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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtatcttctgacctcatatatggtggaacctgtatttagccgattcaactctaatttttgttatccctgtatatttcaggaaaaataattatttgaatctgtttaatatgcctttttaattgaattgttgttacaatggaaaaaaactcattgccttccttgtcatactgtttctttttgtttgtagGGATATGGATCATTTTTACTTCGAGATCTGCCTTTTGATGCCATTCAATTCTGTATATATGAGCAACTTCGAATTGGTTACAAAGTTGTG

Basic information

species Oryza sativa
transcript LOC_Os05g29860.1
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g29860.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G042027_T05 (Zea mays), 3'ss of exon 7
gtatgtatcttctgacctcatatatggtggaacctgtatttagccgattcaactctaatttttgttatccctgtatatttcaggaaaaataattatttgaatctgtttaatatgcctttttaattgaattgttgttacaatggaaaaaaactcattgccttccttgtcatactgtttctttttgtttgtagGGATATGGATCATTTTTACTTCGAGATCTGCCTTTTGATGCCATTCAATTCTGTATATATGAGCAACTTCGAATTGGTTACAAAGTTGTG
|||||| | ||||| | || ||| ||||            || |    |  |   | | || ||||       |  ||| | |    | |  | || |||    || |||  |   ||  || || || |     ||   ||  | || |  ||||        | |||  | ||||||||| |||||||||| ||||| || ||| ||||||||||||| || ||||||||||| || ||||| || |||||||||||||||||||| |||||| |||||
gtatgtgtattctggcatcttatttggt------------taacaatctttatattgacttctgtttgaaggatgaattactgatttactgttgatctgag---gtgtaaattttgttcctattttaaata----tatcttgtgataatatccatta-------tatcac-cggtttcttttggtttgtagGGTTATGGTTCCTTTCTACTTCGAGATCTACCATTTGATGCCATCCAGTTCTGCATTTATGAGCAACTTCGAATTGGCTACAAACTTGTG
















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|29675291|gb|CB671566.1|CB671566
EST:     ATGCTGTTCGTCTCATTGTTGGTAAAGAAGGATTCAGAGGTCTTTACGCT                         GGATATGGATCATTTTTACTTCGAGATCTGCCTTTTGATGCCATTCAATTC
genomic: ATGCTGTTCGTCTCATTGTTGGTAAAGAAGGATTCAGAGGTCTTTACGCTgtatgtatct ... ttgtttgtagGGATATGGATCATTTTTACTTCGAGATCTGCCTTTTGATGCCATTCAATTC
EST: gi|33682562|gb|CF310801.1|CF310801
EST:     ATGCTGTTCGTCTCATTGTTGGTAAAGAAGGATTCAGAGGTCTTTACGCT                         GGATATGGATCATTTTTACTTCGAGATCTGCCTTTTGATGCCATTCAATTC
genomic: ATGCTGTTCGTCTCATTGTTGGTAAAGAAGGATTCAGAGGTCTTTACGCTgtatgtatct ... ttgtttgtagGGATATGGATCATTTTTACTTCGAGATCTGCCTTTTGATGCCATTCAATTC
EST: gi|29675292|gb|CB671567.1|CB671567
EST:     ATGCTGTTCGTCTCATTGTTGGTAAAGAAGGATTCAGAGGTCTTTACGCT                         GGATATGGATCATTTTTACTTCGAGATCTGCCTTTTGATGCCATTCAATTC
genomic: ATGCTGTTCGTCTCATTGTTGGTAAAGAAGGATTCAGAGGTCTTTACGCTgtatgtatct ... ttgtttgtagGGATATGGATCATTTTTACTTCGAGATCTGCCTTTTGATGCCATTCAATTC
EST: gi|33686568|gb|CF314807.1|CF314807
EST:     ATGCTGTTCGTCTCATTGTTGGTAAAGAAGGATTCAGAGGTCTTTACGCT                         GGATATGGATCATTTTTACTTCGAGATCTGCCTTTTGATGCCATTCAATTC
genomic: ATGCTGTTCGTCTCATTGTTGGTAAAGAAGGATTCAGAGGTCTTTACGCTgtatgtatct ... ttgtttgtagGGATATGGATCATTTTTACTTCGAGATCTGCCTTTTGATGCCATTCAATTC
EST: gi|66915672|gb|CX102520.1|CX102520
EST:     GCTGTCCGTCTCATTGTTGGTAAAGAAGGATTCATTAGGTCTTTACGCT                         GGATATGGATCATTTTTACTTCGAGATCTGCCTTTTGATGCCATTCAATTC
genomic: GCTGTTCGTCTCATTGTTGGTAAAGAAGGATTCA-GAGGTCTTTACGCTgtatgtatct ... ttgtttgtagGGATATGGATCATTTTTACTTCGAGATCTGCCTTTTGATGCCATTCAATTC
EST: gi|33683403|gb|CF311642.1|CF311642
EST:     ATGCTGTTCGTCTCATTGTTGGTAAAGAAGGATTCAGAGGTCTTTACGCT                         GGATATGGATCATTTTTACTTCGAGATCTGCCTTTTGATGCCATTCAATTC
genomic: ATGCTGTTCGTCTCATTGTTGGTAAAGAAGGATTCAGAGGTCTTTACGCTgtatgtatct ... ttgtttgtagGGATATGGATCATTTTTACTTCGAGATCTGCCTTTTGATGCCATTCAATTC

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: 54 (upstream exon), 74 (downstream exon)
Score: 8

GTTGTCAAACAAAGAATGCAAACAGGTCAATTCAGGTCTGCACCTGATGCTGTTCGTCTCATTGTTGGTAAAGAAGGATTCAGAGGTCTTTACGCTgtatgtatct ... ttgtttgtagGGATATGGATCATTTTTACTTCGAGATCTGCCTTTTGATGCCATTCAATTCTGTATATATGAGCAACTTCGAATTGGTTACAAAGTTGTG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acaatggaaaaaaactcattgccttccttgtcatactgtttctttttgtttgtagGGATATGGATCATTTTTACTTCGAGATCTGCCTTTTGATGCCATTCAATTCTGTATATATGAGCAACTTCGAATTGGTTACAAAGTTGTG
                                   ctgtttctttttgttt  CT-rich tract
       aaaaaaact  TA-rich tract