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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtggaccactctccttatactgcaccatttaaattcaatacttcattggtggattgagaagtatctccagtttgagtcaacattgtcagacaaatgaagacgtgaaatttcagtgtgcactatgcatataacttgcatcatccgttaggagttccccatgaagtaattttgcaatggtattactgcagATCTTCCACAAGCGAATGCCTCCCGAAGCAATAGATCTTGTGTCCCGTCTCCTTCAGTATTCGCCAAATCTGCGATGTACTGCG

Basic information

species Oryza sativa
transcript LOC_Os06g35530.1
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g35530.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM2G043350_T01 (Zea mays), 3'ss of exon 9
gtatgtggaccactctccttatactgcaccatttaaattcaatacttcattggtggattgagaagtatctccagtttgagtcaacattgtcagacaaatgaagacgtgaaatttcagtgtgcactatgcatataacttgcatcatccgttaggagttccccatgaagtaatttt----gcaatggtattactgcagATCTTCCACAAGCGAATGCCTCCCGAAGCAATAGATCTTGTGTCCCGTCTCCTTCAGTATTCGCCAAATCTGCGATGTACTGCG
                                                                                          || ||||         ||  |||    |||| ||     |||| |  | | | || |  | |  |||||  |||  | | |  |     |||||||  | |||||||||||||||||| |||||||||| ||||||||||||||||| |||||||| |||||||||||||| |||||||||||||  || 
------------------------------------------------------------------------------------------caaacaataatgtttatgttattatcatgtgtaca----atatgatctcccttattc--ttgatgttcctgatggtggagtccttatcacaatggttatgctgcagATCTTCCACAAGAGAATGCCTCCAGAAGCAATAGATCTTGTTTCCCGTCTTCTTCAGTATTCGCCGAATCTGCGATGTAGCGCA
















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|58678104|gb|CK066791.1|CK066791
EST:     ATTACACAGAATTCAAATTTCCGCAGATAAAAGCATGCCCATGGCACAAG                         ATCTTCCACAAGCGAATGCCTCCCGAAGCAATAGATC
genomic: ATTACACAGAATTCAAATTTCCGCAGATAAAAGCATGCCCATGGCACAAGgtatgtggac ... attactgcagATCTTCCACAAGCGAATGCCTCCCGAAGCAATAGATC
EST: gi|29672897|gb|CB669172.1|CB669172
EST:     ATTACACAGAATTCAAATTTCCGCAGATAAAAGCATGCCCATGGCACAAG                         ATCTTCCACAAGCGAATGCCTCCCGAAGCAATAGATCTTGTGTCCCGTCTC
genomic: ATTACACAGAATTCAAATTTCCGCAGATAAAAGCATGCCCATGGCACAAGgtatgtggac ... attactgcagATCTTCCACAAGCGAATGCCTCCCGAAGCAATAGATCTTGTGTCCCGTCTC
EST: gi|33801683|gb|CF326713.1|CF326713
EST:     ATTACACAGAATTCAAATTTCCGCAGATAAAAGCATGCCCATGGCACAAG                         ATCTTCCACAAGCGAATGCCTCCCGAAGCAATAGATCTTGTGTCCCGTCTC
genomic: ATTACACAGAATTCAAATTTCCGCAGATAAAAGCATGCCCATGGCACAAGgtatgtggac ... attactgcagATCTTCCACAAGCGAATGCCTCCCGAAGCAATAGATCTTGTGTCCCGTCTC
EST: gi|38473115|gb|CF957247.1|CF957247
EST:     ATTACACAGAATTCAAATTTCCGCAGATAAAAGCATGCCCATGGCACAAG                         ATCTTCCACAAGCGAATGCCTCCCGAAGCAATAGATCTTGTGTCCCGTCTC
genomic: ATTACACAGAATTCAAATTTCCGCAGATAAAAGCATGCCCATGGCACAAGgtatgtggac ... attactgcagATCTTCCACAAGCGAATGCCTCCCGAAGCAATAGATCTTGTGTCCCGTCTC
EST: gi|29689143|gb|CB685418.1|CB685418
EST:     CAGATAAAAGCATGCCCATGGCACAAG                         ATCTTCCACAAGCGAATGCCTCCCGAAGCAATAGATCTTGTGTCCCGTCTC
genomic: CAGATAAAAGCATGCCCATGGCACAAGgtatgtggac ... attactgcagATCTTCCACAAGCGAATGCCTCCCGAAGCAATAGATCTTGTGTCCCGTCTC
EST: gi|15008260|gb|AU222648.1|AU222648
EST:     ATTACACAGAATTCAAATTTCCGCAGATAAAAGCATGCCCATGGCACAAG                         ATCTTCCACAAGCGAATGCCTCCC
genomic: ATTACACAGAATTCAAATTTCCGCAGATAAAAGCATGCCCATGGCACAAGgtatgtggac ... attactgcagATCTTCCACAAGCGAATGCCTCCC
EST: gi|58680026|gb|CK068713.1|CK068713
EST:     ATTACACAGAATTCAAATTTCCGCAGATAAAAGCATGCCCATGGCACAAG                         ATCTTCCACAAGCGAATGCCTCCCGAAGCAATAGATCTTGTGTCCCGTCTC
genomic: ATTACACAGAATTCAAATTTCCGCAGATAAAAGCATGCCCATGGCACAAGgtatgtggac ... attactgcagATCTTCCACAAGCGAATGCCTCCCGAAGCAATAGATCTTGTGTCCCGTCTC

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: 73 (upstream exon), 74 (downstream exon)
Score: 51

GTTTTGGGTACTCCAACGCGAGAGGAAATCCGTTGTATGAATCCCAATTACACAGAATTCAAATTTCCGCAGATAAAAGCATGCCCATGGCACAAGgtatgtggac ... attactgcagATCTTCCACAAGCGAATGCCTCCCGAAGCAATAGATCTTGTGTCCCGTCTCCTTCAGTATTCGCCAAATCTGCGATGTACTGCG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgcatcatccgttaggagttccccatgaagtaattttgcaatggtattactgcagATCTTCCACAAGCGAATGCCTCCCGAAGCAATAGATCTTGTGTCCCGTCTCCTTCAGTATTCGCCAAATCTGCGATGTACTGCG
                           aagtaatttt  TA-rich tract