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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtttgcactttgtttcatgatggatatgtttcctattgcatttaccatcataatgaataaaaaaaaaactcatacctttcagGTCAGCCTGCCTGATGTTGGCGATTCAACAGTTAATTTAATGAATGCAATATACACAACAATGCAGTCCCATCTTCAAGGCTATAATCTTTGGCAG

Basic information

species Oryza sativa
transcript LOC_Os05g06510.2
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g06510.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM5G864166_T01 (Zea mays), 3'ss of exon 7
--------------------------------gtaagtttgcactttgtttcatgatggatatg-tttcctattgcat------ttaccat--cataatgaataaaaaaaaaactcatacctttcagGTCAGCCTGCCTGATGTTGGCGATTCAACAGTTAATTTAATGAATGCAATATACACAACAATGCAGTCCCATCTTCAAGGCTATAATCTTTGGCAG
                                  |  |||| | |       |||  |    ||  ||  ||||| |        | ||||  ||| || | |||    |||  |||  | |||||||| || || |||||| | || || ||||| ||| |  | |||||  |||||||||||| |||| || ||||| || |||| |||||||||||||||
gtaggttccacaattggtttgttgctgtatccacatatttgtattgctggaaatgtagccagtgactttttattgaaaaaaaaacttccattccatcattattaacgtgaaagttcactcttttcagGTTAGTCTTCCTGATATAGGTGAATCAACTGTTGACCTCATGAACACAATATACACAATAATGGAGCCCCATTTTAAAGGGTATAATCTTTGGCAG
















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|218495263|gb|FG944822.1|FG944822
EST:     CCCTCTGGAGCAACCTGGGTGACTCAATCAATAATGTGAAACTGATTGCA                         GTCAGCCTGCCTGATGTTGGTGATTCAACAGTTAATTTCATGAATGCAATA
genomic: CCCTCTGGAGCAACTTGGGTGAGTCAATCAATAATGTGAAGCTGATTGCAgtaagtttgc ... tacctttcagGTCAGCCTGCCTGATGTTGGCGATTCAACAGTTAATTTAATGAATGCAATA
EST: gi|29661372|gb|CB657647.1|CB657647
EST:     CCCTCTGGAGCAACTTGGGTGAGTCAATCAATAATGTGAAGCTGATTGCA                         GTCAGCCTGCCTGATGTTGGCGATTCAACAGTTAATTTAATGAATGCAATA
genomic: CCCTCTGGAGCAACTTGGGTGAGTCAATCAATAATGTGAAGCTGATTGCAgtaagtttgc ... tacctttcagGTCAGCCTGCCTGATGTTGGCGATTCAACAGTTAATTTAATGAATGCAATA

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: 50 (upstream exon), 39 (downstream exon)
Score: 2

GGGAACTGATATGTTCAATACCCTCTGGAGCAACTTGGGTGAGTCAATCAATAATGTGAAGCTGATTGCAgtaagtttgc ... tacctttcagGTCAGCCTGCCTGATGTTGGCGATTCAACAGTTAATTTAATGAATGCAATATACACAACAATGCAGTCCCATCTTCAAGGCTATAATCTTTGGCAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtttcctattgcatttaccatcataatgaataaaaaaaaaactcatacctttcagGTCAGCCTGCCTGATGTTGGCGATTCAACAGTTAATTTAATGAATGCAATATACACAACAATGCAGTCCCATCTTCAAGGCTATAATCTTTGGCAG
                                             tacctttc  CT-rich tract
            atttaccatcataatg  TA-rich tract