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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttcagtagcttacatttcaattttcttccatcttagctaccatggctctgtttactaaacatgttgcttcaatatttttcagACACTTACATTTGCATGGGTGAACTTCTTCTTTTCGGGTTTTGTTGCAG

Basic information

species Oryza sativa
transcript LOC_Os09g32220.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os09g32220.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G014313_T02 (Zea mays), 3'ss of exon 3
--------------------gttcagtagct-tacatttcaattttcttccatcttagctaccatggctctgtttactaaacatgttgcttcaatatttttcagACACTTACATTTGCATGGGTGAACTTCTTCTTTTCGGGTTTTGTTGCAG
                     || | | |   | || |  | ||  ||       | ||   |     | ||||   | |||||  |   |     |||| ||||||||||||||||||||||||||||| |||||||| ||||| |||||||
gttctgtgttccgtacactgatttacttgtggtgcactatagttggctaatcgtgtggcattctaccgtatgttatattaacatcataacttgtgtttttgcagACACTTACATTTGCATGGGTGAACTTTTTCTTTTCAGGTTTCGTTGCAG

upper sequence: LOC_Os09g32220.1 (Oryza sativa), 3'ss of exon 3
lower sequence: AT4G12590.1 (Arabidopsis thaliana), 3'ss of exon 3
gttcagtagcttacatttcaattttcttccatcttagctaccatggctctgtttactaaacatgttgct-----tcaatatttttcagACACTTACATTTGCATGGGTGAACTTCTTCTTTTCGGGTTTTGTTGCAG
     ||   ||  |||| || |   || |||||  | |     |   ||| | | | || |   || |     | |  ||||| |||||||| || ||||||||||| ||||||||||| || || ||||||||||
-----gtgagttgtatttgaaatg--tttcatctatgtttttgcgttactggtcatttaagaaactgatatcacttaccattttgcagACACTCACTTTTGCATGGGTCAACTTCTTCTTCTCTGGATTTGTTGCAG
















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|58589464|gb|CF987772.1|CF987772
EST:     ACATGGCCATGGACATGATGAAGAAGAACCTCTCTATGATAGTTCCTCAG                         ACACTTACATTTGCATGGGTGAACTTCTTC
genomic: ACATGGCCATGGACATGATGAAGAAGAACCTCTCTATGATAGTTCCTCAGgttcagtagc ... tatttttcagACACTTACATTTGCATGGGTGAACTTCTTC
EST: gi|58686514|gb|CK075201.1|CK075201
EST:     ACATGGGCATGGACATGATGAAGAAGAACCTCTCTATGATAGTTCCTCAG                         ACACTTACATTTGCATGGGTGAACTTCTTCTTTTCAGGTTTTGTTGCAG
genomic: ACATGGCCATGGACATGATGAAGAAGAACCTCTCTATGATAGTTCCTCAGgttcagtagc ... tatttttcagACACTTACATTTGCATGGGTGAACTTCTTCTTTTCGGGTTTTGTTGCAG
EST: gi|87032311|gb|CI264092.1|CI264092
EST:     CTATGATAGTTCCTCAG                         ACACTTACATTTGCATGGGTG-ACTTCTTCTTTTCGGGTTTTGTTGCAG
genomic: CTATGATAGTTCCTCAGgttcagtagc ... tatttttcagACACTTACATTTGCATGGGTGAACTTCTTCTTTTCGGGTTTTGTTGCAG
EST: gi|25806351|gb|CA762312.1|CA762312
EST:     ACATGGCCATGGACATGATGAAGAAGAACCTCTCTATGATGGTTCCTCAG                         ACACTTACATTTGCATGGGTGAACTTCTTCTTTTCAGGTTTTGTTGCAG
genomic: ACATGGCCATGGACATGATGAAGAAGAACCTCTCTATGATAGTTCCTCAGgttcagtagc ... tatttttcagACACTTACATTTGCATGGGTGAACTTCTTCTTTTCGGGTTTTGTTGCAG
EST: gi|86506491|gb|CI149124.1|CI149124
EST:     ACCTCTCTATGATAGTTCCTCAG                         ACACTTACATTTGCATGGGTGAACTTCTTCTTTTCGGGTTTTGTTGCAG
genomic: ACCTCTCTATGATAGTTCCTCAGgttcagtagc ... tatttttcagACACTTACATTTGCATGGGTGAACTTCTTCTTTTCGGGTTTTGTTGCAG
EST: gi|86854905|gb|CI260973.1|CI260973
EST:     CTCTATGATAGTTCCTCAG                         ACACTTACATTTGCATGGGTG-ACTTCTTCTTTTCGGGTTTTGTTGCAG
genomic: CTCTATGATAGTTCCTCAGgttcagtagc ... tatttttcagACACTTACATTTGCATGGGTGAACTTCTTCTTTTCGGGTTTTGTTGCAG
EST: gi|33688252|gb|CF316491.1|CF316491
EST:     ACATGGCCATGGACATGATGAAGAAGAACCTCTCTATGATAGTTCCTCAG                         ACACTTACATTTGCATAGGTGAACTTCTTCTTTTCGGGTTTTGTTGCAG
genomic: ACATGGCCATGGACATGATGAAGAAGAACCTCTCTATGATAGTTCCTCAGgttcagtagc ... tatttttcagACACTTACATTTGCATGGGTGAACTTCTTCTTTTCGGGTTTTGTTGCAG
EST: gi|86543296|gb|CI183502.1|CI183502
EST:     AACCTCTCTATGATAGTTCCTCAG                         ACACTTACATTTGCATGGGTGAACTTCTTCTTTTCGGGTTTTGTTGCAG
genomic: AACCTCTCTATGATAGTTCCTCAGgttcagtagc ... tatttttcagACACTTACATTTGCATGGGTGAACTTCTTCTTTTCGGGTTTTGTTGCAG
EST: gi|117242276|gb|CT842928.1|CT842928
EST:     ACATGGCCATGGACATGATGAAGAAGAACCTCTCTATGATAGTTCCTCAG                         ACACTTACATTTGCATGGGTGAACTTCTTCTTTTCGGGTTTTGTTGCAG
genomic: ACATGGCCATGGACATGATGAAGAAGAACCTCTCTATGATAGTTCCTCAGgttcagtagc ... tatttttcagACACTTACATTTGCATGGGTGAACTTCTTCTTTTCGGGTTTTGTTGCAG

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), 49 (downstream exon)
Score: 84

CCCGAAAGAGGAAGCACAGAAAGCTCAGGCTGCCATGTTTTCAGATCCAAACATGGCCATGGACATGATGAAGAAGAACCTCTCTATGATAGTTCCTCAGgttcagtagc ... tatttttcagACACTTACATTTGCATGGGTGAACTTCTTCTTTTCGGGTTTTGTTGCAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccatcttagctaccatggctctgtttactaaacatgttgcttcaatatttttcagACACTTACATTTGCATGGGTGAACTTCTTCTTTTCGGGTTTTGTTGCAG
                         tactaaa  putative branch site (score: 84)
                                             tatttttc  putative PPT
                                        ttcaatatttttca  TA-rich tract