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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttataagacaattttttttgactaactgtttatgagacaattagtagtgatacttccgtcttttaatgtacactgatgagcgggcaaaatactcatatgtgtgttctatgcttcactctgtgcagATACCAAAGAAAGGGAAGATTTATTCAGTGAATGAAGGGAATGCGAAAAATTGGGACGAGCCTACCGCAAA

Basic information

species Oryza sativa
transcript LOC_Os01g64660.4
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g64660.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GLYMA16G28310.1 (Glycine max), 3'ss of exon 8
gtttataagacaattttttttgactaactgtttatgagacaattagtagtgatacttccgtcttttaatgtacactgatgagcgggcaaaatactcatatgtgtgttctatgcttcactctgtgcagATACCAAAGAAAGGGAAGATTTATTCAGTGAATGAAGGGAATGCGAAAAATTGGGACGAGCCTACCGCAAA
           ||||  | | |||||      ||    | ||  |   || |||    || | |     |   |||  |||| |   |   || |||| ||     | |||| ||  |||||||||||| ||||||||||| || |||||||||||||||||||| ||||| ||||| |||||    ||||| || | 
-----------aattcatatagacta------tagagtataaacacacgt-atatccacgccatcagtgggttact--tgag-gtatatggtaatcatttg----atgtatgatt--ctctgtgcagATCCCAAAGAAAGGTAAAATTTATTCAGTGAATGAAGGAAATGCCAAAAACTGGGATCGTCCTACTGCTAC

upper sequence: LOC_Os01g64660.1 (Oryza sativa), 3'ss of exon 7
lower sequence: EFJ04554 (Selaginella moellendorffii), 3'ss of exon 7
gtttataagacaattttttttgactaactgtttatgagacaattagtagt-gatacttccgtcttttaatgtacactgatgagcgggcaaaatactcatatgtgtgttctatgcttcactctgtgcagATACCAAAGAAAGGGAAGATTTATTCAGTGAATGAAGGGAATGCGAAAAATTGGGACGAGCCTACCGCAAA
                                     |  | || |||   |||  |||| |   ||| |  | |  |||||  | |  | || | ||    ||      ||| ||   ||| |||||||||||||||| || || |||||||| |||||||| || ||||| || || ||||||||||| ||   |  
-------------------------------------gtaagttcgtaaaagatgattcctttcattattaca-atggatgattgtg--agatgcccaagattg------atgattttttctttgcagATACCAAAGAAGGGAAAAATTTATTCCGTGAATGAGGGCAATGCAAAGAACTGGGACGAGCCCACTAGATT

upper sequence: LOC_Os01g64660.1 (Oryza sativa), 3'ss of exon 7
lower sequence: EFJ36627 (Selaginella moellendorffii), 3'ss of exon 6
gtttataagacaattttttttgactaactgtttatgagacaattagta-gtgatacttccgtcttttaatgtacactgatgagcgggcaaaatactcatatgtgtgttctatgcttcactctgtgcagATACCAAAGAAAGGGAAGATTTATTCAGTGAATGAAGGGAATGCGAAAAATTGGGACGAGCCTACCGCAAA
                                     |  | || |||   |||  |||| |   ||| |  | |  |||||    |  | || | ||       | || ||| ||   ||| |||||||||||||||| || || |||||||| |||||||| || ||||| || || ||||||||||| ||   |  
-------------------------------------gtaagttcgtataagatgattcctttcattattaca-atggatgatt--gtgagatgcccaa------gatcgatgattgcttctttgcagATACCAAAGAAGGGAAAAATTTATTCCGTGAATGAGGGCAATGCAAAGAACTGGGACGAGCCCACTAGATT

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|29686739|gb|CB683014.1|CB683014
EST:     CACTTGATCCATCTCTCGGGGAGTTCATATTAACTCATCCAGACATCAAG                         ATACCAAAGAAAGGGAAGATTTATTCAGTGAATGAAGGGAATGCGAAAAAT
genomic: CACTTGATCCATCTCTCGGGGAGTTCATATTAACTCATCCAGACATCAAGgtttataaga ... ctctgtgcagATACCAAAGAAAGGGAAGATTTATTCAGTGAATGAAGGGAATGCGAAAAAT
EST: gi|29621610|gb|CB626621.1|CB626621
EST:     CACTTGATCCATCTCTCGGGGAGTTCATATTAACTCATCCAGACATCAAG                         ATACCAAAGAAAGGGAAGATTTATTCAGTGAATGAAGGGAATGCGAAAAAT
genomic: CACTTGATCCATCTCTCGGGGAGTTCATATTAACTCATCCAGACATCAAGgtttataaga ... ctctgtgcagATACCAAAGAAAGGGAAGATTTATTCAGTGAATGAAGGGAATGCGAAAAAT
EST: gi|58588683|gb|CF986991.1|CF986991
EST:     CACTTGATCCATCTCTCGGGGAGTTCATATTAACTCATCCAGAGATCAAG                         ATACCAAAGAAAGGGAAGATTTATTCAGTGAATGAAGGGAATGCGAAAAAT
genomic: CACTTGATCCATCTCTCGGGGAGTTCATATTAACTCATCCAGACATCAAGgtttataaga ... ctctgtgcagATACCAAAGAAAGGGAAGATTTATTCAGTGAATGAAGGGAATGCGAAAAAT
EST: gi|29613014|gb|CB618027.1|CB618027
EST:     CACTTGATCCATCTCTCGGGGAGTTCATATTAACTCATCCAGACATCAAG                         ATACCAAAGAAAGGGAAGATTTATTCAGTGAATGAAGGGAATGCGAAAAAT
genomic: CACTTGATCCATCTCTCGGGGAGTTCATATTAACTCATCCAGACATCAAGgtttataaga ... ctctgtgcagATACCAAAGAAAGGGAAGATTTATTCAGTGAATGAAGGGAATGCGAAAAAT
EST: gi|29617760|gb|CB622772.1|CB622772
EST:     CACTTGATCCATCTCTCGGGGAGTTCATATTAACTCATCCAGACATCAAG                         ATACCAAAGAAAGGGAAGATTTATTCAGTGAATGAAGGGAATGCGAAAAAT
genomic: CACTTGATCCATCTCTCGGGGAGTTCATATTAACTCATCCAGACATCAAGgtttataaga ... ctctgtgcagATACCAAAGAAAGGGAAGATTTATTCAGTGAATGAAGGGAATGCGAAAAAT
EST: gi|38473796|gb|CF957928.1|CF957928
EST:     CACTTGATCCATCTCTCGGGGAGTTCATATTAACTCATCCAGACATCAAG                         ATACCAAAGAAAGGGAAGATTTATTCAGTGAATGAAGGGAATGCGAAAAAT
genomic: CACTTGATCCATCTCTCGGGGAGTTCATATTAACTCATCCAGACATCAAGgtttataaga ... ctctgtgcagATACCAAAGAAAGGGAAGATTTATTCAGTGAATGAAGGGAATGCGAAAAAT
EST: gi|33820806|gb|CF336207.1|CF336207
EST:     CACTTGATCCATCTCTCGGGGAGTTCATATTAACTCATCCAGACATCAAG                         ATACCAAAGAAAGGGAAGATTTATTCAGTGAATGAAGGGAATGCGAAAAAT
genomic: CACTTGATCCATCTCTCGGGGAGTTCATATTAACTCATCCAGACATCAAGgtttataaga ... ctctgtgcagATACCAAAGAAAGGGAAGATTTATTCAGTGAATGAAGGGAATGCGAAAAAT
EST: gi|27546650|gb|CA764792.2|CA764792
EST:     CACTCGATCCATCTCTCGGGGAGTTCATATTAACTCATCCAGACATCAAG                         ATACCAAAGAAAGGGAAGATTTATTCAGTGAATGAAGGGAATGCGAAAAAT
genomic: CACTTGATCCATCTCTCGGGGAGTTCATATTAACTCATCCAGACATCAAGgtttataaga ... ctctgtgcagATACCAAAGAAAGGGAAGATTTATTCAGTGAATGAAGGGAATGCGAAAAAT
EST: gi|29682614|gb|CB678889.1|CB678889
EST:     CACTTGATCCATCTCTCGGGGAGTTCATATTAACTCATCCAGACATCAAG                         ATACCAAAGAAAGGGAAGATTTATTCAGTGAATGAAGGGAATGCGAAAAAT
genomic: CACTTGATCCATCTCTCGGGGAGTTCATATTAACTCATCCAGACATCAAGgtttataaga ... ctctgtgcagATACCAAAGAAAGGGAAGATTTATTCAGTGAATGAAGGGAATGCGAAAAAT

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: 74 (upstream exon), 71 (downstream exon)
Score: 153

CTTGTTCTGAGTACTGGAAATGGTGTCAATGGCTTCACACTTGATCCATCTCTCGGGGAGTTCATATTAACTCATCCAGACATCAAGgtttataaga ... ctctgtgcagATACCAAAGAAAGGGAAGATTTATTCAGTGAATGAAGGGAATGCGAAAAATTGGGACGAGCCTACCGCAAA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cactgatgagcgggcaaaatactcatatgtgtgttctatgcttcactctgtgcagATACCAAAGAAAGGGAAGATTTATTCAGTGAATGAAGGGAATGCGAAAAATTGGGACGAGCCTACCGCAAA
 cactgat  putative branch site (score: 153)
                                        cttcactct  putative PPT
               aaaatact  TA-rich tract