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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtgggcaagtttgtgtgtgtgacatgatttttgggttttggggtgctagtgatgtaatgattatgttgttcaaagtcacatgaataacttcctccggtgtaatgcagGATTTTGTCGAGTCTGTATTCAGGGAGCGTTTGCATCTGGAACTACCAGACGCAG

Basic information

species Oryza sativa
transcript LOC_Os02g11830.2
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g11830.2 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G141587_T01 (Zea mays), 3'ss of exon 3
gtgagtgggcaagtttgtgtgtgtgacatgatttttgggttttggggtgctagtgatgtaatgattatgttgttcaaagtcacatgaataacttcctccggtgtaatgcagGATTTTGTCGAGTCTGTATTCAGGGAGCGTTTGCATCTGGAACTACCAGACGCAG
|||||||      |||||||    || ||| | |  |  || ||           |||    |  |  |   |    | |||||    | |     || ||  ||||||||||||||||||||||| || ||||| ||||||||  | |||||||||||||| |||
gtgagtgactggttttgtgtac-cgaaatgctatgcgaattatga----------atgcttcgtctgagccatgactaatcaca----ttatgctatctggcataatgcagGATTTTGTCGAGTCTTTACTCAGGAAGCGTTTGTGTATGGAACTACCAGACTCAG

upper sequence: LOC_Os02g11830.2 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G124886_T03 (Zea mays), 3'ss of exon 3
gtgagtgggcaagtttgtgtgtgtgacatgatttttgggttttggggtgctagtgatgtaatgattatgttgttcaaagtcacatgaataacttcctccggtgtaatgcagGATTTTGTCGAGTCTGTATTCAGGGAGCGTTTGCATCTGGAACTACCAGACGCAG
|||||||      |||||||    || ||| | |     || || | ||||  | |||| |     |||  ||    | ||| || |  |      |  || | | ||||||||||||||||||||||| || || ||||| ||  | |||||||||||||| |||
gtgagtgattggttttgtgtac-cgaaatgctatgcaaattatgag-tgct--ttatgtga--gccatggcgt----aatcatattatga----tgtgtggcggattgcagGATTTTGTCGAGTCTGTACTCGGGAAGCGTATGTGTATGGAACTACCAGACTCAG
















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|29613909|gb|CB618922.1|CB618922
EST:     CAGAGGTCGGAGAGGGTCAAGTCCGTGGATCTGCATCCGACCGAGCCATG                         GATTTTGTCGAGTCTGTATTCAGGGAGCGTTTGCATCTGGAACTACCAGAC
genomic: CAGAGGTCGGAGAGGGCCAAGTCCGTGGATCTGCATCCGACCGAGCCATGgtgagtgggc ... tgtaatgcagGATTTTGTCGAGTCTGTATTCAGGGAGCGTTTGCATCTGGAACTACCAGAC
EST: gi|88349632|gb|CI632767.1|CI632767
EST:     CAGAGGTCGGAGAGGGCCAAGTCCGTGGATCTGCATCCGACCGAGCCATG                         GATTTTGTCGAGTCTGTATTCAGGGAGCGTTTGCATCTGGAACTACCAGAC
genomic: CAGAGGTCGGAGAGGGCCAAGTCCGTGGATCTGCATCCGACCGAGCCATGgtgagtgggc ... tgtaatgcagGATTTTGTCGAGTCTGTATTCAGGGAGCGTTTGCATCTGGAACTACCAGAC
EST: gi|88348222|gb|CI637683.1|CI637683
EST:     CAGAGGTCGGAGAGGGCCAAGTCCGTGGATCTGCATCCGACCGAGCCATG                         GATTTTGTCGAGTCTGTATTCAGGGAGCGTTTGCATCTGGAACTACCAGAC
genomic: CAGAGGTCGGAGAGGGCCAAGTCCGTGGATCTGCATCCGACCGAGCCATGgtgagtgggc ... tgtaatgcagGATTTTGTCGAGTCTGTATTCAGGGAGCGTTTGCATCTGGAACTACCAGAC
EST: gi|58685502|gb|CK074189.1|CK074189
EST:     CAGAGGTCGGAGAGGGTCAAGTCCGTGGATCTGCATCCGACCGAGCCATG                         GATTTTGTCGAGTCTGTATTCAGGGAGCGTTTGCATCTGGAACTACCAGAC
genomic: CAGAGGTCGGAGAGGGCCAAGTCCGTGGATCTGCATCCGACCGAGCCATGgtgagtgggc ... tgtaatgcagGATTTTGTCGAGTCTGTATTCAGGGAGCGTTTGCATCTGGAACTACCAGAC
EST: gi|88695800|gb|CI737377.1|CI737377
EST:     CAGAGGTCGGAGAGGGCCAAGTCCGTGGATCTGCATCCGACCGAGCCATG                         GATTTTGTCGAGTCTGTATTCAGGGAGCGTTTGCATCTGGAACTACCAGAC
genomic: CAGAGGTCGGAGAGGGCCAAGTCCGTGGATCTGCATCCGACCGAGCCATGgtgagtgggc ... tgtaatgcagGATTTTGTCGAGTCTGTATTCAGGGAGCGTTTGCATCTGGAACTACCAGAC
EST: gi|58601041|gb|CK011569.1|CK011569
EST:     CAGAGGTCGGAGAGGGTCAAGTCCGTGGATCTGCATCCGACCGAGCCATG                         GATTTTGTCGAGTCTGTATTCAGGGAGCGTTTGCATCTGGAACTACCAGAC
genomic: CAGAGGTCGGAGAGGGCCAAGTCCGTGGATCTGCATCCGACCGAGCCATGgtgagtgggc ... tgtaatgcagGATTTTGTCGAGTCTGTATTCAGGGAGCGTTTGCATCTGGAACTACCAGAC
EST: gi|29680636|gb|CB676911.1|CB676911
EST:     CAGAGGTCGGAGAGGGCCAAGTCCGTGGATCTGCATCCGACCGAGCCATG                         GATTTTGTCGAGTCTGTATTCAGGGAGCGTTTGCATCTGGAACTACCAGAC
genomic: CAGAGGTCGGAGAGGGCCAAGTCCGTGGATCTGCATCCGACCGAGCCATGgtgagtgggc ... tgtaatgcagGATTTTGTCGAGTCTGTATTCAGGGAGCGTTTGCATCTGGAACTACCAGAC
EST: gi|88575756|gb|CI669901.1|CI669901
EST:     CAGAGGTCGGAGAGGGCCAAGTCCGTGGATCTGCATCCGACCGAGCCATG                         GATTTTGTCGAGTCTGTATTCAGGGAGCGTTTGCATCTGGAACTACCAGAC
genomic: CAGAGGTCGGAGAGGGCCAAGTCCGTGGATCTGCATCCGACCGAGCCATGgtgagtgggc ... tgtaatgcagGATTTTGTCGAGTCTGTATTCAGGGAGCGTTTGCATCTGGAACTACCAGAC
EST: gi|3760098|gb|C97356.1|C97356
EST:     CAGAGGTCGGAGAGGGCCAAGTCCGTGGATCTGCATCCGACCGAGCCATG                         GATTTTGTCGAGTCTGTATTCAGGGAGCGTTTGCATCTGGAACTACCAGAC
genomic: CAGAGGTCGGAGAGGGCCAAGTCCGTGGATCTGCATCCGACCGAGCCATGgtgagtgggc ... tgtaatgcagGATTTTGTCGAGTCTGTATTCAGGGAGCGTTTGCATCTGGAACTACCAGAC
EST: gi|29671006|gb|CB667281.1|CB667281
EST:     CAGAGGTCGGAGAGGGCCAAGTCCGTGGATCTGCATCCGACCGAGCCATG                         GATTTTGTCGAGTCTGTATTCAGGGAGCGTTTGCATCTGGAACTACCAGAC
genomic: CAGAGGTCGGAGAGGGCCAAGTCCGTGGATCTGCATCCGACCGAGCCATGgtgagtgggc ... tgtaatgcagGATTTTGTCGAGTCTGTATTCAGGGAGCGTTTGCATCTGGAACTACCAGAC

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), 73 (downstream exon)
Score: 42

AGGAAGCTCGCGCAGAGGTCGGAGAGGGCCAAGTCCGTGGATCTGCATCCGACCGAGCCATGgtgagtgggc ... tgtaatgcagGATTTTGTCGAGTCTGTATTCAGGGAGCGTTTGCATCTGGAACTACCAGACGCAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtaatgattatgttgttcaaagtcacatgaataacttcctccggtgtaatgcagGATTTTGTCGAGTCTGTATTCAGGGAGCGTTTGCATCTGGAACTACCAGACGCAG
                             gaataac  putative branch site (score: 42)
       attatgtt  TA-rich tract