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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtagagtctcttgtattttgaaggtgacttttaagcagtatctttctttttgcgactcatgactatctatatatcagGTTTCATTGTGCAACTACGAAGCCTAGAGGACCACTCTCCCCTTCCCGGTGTTACTCTTGGTGATATCGGCGGAAAATTTGGTAGTGGTGCATACAACAG

Basic information

species Oryza sativa
transcript LOC_Os06g01390.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g01390.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM5G864319_T01 (Zea mays), 3'ss of exon 5
gta-gagtctcttgtattttgaaggtgacttttaagcagtatctt---tctttttgcgactcatgactatctatatatcagGTTTCATTGTGCAACTACGAAGCCTAGAGGACCACTCTCCCCTTCCCGGTGTTACTCTTGGTGATATCGGCGGAAAATTTGGTAGTGGTGCATACAACAG
||| |||| | |||| |||   ||||||  ||||||   | || |       ||||   || |||    ||  | |  ||||||||||||||||||| |||||| ||||||| ||||| || ||||| ||| ||||||| |||||||| || ||||||||||| ||||||||||| |||||
gtaagagtgttttgtgttt---aggtgatatttaagtgttctcctagtctcctttgtttcttatgcacgtccttgtcccagGTTTCATTGTGCAACTGCGAAGCTTAGAGGATCACTCCCCTCTTCCTGGTATTACTCTGGGTGATATTGGTGGAAAATTTGGCAGTGGTGCATATAACAG

upper sequence: LOC_Os06g01390.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G052389_T01 (Zea mays), 3'ss of exon 5
gtagagtctcttgtattttgaaggtgactttt---aagcagtatc-tttctttttgcgactcatgac--------tatctatatatcagGTTTCATTGTGCAACTACGAAGCCTAGAGGACCACTCTCCCCTTCCCGGTGTTACTCTTGGTGATATCGGCGGAAAATTTGGTAGTGGTGCATACAACAG
    ||| | |||  ||| | |  || ||||    | ||||||   | |   |||| |||| |||          | ||  | |  ||||||||||||||||||| |||||| ||||||| ||||| || ||||| |||||||| || |||||||| || ||||| || |||||||||||||| |||||
--gtagtgttttgcttttgggaaatgcctttcttgatgcagtactgtcttcctttgtgacttatggtattacgcatgtcggtgttccagGTTTCATTGTGCAACTGCGAAGCTTAGAGGATCACTCCCCACTTCCTGGTGTTACCCTCGGTGATATTGGTGGAAAGTTCGGTAGTGGTGCATATAACAG
















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|58612003|gb|CK039715.1|CK039715
EST:     AGTTGTGTATGCTCGTCTGATAACTGAAGGAAAGGACTACGGCATACATG                         GTTTCATTGTGCAACTACGAAGCCTAGAGGACCACTCTCCCCTTCCCGGTG
genomic: AGTTGTGTATGCTCGTCTGATAACTGAAGGAAAGGACTACGGCATACATGgtagagtctc ... tatatatcagGTTTCATTGTGCAACTACGAAGCCTAGAGGACCACTCTCCCCTTCCCGGTG
EST: gi|29630576|gb|CB635585.1|CB635585
EST:     AGTTGTGTATGCTCGTCTGATAACTGAAGGAAAGGACTACGGCATACATG                         GTTTCATTGTGCAACTACCAAGCCTAGAGGACCACTCTCCCCTTCCCGGTG
genomic: AGTTGTGTATGCTCGTCTGATAACTGAAGGAAAGGACTACGGCATACATGgtagagtctc ... tatatatcagGTTTCATTGTGCAACTACGAAGCCTAGAGGACCACTCTCCCCTTCCCGGTG
EST: gi|29681783|gb|CB678058.1|CB678058
EST:     CTCGTCTGATAACTGAAGGAAAGGACTACGGCATACATG                         GTTTCATTGTGCAACTACGAAGCCTAGAGGACCACTCTCCCCTTCCCGGTG
genomic: CTCGTCTGATAACTGAAGGAAAGGACTACGGCATACATGgtagagtctc ... tatatatcagGTTTCATTGTGCAACTACGAAGCCTAGAGGACCACTCTCCCCTTCCCGGTG
EST: gi|58663554|gb|CK052240.1|CK052240
EST:     AGTTGTGTATGCTCGTCTGATAACTGAAGGAAAGGACTACGGCATACATG                         GTTTCATTGTGCAACTACGAAGCCTAGAGGACCACTCTCCCCTTCCCGGTG
genomic: AGTTGTGTATGCTCGTCTGATAACTGAAGGAAAGGACTACGGCATACATGgtagagtctc ... tatatatcagGTTTCATTGTGCAACTACGAAGCCTAGAGGACCACTCTCCCCTTCCCGGTG
EST: gi|29666537|gb|CB662812.1|CB662812
EST:     AGTTGTGTATGCTCGTCTGATAACTGAAGGAAAGGACTACGGCATACATG                         GTTTCATTGTGCAACTACGAAGCCTAGAGGACCACTCTCCCCTTCCCGGTG
genomic: AGTTGTGTATGCTCGTCTGATAACTGAAGGAAAGGACTACGGCATACATGgtagagtctc ... tatatatcagGTTTCATTGTGCAACTACGAAGCCTAGAGGACCACTCTCCCCTTCCCGGTG
EST: gi|2443069|gb|C74840.1|C74840
EST:     AGTTGTGTATGCTCGTCTGATAACTGAAGGAAAGGACTACGGCATACATG                         GTTTCATTGTGCAACTACGAAGCCTAGAGGACCACTCTCCCCTTCCCGGTG
genomic: AGTTGTGTATGCTCGTCTGATAACTGAAGGAAAGGACTACGGCATACATGgtagagtctc ... tatatatcagGTTTCATTGTGCAACTACGAAGCCTAGAGGACCACTCTCCCCTTCCCGGTG

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: 52

TGGTGGCCTGGTGGCTTGGGAAAAGCTTCCACTCATGCAGTTGTGTATGCTCGTCTGATAACTGAAGGAAAGGACTACGGCATACATGgtagagtctc ... tatatatcagGTTTCATTGTGCAACTACGAAGCCTAGAGGACCACTCTCCCCTTCCCGGTGTTACTCTTGGTGATATCGGCGGAAAATTTGGTAGTGGTGCATACAACAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggtgacttttaagcagtatctttctttttgcgactcatgactatctatatatcagGTTTCATTGTGCAACTACGAAGCCTAGAGGACCACTCTCCCCTTCCCGGTGTTACTCTTGGTGATATCGGCGGAAAATTTGGTAGTGGTGCATACAACAG
                                         tatctatatat  TA-rich tract