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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtgaagtgttaagatgatgagcatctgtacatcatagagacatactccttgattcttgaaatttatgtccagtcatctgtatcctctcttctgcagGGAGTGTGGACTAGCTCACAAGACAATAATTTTTGTCCTAGAAGAGTTTGACCTCTTTGCTCAG

Basic information

species Oryza sativa
transcript LOC_Os01g49010.2
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g49010.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM5G876520_T04 (Zea mays), 3'ss of exon 1
------gtaagtgaagtgttaagatgatgagcatctgtacatcatagagacatactccttgattcttgaaatttatgtccagtcat-ctgtatcctctcttctgcagGGAGTGTGGACTAGCTCACAAGACAATAATTTTTGTCCTAGAAGAGTTTGACCTCTTTGCTCAG
       | |||||| |  |   || ||| | || ||||     | ||| |||| || ||  ||| | |   || | | || |  |  | ||| |||||||||| |||||||| ||||||||||||||||||||| | ||| | |||||||| || |||||||||||||||
gtgagctttagtgaaataatgccataatgggtat-tgta-----ttgagccatagtctttagttcataattcttttattcatttctgttttatactctcttctgtagGGAGTGCGGACTAGCTCACAAGACAATACTATTTATTCTAGAAGAATTCGACCTCTTTGCTCAG

upper sequence: LOC_Os01g49010.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA20G25850.1 (Glycine max), 3'ss of exon 7
gtaagtgaagtgttaagatgatgagcatctgtacatcatagagacatactccttgattcttgaaatttatgtccagtcatctgtatcctctcttctgcagGGAGTGTGGACTAGCTCACAAGACAATAATTTTTGTCCTAGAAGAGTTTGACCTCTTTGCTCAG
                     |||| |     |  | || |    | |       ||  ||  || || |    |  ||| | |   || | || |  ||||| |||||| |||| || || ||||||||||||||  | || ||||||||||| |||||||||
--------------------gtgagtaa--aaattttattggttgaaaaaggaaaataatttgaagttcta---aagcatttattatcttttttttctagGGAATGTGGATTAGCACATAAAACAATAATTTTTGTTTTGGATGAGTTTGACCTGTTTGCTCAG

upper sequence: LOC_Os01g49010.1 (Oryza sativa), 3'ss of exon 6
lower sequence: Vv01s0011g04400.t01 (Vitis vinifera), 3'ss of exon 6
------------------------------------------------gtaagtgaagtgttaagatgatgagcatctgta-catcatagagacatactccttgattcttgaaatttatgtccagtcatctgtatcctctcttctgcagGGAGTGTGGACTAGCTCACAAGACAATAATTTTTGTCCTAGAAGAGTTTGACCTCTTTGCTCAG---------------------
                                                |   ||  | | |    | ||||| ||| | |    |||| || |  |  |  ||   | |     || |||     || | | | |  |||||| | ||||||||||||| |||||||||||||||| ||||||||  | || ||||||||| ||||  |||||                     
gtgagtgtacacatttggtaggtgattgtgtcctccgtcagtgctgaggcttgttcattttgctaaagatgaccatttttggtttcatggaaaagttgttattctctttct---ttcatgaattttcttatttgtgatctcttgt-cagGGAGTGTGGATTAGCTCACAAGACAATCATTTTTGTATTGGATGAGTTTGACTTCTTCACTCAGGCAAGATTACCTCTCTCTCAT

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|218491615|gb|FG954647.1|FG954647
EST:     GCTTCTTCAGATGACAACACGGAATTCATGATTGACATGTTACG                         GGAGTGTGGACTAGCTCACAAGACAATAATTTTTGTCCTAGAAGAGTTTGA
genomic: GCTTCTTCAGATGACAACACGGAATTCATGATTGACATGTTACGgtaagtgaag ... tcttctgcagGGAGTGTGGACTAGCTCACAAGACAATAATTTTTGTCCTAGAAGAGTTTGA




















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: 44 (upstream exon), 58 (downstream exon)
Score: 2

GCTTCTTCAGATGACAACACGGAATTCATGATTGACATGTTACGgtaagtgaag ... tcttctgcagGGAGTGTGGACTAGCTCACAAGACAATAATTTTTGTCCTAGAAGAGTTTGACCTCTTTGCTCAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atactccttgattcttgaaatttatgtccagtcatctgtatcctctcttctgcagGGAGTGTGGACTAGCTCACAAGACAATAATTTTTGTCCTAGAAGAGTTTGACCTCTTTGCTCAG
     ccttgat  putative branch site (score: 2)
                                  tctgtatcctctcttc  putative PPT
          attcttgaaatttat  TA-rich tract