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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ataaacgaaaaaaatgtcaaacatgttggtagaatggcatttctctgagtattttaattgtagctattgctttgactgatttcaatgctctctatcacagCTTGTCGCAGCATATGTCTTCAGAATTGTGTCAGGAAGAGTTTGGTGTATGCAAACTGGGGAGTCCAAGCACAAGTAGCCCTCCAATTGCTTCGTTTG

Basic information

species Oryza sativa
transcript LOC_Os02g31290.2
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g31290.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G459746_T01 (Zea mays), 3'ss of exon 8
ataaacgaaaaaaatgtcaaacatgttggtagaatggcatttctctgagtattttaattgtagctattgctttgac--tgatttcaatgct-ctctatcacagCTTGTCGCAGCATATGTCTTCAGAATTGTGTCAGGAAGAGTTTGGTGTATGCAAACTGGGGAGTCCAAGCACAAGTAGCCCTCCAATTGCTTCGTTTG
 ||   || || | |   ||   || |  ||   || ||    | |||  |  ||  || ||   | |||| | ||  |||||| |||| |  | ||| |||| ||  | ||||| |||||   ||| | | | || ||||| |||||||||||||||||||| |||| |||||||| |||||||||| |  |||| || |
-tatgtgacaacatt-ctaattttgattttaccgtg-caaacttttgaaaacattggttttaatcactgctctaacattgattttaatgttgttttataacagATTAACACAGCACATGTCCAAAGAGTCGGGGCAAGAAGAATTTGGTGTATGCAAACTGGGCAGTCTAAGCACAAATAGCCCTCCATTGCCTTCATTGG
















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|29628170|gb|CB633181.1|CB633181
EST:     GCAGGCAAGAAAATCAAATTGGAGACCAGCCGTCTGGGTGCTGCTAGGCG                         CTTGTCGCAGCATATGTCTTCAGAATTGTGTCAGGAAGAGTTTGGTGTATG
genomic: GCAGGCAAGAAAATCAAATTGGAGACCAGCCGTCTGGGTGCTGCTAGGCGgtaagtcatt ... tctatcacagCTTGTCGCAGCATATGTCTTCAGAATTGTGTCAGGAAGAGTTTGGTGTATG
EST: gi|29644611|gb|CB649618.1|CB649618
EST:     GCAGGCAAGAAAATCAAATTGGAGACCAGCCGTCTGGGTGCTGCTAGGCG                         CTTGTCGCAGCATATGTCTTCAGAATTGTGTCAGGAAGAGTTTGGTGTATG
genomic: GCAGGCAAGAAAATCAAATTGGAGACCAGCCGTCTGGGTGCTGCTAGGCGgtaagtcatt ... tctatcacagCTTGTCGCAGCATATGTCTTCAGAATTGTGTCAGGAAGAGTTTGGTGTATG
EST: gi|88425200|gb|CI564717.1|CI564717
EST:     GCAGGCAAGAAAATCAAATTGGAGACCAGCCGTCTGGGTGCTGCTAGGCG                         CTTGTCGCAGCATATGTCTTCAGAATTGTGTCAGGAACAGTTTGGTGTATG
genomic: GCAGGCAAGAAAATCAAATTGGAGACCAGCCGTCTGGGTGCTGCTAGGCGgtaagtcatt ... tctatcacagCTTGTCGCAGCATATGTCTTCAGAATTGTGTCAGGAAGAGTTTGGTGTATG

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: 54 (upstream exon), 75 (downstream exon)
Score: 18

ATGTCAGAGCAGCTGAAGCTGCACTTCGTGCATTAAACAGGAATGATATTGCAGGCAAGAAAATCAAATTGGAGACCAGCCGTCTGGGTGCTGCTAGGCGgtaagtcatt ... tctatcacagCTTGTCGCAGCATATGTCTTCAGAATTGTGTCAGGAAGAGTTTGGTGTATGCAAACTGGGGAGTCCAAGCACAAGTAGCCCTCCAATTGCTTCGTTTG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgagtattttaattgtagctattgctttgactgatttcaatgctctctatcacagCTTGTCGCAGCATATGTCTTCAGAATTGTGTCAGGAAGAGTTTGGTGTATGCAAACTGGGGAGTCCAAGCACAAGTAGCCCTCCAATTGCTTCGTTTG
                            gactgat  putative branch site (score: 18)
                                          ctctctatc  putative PPT
     attttaattgta  TA-rich tract