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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CAATCTCGCAGGAAACCAGTTCACTGGAAATTTACCCTACTCGATTTTCTCGATGTCTAATCTTAAGTATTTgtgagtatctttgcaaacatcaagttgattttgcttttaaatttgtataatttggtagagctaaatgttttctctttgtatgtgcag

Basic information

species Oryza sativa
transcript LOC_Os03g08550.1
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g08550.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GRMZM2G330907_T01 (Zea mays), 5'ss of exon 5
CAATCTCGCAGGAAACCAGTTCACTGGAAATTTACCCTACTCGATTTTCTCGATGTCTAATCTTAAGTATTTgtgagtatctttgcaaacatcaagttgattttgcttttaaatttgtataatttggtagagctaaatg---ttttctctttgtatgtgcag
|||||| |||||||| || ||   |||||||||||||||||| ||||   ||||| ||||||||||||||||||||||||  |||||  ||   | |||||||| | ||  ||| ||||| || ||| || | ||||||   |||| |||| |     ||||
CAATCTTGCAGGAAATCAATTTGGTGGAAATTTACCCTACTCAATTTCGACGATGCCTAATCTTAAGTATTTgtgagtattcttgcatccag-gacttgattttacattggaatatgtatcatctggaagggataaatgattttttttcttggcgcacgcag

upper sequence: LOC_Os03g08550.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GRMZM2G153393_T01 (Zea mays), 5'ss of exon 5
CAATCTCGCAGGAAACCAGTTCACTGGAAATTTACCCTACTCGATTTTCTCGATGTCTAATCTTAAGTATTTgtgagtatctttgcaaacatcaagttgattttgcttttaaatttgtataatttggtagagctaaatg----ttttctctttgtatgtgcag
|||||| |||||||| || ||   |||||||||||||||||| ||||   ||||| ||||||||||||||||||||||||  |||||  ||   | |||||||| | ||  ||| ||||| ||| |  || | ||||||    |||| |||| ||   |||||
CAATCTTGCAGGAAATCAATTTGGTGGAAATTTACCCTACTCAATTTCGACGATGCCTAATCTTAAGTATTTgtgagtattcttgcatccag-gacttgattttacattggaatatgtatcatt-gaaagggataaatgatttttttttcttggtgcatgcag
















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|3107717|gb|D43457.1|D43457
EST:     ACTGGAAATTTACCCTACTCGATTTTCTCGATGTCTAATCTTAAGTATTT                         AAATCTAAATCATAACCAATTGCAAGGAAATATAACTGATGTATTTTCCAG
genomic: ACTGGAAATTTACCCTACTCGATTTTCTCGATGTCTAATCTTAAGTATTTgtgagtatct ... gtatgtgcagAAATCTAAATCATAACCAATTGCAAGGAAATATAACTGATGTATTTTCCAG
EST: gi|44665230|gb|CR278664.1|CR278664
EST:     ACTGGAAATTTACCCTACTCGATTTTCTCGATGTCTAATCTTAAGTATTT                         AAATCTAAATCATAACCAATTGCAAGGAAATATAACTGATGTATTTTCCAG
genomic: ACTGGAAATTTACCCTACTCGATTTTCTCGATGTCTAATCTTAAGTATTTgtgagtatct ... gtatgtgcagAAATCTAAATCATAACCAATTGCAAGGAAATATAACTGATGTATTTTCCAG
EST: gi|29644649|gb|CB649656.1|CB649656
EST:     ACTGGAAATTTACCCTACTCGATTTTCTCGATGTCTAATCTTAAGTATTT                         AAATCTAAATCATAACCAATTGCAAGGAAATATAACTGATGTATTTTCCAG
genomic: ACTGGAAATTTACCCTACTCGATTTTCTCGATGTCTAATCTTAAGTATTTgtgagtatct ... gtatgtgcagAAATCTAAATCATAACCAATTGCAAGGAAATATAACTGATGTATTTTCCAG
EST: gi|29624948|gb|CB629959.1|CB629959
EST:     ACTGGAAATTTACCCTACTCGATTTTCTCGATGTCTAATCTTAAGTATTT                         AAATCTAAATCATAACCAATTGCAAGGAAATATAACTGATGTATTTTCCAG
genomic: ACTGGAAATTTACCCTACTCGATTTTCTCGATGTCTAATCTTAAGTATTTgtgagtatct ... gtatgtgcagAAATCTAAATCATAACCAATTGCAAGGAAATATAACTGATGTATTTTCCAG
EST: gi|88386689|gb|CI682838.1|CI682838
EST:     ACTGGAAATTTACCCTACTCGATTTTCTCGATGTCTAATCTTAAGTATTT                         AAATCTAAATCATAACCAATTGCAAGGAAATATAACTGATGTATTTTCCAG
genomic: ACTGGAAATTTACCCTACTCGATTTTCTCGATGTCTAATCTTAAGTATTTgtgagtatct ... gtatgtgcagAAATCTAAATCATAACCAATTGCAAGGAAATATAACTGATGTATTTTCCAG
EST: gi|58661405|gb|CK050085.1|CK050085
EST:     CTTAAGTATTT                         AAATCTAAATCATAACCAATTGCAAGGAAATATAACTGATGTATTGTCGAG
genomic: CTTAAGTATTTgtgagtatct ... gtatgtgcagAAATCTAAATCATAACCAATTGCAAGGAAATATAACTGATGTATTTTCCAG
EST: gi|117225926|gb|CT846035.1|CT846035
EST:     ACTGGAAATTTACCCTACTCGATTTTCTCGATGTCTAATCTTAAGTATTT                         AAATCTAAATCATAACCAATTGCAAGGAAATATAACTGATGTATTT
genomic: ACTGGAAATTTACCCTACTCGATTTTCTCGATGTCTAATCTTAAGTATTTgtgagtatct ... gtatgtgcagAAATCTAAATCATAACCAATTGCAAGGAAATATAACTGATGTATTT
EST: gi|29681108|gb|CB677383.1|CB677383
EST:     ACTGGAAATTTACCCTACTCGATTTTCTCGATGTCTAATCTTAAGTATTT                         AAATCTAAATCATAACCAATTGCAAGGAAATATAACTGATGTATTTTCCAG
genomic: ACTGGAAATTTACCCTACTCGATTTTCTCGATGTCTAATCTTAAGTATTTgtgagtatct ... gtatgtgcagAAATCTAAATCATAACCAATTGCAAGGAAATATAACTGATGTATTTTCCAG

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: 71 (upstream exon), 72 (downstream exon)
Score: 30

CAATCTCGCAGGAAACCAGTTCACTGGAAATTTACCCTACTCGATTTTCTCGATGTCTAATCTTAAGTATTTgtgagtatct ... gtatgtgcagAAATCTAAATCATAACCAATTGCAAGGAAATATAACTGATGTATTTTCCAGCCTCTATAGCTTGACAACACT




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