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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtcgaaacttggaagttaaagcatggccctatgcaagctctgagagtctgagcactgactaattgaaacgctcgtgttgcagTTATTCATGTGCCTAGCTACGAATCTGTCAGGCGCAAGTTCCATTCCAAGTGAGCATTCAGCACCTGGACCTGCGTGGGTTGTTCTGGAATTTCAAGCCG

Basic information

species Oryza sativa
transcript LOC_Os05g44916.1
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g44916.2 (Oryza sativa), 3'ss of exon 11
lower sequence: GRMZM2G005036_T02 (Zea mays), 3'ss of exon 13
gtatgtcgaa-acttggaagttaaagcatggccctatgcaagctctgagagtctgagcactgactaattgaaacgctcgtgttgcagTTATTCATGTGCCTAGCTACGAATCTGTCAGGCGCAAGTTCCATTCCAAGTGAGC--ATTCAGCACCTGGACCTGCGTGGGTTGTTCTGGAATTTCAAGCCG
||||||  |  | ||   |||  |  |||||  |  ||    |    |  || ||      |||||| ||||  |||  | |||||||||||||||| ||||||||||| ||||| || |||||||| || || |||||||   || ||||| | |||| ||| ||   |||||    |  | | |   
gtatgttcagcagtttcgagt--agtcatggtgcattggtgcccgacaaggtatgg----cgactaactgaattgcttttattgcagTTATTCATGTTCCTAGCTACGAGTCTGTTAGCCGCAAGTTTCACTCGAAGTGAGAGGATCCAGCATC-GGACTTGCATGACCTGTTCCAACAACTGATGTG-
















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|89173544|gb|CI041437.1|CI041437
EST:     TGCAAAGAAGATTATTTCTTCGCCGCTTACATTGGCATCATGGGGTGATG                         TTATTCATGTGCCTAGCTACGAATCTGTCAGGCGCAAGTTCCATTCCAAGT
genomic: TGCAAAGAAGATTATTTCTTCGCCGCTTACATTGGCATCATGGGGTGATGgtatgtcgaa ... cgtgttgcagTTATTCATGTGCCTAGCTACGAATCTGTCAGGCGCAAGTTCCATTCCAAGT
EST: gi|88223386|gb|CI223235.1|CI223235
EST:     AGATTATTTCTTCGCCGCTTACATNGGCATCATGGGGTGATG                         TTATTCATGTGCCTAGCTACGAATCTGTCAGGCGCAAGTTCCATTCCAAGT
genomic: AGATTATTTCTTCGCCGCTTACATTGGCATCATGGGGTGATGgtatgtcgaa ... cgtgttgcagTTATTCATGTGCCTAGCTACGAATCTGTCAGGCGCAAGTTCCATTCCAAGT
EST: gi|86496588|gb|CI139221.1|CI139221
EST:     TGCAAAGAAGATTATTTCTTCGCCGCTTACATTGGCATCATGGGGTGATG                         TTATTCATGTGCCTAGCTACGAATCTGTCAGGCGCAAGTTCCATTCCAAGT
genomic: TGCAAAGAAGATTATTTCTTCGCCGCTTACATTGGCATCATGGGGTGATGgtatgtcgaa ... cgtgttgcagTTATTCATGTGCCTAGCTACGAATCTGTCAGGCGCAAGTTCCATTCCAAGT
EST: gi|87036708|gb|CI191330.1|CI191330
EST:     TGCAAAGAAGATTATTTCTTCGCCGCTTACATTGGCATCATGGGGTGATG                         TTATTCATGTGCCTAGCTACGAATCTGTCAGGCGCAAGTTCCATTCCAAGT
genomic: TGCAAAGAAGATTATTTCTTCGCCGCTTACATTGGCATCATGGGGTGATGgtatgtcgaa ... cgtgttgcagTTATTCATGTGCCTAGCTACGAATCTGTCAGGCGCAAGTTCCATTCCAAGT
EST: gi|88993445|gb|CI257873.1|CI257873
EST:     TGCAAAGAAGATTATTTCTTCGCCGCTTACATTGGCATCATGGGGTGATG                         TTATTCATGTGCCTAGCTACGAATCTGTCAGGCGCAAGTTCCATTCCAAGT
genomic: TGCAAAGAAGATTATTTCTTCGCCGCTTACATTGGCATCATGGGGTGATGgtatgtcgaa ... cgtgttgcagTTATTCATGTGCCTAGCTACGAATCTGTCAGGCGCAAGTTCCATTCCAAGT
EST: gi|33654803|gb|CF277417.1|CF277417
EST:     TCGCCGCTTACATTGGCATCATGGGGTGATG                         TTATTCATGTGCCTAGCTACGAATCTGTCAGGCGCAAGTTCCATTCCAAGT
genomic: TCGCCGCTTACATTGGCATCATGGGGTGATGgtatgtcgaa ... cgtgttgcagTTATTCATGTGCCTAGCTACGAATCTGTCAGGCGCAAGTTCCATTCCAAGT

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: 45 (upstream exon), 31 (downstream exon)
Score: 2

TACTTCCTGAAAACTGTTGAGGAGATCACTTTAAATGACATTTCTTCAACTGCAAAGAAGATTATTTCTTCGCCGCTTACATTGGCATCATGGGGTGATGgtatgtcgaa ... cgtgttgcagTTATTCATGTGCCTAGCTACGAATCTGTCAGGCGCAAGTTCCATTCCAAGTGAGCATTCAGCACCTGGACCTGCGTGGGTTGTTCTGGAATTTCAAGCCG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cctatgcaagctctgagagtctgagcactgactaattgaaacgctcgtgttgcagTTATTCATGTGCCTAGCTACGAATCTGTCAGGCGCAAGTTCCATTCCAAGTGAGCATTCAGCACCTGGACCTGCGTGGGTTGTTCTGGAATTTCAAGCCG
                             gactaat  putative branch site (score: 2)
                                taattgaaa  TA-rich tract