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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGCTGCGGTATTCCATAATGCAAGCACACGGTTCTGTGATGGGGCTCGCTTTGGTCTAGGTGCTGAGgtatgtcctttaaatttgtatcactttataacttggacattttcgttaactagttatcaaaaaaaaatagttatcgaaaatatatgttgttactattgaatggtcagcgtttcattcagtcccctattttctttcctttatcaaatatag

Basic information

species Oryza sativa
transcript LOC_Os01g62900.1
intron # 18
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g62900.1 (Oryza sativa), 5'ss of exon 18
lower sequence: GRMZM2G028535_T02 (Zea mays), 5'ss of exon 18
TGCTGCGGTATTCCATAATGCAAGCACACGGTTCTGTGATGGGGCTCGCTTTGGTCTAGGTGCTGAGgtatgtcctttaaatttgtatcactttataacttggacattttcgttaactagttatcaaaaaaaaatagttatcgaaaatatatgttgttactattgaatggtcagcgtttcattcagtcccctattttctttcctttatcaaatatag
||| || || || ||||||||||||||| |||| ||||||||| | || ||||| |||||||||||||||  | ||||        |||  ||| ||| |            ||| | | ||||   |  |||| |||||  |    || ||||    |  ||| | | |    | || |   |                                 
TGCCGCTGTGTTTCATAATGCAAGCACAAGGTTTTGTGATGGGACGCGTTTTGGGCTAGGTGCTGAGgtactttctttggcc----atctgtttttaattc-----------ttatcgatttatatcatgaaaacagtta--ggctttacatgtgaagatcatttatttgaactctttgcgcgc---------------------------------

upper sequence: LOC_Os01g62900.1 (Oryza sativa), 5'ss of exon 18
lower sequence: GLYMA07G16510.1 (Glycine max), 5'ss of exon 15
TGCTGCGGTATTCCATAATGCAAGCACACGGTTCTGTGATGGGGCTCGCTTTGGTCTAGGTGCTGAGgta-tgtcctttaaatttgtatcactttataacttggacattttcgttaactagttatcaaaaaaaaatagttatcgaaaatatatgttgttactattgaatggtcagcgtttcattcagtcccctattttctttcctttatcaaatatag
|||||| |||||||| |||||||| ||| |||||||||||||  |||||||||| || ||||| |||||  | | ||||  ||  | ||    | ||||          || |      ||||||  ||       | || || |   |   || | ||| | ||||   |                                               
TGCTGCTGTATTCCACAATGCAAGTACAAGGTTCTGTGATGGAACTCGCTTTGGCCTTGGTGCAGAGgtggtctactttccataagcatattgtaataa----------ttagcagcacagttattcaa------catttctcaactgttcttggttttattgttgatcag-----------------------------------------------

upper sequence: LOC_Os01g62900.1 (Oryza sativa), 5'ss of exon 18
lower sequence: GLYMA18G40770.1 (Glycine max), 5'ss of exon 20
TGCTGCGGTATTCCATAATGCAAGCACACGGTTCTGTGATGGGGCTCGCTTTGGTCTAGGTGCTGAGgta-tgtcctttaaatttgtatcactttataacttggacattttcgttaactagttatcaaaaaaaaatagttatcgaaaatatatgttgttactattgaatggtcagcgtttcattcagtcccctattttctttcctttatcaaatatag
|||||| |||||||| || ||||| ||| |||| |||||||| ||||||||||| || ||||| |||||  ||| ||||  ||  |  |    | ||||          || |      ||||||  |||        || || |   | | ||   ||| | ||||   |                                               
TGCTGCTGTATTCCACAACGCAAGTACAAGGTTTTGTGATGGAGCTCGCTTTGGCCTTGGTGCAGAGgtggtgtactttccataagcttattgtaataa----------ttagcagcacagttattcaaa------ttttctcaactgtttttggctttattgttgatcag-----------------------------------------------

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|428854|gb|D25010.1|D25010
EST:     ATGCAAGCACACGGTTCTGTGATGGGGCTCGCTTTGGTCTAGGTGCTGAG                         GTTGGCATAAGCACAGGGCGCATACATGCTCGGGGGCCTGTTGGCGTTGAT
genomic: ATGCAAGCACACGGTTCTGTGATGGGGCTCGCTTTGGTCTAGGTGCTGAGgtatgtcctt ... tcaaatatagGTTGGCATAAGCACAGGGCGCATACATGCTCGGGGGCCTGTTGGCGTTGAT
EST: gi|38471160|gb|CF955291.1|CF955291
EST:     AGCACACGGTTCTGTGATGGGGCTCGCTTTGGTCTAGGTGCTGAG                         GTTGGCATAAGCACAGGGCGCATACATGCTCGGGGGCCTGTTGGCGTTGAT
genomic: AGCACACGGTTCTGTGATGGGGCTCGCTTTGGTCTAGGTGCTGAGgtatgtcctt ... tcaaatatagGTTGGCATAAGCACAGGGCGCATACATGCTCGGGGGCCTGTTGGCGTTGAT
EST: gi|88261597|gb|CI365173.1|CI365173
EST:     GGCTCGCTT-GGTGTAGG-GCTGAG                         GT-GGCATAAGCACAGGGCGCATACATGCTCGGGGGCCTGTTGGCGTTGAT
genomic: GGCTCGCTTTGGTCTAGGTGCTGAGgtatgtcctt ... tcaaatatagGTTGGCATAAGCACAGGGCGCATACATGCTCGGGGGCCTGTTGGCGTTGAT

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: 47 (upstream exon), 42 (downstream exon)
Score: 6

TGCTGCGGTATTCCATAATGCAAGCACACGGTTCTGTGATGGGGCTCGCTTTGGTCTAGGTGCTGAGgtatgtcctt ... tcaaatatagGTTGGCATAAGCACAGGGCGCATACATGCTCGGGGGCCTGTTGGCGTTGATGGACTCCTAACAACTCGATG




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