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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCTGTGACCCATTCTGTTGCCAACTGTGTCAAACGAGTTGTGGTCATCGTCTCATCCGTTCTCTTCTTCAGAACTCCGATTTCACCTATTAATGCCCTTGgtaacctcacaaccaaattcaactgatcctaacagctcgcttttcaatttacccgtactgaattttgtccttttttctgcattcag

Basic information

species Oryza sativa
transcript LOC_Os05g07870.1
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g07870.1 (Oryza sativa), 5'ss of exon 8
lower sequence: GRMZM2G008642_T01 (Zea mays), 5'ss of exon 6
CCTGTGACCCATTCTGTTGCCAACTGTGTCAAACGAGTTGTGGTCATCGTCTCATCCGTTCTCTTCTTCAGAACTCCGATTTCACCTATTAATGCCCTTGgtaacctcacaaccaa-attcaactgatcctaacagctcgcttttcaatttacccgta-ctgaatttt--gtccttttttctgcattcag
|| ||||||||||| |||||||||| | | ||||| || |||||||| || ||||||||||||||||| |||||||  ||||||||||| |||||| | ||||        |  || ||||  |         |   |  |||  ||  | | |  |  ||||||| |  ||  |||| | ||| | |||
CCCGTGACCCATTCGGTTGCCAACTCTCTTAAACGTGTGGTGGTCATTGTGTCATCCGTTCTCTTCTTTAGAACTCTAATTTCACCTATAAATGCCTTAGgtacagcagtgattaatattcttcatgcaaatgccagttacttaccatctcatcaatgtctgaattgtaagtttttttctttgcctgcag

upper sequence: LOC_Os05g07870.1 (Oryza sativa), 5'ss of exon 8
lower sequence: GRMZM2G512279_T01 (Zea mays), 5'ss of exon 4
CCTGTGACCCATTCTGTTGCCAACTGTGTCAAACGAGTTGTGGTCATCGTCTCATCCGTTCTCTTCTTCAGAACTCCGATTTCACCTATTAATGCCCTTGgtaacctcacaaccaa-attcaactgatcctaacagctcgcttttcaatttacccgta-ctgaattttgtccttttt-tctgcattcag
|| ||||||||||| ||||| |||| | | ||||| || |||||||| || ||||||||||||||||| |||||||  ||||||||||| |||||| | ||||        |  || ||||  |         |   |   |   |   | | | ||  ||||||| |    ||||| | ||| | |||
CCCGTGACCCATTCGGTTGCTAACTCTTTTAAACGTGTGGTGGTCATTGTGTCATCCGTTCTCTTCTTTAGAACTCTAATTTCACCTATAAATGCCTTAGgtacagaagtgattaatattcttcatgcaagtgccagttattgaacgtctcatcagtgtctgaattgtaagttttttctttgcctgcag
















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|66924213|gb|CX111061.1|CX111061
EST:     CTCATCCGTTCTCTTCTTCAGAACTCCGATTTCACCTATTAATGCCCTTG                         GAACTGGCGTTGCTCTAGCTGGAGTTTTCCTGTACTCTAGGGTCAAAAAAG
genomic: CTCATCCGTTCTCTTCTTCAGAACTCCGATTTCACCTATTAATGCCCTTGgtaacctcac ... ctgcattcagGAACTGGCGTTGCTCTAGCTGGAGTTTTCCTGTACTCTAGGTTCAAAAAAG
EST: gi|88552763|gb|CI482801.1|CI482801
EST:     GTCATCCGTTCTCTTCTTCAGAACTCCGATTTCACCTATTAATGCCCTTG                         GAACTGGCGTTGCTCTAGCTGGAGTTTTCCTGTACTTTAGGTTCAAAAAAG
genomic: CTCATCCGTTCTCTTCTTCAGAACTCCGATTTCACCTATTAATGCCCTTGgtaacctcac ... ctgcattcagGAACTGGCGTTGCTCTAGCTGGAGTTTTCCTGTACTCTAGGTTCAAAAAAG
EST: gi|29642963|gb|CB647970.1|CB647970
EST:     CTCATCCGTTCTCTTCTTCAGAACTCCGATTTCACCTATTAATGCCCTTG                         GAACTGGCGTTGCTCTAGCTGGAGTTTTCCTGTACTCTAGGTTCAAAAAAG
genomic: CTCATCCGTTCTCTTCTTCAGAACTCCGATTTCACCTATTAATGCCCTTGgtaacctcac ... ctgcattcagGAACTGGCGTTGCTCTAGCTGGAGTTTTCCTGTACTCTAGGTTCAAAAAAG
EST: gi|29659992|gb|CB656267.1|CB656267
EST:     CTCATCCGTTCTCTTCTTCAGAACTCCGATTTCACCTATTAATGCCCTTG                         GAACTGGCGTTGCTCTAGCTGGAGTTTTCCTGTACTCTAGGTTCAAAAAAG
genomic: CTCATCCGTTCTCTTCTTCAGAACTCCGATTTCACCTATTAATGCCCTTGgtaacctcac ... ctgcattcagGAACTGGCGTTGCTCTAGCTGGAGTTTTCCTGTACTCTAGGTTCAAAAAAG
EST: gi|88661888|gb|CI461859.1|CI461859
EST:     CTCATCCGTTCTCTTCTTCAGAACTCCGATTTCACCTATTAATGCCCTTG                         GAACTGGCGTTGCTCTAGCTGGAGTTTTCCTGTACTCTAGGTTCAAAAAAG
genomic: CTCATCCGTTCTCTTCTTCAGAACTCCGATTTCACCTATTAATGCCCTTGgtaacctcac ... ctgcattcagGAACTGGCGTTGCTCTAGCTGGAGTTTTCCTGTACTCTAGGTTCAAAAAAG
EST: gi|88532797|gb|CI461430.1|CI461430
EST:     CTCATCCGTTCTCTTCTTCAGAACTCCGATTTCACCTATTAATGCCCTTG                         GAACTGGCGTTGCTCTAGCTGGAGTTTTCCTGTACTCTAGGTTCAAAAAAG
genomic: CTCATCCGTTCTCTTCTTCAGAACTCCGATTTCACCTATTAATGCCCTTGgtaacctcac ... ctgcattcagGAACTGGCGTTGCTCTAGCTGGAGTTTTCCTGTACTCTAGGTTCAAAAAAG

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: 74 (upstream exon), 75 (downstream exon)
Score: 53

CCTGTGACCCATTCTGTTGCCAACTGTGTCAAACGAGTTGTGGTCATCGTCTCATCCGTTCTCTTCTTCAGAACTCCGATTTCACCTATTAATGCCCTTGgtaacctcac ... ctgcattcagGAACTGGCGTTGCTCTAGCTGGAGTTTTCCTGTACTCTAGGTTCAAAAAAGCTAAACCAAAGGCTAAGACTGCATGAGTCAACATACACAGCTGCAATTT




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