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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagattgactgcccgtttttcagagtgtgcctgtctttattcctcattatatcatggcactatagatttgactgaactgctacctctagGTGTGCTACTCCTGGTGGGTGCTCTCAAGCTTGATAATGATTGATAGAGTGCACTGGATTGACAAGGACAAACTTGCAAAATTCATACTAAATTGCCAG

Basic information

species Oryza sativa
transcript LOC_Os08g40140.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os08g40140.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G124557_T02 (Zea mays), 3'ss of exon 7
gtgagattgact-----gcccgtttttcagagtgtgcctgtctttattcctcattatatcatggcactatagatttgactgaac--tgcta---cctctagGTGTGCTACTCCTGGTGGGTGCTCTCAAGCTTGATAATGATTGATAGAGTGCACTGGATTGACAAGGACAAACTTGCAAAATTCATACTAAATTGCCAG
||||| || |||      |  ||  | |   || ||| |   |   | | |  ||  |  |   | |||| ||||| | |||||  | | |    ||| |||| |||||||| ||||||||||| || ||| |  | |||||||| |||||||| |||||||||||||| || ||  | ||||||||||| || || |||
gtgaggtttactctgtcacaagtcatgcgtggtctgcattcttcagtacatgtttccacgagcccgctatggatttaattgaaccctaccaaattctcaagGTTTGCTACTCGTGGTGGGTGCTATCGAGCCTAGTCATGATTGACAGAGTGCATTGGATTGACAAGGAAAAGCTAACGAAATTCATACTGAACTGTCAG

upper sequence: LOC_Os08g40140.1 (Oryza sativa), 3'ss of exon 6
lower sequence: Vv12s0134g00150.t01 (Vitis vinifera), 3'ss of exon 7
gtgagattgact-gcccgtttttcagagtgtgcctgtct-----ttattcctcattatatcatggcactatagatttg-actgaactgcta--------cctctagGTGTGCTACTCCTGGTGGGTGCTCTCAAGCTTGATAATGATTGATAGAGTGCACTGGATTGACAAGGACAAACTTGCAAAATTCATACTAAATTGCCAG
||   ||    | |||  | ||||    | |  || ||        || | |    ||   ||||  ||     ||   |||||| |   |         ||  |||| || ||||| ||||||||||| ||||||||||| |||||||| ||||  || |||||||||||||| || ||    ||||| ||| || | || |||
gtacaatccctttgcctttctttccttttttctctttcaagggaccatactttcccatgcaatggttcttggtcttcacactgaagtttcaattgtatctcttcagGTCTGTTACTCATGGTGGGTGCTTTCAAGCTTGATCATGATTGACAGAGCTCATTGGATTGACAAGGATAAGCTCATTAAATTTATAATAGACTGTCAG

upper sequence: LOC_Os08g40140.1 (Oryza sativa), 3'ss of exon 6
lower sequence: Vv15s0024g00080.t01 (Vitis vinifera), 3'ss of exon 7
---------------------gtgagattgactgcccgtttttcagagtgtgcctgtctttattcctcattata-tcatggcactatagatttgactg--aactgctac-------ctctagGTGTGCTACTCCTGGTGGGTGCTCTCAAGCTTGATAATGATTGATAGAGTGCACTGGATTGACAAGGACAAACTTGCAAAATTCATACTAAATTGCCAG
                      |    ||   |    ||| || |   |      | | | ||| |  || | | ||||     ||    | | |||   |  | |||        ||  |||| || ||||| ||||||||||| |||||| |||| |||||||| ||||  || |||||||||||||| || ||    ||||||||  || |||| |||
gtatgattctttttttcttccatatatttatttatttgttatttattttagagaagccataatttcctataaaaatcatttttatagttttcttactataagttcctattgtatcacttcagGTCTGTTACTCATGGTGGGTGCTATCAAGCCTGATCATGATTGACAGAGCTCATTGGATTGACAAGGAAAAGCTCATTAAATTCATCTTAGATTGTCAG

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|58681560|gb|CK070247.1|CK070247
EST:     GTCAGTGCAAAGAGGGAGGGCTCAATGGACGGCCTGAGAAACTTGCTGAT                         GTGTGCTACTCCTGGTGGGTGCTCTCAAGCTTGATAATGATTGATAGAGTG
genomic: GTCAGTGCAAAGAGGGAGGGCTCAATGGACGGCCTGAGAAACTTGCTGATgtgagattga ... ctacctctagGTGTGCTACTCCTGGTGGGTGCTCTCAAGCTTGATAATGATTGATAGAGTG
EST: gi|88220590|gb|CI220150.1|CI220150
EST:     TGAGAAACTTGCTGAT                         GTGTGCTACTCCTGGTGGGTGCTCTCAAGCTTGATAATGATTGATAGAGTG
genomic: TGAGAAACTTGCTGATgtgagattga ... ctacctctagGTGTGCTACTCCTGGTGGGTGCTCTCAAGCTTGATAATGATTGATAGAGTG

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: 70 (upstream exon), 74 (downstream exon)
Score: 9

CTCGTTGCATCACATTGATAGAGATCTCCTTGGATGGTGGCTTTGTGAGCGTCAGTGCAAAGAGGGAGGGCTCAATGGACGGCCTGAGAAACTTGCTGATgtgagattga ... ctacctctagGTGTGCTACTCCTGGTGGGTGCTCTCAAGCTTGATAATGATTGATAGAGTGCACTGGATTGACAAGGACAAACTTGCAAAATTCATACTAAATTGCCAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctttattcctcattatatcatggcactatagatttgactgaactgctacctctagGTGTGCTACTCCTGGTGGGTGCTCTCAAGCTTGATAATGATTGATAGAGTGCACTGGATTGACAAGGACAAACTTGCAAAATTCATACTAAATTGCCAG
                               atttgac  putative branch site (score: 9)
                                             ctacctct  putative PPT
           attatatcat  TA-rich tract