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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAAAATCTAGTGGTCTAAATAGCTTCGGCCTGATGTGGTGCAACGgtattattttgatgacctgtttcatattcataatatccagattaaaccatatttgccttagcattcatatcctatccatttggattccag

Basic information

species Oryza sativa
transcript LOC_Os02g40030.1
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g40030.2 (Oryza sativa), 5'ss of exon 6
lower sequence: GRMZM2G020976_T01 (Zea mays), 5'ss of exon 6
GAAAATCTAGTGGTCTAAATAGCTTCGGCCTGATGTGGTGCAACGgtattattttgatgacctgtttca---------------tattcataatatccagattaaaccatatttgccttagcattcatatcctatccatttggattccag
||||||||||||| || |||||||| ||||||||||||||||| ||||||||| ||||  ||  |||                 | || ||       |  || |||    | |  ||||  ||   ||| |    | | |||||| |||
GAAAATCTAGTGGCCTTAATAGCTTTGGCCTGATGTGGTGCAATGgtattattctgattgcccttttttcttctcgaacactgttttttattgctcttaatttcaacttcttatatcttaagatct-tatacccctcttctggattacag

upper sequence: LOC_Os02g40030.2 (Oryza sativa), 5'ss of exon 6
lower sequence: GRMZM2G133226_T04 (Zea mays), 5'ss of exon 6
GAAAATCTAGTGGTCTAAATAGCTTCGGCCTGATGTGGTGCAACGgtattattttgatgacctgtttcatattc---ataatatccagatt------------aaaccatatttgccttagcattcatatcctat---ccatttggattccag
||||||||||||| || |||||||| ||||||||||||||||| ||||| ||||||||  ||  |||    |     | | |||   ||||            | | || | || | |  |  || | ||| |||   |  |||||||| |||
GAAAATCTAGTGGCCTCAATAGCTTTGGCCTGATGTGGTGCAATGgtatcattttgattgcccttttttcttcttgaacactattttgattgctcttaacttcagatcaaactt-cttatgtcttaaaatcttatatcctgtttggatttcag

upper sequence: LOC_Os02g40030.2 (Oryza sativa), 5'ss of exon 6
lower sequence: GLYMA17G32030.1 (Glycine max), 5'ss of exon 6
GAAAATCTAGTGGTCTAAATAGCTTCGGCCTGATGTGGTGCAACGgta---ttat--tttgatgacctgtttcatattcataatatccagattaaaccatatttgccttagcattcatatcctatccatttggattccag
| ||| |||||||||| |||||||| ||||| ||||||||||| ||||   ||||  ||||   |   |  |  ||  | ||   |    |||  | |  | ||  ||||   || | || || | |  ||  |||  ||
GGAAAACTAGTGGTCTTAATAGCTTTGGCCTAATGTGGTGCAATGgtaagcttatgatttgtataatggcctgttaaacttaccctttttattgtaacgaaatt-tctta--tttgaaatacttttctattttattatag

upper sequence: LOC_Os02g40030.2 (Oryza sativa), 5'ss of exon 6
lower sequence: GLYMA14G14360.1 (Glycine max), 5'ss of exon 6
GAAAATCTAGTGGTCTAAATAGCTTCGGCCTGATGTGGTGCAACGgta---ttattt------tgatgacctgtttcatattcataatatccagattaaaccatatttgccttagcattcatatcctatccatttggattccag
| ||| |||||||||| |||||||| ||||| ||||||||||| ||||   |||| |        ||| ||||||  |  ||| ||   |    |||  | || | |   ||||   || | || || | |  ||  |||  ||
GGAAAACTAGTGGTCTTAATAGCTTTGGCCTAATGTGGTGCAATGgtaagcttatatattgtacaatggcctgttaaactttcttaccctttttattgtaacagaat-atctta--tttgaaatacttttctattttattatag

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|29670135|gb|CB666410.1|CB666410
EST:     GAAAATCTAGTGGTCTAAATAGCTTCGGCCTGATGTGGTGCAACG                         GACTTGTCTGTGGGCCTTCAGTACTTTTTCTGACATATATTCAGGGTGACC
genomic: GAAAATCTAGTGGTCTAAATAGCTTCGGCCTGATGTGGTGCAACGgtattatttt ... tggattccagGACTTGTCTGTGGGCCTTCAGTACTTTTTCTGACATATATTCAGGGTGACC
EST: gi|29671157|gb|CB667432.1|CB667432
EST:     GAAAATCTAGTGGTCTAAATAGCTTCGGCCTGATGTGGTGCAACG                         GACTTGTCTGTGGGCCTTCAGTACTTTTTCTGACATATATTCAGGGTGACC
genomic: GAAAATCTAGTGGTCTAAATAGCTTCGGCCTGATGTGGTGCAACGgtattatttt ... tggattccagGACTTGTCTGTGGGCCTTCAGTACTTTTTCTGACATATATTCAGGGTGACC
EST: gi|29672145|gb|CB668420.1|CB668420
EST:     GAAAATCTAGTGGTCTAAATAGCTTCGGCCTGATGTGGTGCAACG                         GACTTGTCTGTGGGCCTTCAGTACTTTTTCTGACATATATTCAGGGTGACC
genomic: GAAAATCTAGTGGTCTAAATAGCTTCGGCCTGATGTGGTGCAACGgtattatttt ... tggattccagGACTTGTCTGTGGGCCTTCAGTACTTTTTCTGACATATATTCAGGGTGACC
EST: gi|25806370|gb|CA762331.1|CA762331
EST:     GAAAATCTAGTGGTCTAAATAGCTTCGGCCTGATGTGGTGCAACG                         GACTTGTCTGTGGGCCTTCAGTACTTTTTCTGACATATATTCAGGGTGACC
genomic: GAAAATCTAGTGGTCTAAATAGCTTCGGCCTGATGTGGTGCAACGgtattatttt ... tggattccagGACTTGTCTGTGGGCCTTCAGTACTTTTTCTGACATATATTCAGGGTGACC
EST: gi|58683170|gb|CK071857.1|CK071857
EST:     TAGTGGTCTAAATAGCTTCGGCCTGATGTGGTGCAACG                         GACTTGTCTGTGGGCCTTCAGTACTTTTTCTGACATATATTCAGGGTGACC
genomic: TAGTGGTCTAAATAGCTTCGGCCTGATGTGGTGCAACGgtattatttt ... tggattccagGACTTGTCTGTGGGCCTTCAGTACTTTTTCTGACATATATTCAGGGTGACC
EST: gi|29670136|gb|CB666411.1|CB666411
EST:     GAAAATCTAGTGGTCTAAATAGCTTCGGCCTGATGTGGTGCAACG                         GACTTGTCTGTGGGCCTTCAGTACTTTTTCTGACATATATTCAGGGTGACC
genomic: GAAAATCTAGTGGTCTAAATAGCTTCGGCCTGATGTGGTGCAACGgtattatttt ... tggattccagGACTTGTCTGTGGGCCTTCAGTACTTTTTCTGACATATATTCAGGGTGACC
EST: gi|29672495|gb|CB668770.1|CB668770
EST:     GAAAATCTAGTGGTCTAAATAGCTTCGGCCTGATGTGGTGCAACG                         GACTTGTCTGTGGGCCTTCAGTACTTTTTCTGACATATATTCAGGGTGACC
genomic: GAAAATCTAGTGGTCTAAATAGCTTCGGCCTGATGTGGTGCAACGgtattatttt ... tggattccagGACTTGTCTGTGGGCCTTCAGTACTTTTTCTGACATATATTCAGGGTGACC
EST: gi|2310116|gb|C26271.1|C26271
EST:     GAAAATCTAGTGGTCTAAATAGCTTCGGCCTGATGTGGTGCAACG                         GACTTGTCTGTGGGCCTTCAGTACTTTTTCTGACATATATTCAGGGTGACC
genomic: GAAAATCTAGTGGTCTAAATAGCTTCGGCCTGATGTGGTGCAACGgtattatttt ... tggattccagGACTTGTCTGTGGGCCTTCAGTACTTTTTCTGACATATATTCAGGGTGACC

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: 45 (upstream exon), 75 (downstream exon)
Score: 29

GAAAATCTAGTGGTCTAAATAGCTTCGGCCTGATGTGGTGCAACGgtattatttt ... tggattccagGACTTGTCTGTGGGCCTTCAGTACTTTTTCTGACATATATTCAGGGTGACCTGAAGAAGGCTATAGAATTTCCCTACCTCTATTCCCCTGGGTTTCAG




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