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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgaatgccatttctctatcagattgttttaaccttgtagccaatacctcgtcttgcttaagaattgaaccatttggcgcttgtcgctgaatattgcacttcttttcaaccacaattttattatcagtatatgcttagggagaaaaaaaaattcacctttatgtcacagcttacttctgtccaatcattttttgcagGGTTTGACCGGGCTCCTGCAGTCACCAATCAAGGGTGCCGAGAAACATGGTCTTCCTGGAGTTATCTCAG

Basic information

species Oryza sativa
transcript LOC_Os08g02350.1
intron # 30
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os08g02350.1 (Oryza sativa), 3'ss of exon 30
lower sequence: Vv15s0024g00240.t01 (Vitis vinifera), 3'ss of exon 28
gtgaatgccatttctctatcagattgttttaaccttgtagccaatacctcgtcttgcttaagaattgaaccatttggcgcttgtcgctgaatattgcacttcttttcaaccacaattttattatcagtatatgcttagggagaaaaaaaaattcacctttatgtcacagcttacttctgtccaatcattttttgcagGGTTTGACCGGGCTCCTGCAGTCACCAATCAAGGGTGCCGAGAAACATGGTCTTCCTGGAGTTATCTCAG
                                                                                           |  ||| |  | ||   |   || |  ||  || | ||  ||| | |       |   ||||        | |||      ||||   |||   ||||| || |||||  | || || ||||| || || ||||| || ||||| |||||||||||||||||||| ||| ||||||
------------------------------------------------------------------------------------------gtgatgccccaccttctcaaggca-tgatagaataactagctgcattgtattgttatgcaatttggtggcttttca------actttgttccttccatttattccagGGACTCACTGGTCTCCTCCAATCGCCAATTAAAGGTGCTGAGAAACATGGTCTTCCTGGTGTTCTCTCAG
















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|58691014|gb|CK079701.1|CK079701
EST:     AGTGCTAAACGGATTTTTAGAG                         GGTTTGACCGGGCTCCTGCAGTCACCAATCAAGGGTGCCGAGAAACATGGT
genomic: AGTGCTAAACGGATTTTTAGAGgtgaatgcca ... ttttttgcagGGTTTGACCGGGCTCCTGCAGTCACCAATCAAGGGTGCCGAGAAACATGGT
EST: gi|58692108|gb|CK080795.1|CK080795
EST:     AGAGGCAGCTAAGTTTGCATGGGGAAGGAGTGCTAAACGGATTTTTAGAG                         GGTTTGACCGGGCTCCTGCAGTCACCAATCAAGGGTGCCGAGAAACATGGT
genomic: AGAGGCAGCTAAGTTTGCATGGGGAAGGAGTGCTAAACGGATTTTTAGAGgtgaatgcca ... ttttttgcagGGTTTGACCGGGCTCCTGCAGTCACCAATCAAGGGTGCCGAGAAACATGGT
EST: gi|58666488|gb|CK055174.1|CK055174
EST:     GTTTGCATGGGGAAGGAGTGCTAAACGGATTTTTAGAG                         GGTTTGACCGGGCTCCTGCAGTCACCAATCAAGGGTGCCGAGAAACATGGT
genomic: GTTTGCATGGGGAAGGAGTGCTAAACGGATTTTTAGAGgtgaatgcca ... ttttttgcagGGTTTGACCGGGCTCCTGCAGTCACCAATCAAGGGTGCCGAGAAACATGGT
EST: gi|58605498|gb|CK033531.1|CK033531
EST:     AGAGGCAGCTAAGTTTGCATGGGGAAGGAGTGCTAAACGGATTTTTAGAG                         GGTTTGACCGGGCTCCTGCAGTCACCAATCAAGGGTGCCGAGAAACATGGT
genomic: AGAGGCAGCTAAGTTTGCATGGGGAAGGAGTGCTAAACGGATTTTTAGAGgtgaatgcca ... ttttttgcagGGTTTGACCGGGCTCCTGCAGTCACCAATCAAGGGTGCCGAGAAACATGGT

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: 48 (upstream exon), 62 (downstream exon)
Score: 5

TGTTGCTTTTACATATGATGAGCAAGCTGCTTCTAAAATGGATGAACGGGAGAGGCAGCTAAGTTTGCATGGGGAAGGAGTGCTAAACGGATTTTTAGAGgtgaatgcca ... ttttttgcagGGTTTGACCGGGCTCCTGCAGTCACCAATCAAGGGTGCCGAGAAACATGGTCTTCCTGGAGTTATCTCAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaaaaaaaattcacctttatgtcacagcttacttctgtccaatcattttttgcagGGTTTGACCGGGCTCCTGCAGTCACCAATCAAGGGTGCCGAGAAACATGGTCTTCCTGGAGTTATCTCAG
                         agcttac  putative branch site (score: 5)
                                          tcatttttt  putative PPT
                                        aatcatttttt  TA-rich tract