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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GATTGAACTCTTCACTCATGTCCCAGTTCTGCGTAACTTTGTTGAACATTTGAAACGGAAAAATTTCAACGTTTGTGCTGTGTACCTTCTTGATTCACAGgtttggactcttggatcactaaccaaatatatttatccttgagaaaacatactgagcccaaacacaactacacaagtcttacttgagttttgttttgcttggttaag

Basic information

species Oryza sativa
transcript LOC_Os03g50620.1
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g50620.2 (Oryza sativa), 5'ss of exon 5
lower sequence: GRMZM2G131324_T01 (Zea mays), 5'ss of exon 6
GATTGAACTCTTCACTCATGTCCCAGTTCTGCGTAACTTTGTTGAACATTTGAAACGGAAAAATTTCAACGTTTGTGCTGTGTACCTTCTTGATTCACAGgtttggactcttggatcactaaccaaatatatttatccttgagaaaacatactgagcccaaacacaactacacaagtcttacttgagttttgttttgcttggttaag
||||||||||||||| ||||| ||||||||||| |||||||| || ||  ||||||| ||||||||||||||||| ||||| ||||||||||||||||||||||| | || || ||        |||| |  || ||  |||  | | ||| ||| || |||         || |  | |   |  ||||  |||| | || |  ||
GATTGAACTCTTCACACATGTTCCAGTTCTGCGGAACTTTGTCGAGCACCTGAAACGAAAAAATTTCAACGTTTGCGCTGTTTACCTTCTTGATTCACAGgtttgaa-tcatgaat------ataaattttcttgtcaatga--agatatattgaaccaaaa---------accaagcctgagtacgtttgttttttcatgatccag

upper sequence: LOC_Os03g50620.2 (Oryza sativa), 5'ss of exon 5
lower sequence: GRMZM2G154716_T01 (Zea mays), 5'ss of exon 8
GATTGAACTCTTCACTCATGTCCCAGTTCTGCGTAACTTTGTTGAACATTTGAAACGGAAAAATTTCAACGTTTGTGCTGTGTACCTTCTTGATTCACAGgtttggactcttggatcactaaccaaatatatttatccttgagaaaacatactgagcccaaacacaactacacaagtcttacttgagttttgttttgcttggttaag
||||||||||||||| ||||| ||||||||||| |||||||| || ||  |||||||||||| |||||||||||| ||||| |||||||||||||||| |||||| | || || ||        | | || ||  |      ||| | ||| ||| || |||| |||        | |  | |   ||| | |||| | || |  ||
GATTGAACTCTTCACACATGTTCCAGTTCTGCGGAACTTTGTCGAGCACCTGAAACGGAAAATTTTCAACGTTTGCGCTGTTTACCTTCTTGATTCACGGgtttgaa-tcatgaat--------agaaattttcttgacaatgaatatatattgaaccaaaacccaa--------gcccgagtacggttat-tttttcatgatccag

upper sequence: LOC_Os03g50620.2 (Oryza sativa), 5'ss of exon 5
lower sequence: GLYMA08G39880.1 (Glycine max), 5'ss of exon 6
GATTGAACTCTTCACTCATGTCCCAGTTCTGCGTAACTTTGTTGAACATTTGAAACGGAAAAATTTCAACGTTTGTGCTGTGTACCTTCTTGATTCACAGgtttg-gactcttggatcactaaccaaatatatttatccttgagaaaacatactgagcccaaacacaactacacaagtcttacttgagtt-ttgttttgcttggttaag----------------------
||| ||||| |   | ||||||||||| ||    || ||||| ||||||||||||||||||||||| |  ||||||||||| ||| | ||||||||||||||||| |    || | | |  ||  |  |   ||||   |   |      |  |   || | | ||  |     |     || || | || || | ||  |||  |                         
GATAGAACTATATTCACATGTCCCAGTGCTTAAGAATTTTGTGGAACATTTGAAACGGAAAAATTTTAGTGTTTGTGCTGTTTACTTACTTGATTCACAGgtttgtggtagtttgttgagaaaatattttcttttaagttattggctctctcatattcctatagacttcctgttattgtatattttaattattatctttgttgactctaataatattaaaatgttttccag

upper sequence: LOC_Os03g50620.2 (Oryza sativa), 5'ss of exon 5
lower sequence: Vv00s0174g00200.t01 (Vitis vinifera), 5'ss of exon 5
GATTGAACTCTTCACTCATGTCCCAGTTCTGCGTAACTTTGTTGAACATTTGAAACGGAAAAATTTCAACGTTTGTGCTGTGTACCTTCTTGATTCACAGgtttg--gactcttggatcactaaccaaatatatttatccttgagaaaacatactgagcccaaacacaactacacaagtcttacttgagttttgttttgcttggttaag
||| || || ||  | ||||| ||| | || || || ||||| || |||||||| || || |||||||| ||||||||||||||||| |||||||||||||||||  || | ||    |     |  ||| |  ||||  |   ||     || ||     |   | |  |       | ||  |     ||| |  |    |      
GATAGAGCTTTTTTCGCATGTTCCAATGCTTCGGAATTTTGTGGACCATTTGAAGCGTAAGAATTTCAATGTTTGTGCTGTGTACCTGCTTGATTCACAGgtttgtagaattttctcccttgggcataattttattattttaatgactggttattgcttgtattgagagttcttttttttttcttcttcctttttaatatcag------

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|58611474|gb|CK039186.1|CK039186
EST:     TGAAACGGAAAAATTTCAACGTTTGTGCTGTGTACCTTCTTGATTCACAG                         TTTGTTAGTGATGTGACAAAATACATC
genomic: TGAAACGGAAAAATTTCAACGTTTGTGCTGTGTACCTTCTTGATTCACAGgtttggactc ... cttggttaagTTTGTTAGTGATGTGACAAAATACATC
EST: gi|157650986|gb|EX450620.1|EX450620
EST:     GTACCTTCTTGATTCACAG                         TTTGTTAGTGATGTGACAAAATACATCAGTGGTTGCATGGCTTCTCTTTCT
genomic: GTACCTTCTTGATTCACAGgtttggactc ... cttggttaagTTTGTTAGTGATGTGACAAAATACATCAGTGGTTGCATGGCTTCTCTTTCT
EST: gi|27578010|gb|CB000705.1|CB000705
EST:     TGAAACGGAAAAATTTCAACGTTTGTGCTGTGTACCTTCTTGATTCACAG                         TTTGTTAGTGATGTGACAAAATACATCAGTGGTTGCATGGCTTCTCTTTCT
genomic: TGAAACGGAAAAATTTCAACGTTTGTGCTGTGTACCTTCTTGATTCACAGgtttggactc ... cttggttaagTTTGTTAGTGATGTGACAAAATACATCAGTGGTTGCATGGCTTCTCTTTCT
EST: gi|426369|gb|D22232.1|D22232
EST:     TGAAACGGAAAAATTTCAACGNTTGTGCTGTGTACCTTCTTGATTCACAG                         TTTGTTAGTGATGT
genomic: TGAAACGGAAAAATTTCAACGTTTGTGCTGTGTACCTTCTTGATTCACAGgtttggactc ... cttggttaagTTTGTTAGTGATGT
EST: gi|29689065|gb|CB685340.1|CB685340
EST:     TGAAACGGAAAAATTTCAACGTTTGTGCTGTGTACCTTCTTGATTCACAG                         TTTGTTAGTGATGTGACAAAATACATCAGTGGTTGCATGGCTTCTCTTTCT
genomic: TGAAACGGAAAAATTTCAACGTTTGTGCTGTGTACCTTCTTGATTCACAGgtttggactc ... cttggttaagTTTGTTAGTGATGTGACAAAATACATCAGTGGTTGCATGGCTTCTCTTTCT

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: 75 (upstream exon), 73 (downstream exon)
Score: 27

GATTGAACTCTTCACTCATGTCCCAGTTCTGCGTAACTTTGTTGAACATTTGAAACGGAAAAATTTCAACGTTTGTGCTGTGTACCTTCTTGATTCACAGgtttggactc ... cttggttaagTTTGTTAGTGATGTGACAAAATACATCAGTGGTTGCATGGCTTCTCTTTCTGCCATGATTCAGCTTGAACTTCCTCATATCAACATTCTTTCAAAGATGG




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