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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GATTGAACTCTTCACTCATGTCCCAGTTCTGCGTAACTTTGTTGAACATTTGAAACGAAAAAATTTCAACGTTTGTGCCGTGTACTTTCTTGATTCACAGgtttggactcttggatcactaaccaaatatatttatccttgaaaaaagatactggccccaaacacaagtagacaagtctgacttgagttttgtttttcttggttaag

Basic information

species Oryza sativa
transcript LOC_Os03g21914.1
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g21914.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GRMZM2G131324_T01 (Zea mays), 5'ss of exon 6
GATTGAACTCTTCACTCATGTCCCAGTTCTGCGTAACTTTGTTGAACATTTGAAACGAAAAAATTTCAACGTTTGTGCCGTGTACTTTCTTGATTCACAGgtttggactcttggatcactaaccaaatatatttatccttgaaaaaagatactggccccaaacacaagtagacaagtctgacttgagttttgtttttcttggttaag
||||||||||||||| ||||| ||||||||||| |||||||| || ||  ||||||||||||||||||||||||| || || ||| ||||||||||||||||||| | || || ||        |||| |  || ||  |||| |   ||| ||  || |||          |||| |||| |   ||||  |||||| || |  ||
GATTGAACTCTTCACACATGTTCCAGTTCTGCGGAACTTTGTCGAGCACCTGAAACGAAAAAATTTCAACGTTTGCGCTGTTTACCTTCTTGATTCACAGgtttgaa-tcatgaat------ataaattttcttgtcaatgaagat--atattgaaccaaaa--------accaagcctgagt-acgtttgttttttcatgatccag

upper sequence: LOC_Os03g21914.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GRMZM2G154716_T01 (Zea mays), 5'ss of exon 8
GATTGAACTCTTCACTCATGTCCCAGTTCTGCGTAACTTTGTTGAACATTTGAAACGAAAAAATTTCAACGTTTGTGCCGTGTACTTTCTTGATTCACAGgtttggactcttggatcactaaccaaatatatttatccttgaaaaaagatactggccccaaacacaagtagacaagtctgacttgagttttgtttttcttggttaag
||||||||||||||| ||||| ||||||||||| |||||||| || ||  ||||||| |||| |||||||||||| || || ||| |||||||||||| |||||| | || || ||        |||| |  ||  |  |||| |   ||| ||  || |||| ||||         | || |   ||| | |||||| || |  ||
GATTGAACTCTTCACACATGTTCCAGTTCTGCGGAACTTTGTCGAGCACCTGAAACGGAAAATTTTCAACGTTTGCGCTGTTTACCTTCTTGATTCACGGgtttgaa-tcatgaatag------aaattttcttgacaatgaatat--atattgaaccaaaacccaagc--------ccgagtacggttat-tttttcatgatccag

upper sequence: LOC_Os03g21914.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GLYMA08G39880.1 (Glycine max), 5'ss of exon 6
GATTGAACTCTTCACTCATGTCCCAGTTCTGCGTAACTTTGTTGAACATTTGAAACGAAAAAATTTCAACGTTTGTGCCGTGTACTTTCTTGATTCACAGgtttggactcttggatcactaaccaaatatatttatccttgaaaaaagatac----tggccccaaacacaagtagacaa-gtctgacttgagttttgtttttcttggttaag----------------------
||| ||||| |   | ||||||||||| ||    || ||||| |||||||||||||| |||||||| |  |||||||| || ||||| |||||||||||||||||   |  | | |   | |  |||||| ||  |    |  |   | |      |   || | | ||     |  |  || |   || | | || | ||| |||  |                         
GATAGAACTATATTCACATGTCCCAGTGCTTAAGAATTTTGTGGAACATTTGAAACGGAAAAATTTTAGTGTTTGTGCTGTTTACTTACTTGATTCACAGgtttg---tggtagtttgttgagaaaatattttcttttaagttattggctctctcatattcctatagacttcctgttattgtatattttaattattatctttgttgactctaataatattaaaatgttttccag

upper sequence: LOC_Os03g21914.1 (Oryza sativa), 5'ss of exon 5
lower sequence: Vv00s0174g00200.t01 (Vitis vinifera), 5'ss of exon 5
GATTGAACTCTTCACTCATGTCCCAGTTCTGCGTAACTTTGTTGAACATTTGAAACGAAAAAATTTCAACGTTTGTGCCGTGTACTTTCTTGATTCACAGgtttggactcttggatcactaaccaaatatatttatccttgaaaaaagatactggccccaaacacaagtagacaagtctgacttgagttttgtttttcttggttaag--
||| || || ||  | ||||| ||| | || || || ||||| || |||||||| || || |||||||| |||||||| |||||| | ||||||||||||||||| |   ||   || ||      |||  |||||  ||  ||  |    ||||       |     | || |  |||   ||   | || ||  | ||   ||    
GATAGAGCTTTTTTCGCATGTTCCAATGCTTCGGAATTTTGTGGACCATTTGAAGCGTAAGAATTTCAATGTTTGTGCTGTGTACCTGCTTGATTCACAGgtttgtagaattttctcccttgg-gcataattttattattttaatga----ctggttattg-cttgtattgagagttcttttttttttcttcttcctttttaatatcag

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|218497501|gb|FG955303.1|FG955303
EST:     TGAAACGGAAAAATTTCAACGTTTGTGCTGTGTACCTTCTTGATTCACAG                         TTTGTTAGTGATGTGACAAAATACATCAGTGGTTGCATGGCTTCTCTTTCT
genomic: TGAAACGAAAAAATTTCAACGTTTGTGCCGTGTACTTTCTTGATTCACAGgtttggactc ... cttggttaagTTTGTTAGTGATGTGACAAAATACATCAGTGGTTGCATGGCTTCTCTTTCT
EST: gi|163929298|gb|EG711035.1|EG711035
EST:     TGAAACGAAAAAATTTCAACGTTTGTGCCGTGTACTTTCTTGATTCACAG                         TTTGTTAGTGATGTGACAAAATACATCAGTGGTTGCATGGCTTCTCTTTCT
genomic: TGAAACGAAAAAATTTCAACGTTTGTGCCGTGTACTTTCTTGATTCACAGgtttggactc ... cttggttaagTTTGTTAGTGATGTGACAAAATACATCAGTGGTTGCATGGCTTCTCTTTCT
EST: gi|58656588|gb|CK045268.1|CK045268
EST:     TGAAACGGAAAAATTTCAACGTTTGTGCCGTGTACTTTCTTGATTCACAG                         TTTGTTAGTGATGTGACAAAATACATCAGTGGTTGCATGGCTTCTCTTTCT
genomic: TGAAACGAAAAAATTTCAACGTTTGTGCCGTGTACTTTCTTGATTCACAGgtttggactc ... cttggttaagTTTGTTAGTGATGTGACAAAATACATCAGTGGTTGCATGGCTTCTCTTTCT
EST: gi|27546018|gb|CA764157.2|CA764157
EST:     TGAAACGGAAAAATTTCAACGTTTGTGCCGTGTACTTTCTTGATTCACAG                         TTTGTTAGTGATGTGACAAAATACATCAGTGGTTGCATGGCTTCTCTTTCT
genomic: TGAAACGAAAAAATTTCAACGTTTGTGCCGTGTACTTTCTTGATTCACAGgtttggactc ... cttggttaagTTTGTTAGTGATGTGACAAAATACATCAGTGGTTGCATGGCTTCTCTTTCT
EST: gi|33679512|gb|CF307751.1|CF307751
EST:     TGAAACGGAAAAATTTCAACGTTTGTGCTGTGTACCTTCTTGATTCACAG                         TTTGTTAGTGATGTGACAAAATACATCAGTGGTTGCATGGCTTCTCTTTCT
genomic: TGAAACGAAAAAATTTCAACGTTTGTGCCGTGTACTTTCTTGATTCACAGgtttggactc ... cttggttaagTTTGTTAGTGATGTGACAAAATACATCAGTGGTTGCATGGCTTCTCTTTCT
EST: gi|86886652|gb|CI312537.1|CI312537
EST:     CAACGTTTGGTGCCNGTG-ACTTTTCCTTGATTCCCCAG                         TTTGTTAGTGATGTGACAAAATACATCAGTGGTTGCATGGCTTCTCTTTC
genomic: CAACGTTT-GTGCC-GTGTAC-TTT-CTTGATT-CACAGgtttggactc ... cttggttaagTTTGTTAGTGATGTGACAAAATACATCAGTGGTTGCATGGCTTCTCTTTC
EST: gi|44673938|gb|CR287372.1|CR287372
EST:     TGAAACGGAAAAATTTCAACGTTTGTGCCGTGTACTTTCTTGATTCACAG                         TTTGTTAGTGATGTGACAAAATACATCAGTGGTTGCATGGCTTCTCTTTCT
genomic: TGAAACGAAAAAATTTCAACGTTTGTGCCGTGTACTTTCTTGATTCACAGgtttggactc ... cttggttaagTTTGTTAGTGATGTGACAAAATACATCAGTGGTTGCATGGCTTCTCTTTCT
EST: gi|8857451|gb|AU094769.1|AU094769
EST:     GAAACGAAAAAATTNCAACCGTTTGTCCCGTGTACTTTCTTGATTCNCAG                         TTTGTTAGTGATGTGACAAAATACATCCAGTGGTTGCATGGCTTCTCTTTC
genomic: GAAACGAAAAAATTTCAA-CGTTTGTGCCGTGTACTTTCTTGATTCACAGgtttggactc ... cttggttaagTTTGTTAGTGATGTGACAAAATACAT-CAGTGGTTGCATGGCTTCTCTTTC
EST: gi|218503197|gb|FG958153.1|FG958153
EST:     TGAAACGGAAAAATTTCAACGTTTGTGCCGTGTACTTTCTTGATTCACAG                         TTTGTTAGTGATGTGACAAAATACATCAGTGGTTGCATGGCTTCTCTTTCT
genomic: TGAAACGAAAAAATTTCAACGTTTGTGCCGTGTACTTTCTTGATTCACAGgtttggactc ... cttggttaagTTTGTTAGTGATGTGACAAAATACATCAGTGGTTGCATGGCTTCTCTTTCT
EST: gi|58671472|gb|CK060158.1|CK060158
EST:     TGAAACGGAAAAATTTCAACGTTTGTGCTGTGTACCTTCTTGATTCACAG                         TTTGTTAGTGATGTGACAAAATACATCAGTGGTTGCATGGCTTCTCTTTCT
genomic: TGAAACGAAAAAATTTCAACGTTTGTGCCGTGTACTTTCTTGATTCACAGgtttggactc ... 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: 58 (upstream exon), 46 (downstream exon)
Score: 33

GATTGAACTCTTCACTCATGTCCCAGTTCTGCGTAACTTTGTTGAACATTTGAAACGAAAAAATTTCAACGTTTGTGCCGTGTACTTTCTTGATTCACAGgtttggactc ... cttggttaagTTTGTTAGTGATGTGACAAAATACATCAGTGGTTGCATGGCTTCTCTTTCTGCCATGATTCAGCTTGAACTTCCTCATATCAACATTCTTTCAAAGATGG




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