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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTGCGGGATCGCCTTGTGAAAATTGTGACAGACTATCGAACAGAAACTTCATTAAGACATGGGTGCAATGATATACTTAAGgttaatattcaagaaaaagatatacttaaggttagttgtctatttattaccccacatctatcttgacgtttgatgaccctgccatgtacag

Basic information

species Oryza sativa
transcript LOC_Os04g11880.1
intron # 18
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g11880.1 (Oryza sativa), 5'ss of exon 18
lower sequence: GRMZM2G040247_T01 (Zea mays), 5'ss of exon 18
GTTGCGGGATCGCCTTGTGAAAATTGTGACAGACTATCGAACAGAAACTTCATTAAGACATGGGTGCAATGATATACTTAAGgttaatattcaagaaaaagatatacttaaggttagttgtctatttattaccccacatct---atcttgacgtttgatgaccctgccatgtacag
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GTTGCGGGATCGTCTTGTGAAAATTGTGACGGATTACCGGACAGAAACTTCATTGCGAAATGGATGCAACGATATACTTAAGgtttactttctttcgtatactgtgct----gctccatgtct--caaccatcttgaattttggacattttcatccga--aacttgctttgttcag
















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|8527531|gb|AU092346.1|AU092346
EST:     TNTCCGAACCAGAAACTTCATTAAGACATGGNTGCAATGATATACTTAAG                         GCTGATTGCGT-AACCTTTTGGTAAAATATTATCACGAGGCTCGGCGTGGA
genomic: TAT-CGAA-CAGAAACTTCATTAAGACATGGGTGCAATGATATACTTAAGgttaatattc ... ccatgtacagGCTGATTGCGTAAACCTTTTGGTAAAATATTATCACGAGGCTCGGCGTGGA
EST: gi|55409184|gb|CV721560.1|CV721560
EST:     ACTATCGAACAGAAACTTCATTAAGACATGGGTGCAATGATATACTTAAG                         GCTGATTGCGTAAACCTTTTG
genomic: ACTATCGAACAGAAACTTCATTAAGACATGGGTGCAATGATATACTTAAGgttaatattc ... ccatgtacagGCTGATTGCGTAAACCTTTTG
EST: gi|218488547|gb|FG955820.1|FG955820
EST:     ACTATCGAACAGAAACTTCATTAAGACATGGGTGCAATGATATACTTAAG                         GCTGATTGCGTAAACCTTTTGGTAAAATATTATCACGAGGCTCGGCGTGGA
genomic: ACTATCGAACAGAAACTTCATTAAGACATGGGTGCAATGATATACTTAAGgttaatattc ... ccatgtacagGCTGATTGCGTAAACCTTTTGGTAAAATATTATCACGAGGCTCGGCGTGGA
EST: gi|58688189|gb|CK076876.1|CK076876
EST:     ACTATCGAACAGAAACTTCATTAAGACATGGGTGCAATGATATACTTAAG                         GCTGATTGCGTAAACCTTTTGGTAAAATATTATCACGAGGCTCGGCGTGGA
genomic: ACTATCGAACAGAAACTTCATTAAGACATGGGTGCAATGATATACTTAAGgttaatattc ... ccatgtacagGCTGATTGCGTAAACCTTTTGGTAAAATATTATCACGAGGCTCGGCGTGGA
EST: gi|218492660|gb|FG966164.1|FG966164
EST:     ACTATCGAACAGAAACTTCATTAAGACATGGGTGCAATGATATACTTAAG                         GCTGATTGCGTAAACCTTTTGGTAAAATATT
genomic: ACTATCGAACAGAAACTTCATTAAGACATGGGTGCAATGATATACTTAAGgttaatattc ... ccatgtacagGCTGATTGCGTAAACCTTTTGGTAAAATATT

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: 72 (upstream exon), 70 (downstream exon)
Score: 26

GTTGCGGGATCGCCTTGTGAAAATTGTGACAGACTATCGAACAGAAACTTCATTAAGACATGGGTGCAATGATATACTTAAGgttaatattc ... ccatgtacagGCTGATTGCGTAAACCTTTTGGTAAAATATTATCACGAGGCTCGGCGTGGAGTCTACATGGCTAGTATGGACGAGGAGGTGACAGGAACTAGGGTTGCTG




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