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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGCTTGAATACTTTGAATCAAAAGTTATCGAGCAACAGGAAGCTGCACGCAATGGAACTCGGAAACCTGATGCATCAATTGCTAGTAAAGGGCATCTAAGgtaaaatatagttaaatttcaccaacctaaagtatcgtaacttcttagagacttctcttttgcatttatagatatctaggtacagtatactttttataacatcttcactttgtactgactgttctactttgcgtttgcag

Basic information

species Oryza sativa
transcript LOC_Os07g23990.1
intron # 20
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os07g23990.1 (Oryza sativa), 5'ss of exon 20
lower sequence: GLYMA07G06160.1 (Glycine max), 5'ss of exon 22
GGCTTGAATACTTTGAATCAAAAGTTATCGAGCAACAGGAAGCTGCACGCAATGGAACTCGGAAACCTGATGCATCAATTGCTAGTAAAGGGCATCTAAGgtaaaatatagttaaatttcaccaacctaaagtatcgtaacttcttagagacttctcttttgcatttatagatatctaggtacagtatactttttataacatcttcactttgtactgactgttctactttgcgtttgcag
||||||| || ||||| || || | | | || || || |||||||| || ||||| ||||| ||||||||||||||||| ||||| ||||| ||||| |||||  ||| | ||||   |   |||  |  | | |  ||  |  || |  | |    | ||||||    |  ||  |   |   | ||| ||| | | |  ||||                                   
GGCTTGAGTATTTTGAGTCCAAGGCTTTTGAACAGCAAGAAGCTGCTCGAAATGGTACTCGAAAACCTGATGCATCAATAGCTAGCAAAGGCCATCTTAGgtatgataaaattaa-ccttggcaatgtgga-tctgatacttcattggctaat----tgttgcatcaggaagtacttctctcatgcatattttatttgatgtcttt----------------------------------

upper sequence: LOC_Os07g23990.1 (Oryza sativa), 5'ss of exon 20
lower sequence: GLYMA16G02770.1 (Glycine max), 5'ss of exon 22
GGCTTGAATACTTTGAATCAAAAGTTATCGAGCAACAGGAAGCTGCACGCAATGGAACTCGGAAACCTGATGCATCAATTGCTAGTAAAGGGCATCTAAGgtaaaatatagttaaatttcaccaacctaaagtatcgtaacttcttagagacttctcttttgcatttatagatatctaggtacagtatactttttataacatcttcactttgtactgactgttctactttgcgtttgcag
||||||| || |||||||| || | | | || || || |||||||| || ||||| ||||| ||||||||||||||||| || || ||||| ||||| |||||   || | ||||   |   |||  |  | | |  ||  |  || |  | |    | ||||||    | | |  |   |   | ||| ||| | |    ||||                                   
GGCTTGAGTATTTTGAATCCAAGGCTTTTGAACAGCAAGAAGCTGCTCGAAATGGTACTCGAAAACCTGATGCATCAATAGCCAGCAAAGGCCATCTTAGgtatggtaaaattaa-ccttggcaatgtgga-tctgatacttcattggctaat----tgttgcatcaggaaaaacttctctcatgcatattttatttggtgtcttt----------------------------------

upper sequence: LOC_Os07g23990.1 (Oryza sativa), 5'ss of exon 20
lower sequence: Vv15s0046g00740.t01 (Vitis vinifera), 5'ss of exon 22
GGCTTGAATACTTTGAATCAAAAGTTATCGAGCAACAGGAAGCTGCACGCAATGGAACTCGGAAACCTGATGCATCAATTGCTAGTAAAGGGCATCTAAGgtaaaatatagttaaatttcaccaacctaaagtatcgtaacttcttagagacttctcttttgcatttatagatatctaggtacagtatactttttataacatcttcactttgtactgactgttctactttgcgtttgcag
|||| || |||||||| ||||| | | | || || || ||||||||| | ||||| ||||| |||||||||||||| || || || ||||| || ||||||||    |   ||    ||  |      ||  |    | ||   |  |  | |  || |  ||||    || |     ||| ||   |      |   |  |      ||                              
GGCTCGAGTACTTTGAGTCAAAGGCTTTTGAACAGCAAGAAGCTGCAAGAAATGGGACTCGAAAACCTGATGCATCCATAGCCAGCAAAGGCCACCTAAGgtatgccagcattgtccttggc------aagat----tgaccattctgcaattgatcat--gcataagaagttgatagggtgcacagttgcccctgctattttgatgattca----------------------------

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|29627547|gb|CB632558.1|CB632558
EST:     AATGGAACTCGGAAACCTGATGCATCAATTGCTAGTAAAGGGCATCTAAG                         TGTATCTGATCTTCTTGATTATATAAATCCCAATGAAGAAAGCAAAGGAAG
genomic: AATGGAACTCGGAAACCTGATGCATCAATTGCTAGTAAAGGGCATCTAAGgtaaaatata ... gcgtttgcagTGTATCTGATCTTCTTGATTATATAAATCCCAATGAAGAAAGCAAAGGAAG
EST: gi|29625529|gb|CB630540.1|CB630540
EST:     AATGGAACTCGGAAACCTGATGCATCAATTGCTAGTAAAGGGCATCTAAG                         TGTATCTGATCTTCTTGATTATATAAATCCCAATGAAGAAAGCAAAGGAAG
genomic: AATGGAACTCGGAAACCTGATGCATCAATTGCTAGTAAAGGGCATCTAAGgtaaaatata ... gcgtttgcagTGTATCTGATCTTCTTGATTATATAAATCCCAATGAAGAAAGCAAAGGAAG
EST: gi|29675752|gb|CB672027.1|CB672027
EST:     AATGGAACTCGGAAACCTGATGCATCAATTGCTAGTAAAGGGCATCTAAG                         TGTATCTGATCTTCTTGATTATATAAATCCCAATGAAGAAAGCAAAGGAAG
genomic: AATGGAACTCGGAAACCTGATGCATCAATTGCTAGTAAAGGGCATCTAAGgtaaaatata ... gcgtttgcagTGTATCTGATCTTCTTGATTATATAAATCCCAATGAAGAAAGCAAAGGAAG

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: 64 (upstream exon), 69 (downstream exon)
Score: 16

GGCTTGAATACTTTGAATCAAAAGTTATCGAGCAACAGGAAGCTGCACGCAATGGAACTCGGAAACCTGATGCATCAATTGCTAGTAAAGGGCATCTAAGgtaaaatata ... gcgtttgcagTGTATCTGATCTTCTTGATTATATAAATCCCAATGAAGAAAGCAAAGGAAGAGATTCTGAATCAAGTAAAAGGAGGTACTCAAGCATAAAG




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