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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGCCAATCGTACAGATGCTTGTTTTATCCGTGTAATTGGCAGTGAGTTAGTTCAAAAATATGTTGGTGAAGGGGCACGGATGGTCCGGGAATTATTTCAGgtatgtgcaacattgtgaaaactcacaagaacttatcaattttctgcacttaaagtgcttctgtttgacaagcatgtttctgaaaaaaaaaatgttgacttggtttag

Basic information

species Oryza sativa
transcript LOC_Os02g54340.1
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g54340.2 (Oryza sativa), 5'ss of exon 7
lower sequence: GRMZM2G181359_T01 (Zea mays), 5'ss of exon 7
GGCCAATCGTACAGATGCTTGTTTTATCCGTGTAATTGGCAGTGAGTTAGTTCAAAAATATGTTGGTGAAGGGGCACGGATGGTCCGGGAATTATTTCAGgtatgtgcaacattgtgaaaactcacaagaacttatcaattttctgcacttaaagtgcttctgtttgacaagcatgtttctgaaaaaaaaaatgttgacttggtttag
 || ||||| || ||||||||||| |||||||||||||| |||||||||||||| || ||||| || ||||| || ||||||||| ||||| | || ||||||| |  |    |||||  |     ||  | |   | | | | | ||      || | | ||||  |||    | |||||||||  ||   |  |    | |     
AGCAAATCGGACTGATGCTTGTTTCATCCGTGTAATTGGAAGTGAGTTAGTTCAGAAGTATGTCGGCGAAGGTGCTCGGATGGTCAGGGAACTTTTCCAGgtatatatatggctgtga--atctgtaaatattatcccagtcttttcat-----gtacgtgtgttcaaca----tatttctgaaatgaattcttctatggtag-----

upper sequence: LOC_Os02g54340.2 (Oryza sativa), 5'ss of exon 7
lower sequence: GLYMA19G45140.1 (Glycine max), 5'ss of exon 7
GGCCAATCGTACAGATGCTTGTTTTATCCGTGTAATTGGCAGTGAGTTAGTTCAAAAATATGTTGGTGAAGGGGCACGGATGGTCCGGGAATTATTTCAGgtatgtgcaacattgtgaaaactcacaagaacttatcaattttctgcacttaaagtgcttctgtttgacaagcatgtttctgaaaaaaaaaatgttgacttggtttag
||| ||| | || ||||||||||||||  | || ||||| |||||| ||||||| |||||||||||||| || || || ||||| || ||| ||||||||||      |  || |  || |  |||      ||     |||| |  | ||    | |   | |||      |||| ||      ||  |||  || |  |  | |||
GGCTAATAGGACTGATGCTTGTTTTATAAGAGTTATTGGAAGTGAGCTAGTTCAGAAATATGTTGGTGAGGGTGCTCGAATGGTTCGTGAACTATTTCAGgtg-----agaatggctaagatgcac-----ttt-----ttttttaaattttttttcccgttatttccatgacatgatttcatcgaactaaaattttatgtcctctag

upper sequence: LOC_Os02g54340.2 (Oryza sativa), 5'ss of exon 7
lower sequence: GLYMA03G42370.2 (Glycine max), 5'ss of exon 7
GGCCAATCGTACAGATGCTTGTTTTATCCGTGTAATTGGCAGTGAGTTAGTTCAAAAATATGTTGGTGAAGGGGCACGGATGGTCCGGGAATTATTTCAGgtatgtgcaacattgtgaaaactcacaagaacttatcaattttctgcacttaaagtgcttctgtttgacaagcatgtttctgaaaaaaaaaatgttgacttggtttag
||| ||| | || ||||||||||||||  | || ||||| |||||| ||||||| |||||||||||||| || || || ||||| || ||| ||||||||||   ||       |  || |  |||       |||  ||||| |    ||    || |||    ||||| |  |   |||||  ||||     ||||  |  | |||
GGCTAATAGGACTGATGCTTGTTTTATAAGAGTTATTGGAAGTGAGCTAGTTCAGAAATATGTTGGTGAGGGTGCTCGAATGGTTCGTGAACTATTTCAGgtgaatg-------gctaagatgcacc---ttctatttattttatat-ttttcgttgtttcca--tgacatgatttcatctgactaaaat----ttgatgtcctctag

upper sequence: LOC_Os02g54340.2 (Oryza sativa), 5'ss of exon 7
lower sequence: GLYMA16G01810.1 (Glycine max), 5'ss of exon 7
GGCCAATCGTACAGATGCTTGTTTTATCCGTGTAATTGGCAGTGAGTTAGTTCAAAAATATGTTGGTGAAGGGGCACGGATGGTCCGGGAATTATTTCAGgtatgtgcaacattgtgaaaactcacaagaacttatcaattttctgcacttaaagtgcttctgtttgacaagcatgtt-tctgaaaaaaaaaatgttgacttggtttag
||| ||| | || ||||||||||||||  | || ||||| |||||| ||||||| |||||||| ||||| |||||  ||||||| || ||| |||||||||||  |   ||||        |   | ||   ||     || | | ||  | || | |     |||||| |  || || |||     |                     
GGCTAATAGGACTGATGCTTGTTTTATAAGGGTTATTGGAAGTGAGCTAGTTCAGAAATATGTCGGTGAGGGGGCTAGGATGGTTCGTGAACTATTTCAGgtaaat---acataagacgtgccttctagcttttgatcgttgtttcca--tgaaattcaatcatttgactaaaattttatctcttgtag--------------------

upper sequence: LOC_Os02g54340.2 (Oryza sativa), 5'ss of exon 7
lower sequence: GLYMA07G05220.1 (Glycine max), 5'ss of exon 7
GGCCAATCGTACAGATGCTTGTTTTATCCGTGTAATTGGCAGTGAGTTAGTTCAAAAATATGTTGGTGAAGGGGCACGGATGGTCCGGGAATTATTTCAGgta---tgtgcaacattgtgaaaactcacaagaacttatcaattttctgcacttaaagtgcttctgtttgacaagcatgtttctgaaaaaaaaaatgttgacttggtttag
||| ||| | || ||||||||||||||  | || ||||| |||||| ||||||| |||||||||||||| |||||  ||||||| || ||| |||||||||||   ||  ||| | |  |    ||  |      |||||| || | | || | ||| |   ||  |||||| |  || ||||| |     |                   
GGCTAATAGGACTGATGCTTGTTTTATAAGGGTTATTGGAAGTGAGCTAGTTCAGAAATATGTTGGTGAGGGGGCTAGGATGGTTCGTGAACTATTTCAGgtaaaatgcacaagact-cgtcctctagcttttttttatca-ttgtttcca-tgaaaataaatc-atttgactaaaat-tttctcatttttag------------------

upper sequence: LOC_Os02g54340.2 (Oryza sativa), 5'ss of exon 7
lower sequence: GLYMA03G42370.4 (Glycine max), 5'ss of exon 7
GGCCAATCGTACAGATGCTTGTTTTATCCGTGTAATTGGCAGTGAGTTAGTTCAAAAATATGTTGGTGAAGGGGCACGGATGGTCCGGGAATTATTTCAGgtatgtgcaacattgtgaaaactcacaagaacttatcaattt---tctgcacttaaagtgcttctgtttgacaagcatgtttctgaaaaaaaaaatgttgacttggtttag
||| ||| | || ||||||||||||||  | || ||||| |||||| ||||||| |||||||||||||| || || || ||||| || ||| ||||||||||   ||    |   || |   ||     |  ||||   |||   | |   | | |  || ||   | |||| |  || ||  ||      | |  |    ||      ||
GGCTAATAGGACTGATGCTTGTTTTATAAGAGTTATTGGAAGTGAGCTAGTTCAGAAATATGTTGGTGAGGGTGCTCGAATGGTTCGTGAACTATTTCAGgtgaatg-gctaagatgcaccttctatttattttatatttttcgttgtttccatgacatgatttcatctgactaaaat-ttgatgtcctctagatggcccgctctaagaag

upper sequence: LOC_Os02g54340.2 (Oryza sativa), 5'ss of exon 7
lower sequence: PP1S49_256V6.1 (Physcomitrella patens), 5'ss of exon 7
GGCCAATCGTACAGATGCTTGTTTTATCCGTGTAATTGGCAGTGAGTTAGTTCAAAAATATGTTGGTGAAGGGGCACGGATGGTCCGGGAATTATTTCAGgtatgtgcaacattgtgaaaactcacaa----gaacttatcaattttctgcacttaaagtgcttctgtttgacaagcatgtttctgaaaaaaaaaatgttgacttggtttag
 |||||| | ||||||||||| || || ||||| |||||||||||| | ||||| |||||||| || || || || ||||||||||| ||  | || |||| | ||  | | ||     |  |||||     ||  ||    ||  | || | ||| ||     || |     |  |||    ||| ||     | |  | || |       
TGCCAATAGGACAGATGCTTGCTTCATTCGTGTTATTGGCAGTGAGCTTGTTCAGAAATATGTAGGAGAGGGTGCTCGGATGGTCCGTGAGCTTTTCCAGgcaagtcaatcgtta-atcacttcacatccctgaggtttgatatggtttggatttagaga----ctatcctttagtcattcgcctggaacctgta-tactcacatc------

upper sequence: LOC_Os02g54340.2 (Oryza sativa), 5'ss of exon 7
lower sequence: EFJ29161 (Selaginella moellendorffii), 5'ss of exon 7
GGCCAATCGTACAGATGCTTGTTTTATCCGTGTAATTGGCAGTGAGTTAGTTCAAAAATATGTTGGTGAAGGGGCACGGATGGTCCGGGAATTATTTCAGgtatgtgcaacattgtgaaaactcacaagaac--ttatcaattttctgcacttaaagtgcttctgtttgacaagcatgtttctgaaaaaaaaaatgttgacttggtttag
|||||||||||||||||| || || || || || |||||||| ||| | || || || || ||||||||||| || || ||||| || || ||||| |||||||||   |   ||||   | ||     |    |  | ||  || |    ||    | ||  | ||     ||                                    
GGCCAATCGTACAGATGCCTGCTTCATTCGAGTTATTGGCAGCGAGCTCGTCCAGAAGTACGTTGGTGAAGGAGCTCGAATGGTGCGCGAGTTATTCCAGgtatgttacattctgtgtttattcctggcagtggtcttaaaagttttttttttccctttctctttttctttcag------------------------------------

upper sequence: LOC_Os02g54340.2 (Oryza sativa), 5'ss of exon 7
lower sequence: EFJ13722 (Selaginella moellendorffii), 5'ss of exon 7
GGCCAATCGTACAGATGCTTGTTTTATCCGTGTAATTGGCAGTGAGTTAGTTCAAAAATATGTTGGTGAAGGGGCACGGATGGTCCGGGAATTATTTCAGgtatgtgcaacattgtgaaaactc---acaagaacttatcaattttctgcacttaaagtgcttctgtttgacaagcatgtttctgaaaaaaaaaatgttgacttggtttag
|||||||||||||||||| || || || || || |||||||| ||| | || || || || ||||||||||| || || ||||| || || ||||| |||||||||   |    |||   | ||    ||      |   |||||| |    ||       |||| |||  |   ||                                  
GGCCAATCGTACAGATGCCTGCTTCATTCGAGTTATTGGCAGCGAGCTCGTCCAGAAGTACGTTGGTGAAGGAGCTCGAATGGTGCGCGAGTTATTCCAGgtatgttacattccgtgtttattcctggcagtggtcttaaaattttttatttttttttcctttctctttttctttcag---------------------------------

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|29622230|gb|CB627241.1|CB627241
EST:     TTCAAAAATATGTTGGTGAAGGGGCACGGATGGTCCGGGAATTATTTCAG                         ATGGCCCGCTCGAAGAAAGCATGCATTGTCTTCTTTGATGAGGTTGATGCT
genomic: TTCAAAAATATGTTGGTGAAGGGGCACGGATGGTCCGGGAATTATTTCAGgtatgtgcaa ... cttggtttagATGGCCCGCTCGAAGAAAGCATGCATTGTCTTCTTTGATGAGGTTGATGCT
EST: gi|58654487|gb|CK043167.1|CK043167
EST:     TTCAAAAATATGTTGGTGAAGGGGCACGGATGGTCCGGGAATTATTTCAG                         ATGGCCCGCTCGAAGAAAGCATGCATTGTCTTCTTTGATGAGGTTGATGCT
genomic: TTCAAAAATATGTTGGTGAAGGGGCACGGATGGTCCGGGAATTATTTCAGgtatgtgcaa ... cttggtttagATGGCCCGCTCGAAGAAAGCATGCATTGTCTTCTTTGATGAGGTTGATGCT
EST: gi|84117608|gb|CD151375.1|CD151375
EST:     TCAAAAATATGTTGGTGAAGGGGCGACGGATGGTCCGGGAATTATTTCAG                         ATGGCCCGCTCGAAGAAAGCATGCATTGTC
genomic: TCAAAAATATGTTGGTGAAGGGGC-ACGGATGGTCCGGGAATTATTTCAGgtatgtgcaa ... cttggtttagATGGCCCGCTCGAAGAAAGCATGCATTGTC
EST: gi|58673769|gb|CK062455.1|CK062455
EST:     TTCAAAAATATGTTGGTGAAGGGGCACGGATGGTCCGGGAATTATTTCAG                         ATGGCCCGCTCGAAGAAAGCATGCATTGTCTTCTTTGATGAGGTTGATGCT
genomic: TTCAAAAATATGTTGGTGAAGGGGCACGGATGGTCCGGGAATTATTTCAGgtatgtgcaa ... cttggtttagATGGCCCGCTCGAAGAAAGCATGCATTGTCTTCTTTGATGAGGTTGATGCT
EST: gi|58685776|gb|CK074463.1|CK074463
EST:     TTCAAAAATATGTTGGTGAAGGGGCACGGATGGTCCGGGAATTATTTCAG                         ATGGCCCGCTCGAAGAAAGCATGCATTGTCTTCTTTGATGAGGTTGATGCT
genomic: TTCAAAAATATGTTGGTGAAGGGGCACGGATGGTCCGGGAATTATTTCAGgtatgtgcaa ... cttggtttagATGGCCCGCTCGAAGAAAGCATGCATTGTCTTCTTTGATGAGGTTGATGCT
EST: gi|8857968|gb|AU095286.1|AU095286
EST:     TTCAAAAATATGTTGGTGAAGGGGCACGGATGGTCCGGGAATTATTTCAG                         ATGGCCCGCTCGAAGAAAAGCATGCATTGTCTTCTTTGATGAGGTTGATGC
genomic: TTCAAAAATATGTTGGTGAAGGGGCACGGATGGTCCGGGAATTATTTCAGgtatgtgcaa ... cttggtttagATGGCCCGCTCGAAGAAA-GCATGCATTGTCTTCTTTGATGAGGTTGATGC
EST: gi|58600395|gb|CK010923.1|CK010923
EST:     TTCAAAAATATGTTGGTGAAGGGGCACGGATGGTCCGGGAATTATTTCAG                         ATGGCCCGCTCGAAGAAAGCATGCATTGTCTTCTTTGATGAGGTTGATGCT
genomic: TTCAAAAATATGTTGGTGAAGGGGCACGGATGGTCCGGGAATTATTTCAGgtatgtgcaa ... cttggtttagATGGCCCGCTCGAAGAAAGCATGCATTGTCTTCTTTGATGAGGTTGATGCT

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: 67 (upstream exon), 70 (downstream exon)
Score: 19

GGCCAATCGTACAGATGCTTGTTTTATCCGTGTAATTGGCAGTGAGTTAGTTCAAAAATATGTTGGTGAAGGGGCACGGATGGTCCGGGAATTATTTCAGgtatgtgcaa ... cttggtttagATGGCCCGCTCGAAGAAAGCATGCATTGTCTTCTTTGATGAGGTTGATGCTATTGGAGGTGCTCGCTTCGATGATGGGGTTGGGGGTGATAATGAGGTTC




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