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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCTTTCTCAGAAGAGGAGATACGGAACTTTATGGTGCAGATACTGCAAGGTCTTGCATATATGCATAACAACGGTTATTTCCATCGTGACCTGAAACCTGgtatacctttcgactatattctgttgaagttataggctgtctatataccctagaagttaattagccttctctctttcctctttag

Basic information

species Oryza sativa
transcript LOC_Os03g63020.3
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g63020.1 (Oryza sativa), 5'ss of exon 6
lower sequence: GRMZM2G045241_T07 (Zea mays), 5'ss of exon 2
GCTTTCTCAGAAGAGGAGATACGGAACTTTATGGTGCAGATACTGCAAGGTCTTGCATATATGCATAACAACGGTTATTTCCATCGTGACCTGAAACCTGgta-tacctttcgactatattctgttgaagttataggctgtctatataccctagaagttaattagccttctctctttcctctttag--
|||||| | |||  ||| ||| ||||||||||||| |||||||||||||||||||||||||||||||| || || ||||| || |||||  | |||||||||| |   | | |   |||||   ||| | ||||    | ||| | |  |    ||  |||||||  || |  |||   | | |    
GCTTTCCCTGAAAGGGATATAAGGAACTTTATGGTCCAGATACTGCAAGGTCTTGCATATATGCATAATAATGGGTATTTTCACCGTGATTTAAAACCTGgtaatgtgtcttgttgatattacattggaattat--cttatctttctttctgtcaaaataattagtttttttccttctatttgtgcag

upper sequence: LOC_Os03g63020.1 (Oryza sativa), 5'ss of exon 6
lower sequence: AT4G13020.1 (Arabidopsis thaliana), 5'ss of exon 6
GCTTTCTCAGAAGAGGAGATACGGAACTTTATGGTGCAGATACTGCAAGGTCTTGCATATATGCATAACAACGGTTATTTCCATCGTGACCTGAAACCTGgtatacctttcgactatattctgttgaagttataggctgtctatataccctagaagt-taattagccttctctctttcctctttag--
 |||| || ||||  || ||| | |  ||||||   ||||| |||||||| || ||| | |||||||| ||||||||||||||||| |||||||||||||||||   ||   ||| | |  |||   | ||  |    || |     |  |  | || | || | |    | | ||   | | |    
CCTTTTTCTGAAGGAGAAATAAGAAGTTTTATGTCTCAGATGCTGCAAGGGCTCGCACACATGCATAAAAACGGTTATTTCCATCGAGACCTGAAACCTGgtatgttttggtactttgtattgtattaattg-aaatggttttcgctctttgaatgtcttataaacaagttttgttctgtttctgaag
















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|29656191|gb|CB652466.1|CB652466
EST:     TCTTGCATATATGCATAACAACGGTTATTTCCATCGTGACCTGAAACCTG                         AAAATCTGTTG
genomic: TCTTGCATATATGCATAACAACGGTTATTTCCATCGTGACCTGAAACCTGgtataccttt ... tcctctttagAAAATCTGTTG
EST: gi|25798660|gb|CA754621.1|CA754621
EST:     TCTTGCATATATGCATAACAACGGTTATTTCCATCGTGACCTGAAACCTG                         AAAATCTGTTGGTGACAGATGGC
genomic: TCTTGCATATATGCATAACAACGGTTATTTCCATCGTGACCTGAAACCTGgtataccttt ... tcctctttagAAAATCTGTTGGTGACAGATGGC
EST: gi|58694135|gb|CK082822.1|CK082822
EST:     TCTTGCATATATGCATAACAACGGTTATTTCCATCGTGACCTGAAACCTG                         AAAATCTGTTGGTGACAGATGGCACTGTTAAAATTGCTGACTTTGGGTTGG
genomic: TCTTGCATATATGCATAACAACGGTTATTTCCATCGTGACCTGAAACCTGgtataccttt ... tcctctttagAAAATCTGTTGGTGACAGATGGCACTGTTAAAATTGCTGACTTTGGGTTGG
EST: gi|29663526|gb|CB659801.1|CB659801
EST:     TCTTGCATATATGCATAACAACGGTTATTTCCATCGTGACCTGAAAACTG                         AAAATCTGTTGGTGACAGATGGCACTGTTAAAATTGCTGAC
genomic: TCTTGCATATATGCATAACAACGGTTATTTCCATCGTGACCTGAAACCTGgtataccttt ... tcctctttagAAAATCTGTTGGTGACAGATGGCACTGTTAAAATTGCTGAC
EST: gi|58656490|gb|CK045170.1|CK045170
EST:     TCTTGCATATATGCATAACAACGGTTATTTCCATCGTGACCTGAAACCTG                         AAAATCTGTTGGTGACAGATGGCACTGTTAAAATTGCTGACTTTGGGTTGG
genomic: TCTTGCATATATGCATAACAACGGTTATTTCCATCGTGACCTGAAACCTGgtataccttt ... tcctctttagAAAATCTGTTGGTGACAGATGGCACTGTTAAAATTGCTGACTTTGGGTTGG
EST: gi|58692426|gb|CK081113.1|CK081113
EST:     TCTTGCATATATGCATAACAACGGTTATTTCCATCGTGACCTGAAACCTG                         AAAATCTGTTGGTGACAGATGGCACTGTTAAAATTGCTGACTTTGGGTTGG
genomic: TCTTGCATATATGCATAACAACGGTTATTTCCATCGTGACCTGAAACCTGgtataccttt ... tcctctttagAAAATCTGTTGGTGACAGATGGCACTGTTAAAATTGCTGACTTTGGGTTGG
EST: gi|29613119|gb|CB618132.1|CB618132
EST:     TCTTGCATATATGCATAACAACGGTTATTTCCATCGTGACCTGAAACCTG                         AAAATCTGTTGGTGACAGATGGCACTGTTAAAATTGCTGACTTTGGGTTGG
genomic: TCTTGCATATATGCATAACAACGGTTATTTCCATCGTGACCTGAAACCTGgtataccttt ... tcctctttagAAAATCTGTTGGTGACAGATGGCACTGTTAAAATTGCTGACTTTGGGTTGG
EST: gi|58675001|gb|CK063688.1|CK063688
EST:     TCTTGCATATATGCATAACAACGGTTATTTCCATCGTGACCTGAAACCTG                         AAAATCTGTTGGTGACAGATGGCACTGTTAAAATTGCTGACTTTGGGTTGG
genomic: TCTTGCATATATGCATAACAACGGTTATTTCCATCGTGACCTGAAACCTGgtataccttt ... tcctctttagAAAATCTGTTGGTGACAGATGGCACTGTTAAAATTGCTGACTTTGGGTTGG
EST: gi|86848584|gb|CI293908.1|CI293908
EST:     TCTTGCATATATGCATAACAACGGTTATTTCCATCGTGACCTGAAACCTG                         AAAATCTGTTGGTGACAGATGGCACTGTTAAAATTGCTGACTTTGGGTTGG
genomic: TCTTGCATATATGCATAACAACGGTTATTTCCATCGTGACCTGAAACCTGgtataccttt ... tcctctttagAAAATCTGTTGGTGACAGATGGCACTGTTAAAATTGCTGACTTTGGGTTGG
EST: gi|33381171|gb|CF196514.1|CF196514
EST:     TCTTGCATATATGCATAACAACGGTTATTTCCATCGTGACCTGAAACCTG                         AAAATCTGTTGGTGACAGATGGCACTGTTAAAATTGCTGACTTTGGGTTGG
genomic: TCTTGCATATATGCATAACAACGGTTATTTCCATCGTGACCTGAAACCTGgtataccttt ... tcctctttagAAAATCTGTTGGTGACAGATGGCACTGTTAAAATTGCTGACTTTGGGTTGG

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), 70 (downstream exon)
Score: 28

GCTTTCTCAGAAGAGGAGATACGGAACTTTATGGTGCAGATACTGCAAGGTCTTGCATATATGCATAACAACGGTTATTTCCATCGTGACCTGAAACCTGgtataccttt ... tcctctttagAAAATCTGTTGGTGACAGATGGCACTGTTAAAATTGCTGACTTTGGGTTGGCAAGAGAAGTATCTTCCAGTCCTCCTTATACTGACTATGTTTCCACCAG




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