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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatcagatccatccttcaaatcatccgtttatcactgctttattgaatcatcttgagcatttgtagcatgtgctaactatacccacggattggcattaccagGAAAGCACTTATCCATGCTTCCAGTTGAGCCTAAATTGGGGAAGATGCTGATTTTTGGTGCTATTTTTAATTGCCTTGATCCCATATTAACCATTGTTTC

Basic information

species Oryza sativa
transcript LOC_Os01g02884.1
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g02884.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G373175_T02 (Zea mays), 3'ss of exon 13
gtatcagatccatccttcaaatcatccgtttatc-----actgctttatt--gaatcatcttgagcatttgtagc--atgtgctaactatacccacggattggcattaccagGAAAGCACTTATCCATGCTTCCAGTTGAGCCTAAATTGGGGAAGATGCTGATTTTTGGTGCTATTTTTAATTGCCTTGATCCCATATTAACCATTGTTTC
||| | ||| || || | | || |    ||||        |||||||| |  | ||| |||  ||| ||||||||   |||||| |  || |  || | ||| ||||  ||||||||||||| || |||||||||||||| ||||| || || |||||||| |||||||| |||||||||||||| || ||||||||||||||||| |||||
gtacctgattcacccataagattaaatttttacataacagctgctttactccgcatc-tctgtagcttttgtagcttgtgtgctgataatgcttactgcttgtcattttcagGAAAGCACTTGTCTATGCTTCCAGTTGAACCTAAGTTAGGAAAGATGCTTATTTTTGGGGCTATTTTTAATTGTCTGGATCCCATATTAACCATAGTTTC

upper sequence: LOC_Os01g02884.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GLYMA09G18490.1 (Glycine max), 3'ss of exon 8
gtatcagatccatccttcaaatcatccgtttatcactgctttattgaatcatcttgagcatttgtagcatgtgctaactatacccacggattggca-ttaccagGAAAGCACTTATCCATGCTTCCAGTTGAGCCTAAATTGGGGAAGATGCTGATTTTTGGTGCTATTTTTAATTGCCTTGATCCCATATTAACCATTGTTTC
      | |  | | ||   |||   | |  |   |||||| | ||| | || ||      || ||   | |   | |   |     ||  || || ||  ||||  |  ||||  | ||||||||  | || || ||| | || |||||||| || ||||||| ||| || |||||||| |||||||||||||| |||||| |
---gttggttgaccatt---atccggcatgaaaatctgctt-actga-ttattttc----cttataaagtataa-agcccaatagttggtctgtcaattgacagGGCACAACTTGACAATGCTTCCCATGGAACCCAAACTTGGCAAGATGCTTATATTTGGTGTTATCTTCAATTGCCTGGATCCCATATTAACTATTGTTGC

upper sequence: LOC_Os01g02884.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GLYMA20G25800.1 (Glycine max), 3'ss of exon 16
gtatcagatccatccttcaaatcatccgtt-tatcactgctttatt-gaatcatcttgagcatttgtagcatgtgctaactatacccacggattggcattaccagGAAAGCACTTATCCATGCTTCCAGTTGAGCCTAAATTGGGGAAGATGCTGATTTTTGGTGCTATTTTTAATTGCCTTGATCCCATATTAACCATTGTTTC
                |    | |||| || ||   |||    ||| |  | |||||   |  ||| |         |  | ||     ||  |   |||  ||||      | |  | ||||||||  | || || ||| | || |||||||| || || ||||||||||| |||||||| ||||||||||||||  | ||| |
---------------gttggttgatcccttctagtcctggaaaatttggcttatcttttcctcttgaaatgatgaagacttgtatttg-ggccttcaattgacagGGCGCTGCCTGACAATGCTTCCTATGGAACCCAAACTTGGCAAGATGCTAATATTAGGTGCTATTTTCAATTGCCTGGATCCCATATTAACTGTGGTTGC

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), 73 (downstream exon)
Score: 22

GTAGAAAATGCCATTGAATATCTCAAAGTCATTGGAGCGTTTGATCGTAATGAAGAGTTAACAATTCTAGgtatcagatc ... gcattaccagGAAAGCACTTATCCATGCTTCCAGTTGAGCCTAAATTGGGGAAGATGCTGATTTTTGGTGCTATTTTTAATTGCCTTGATCCCATATTAACCATTGTTTC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcatcttgagcatttgtagcatgtgctaactatacccacggattggcattaccagGAAAGCACTTATCCATGCTTCCAGTTGAGCCTAAATTGGGGAAGATGCTGATTTTTGGTGCTATTTTTAATTGCCTTGATCCCATATTAACCATTGTTTC
                       tgctaac  putative branch site (score: 22)
                          taactata  TA-rich tract