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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtactatgaataaaaacatgatgaccatctcacataattttaacaagaataagctgactgaccatacgttggtgctcagGTCCTGGAGCTTGACAGCATGAATGTGAAGGCTTTTTACAGAAGGGCACAGGCACACATGTATCTTGTTGACTTTGATTTGGCAGAACTGGATATCAAGA

Basic information

species Oryza sativa
transcript LOC_Os02g28980.1
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g28980.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM2G336858_T01 (Zea mays), 3'ss of exon 7
gtactatgaataaaaacatgatgaccatctcacataattttaacaagaataag-ctg-actgaccatacgt--tggtgctcagGTCCTGGAGCTTGACAGCATGAATGTGAAGGCTTTTTACAGAAGGGCACAGGCACACATGTATCTTGTTGACTTTGATTTGGCAGAACTGGATATCAAGA
|||||||      |   | |   |  | ||     |||| ||| ||||| ||  |||   | || ||| ||  ||||  | ||||||||||   ||||| ||  || |||||||| || |||||||||||||||||||||||| ||||||||||  |||||||||||||    ||||||||||
gtactatactctgagtaaagtgaaataacttg-ggaattataataagaaaaaaactgtggttacaataagtattggtatttagGTCCTGGAATCTGACAACACAAACGTGAAGGCCTTGTACAGAAGGGCACAGGCACACATGCATCTTGTTGATCTTGATTTGGCAGAGGCAGATATCAAGA
















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|29665077|gb|CB661352.1|CB661352
EST:     GTAAGCTGAAGCTTAAAGACTACAAGGAAGCAAAGGAACTGTGTACTGAG                         GTCCTGGAGCTTGACAGCATGAATGTGAAGGCTTTTTACAGAAGGGCACAG
genomic: GTAAGCTGAAGCTTAAAGACTACAAGGAAGCAAAGGAACTGTGTACTGAGgtactatgaa ... tggtgctcagGTCCTGGAGCTTGACAGCATGAATGTGAAGGCTTTTTACAGAAGGGCACAG
EST: gi|218501934|gb|FG968124.1|FG968124
EST:     GTAAGCTGAAGCTTAAAGACTACAAGGAAGCAAAGGAACTGTGTACTGAG                         GTCCTGGAGCTTGACAGCATGAATGTGAAGGCTTTTTACAGAAGGGCACAG
genomic: GTAAGCTGAAGCTTAAAGACTACAAGGAAGCAAAGGAACTGTGTACTGAGgtactatgaa ... tggtgctcagGTCCTGGAGCTTGACAGCATGAATGTGAAGGCTTTTTACAGAAGGGCACAG
EST: gi|29644965|gb|CB649972.1|CB649972
EST:     GTAAGCTGAAGCTTAAAGACTACAAGGAAGCAAAGGAACTGTGTACTGAG                         GTCCTGGAGCTTGACAGCATGAATGTGAAGGCTTTTTACAGAAGGGCACAG
genomic: GTAAGCTGAAGCTTAAAGACTACAAGGAAGCAAAGGAACTGTGTACTGAGgtactatgaa ... tggtgctcagGTCCTGGAGCTTGACAGCATGAATGTGAAGGCTTTTTACAGAAGGGCACAG
EST: gi|58677214|gb|CK065901.1|CK065901
EST:     GTAAGCTGAAGCTTAAAGACTACAAGGAAGCAAAGGAACTGTGTACTGAG                         GTCCTGGAGCTTGACAGCATGAATGTGAAGGCTTTTTACAGAAGGGCACAG
genomic: GTAAGCTGAAGCTTAAAGACTACAAGGAAGCAAAGGAACTGTGTACTGAGgtactatgaa ... tggtgctcagGTCCTGGAGCTTGACAGCATGAATGTGAAGGCTTTTTACAGAAGGGCACAG

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: 75 (upstream exon), 70 (downstream exon)
Score: 52

GCAGCTGTCCAAACCACTCAAGGTGAGTTGCAAGCTCAACAATGCTGCATGTAAGCTGAAGCTTAAAGACTACAAGGAAGCAAAGGAACTGTGTACTGAGgtactatgaa ... tggtgctcagGTCCTGGAGCTTGACAGCATGAATGTGAAGGCTTTTTACAGAAGGGCACAGGCACACATGTATCTTGTTGACTTTGATTTGGCAGAACTGGATATCAAGA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccatctcacataattttaacaagaataagctgactgaccatacgttggtgctcagGTCCTGGAGCTTGACAGCATGAATGTGAAGGCTTTTTACAGAAGGGCACAGGCACACATGTATCTTGTTGACTTTGATTTGGCAGAACTGGATATCAAGA
                               gactgac  putative branch site (score: 52)
       acataattttaacaag  TA-rich tract