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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtgcctaacactaccaataaatatggtattcttaatataaagaatgtagaagggaaaagtcgaataattgttttatatggtgcagACGAATCGGTGATATTGAAAACGGAAGCTCTTCTTCACTGGCATTCATCGGTAACATGACATCGTTGAGCATCCT

Basic information

species Oryza sativa
transcript LOC_Os04g52600.1
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g52600.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM2G155837_T02 (Zea mays), 3'ss of exon 9
gtaagtgcctaacactaccaataaatatggtattcttaatataaagaatgtagaagggaaaagtcgaataattgttttatatggtgcagACGAATCGGTGATATTGAAAACGGAAGCTCTTCTTCACTGGCATTCATCGGTAACATGACATCGTTGAGCATCCT----------------------------
||||||       |  |  | ||| |||  |  |||   | ||| |  |       ||||  ||  | ||  | |||  | |||||||||||||| ||||| |||| ||| |||||   ||||||| ||  ||||||| ||||||||||||| |||| ||   |                            
gtaagtaatggctagaataactaagtattattctctagttgtaatgt-tactttctggaagtgtgaagtacctatttc-tgtggtgcagACGAATAGGTGACATTGTAAATGGAAG---TTCTTCAATGATATTCATCAGTAACATGACATCTTTGAACACATTGTATGGATAACTTTGTCATCAATCAATG
















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|88574965|gb|CI666734.1|CI666734
EST:     CAAGGTCCAATTCCTTCTGCTCTTTCTAATCTTGTCCAACTATCAAGCTT                         ACGAATCGGCGATATTGAAAACGGAAGCTCTTCTTCACTGGCATTCATCGG
genomic: CAAGGTCCAATTCCTTCTGCTCTTTCTAATCTTGTCCAACTATCAAGCTTgtaagtgcct ... tatggtgcagACGAATCGGTGATATTGAAAACGGAAGCTCTTCTTCACTGGCATTCATCGG
EST: gi|88302417|gb|CI668263.1|CI668263
EST:     CAAGGTCCAATTCCTTCTGCTCTTTCTAATCTTGTCCAACTATCAAGCTT                         ACGAATCGGTGATATTGAAAACGGAAGCTCTTCTTCACTGGCATTCATCGG
genomic: CAAGGTCCAATTCCTTCTGCTCTTTCTAATCTTGTCCAACTATCAAGCTTgtaagtgcct ... tatggtgcagACGAATCGGTGATATTGAAAACGGAAGCTCTTCTTCACTGGCATTCATCGG
EST: gi|88570904|gb|CI662277.1|CI662277
EST:     CAAGGTCCAATTCCTTCTGCTCTTTCTAATCTTGTCCAACTATCAAGCTT                         ACGAATCGGTGATATTGAAAACGGAAGCTCTTCTTCACTGGCATTCATCGG
genomic: CAAGGTCCAATTCCTTCTGCTCTTTCTAATCTTGTCCAACTATCAAGCTTgtaagtgcct ... tatggtgcagACGAATCGGTGATATTGAAAACGGAAGCTCTTCTTCACTGGCATTCATCGG

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: 55 (upstream exon), 45 (downstream exon)
Score: 10

GCGGTTTCAAGGCAATTCTTTTCAAGGTCCAATTCCTTCTGCTCTTTCTAATCTTGTCCAACTATCAAGCTTgtaagtgcct ... tatggtgcagACGAATCGGTGATATTGAAAACGGAAGCTCTTCTTCACTGGCATTCATCGGTAACATGACATCGTTGAGCATCCT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttaatataaagaatgtagaagggaaaagtcgaataattgttttatatggtgcagACGAATCGGTGATATTGAAAACGGAAGCTCTTCTTCACTGGCATTCATCGGTAACATGACATCGTTGAGCATCCT
 tcttaat  putative branch site (score: 10)
                                aataattgttttatat  TA-rich tract