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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCTGCCCTGCTTGTCGTGGATGCGGACGTACAGGTTGAAGGAGGATCTGCAGGCCGACCTCGCCGCTGGCATCACCGTCGGCGTCATGCTCGTGCCCCAAgtacattctttaccctcgtgattcgcaacatttcgtattgctatgcacggcttcaactgttcctaatcctggttatcaaacgggaaagatatggttatat...

Basic information

species Oryza sativa
transcript LOC_Os09g06499.2
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os09g06499.2 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G068212_T01 (Zea mays), 5'ss of exon 1
TCTGCCCTGCTTGTCGTGGATGCGGACGTACAGGTTGAAGGAGGATCTGCAGGCCGACCTCGCCGCTGGCATCACCGTCGGCGTCATGCTCGTGCCCCAAgtacattctttaccctcgtgattcgcaacatttcgtattgctatgcacggcttcaactgttcctaatcctggttatcaaacgggaaagatatggttatat------
  |||| ||  || ||||||  ||||  ||||| | |||| |||| || ||||||||||||||| | ||||||||||| || |||||||| |||||||| |||||  |  |  | ||  ||          ||  | |||  || | | |  | |   | |  |  |  || |||| |       |   | |  ||  |       
CTTGCCGTGTGTGGCGTGGACACGGAACTACAGATGGAAGCAGGACCTCCAGGCCGACCTCGCCTCGGGCATCACCGTTGGAGTCATGCTTGTGCCCCAGgtacacccactggc-tcccgacgtatg----ttttttttgagatactccgtct-actagattgttgtgttgcttataaggatttgagtgtctccttggagaaacga
















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|29643060|gb|CB648067.1|CB648067
EST:     AGGCCGACCTCGCCGCTGGCATCACCGTCGGCGTCATGCTCGTGCCCCAA                         GCAATGTCATATGCAAAGTTGGCTGGGCTTCACCCAATATATGAGGTTAT
genomic: AGGCCGACCTCGCCGCTGGCATCACCGTCGGCGTCATGCTCGTGCCCCAAgtacattctt ... tgtattgtagGCAATGTCATATGCAAAGTTGGCTGGGCTTCACCCAATATATG-GGTTAT
EST: gi|29678820|gb|CB675095.1|CB675095
EST:     AGGCCGACCTCGCCGCTGGCATCACCGTCGGCGTCATGCTCGTGCCCCAA                         GCAATGTCATATGCAAAGTTGGCTGGGCTTCACCCAATATATGGGTTAT
genomic: AGGCCGACCTCGCCGCTGGCATCACCGTCGGCGTCATGCTCGTGCCCCAAgtacattctt ... tgtattgtagGCAATGTCATATGCAAAGTTGGCTGGGCTTCACCCAATATATGGGTTAT
EST: gi|117236351|gb|CT842269.1|CT842269
EST:     AGGCCGACCTCGCCGCTGGCATCACCGTCGGCGTCATGCTCGTGCCCCAA                         GCAATGTCATATGCAAAGTTGGCTGGGCTTCACCCAATATATGGGTTAT
genomic: AGGCCGACCTCGCCGCTGGCATCACCGTCGGCGTCATGCTCGTGCCCCAAgtacattctt ... tgtattgtagGCAATGTCATATGCAAAGTTGGCTGGGCTTCACCCAATATATGGGTTAT
EST: gi|29614648|gb|CB619661.1|CB619661
EST:     AGGCCGACCTCGCCGCTGGCATCACCGTCGGCGTCATGCTCGTGCCCCAA                         GCAATGTCATATGCAAAGTTGGCTGGGCTTCACCCAATATATGGGTTAT
genomic: AGGCCGACCTCGCCGCTGGCATCACCGTCGGCGTCATGCTCGTGCCCCAAgtacattctt ... tgtattgtagGCAATGTCATATGCAAAGTTGGCTGGGCTTCACCCAATATATGGGTTAT
EST: gi|29674506|gb|CB670781.1|CB670781
EST:     AGGCCGACCTCGCCGCTGGCATCACCGTCGGCGTCATGCTCGTGCCCCAA                         GCAATGTCATATGCAAAGTTGGCTGGGCTTCACCCAATATATGGGTTAT
genomic: AGGCCGACCTCGCCGCTGGCATCACCGTCGGCGTCATGCTCGTGCCCCAAgtacattctt ... tgtattgtagGCAATGTCATATGCAAAGTTGGCTGGGCTTCACCCAATATATGGGTTAT
EST: gi|38474049|gb|CF958181.1|CF958181
EST:     AGGCCGACCTCGCCGCTGGCATCACCGTCGGCGTCATGCTCGTGCCCCAA                         GCAATGTCATATGCAAAGTTGGCTGGGCTTCACCCAATATATGGGTTAT
genomic: AGGCCGACCTCGCCGCTGGCATCACCGTCGGCGTCATGCTCGTGCCCCAAgtacattctt ... tgtattgtagGCAATGTCATATGCAAAGTTGGCTGGGCTTCACCCAATATATGGGTTAT

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: 48 (upstream exon), 48 (downstream exon)
Score: 7

TCTGCCCTGCTTGTCGTGGATGCGGACGTACAGGTTGAAGGAGGATCTGCAGGCCGACCTCGCCGCTGGCATCACCGTCGGCGTCATGCTCGTGCCCCAAgtacattctt ... tgtattgtagGCAATGTCATATGCAAAGTTGGCTGGGCTTCACCCAATATATGGGTTAT




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