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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTCACCGCATCTGGTCATACTGAATTGCGAATCAATGCTATCATGATCACCAGCACAGTCATTGTTGTTCTGTTCAGCACAATGgtaaggatgtaatgctttctctctgttattatcttggatggttattttctgctcagcaggtgtatttctagcaatctgttgatagatttgtgcacttttg...

Basic information

species Oryza sativa
transcript LOC_Os05g05590.1
intron # 14
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g05590.1 (Oryza sativa), 5'ss of exon 14
lower sequence: GRMZM2G063492_T01 (Zea mays), 5'ss of exon 14
TTCACCGCATCTGGTCATACTGAATTGCGAATCAATGCTATCATGATCACCAGCACAGTCATTGTTGTTCTGTTCAGCACAATGgtaaggatgtaatgctttctctctgttattatcttggatggttattttctgctcagcaggt-gtatttctagcaatctgttgatagatttgtgcacttttg
|| || ||||||||||| |||||| ||||| |||||||||||||||||||||||||||| ||||||||||| ||||||||||||||||| | || | |||| |||||| | ||| | | || | || || || | | | |
TTTACAGCATCTGGTCACACTGAAGTGCGAGTCAATGCTATCATGATCACCAGCACAGTTATTGTTGTTCTATTCAGCACAATGgtaagccgtctgctataccttattattatcatcttgttcttcatagatgtgcgtgttacatagtccagcacaaaacatgacaatgaaacggccaagggta-

upper sequence: LOC_Os05g05590.1 (Oryza sativa), 5'ss of exon 14
lower sequence: GLYMA19G42900.1 (Glycine max), 5'ss of exon 13
TTCACCGCATCTGGTCATACTGAATTGCGAATCAATGCTATCATGATCACCAGCACAGTCATTGTTGTTCTGTTCAGCACAATGgtaagg-atgtaatgctttctctctgttattatcttggatggttattttctgctcagcaggtgtatttctagcaatctgttgatagatttgtgcacttttg--
|||||| || ||||| |||||| ||||| |||||| ||||||||||||||||| | | |||||| || |||||||||||||||| | | ||| | | | | || |||||| || | || | | || || | | | ||| | | ||
TTCACCTTGTCGGGTCACACTGAACAGCGAACCAATGCCATCATGATCACCAGCACCATTACTGTTGTGCTTGTCAGCACAATGgtaagacgcatgcttcttctaaatttgtttgacatttcatggtt-ttgttaatatagagattttgctttctgc--ttcgatcataattactcctaggttaacc

upper sequence: LOC_Os05g05590.1 (Oryza sativa), 5'ss of exon 14
lower sequence: GLYMA10G30020.1 (Glycine max), 5'ss of exon 14
TTCACCGCATCTGGTCATACTGAATTGCGAATCAATGCTATCATGATCACCAGCACAGTCATTGTTGTTCTGTTCAGCACAATGgtaaggatgtaatgctttctctctgttattatcttggatggttattttctgctcagcaggtgtatttctagcaatctgttgatagatttgtgcacttttg----
|||||| || || || ||| | |||||| |||||| ||||||||||| ||||| ||| |||||| || ||||||||| ||||||| || | || ||| | | | ||| | | | || | || |||| | || | | | | | | |||| |
TTCACCATGTCGGGGCACACTTCACTGCGAAGCAATGCAATCATGATCACAAGCACCATCACTGTTGTGCTTTTCAGCACAGTGgtaag-atatt-tgttttgtagtttctgacatccttagccagtgtccattggtttctttgt-tattagaggttattttgtctttgttgcat-cactgatattca

upper sequence: LOC_Os05g05590.1 (Oryza sativa), 5'ss of exon 14
lower sequence: GLYMA20G37370.1 (Glycine max), 5'ss of exon 14
TTCACCGCATCTGGTCATACTGAATTGCGAATCAATGCTATCATGATCACCAGCACAGTCATTGTTGTTCTGTTCAGCACAATGgtaagg-atgtaatgctttctctctgttattatct-tggatggttatt--ttctgctcagcaggtgtatttctagcaa-tctgttgatagatttgtgcacttttg
|||||| || || || ||| | | ||| |||||| ||||||||||| ||||| ||| |||||| || ||||||||| ||||||| || | | | | |||| || | || ||| || | | | ||| | || | | ||||| | | | |
TTCACCATGTCGGGGCACACTTCACTAAGAAGCAATGCAATCATGATCACAAGCACCATCACTGTTGTGCTTTTCAGCACAGTGgtaagatatttgttttgtagtttctgacatccttagccagtgtccattggttttttttatcagaggaggttattttgtctttgttgcatcactgataatc-----

upper sequence: LOC_Os05g05590.1 (Oryza sativa), 5'ss of exon 14
lower sequence: GLYMA03G40290.1 (Glycine max), 5'ss of exon 13
TTCACCGCATCTGGTCATACTGAATTGCGAATCAATGCTATCATGATCACCAGCACAGTCATTGTTGTTCTGTTCAGCACAATGgtaagg-atgtaatgctttctctctgttattatcttggatggtt-attttctgctcagcaggtgtatttctagcaatctgttgatagatttgtg--cacttttg-
|||||| || ||||| |||||| |||||| |||||| ||||||||||||||||| | | |||||| || |||||||||||||||| | | | | || ||| | | | || || || || | | | | | | |||| | ||| | || || ||| |
TTCACCTTGTCCGGTCACACTGAACTGCGAACCAATGCCATCATGATCACCAGCACCATTACTGTTGTGCTTGTCAGCACAATGgtaagacgcatgacgaatgcttcttgtaaatttgtttgaaatttcatggttttgttaataaggagatttt-----gctttttgcttcgttcatgattactcctag

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|29685383|gb|CB681658.1|CB681658
EST:     ATGCTATCATGATCACCAGCACAGTCATTGTTGTTCTGTTCAGCACAATG                         GNNNNNNNNNNNNNNACCAAGCCTCTCCTCAATCTCCTCATCCCACCAAGG
genomic: ATGCTATCATGATCACCAGCACAGTCATTGTTGTTCTGTTCAGCACAATGgtaaggatgt ... tttgtttcagGTTTTTGGTTTTTTTACCAAGCCTCTCCTCAATCTCCTCATCCCACCAAGG
EST: gi|29677873|gb|CB674148.1|CB674148
EST:     ATGCTATCATGATCACCAGCACAGTCATTGTTGTTCTGTTCAGCACAATG                         GNNNNNNNNNNNNNNACCAAGCCTCTCCTCAATCTCCTCATCCCACCAAGG
genomic: ATGCTATCATGATCACCAGCACAGTCATTGTTGTTCTGTTCAGCACAATGgtaaggatgt ... tttgtttcagGTTTTTGGTTTTTTTACCAAGCCTCTCCTCAATCTCCTCATCCCACCAAGG
EST: gi|29675121|gb|CB671396.1|CB671396
EST:     ATGCTATCATGATCACCAGCACAGTCATTGTTGTTCTGTTCAGCACAATG                         GNNNNNNNNNNNNNNACCAAGCCTCTCCTCAATCTCCTCATCCCACCAAGG
genomic: ATGCTATCATGATCACCAGCACAGTCATTGTTGTTCTGTTCAGCACAATGgtaaggatgt ... tttgtttcagGTTTTTGGTTTTTTTACCAAGCCTCTCCTCAATCTCCTCATCCCACCAAGG
EST: gi|29672522|gb|CB668797.1|CB668797
EST:     ATGCTATCATGATCACCAGCACAGTCATTGTTGTTCTGTTCAGCACAATG                         GNNNNNNNNNNNNNNACCAAGCCTCTCCTCAATCTCCTCATCCCACCAAGG
genomic: ATGCTATCATGATCACCAGCACAGTCATTGTTGTTCTGTTCAGCACAATGgtaaggatgt ... tttgtttcagGTTTTTGGTTTTTTTACCAAGCCTCTCCTCAATCTCCTCATCCCACCAAGG
EST: gi|29672523|gb|CB668798.1|CB668798
EST:     ATGCTATCATGATCACCAGCACAGTCATTGTTGTTCTGTTCAGCACAATG                         GNNNNNNNNNNNNNNACCAAGCCTCTCCTCAATCTCCTCATCCCACCAAGG
genomic: ATGCTATCATGATCACCAGCACAGTCATTGTTGTTCTGTTCAGCACAATGgtaaggatgt ... tttgtttcagGTTTTTGGTTTTTTTACCAAGCCTCTCCTCAATCTCCTCATCCCACCAAGG
EST: gi|29628631|gb|CB633642.1|CB633642
EST:     ATGCTATCATGATCACCAGCACAGTCATTGTTGTTCTGTTCAGCACAATG                         GNNNNNNNNNNNNNNACCAAGCCTCTCCTCAATCTCCTCATCCCACCAAGG
genomic: ATGCTATCATGATCACCAGCACAGTCATTGTTGTTCTGTTCAGCACAATGgtaaggatgt ... tttgtttcagGTTTTTGGTTTTTTTACCAAGCCTCTCCTCAATCTCCTCATCCCACCAAGG

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: 45 (upstream exon), 69 (downstream exon)
Score: 8

TTCACCGCATCTGGTCATACTGAATTGCGAATCAATGCTATCATGATCACCAGCACAGTCATTGTTGTTCTGTTCAGCACAATGgtaaggatgt ... tttgtttcagGTTTTTGGTTTTTTTACCAAGCCTCTCCTCAATCTCCTCATCCCACCAAGGCCTGACATAGCAGCTGATCTCTCAAGCCAGTCAATCATAGACCCACTTC




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