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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTCCAGCCAAGCATCTTCTTCCGGTGCCAAGACCAGATCCAGAGGTCGTTGCTATGCTAACATCAGGATTGACTGCTTCAATTGCCCTTGAGAAGgttagtatacagttcttttgtttctttgctacataacatgtggctttgacctcatacttggtgaaccaacgtttaagtttggtgtggtctacatgaatataacttcattatctgatttgcgttgatttctgctgcctttag

Basic information

species Oryza sativa
transcript LOC_Os09g28570.1
intron # 11
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os09g28570.3 (Oryza sativa), 5'ss of exon 11
lower sequence: GRMZM2G368058_T01 (Zea mays), 5'ss of exon 6
GTTCCAGCCAAGCATCTTCTTCCGGTGCCAAGACCAGATCCAGAGGTCGTTGCTATGCTAACATCAGGATTGACTGCTTCAATTGCCCTTGAGAAGgttag-----tatacagttcttttgtttctttgctacataacatgtggctt-tgacctcatacttggtgaaccaacgtttaagtttggtgtggtctacatgaatataacttcattatctg---atttgcgtt-gatttctgctgcctttag--------
 || |||||||   |||| |||| |||||||||||||| |||||||| ||||||||||||||||||||||||||||| || || || ||||| ||||||       |  | | |||||   ||| |   |    |  ||| || | | |    | ||   |  ||     || |   | |    |      |      |||||| ||  ||   ||   || ||  || ||||| |||||| |||          
ATTTCAGCCAAAAGTCTTATTCCAGTGCCAAGACCAGACCCAGAGGTGGTTGCTATGCTAACATCAGGATTGACTGCATCCATCGCTCTTGAAAAGgttctgttcctccatatttcttagttttttccacggtttggcatatgccatgtatttttatctctattgtgttcacataagattcaaattccaagtttgaagatataattttcttccttgcttatctggattcgatttatgctgcatttcttccattag

upper sequence: LOC_Os09g28570.3 (Oryza sativa), 5'ss of exon 11
lower sequence: GRMZM2G147191_T02 (Zea mays), 5'ss of exon 11
GTTCCAGCCAAGCATCTTCTTCCGGTGCCAAGACCAGATCCAGAGGTCGTTGCTATGCTAACATCAGGATTGACTGCTTCAATTGCCCTTGAGAAGgttagtatacagttcttttgtttctttgctacataacatgtggctttgacctc-atacttggtgaaccaacgtttaagtttggtgtggtctacatgaatataacttcattatctgatttgcgttgatttctgctgcctttag
||||||||||| ||||||||||| |||||||||||||| || ||||| ||||| ||| | ||||||||| ||||||| ||||||   ||||| ||||||  | |    | |   || || ||| ||  |           | ||   || || ||   | ||     | || | ||| |   | | ||                                                  
GTTCCAGCCAAACATCTTCTTCCAGTGCCAAGACCAGACCCTGAGGTTGTTGCAATGTTGACATCAGGACTGACTGCATCAATTAGTCTTGAAAAGgtttattttatatacccctgcttgttttctttacttttgagcaatctgttttctatcctaaattaatt--tggttgatttttgctggctttag-------------------------------------------------

upper sequence: LOC_Os09g28570.3 (Oryza sativa), 5'ss of exon 11
lower sequence: GLYMA02G15070.1 (Glycine max), 5'ss of exon 11
GTTCCAGCCAAGCATCTTCTTCCGGTGCCAAGACCAGATCCAGAGGTCGTTGCTATGCTAACATCAGGATTGACTGCTTCAATTGCCCTTGAGAAGgttagtatacagttcttttgtttctttgctacataacatgtggctttgacctcatacttggtgaaccaacgtttaagtttggtgtggtctacatgaatataacttcattatctga----tttgcgttgatttctgctgcctttag------------------------
 ||||  | || |||  |||||||||||| ||||||||||| || || ||||| ||||| ||||| ||||||||||| |||||||| || || ||||||    ||   |  | |||| || ||||| ||  |  | |   | |  | |  || ||  |  ||  |  ||| |  |   |||     |      | |    | ||  ||||      || |  ||  || |  ||     ||                        
ATTCCTTCAAAACATGCTCTTCCGGTGCCTAGACCAGATCCTGAAGTTGTTGCCATGCTTACATCGGGATTGACTGCCTCAATTGCTCTAGAAAAGgttgac-taatataatgttgtctccttgcttca-gatgtatccttatttcttagtatttattatactcatctttgatatcaatgtaaatcaagccttttttttattatcttctgtgaatcttccactggcttgtcttgatcaaagtttccttttttgtacactcaaaag

upper sequence: LOC_Os09g28570.3 (Oryza sativa), 5'ss of exon 11
lower sequence: AT1G49670.1 (Arabidopsis thaliana), 5'ss of exon 11
GTTCCAGCCAAGCATCTTCTTCCGGTGCCAAGACCAGATCCAGAGGTCGTTGCTATGCTAACATCAGGATTGACTGCTTCAATTGCCCTTGAGAAGgt--tagtatacagttcttttgtttctttgcta-cataacatgtggctttgacctcatacttggtgaaccaacgtttaagtttggtgtggtctacatgaatataacttcattatctgatttgcgttgatttctgctgcctttag-------------
||  |  | |||||| ||||||| || ||||||||||||||||| || ||||| ||||| || || ||||| ||||| | ||| |||||||| |||||  |  ||   |||    ||   | | || |  |||    | |   ||    |||  |  |     |     || |   ||    |  || |  ||     ||| ||  |  |   |||  |  |||  | | ||   | |               
GTATCTTCTAAGCATGTTCTTCCTGTTCCAAGACCAGATCCAGAAGTTGTTGCCATGCTTACCTCGGGATTAACTGCATTAATCGCCCTTGAAAAGgtcgtgctaacgagtgtcattaactgtctgttttcatcgtttttcatttcagactctcaaattcctcatttttgtatgtattaatagctgtatg-atattcttaagttgctagttcaattatctctgacattttctttatcttatgggaattcacag

upper sequence: LOC_Os09g28570.3 (Oryza sativa), 5'ss of exon 11
lower sequence: AT1G49670.2 (Arabidopsis thaliana), 5'ss of exon 11
GTTCCAGCCAAGCATCTTCTTCCGGTGCCAAGACCAGATCCAGAGGTCGTTGCTATGCTAACATCAGGATTGACTGCTTCAATTGCCCTTGAGAAGgt--tagtatacagttcttttgtttctttgctacataacatgtggctttgacctcatacttggtgaaccaacgtttaagtttggtgtggtctacatgaatataacttcattatctgatttgcgttgatttctgctgcctttag
||  |  | |||||| ||||||| || ||||||||||||||||| || ||||| ||||| || || ||||| ||||| | ||| |||||||| |||||  |  ||   |||    ||   | | || |      |||  |  ||| |  ||| |||     |  |  | |||  || ||   |  |                                                     
GTATCTTCTAAGCATGTTCTTCCTGTTCCAAGACCAGATCCAGAAGTTGTTGCCATGCTTACCTCGGGATTAACTGCATTAATCGCCCTTGAAAAGgtcgtgctaacgagtgtcattaactgtctgtttt----cat-cgtttttcatttcagactctcaaattcctcatttttgtatgtattaatag---------------------------------------------------

upper sequence: LOC_Os09g28570.3 (Oryza sativa), 5'ss of exon 11
lower sequence: Vv03s0063g00610.t01 (Vitis vinifera), 5'ss of exon 11
GTTCCAGCCAAGCATCTTCTTCCGGTGCCAAGACCAGATCCAGAGGTCGTTGCTATGCTAACATCAGGATTGACTGCTTCAATTGCCCTTGAGAAGgttagta--tacagttcttttgtttctttgctacataacatgtggctttgacctcatacttg---gtgaaccaacgtttaagtttggtgtggtctacatgaatataacttcattatctgatttgcgttgatttctgctgcctttag-------------------------------------------------
|||||  |||||||  | ||||| ||| |||||||||||||||| || ||||| |||||||| |||||| | || || ||||||||  | || |||||  ||   | ||  | | |    || |||    | |   |||   ||  |    ||   ||    ||     |  ||||  ||        ||   |    | |  | |  | ||    | | | ||  |||   |  || |||                                                  
GTTCCTTCCAAGCACATCCTTCCCGTGGCAAGACCAGATCCAGAAGTTGTTGCGATGCTAACCTCAGGACTTACAGCATCAATTGCTTTAGAAAAGgtatgttacttcaagtgtctgtcctccttgtccaagattttgttaattgcaatatatgtatgtaaatgtttatatatttacattcaactaattcattaattttctggccttctgatgctgtattctttctttttgtcatccattactgagacagttaattgtcttgttctgacaattcttttatggaacttgtag

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|58684560|gb|CK073247.1|CK073247
EST:     TCGTTGCTATGCTAACATCAGGATTGACTGCTTCAATTGCCCTTGAGAAG                         GCAGGCCAAATGGCATCAGGGCAAGTTGTTCTAGTTACAGCTGCTGCTGGT
genomic: TCGTTGCTATGCTAACATCAGGATTGACTGCTTCAATTGCCCTTGAGAAGgttagtatac ... ctgcctttagGCAGGCCAAATGGCATCAGGGCAAGTTGTTCTAGTTACAGCTGCTGCTGGT




















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: 71 (upstream exon), 68 (downstream exon)
Score: 42

GTTCCAGCCAAGCATCTTCTTCCGGTGCCAAGACCAGATCCAGAGGTCGTTGCTATGCTAACATCAGGATTGACTGCTTCAATTGCCCTTGAGAAGgttagtatac ... ctgcctttagGCAGGCCAAATGGCATCAGGGCAAGTTGTTCTAGTTACAGCTGCTGCTGGTGGAACAGGACAATTTGCTGTGCAG




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