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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ggtattaccaaaacttggtaaggtttattttggctacaatctaaacaagcccctagcccctagtgactgagttcgcgttttggttgtgttgtgtgtatagGTGAAGAATGGTGGTGATTGCCAGTCCGTGCTCGACTATGTGCATGGATTATATCAAGATTTGGGCATACAGGACCTGACCATCCAAACCGATGAATAAG

Basic information

species Oryza sativa
transcript LOC_Os02g58580.5
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g58580.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G017365_T03 (Zea mays), 3'ss of exon 8
ggtattaccaaaacttggtaaggtttattttggctacaatctaaacaagcccctagcccctagtgactgagttcgcgttttggttgtgttgtg-tgtatagGTGAAGAATGGTGGTGATTGCCAGTCCGTGCTCGACTATGTGCATGGATTATATCAAGATTTGGGCATACAGGACCTGACCATCCAAACCGATGAATAAG
                 ||||        ||| |    | ||  | ||| || |       | |||   | | |     ||| |||| ||| | ||||||||||||||  || | |||   || | | || || || ||   |||||| |||||||| ||||||||||||||||| |||||  ||||||| ||||| |  |
-----------------gtaaaacc---cttgacacagagctgca-aagtccatcatttgcactgaagcattcctgacgttgcttgttttgcgctgtatagGTGAAGAGCGGCGCTGACGACCGGGCAGTCCTTGAATACACGCATGGTTTATATCAGGATTTGGGCATACAGGATCTGACGGTCCAAACTGATGAGTTTG
















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|88487175|gb|CI424446.1|CI424446
EST:     GATTTTGGGAGCTTGTACCTGGTCACGCTGTTGGATCTCTCGACATCCGG                         GTGAAGAATGGTGGTGATTGCCAGTCCGTGCTCGACTATGTGCATGGATTA
genomic: GATTTTGGGAGCTTGTACCTGGTCACGCTGTTGGATCTCTCGACATCCGGgtacatcttt ... gtgtgtatagGTGAAGAATGGTGGTGATTGCCAGTCCGTGCTCGACTATGTGCATGGATTA
EST: gi|86887374|gb|CI313277.1|CI313277
EST:     GATTTTGGGAGCTTGTACCTGGTCACGCTGTTGGATCTCTCGACATCCGG                         GTGAAGAATGGTGGTGATTGCCAGTCCGTGCTCGACTATGTGCATGGATTA
genomic: GATTTTGGGAGCTTGTACCTGGTCACGCTGTTGGATCTCTCGACATCCGGgtacatcttt ... gtgtgtatagGTGAAGAATGGTGGTGATTGCCAGTCCGTGCTCGACTATGTGCATGGATTA
EST: gi|88486200|gb|CI423471.1|CI423471
EST:     GATTTTGGGAGCTTGTACCTGGTCACGCTGTTGGATCTCTCGACATCCGG                         GTGAAGAATGGTGGTGATTGCCAGTCCGTGCTCGACTATGTGCATGGATTA
genomic: GATTTTGGGAGCTTGTACCTGGTCACGCTGTTGGATCTCTCGACATCCGGgtacatcttt ... gtgtgtatagGTGAAGAATGGTGGTGATTGCCAGTCCGTGCTCGACTATGTGCATGGATTA
EST: gi|86507803|gb|CI150436.1|CI150436
EST:     GATTTTGGGAGCTTGTACCTGGTCACGCTGTTGGATCTCTCGACATCCGG                         GTGAAGAATGGTGGTGATTGCCAGTCCGTGCTCGACTATGTGCATGGATTA
genomic: GATTTTGGGAGCTTGTACCTGGTCACGCTGTTGGATCTCTCGACATCCGGgtacatcttt ... gtgtgtatagGTGAAGAATGGTGGTGATTGCCAGTCCGTGCTCGACTATGTGCATGGATTA
EST: gi|86862201|gb|CI330735.1|CI330735
EST:     GATTTTGGGAGCTTGTACCTGGTCACGCTGTTGGATCTCTCGACATCCGG                         GTGAAGAATGGTGGTGATTGCCAGGTCCGTGCTCGACTATGTGCATGGATT
genomic: GATTTTGGGAGCTTGTACCTGGTCACGCTGTTGGATCTCTCGACATCCGGgtacatcttt ... gtgtgtatagGTGAAGAATGGTGGTGATTGCCA-GTCCGTGCTCGACTATGTGCATGGATT
EST: gi|88486115|gb|CI423386.1|CI423386
EST:     TGGTCACGCTGTTGGATCTCTCGACATCCGG                         GTGAAGAATGGTGGTGATTGCCAGTCCGTGCTCGACTATGTGCATGGATTA
genomic: TGGTCACGCTGTTGGATCTCTCGACATCCGGgtacatcttt ... gtgtgtatagGTGAAGAATGGTGGTGATTGCCAGTCCGTGCTCGACTATGTGCATGGATTA
EST: gi|8858691|gb|AU096009.1|AU096009
EST:     GATTTTGGGAGCTTGTACCTGGTCACGCTGTTGGATCTCTCGACATCCGG                         GTGAAGAATGGTGGTGATTGCCAGTCCGTGCTCGACTATGTGCATGGATTA
genomic: GATTTTGGGAGCTTGTACCTGGTCACGCTGTTGGATCTCTCGACATCCGGgtacatcttt ... gtgtgtatagGTGAAGAATGGTGGTGATTGCCAGTCCGTGCTCGACTATGTGCATGGATTA
EST: gi|29661174|gb|CB657449.1|CB657449
EST:     GATTTTGGGAGCTTGTACCTGGTCACGCTGTTGGATCTCTCGACATCCGG                         GTGAAGAATGGTGGTGATTGCCAGTCCGTGCTCGACTATGTGCATGGATTA
genomic: GATTTTGGGAGCTTGTACCTGGTCACGCTGTTGGATCTCTCGACATCCGGgtacatcttt ... gtgtgtatagGTGAAGAATGGTGGTGATTGCCAGTCCGTGCTCGACTATGTGCATGGATTA
EST: gi|88484745|gb|CI422016.1|CI422016
EST:     CTCGACATCCGG                         GTGAAGAATGGTGGTGATTGCCAGTCCGTGCTCGACTATGTGCATGGATTA
genomic: CTCGACATCCGGgtacatcttt ... gtgtgtatagGTGAAGAATGGTGGTGATTGCCAGTCCGTGCTCGACTATGTGCATGGATTA
EST: gi|89170146|gb|CI039423.1|CI039423
EST:     GATTTTGGGAGCTTGTACCTGGTCACGCTGTTGGATCTCTCGACATCCGG                         GTGAAGAATGGTGGTGATTGCCAGTCCGTGCTCGACTATGTGCATGGATTA
genomic: GATTTTGGGAGCTTGTACCTGGTCACGCTGTTGGATCTCTCGACATCCGGgtacatcttt ... gtgtgtatagGTGAAGAATGGTGGTGATTGCCAGTCCGTGCTCGACTATGTGCATGGATTA

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: 71 (upstream exon), 66 (downstream exon)
Score: 12

ATAACTGCGTGCGAGGATGTTTCTGAAGTATGTCAAGGTCGATTTTGGGAGCTTGTACCTGGTCACGCTGTTGGATCTCTCGACATCCGGgtacatcttt ... gtgtgtatagGTGAAGAATGGTGGTGATTGCCAGTCCGTGCTCGACTATGTGCATGGATTATATCAAGATTTGGGCATACAGGACCTGACCATCCAAACCGATGAATAAG




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Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ggtattaccaaaacttggtaaggtttattttggctacaatctaaacaagcccctagcccctagtgactgagttcgcgttttggttgtgttgtgtgtatagGTGAAGAATGGTGGTGATTGCCAGTCCGTGCTCGACTATGTGCATGGATTATATCAAGATTTGGGCATACAGGACCTGACCATCCAAACCGATGAATAAG

- - - accaaaa
- - - - - - - - - - - - - - - tggctac
- - - - - - - - - - - - - - - - - - - - -taaacaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gtgactg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ttgtgtt