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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtagtaatattatttataaaatttggaatagggatcaatcctgtttggtgcctgttcccttggatttttccctttgcagatcttgatcatgtaaaacttgttgatccttcatgttagattttattgaaggataaagatggctcgaaatatttcccatgtattacaactagtttggatttcattacagGCTGAGGCAGCTTGGCAGTTCTTGAACGTCATGAGATCCTATCTGGAGTCGCTTTGTTCTGACCTGCCATCTCATACCATCACCAATGTACAGTCAAATA

Basic information

species Oryza sativa
transcript LOC_Os03g05200.1
intron # 15
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g05200.1 (Oryza sativa), 3'ss of exon 15
lower sequence: GRMZM2G107651_T01 (Zea mays), 3'ss of exon 12
gtagtaatattatttataaaatttggaatagggatcaatcctgtttggtgcctgttcccttggatttttccctttgcagatcttgatcatgtaaaacttgttgatccttcatgttagattttattgaaggataaagatggctcgaaatatttcccatgtattacaactagtttggatttcattacagGCTGAGGCAGCTTGGCAGTTCTTGAACGTCATGAGATCCTATCTGGAGTCGCTTTGTTCTGACCTGCCATCTCATACCATCACCAATGTACAGTCAAATA
   ||| || | ||| ||  | ||   | |   |||| |    |||   |  ||| || ||   |||||   | |  |||     || ||      ||      |   |||| | |  || |||||       ||  | | |    |   |    |   ||||||     | ||||| | ||| |||||||| | ||||||| ||||||| ||  | |||||| ||||  |||| || ||||| ||||||||||  | ||||||||| || ||||||||||||||||
---gtactaatttttttaccactttatagatttatcattttactttctagtttgtaccattcattttttttttctctagaaggaaattat------ctctgcacttgatcatttaaacttctattggttatccaatttagtttttga--atgataaaacattaca-----tatggatattattgcagGCTGATGTAGCTTGGAAGTTCTTAAATATAATGAGAACCTACTTGGAATCACTTTGCTCTGACCTGCGCTTTCATACCATTACAAATGTACAGTCAAATA
















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|38477933|gb|CF962066.1|CF962066
EST:     GAATGCCCTGGGGTAAGAGACATCCAATTTACAAATGCAATGAAGTTCAG                         GCTGAGGCAGCTTGGCAGTTCTTGAACGTCATGAGATCCTATCTGGAGTCG
genomic: GAATGCCCT-GGCTAAGAGACATCCAATTTACAAATGCAATGAAGTTCAGgtagtaatat ... ttcattacagGCTGAGGCAGCTTGGCAGTTCTTGAACGTCATGAGATCCTATCTGGAGTCG
EST: gi|29614852|gb|CB619865.1|CB619865
EST:     AGAATGCCCTGGCTAAGAGACATCCAATTTACAAATGCAATGAAGTTCAG                         GCTGAGGCAGCTTGGCAGTTCTTGAACGTCATGAGATCCTATCTGGAGTCG
genomic: AGAATGCCCTGGCTAAGAGACATCCAATTTACAAATGCAATGAAGTTCAGgtagtaatat ... ttcattacagGCTGAGGCAGCTTGGCAGTTCTTGAACGTCATGAGATCCTATCTGGAGTCG
EST: gi|25807379|gb|CA763340.1|CA763340
EST:     AGAATGCCCTGGCTAAGAGACATCCAATCTACAAATGCAATGAAGTTCAG                         GCTGAGGCAGCTTGGCAGTTCTTGAACGTCATGAGATCCTATCTGGAGTCG
genomic: AGAATGCCCTGGCTAAGAGACATCCAATTTACAAATGCAATGAAGTTCAGgtagtaatat ... ttcattacagGCTGAGGCAGCTTGGCAGTTCTTGAACGTCATGAGATCCTATCTGGAGTCG

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: 57 (upstream exon), 73 (downstream exon)
Score: 19

CAAAGAACTTGTTTCTGATCTCAGTCCAATTCATGCTAGACTTTCATGTGAGAATGCCCTGGCTAAGAGACATCCAATTTACAAATGCAATGAAGTTCAGgtagtaatat ... ttcattacagGCTGAGGCAGCTTGGCAGTTCTTGAACGTCATGAGATCCTATCTGGAGTCGCTTTGTTCTGACCTGCCATCTCATACCATCACCAATGTACAGTCAAATA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaagatggctcgaaatatttcccatgtattacaactagtttggatttcattacagGCTGAGGCAGCTTGGCAGTTCTTGAACGTCATGAGATCCTATCTGGAGTCGCTTTGTTCTGACCTGCCATCTCATACCATCACCAATGTACAGTCAAATA
                                            tttcatt  CT-rich tract
            aaatattt  TA-rich tract