTTTTGGAATTAAGCAA
genomic: AC-TGGCTCAGAGAGCAAGGGACAACAGCCTTAAGCCAGAGGATTATGAGgtataggccg ... tgtcttgcagGGTGGCACTTTCACTGTGTCAAACTTGGGAGGCCCTTTTGGAATTAAGCAA
EST: gi|86871900|gb|CI332072.1|CI332072
EST:     AGCCTTAAGCCAGAGGATTATGAG                         GGTGGCACTTTCACTGTGTCAAACTTGGGAGGCCCTTTTGGAATTAAGCAA
genomic: AGCCTTAAGCCAGAGGATTATGAGgtataggccg ... tgtcttgcagGGTGGCACTTTCACTGTGTCAAACTTGGGAGGCCCTTTTGGAATTAAGCAA
EST: gi|89198662|gb|CI016747.1|CI016747
EST:     AACTGGCTCAGAGAGCAAGGGACNACAGCCTTAAGCCAGAGGATTATGAG                         GGTGGCACTTTCACTGTGTCAAACTTGGGAGGCCCTTTTGGAATTAAGCAA
genomic: AACTGGCTCAGAGAGCAAGGGACAACAGCCTTAAGCCAGAGGATTATGAGgtataggccg ... tgtcttgcagGGTGGCACTTTCACTGTGTCAAACTTGGGAGGCCCTTTTGGAATTAAGCAA

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: 36 (upstream exon), 73 (downstream exon)
Score: 9

GATGCTGACAAGAAGGGCCTAGCCACTATCGCTGATGAGGTGAAGCAACTGGCTCAGAGAGCAAGGGACAACAGCCTTAAGCCAGAGGATTATGAGgtataggccg ... tgtcttgcagGGTGGCACTTTCACTGTGTCAAACTTGGGAGGCCCTTTTGGAATTAAGCAATTCTGTGCCATCGTAAATCCTCCACAATCAGCAATTTTGGCTATTGGCT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatatttgattcgatagtatttttcctttgacaatttggatgcaatgtcttgcagGGTGGCACTTTCACTGTGTCAAACTTGGGAGGCCCTTTTGGAATTAAGCAATTCTGTGCCATCGTAAATCCTCCACAATCAGCAATTTTGGCTATTGGCT
                         ctttgac  putative branch site (score: 9)
             atagtattttt  TA-rich tract