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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTGATTGCGATGAGCACAAGAGTGTGTGCAGCAAGTATGGAGTTTCTGGGTACCCAACAATTCAATGGTTCCCCAAAGGATCCCTGGAGCCCAAAAAgtgaggctgcataacttttgttcaaatacttttgaacatctacaccagacaaaattttcatgatttatatcactacaaccatgtag

Basic information

species Oryza sativa
transcript LOC_Os01g23740.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g23740.2 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G128171_T04 (Zea mays), 5'ss of exon 3
GTTGATTGCGATGAGCACAAGAGTGTGTGCAGCAAGTATGGAGTTTCTGGGTACCCAACAATTCAATGGTTCCCCAAAGGATCCCTGGAGCCCAAAAAgtgaggctgcataacttttgttcaaatacttttgaacatctacaccagacaaaattt-----tcatgatttatatcactacaaccatgtag
|||||||| ||||||||||||||| |||||||||||||||||||||| ||||| |||||||| ||||||||||| ||||||||| |||||||||||||||||||  ||        |||| ||||  ||    |   ||        |||  | |     |  |||   | ||  ||    | |  |||
GTTGATTGTGATGAGCACAAGAGTTTGTGCAGCAAGTATGGAGTTTCCGGGTATCCAACAATCCAATGGTTCCCGAAAGGATCCTTGGAGCCCAAAAAgtgagggagcgcg-----tgtttaaatttttccatat-cctttgtttaccaagttctgtgaattctgacagaaattcctttggcaaattag

upper sequence: LOC_Os01g23740.2 (Oryza sativa), 5'ss of exon 3
lower sequence: GLYMA02G01750.1 (Glycine max), 5'ss of exon 3
GTTGATTGCGATGAGCACAAGAGTGTGTGCAGCAAGTATGGAGTTTCTGGGTACCCAACAATTCAATGGTTCCCCAAAGGATCCCTGGAGCCCAAAAAgtgaggc--tgcataacttttgttcaaatacttttgaacatctacaccagacaaaattttcatgattta--tatcactacaaccatgtag------------------------------------------
||||| || ||||||||||||||| |||||||||| |||||||| |||||||||||||||||||| ||||| || |||||||| || || ||||||||||||||   |   |  || |||    |  || ||   |||  |  |  |    || |  |  | |||||  | ||| | ||    | |                                            
GTTGACTGTGATGAGCACAAGAGTTTGTGCAGCAAATATGGAGTCTCTGGGTACCCAACAATTCAGTGGTTTCCAAAAGGATCTCTTGAACCCAAAAAgtgaggagatttttgtctattggaatataacattgacacaattttat-atcttaattcatagttatttacctgtcatttcacatttatcattccttttgcattcaatacttgattttggaaaattcccatag

upper sequence: LOC_Os01g23740.2 (Oryza sativa), 5'ss of exon 3
lower sequence: GLYMA06G24520.1 (Glycine max), 5'ss of exon 4
GTTGATTGCGATGAGCACAAGAGTGTGTGCAGCAAGTATGGAGTTTCTGGGTACCCAACAATTCAATGGTTCCCCAAAGGATCCCTGGAGCCCAAAAAgtgaggc--tgcataacttttgttcaaatacttttgaacatctacaccagacaaaattttcatgatttatatcactacaaccatgtag--------------------------------------------
||||| || ||||||||||||||| |||||||||| |||||||| |||||||||||||||||||| ||||| || |||||||| || || ||||||||||||||   |   |  || |||    |  || ||   |||  |  |  |    || |  |  | |||||  |  |      ||| ||                                             
GTTGACTGTGATGAGCACAAGAGTTTGTGCAGCAAATATGGAGTCTCTGGGTACCCAACAATTCAGTGGTTTCCAAAAGGATCTCTTGAACCCAAAAAgtgaggagatttttgtctattggaatataacattgacacaattttat-atcttaattcatagttatttacctgtcatttctcatttatcattccttttgcattcaatacttgattttggaaaattcccatag

upper sequence: LOC_Os01g23740.2 (Oryza sativa), 5'ss of exon 3
lower sequence: GLYMA10G01820.1 (Glycine max), 5'ss of exon 4
GTTGATTGCGATGAGCACAAGAGTGTGTGCAGCAAGTATGGAGTTTCTGGGTACCCAACAATTCAATGGTTCCCCAAAGGATCCCTGGAGCCCAAAAAgtgaggctgcataacttttgttcaaatacttt-tgaaca----tctacaccaga---caaaatt-ttcatgatttatatcactacaaccatgtag-------------------------------------
||||| || |||||||| |||||| ||||||||||||||||||| |||||||||||||||||||| ||||| || |||||||| || ||  |||||||||||||    ||    | | ||  ||||     || | |    | || | |  |   || | || || |    | || ||||  | | |||                                         
GTTGACTGTGATGAGCATAAGAGTTTGTGCAGCAAGTATGGAGTCTCTGGGTACCCAACAATTCAGTGGTTTCCAAAAGGATCTCTTGAAGCCAAAAAgtgagg--agatcttctctattggaatataacatggagacgattttatatctcaattcatagttatttacctgtcatttcacatctatcattccttttgcattcaatatttgattttggaaaattcccatag

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|58598802|gb|CK009330.1|CK009330
EST:     GGGTACCCAACAATTCAATGGTTCCCCAAAGGATCCCTGGAGCCCAAAAA                         GTATGAAGGACAACGCAGTGCAGAGGCCCTTGCTGAATTTGTTAACACTGA
genomic: GGGTACCCAACAATTCAATGGTTCCCCAAAGGATCCCTGGAGCCCAAAAAgtgaggctgc ... aaccatgtagGTATGAAGGACAACGCAGTGCAGAGGCCCTTGCTGAATTTGTTAACACTGA




















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), 56 (downstream exon)
Score: 54

GTTGATTGCGATGAGCACAAGAGTGTGTGCAGCAAGTATGGAGTTTCTGGGTACCCAACAATTCAATGGTTCCCCAAAGGATCCCTGGAGCCCAAAAAgtgaggctgc ... aaccatgtagGTATGAAGGACAACGCAGTGCAGAGGCCCTTGCTGAATTTGTTAACACTGAAGGAG




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