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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agatagttagattagcttaaccaaaatctgcttctgccataccctgttttggctgttagcaatttaatgctgaaaacatcacgttatttactctttgcagGAGTTTGAACCTTTGATTCAGAAGCCATATAGCATTGTCTATTTCCATTCTGCTGCATCATTACAACC

Basic information

species Oryza sativa
transcript LOC_Os10g30750.1
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os10g30750.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM5G836588_T01 (Zea mays), 3'ss of exon 9
agatagttagattagcttaaccaaaatctgcttctgccataccctgttttggctgttagcaat---ttaatgctgaaaacatcacgttatttactctttgcagGAGTTTGAACCTTTGATTCAGAAGCCATATAGCATTGTCTATTTCCATTCTGCTGCATCATTACAACC
   |   ||  ||   ||    || |    | |||  || |   ||| |||| | ||  ||||   ||||| |||||||        ||||| || | |  |||||||||||||||||||||||||||||||||  ||||| |||||||| || || ||||||||||||||
ttgtgcgtatgttgtttt--ttaagacactcatcttgcagattttgtattgggttttctcaataagttaattctgaaaattgtgtcatattttctgtct-tagGAGTTTGAACCTTTGATTCAGAAGCCATATACAATTGTATATTTCCACTCCGCAGCATCATTACAACC
















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|38470669|gb|CF954800.1|CF954800
EST:     TTCTTCTTCGCTGCTTGGATCTTGAACGGTTTGTTCTACATGTAGTAAAG                         GAGTTTGAACCTTTGATTCAGAAGCCATATAGCATTGTCTATTTCCATTCT
genomic: TTCTTCTTCGCTGCTTGGATCTTGAACGGTTTGTTCTACATGTAGTAAAGgtaattgtcc ... ctctttgcagGAGTTTGAACCTTTGATTCAGAAGCCATATAGCATTGTCTATTTCCATTCT
EST: gi|29672652|gb|CB668927.1|CB668927
EST:     ACATGTAGTAAAG                         GAGTTTGAACCTTTGATTCAGAAGCCATATAGCATTGTCTATTTCCATTCT
genomic: ACATGTAGTAAAGgtaattgtcc ... ctctttgcagGAGTTTGAACCTTTGATTCAGAAGCCATATAGCATTGTCTATTTCCATTCT
EST: gi|58600810|gb|CK011338.1|CK011338
EST:     TTCTTCTTCGCTGCTTGGATCTTGAACGGTTTGTTCTACATGTAGTAAAG                         GAGTTTGAACCTTTGATTCAGAAGCCATATAGCATTGTCTATTTCCATTCT
genomic: TTCTTCTTCGCTGCTTGGATCTTGAACGGTTTGTTCTACATGTAGTAAAGgtaattgtcc ... ctctttgcagGAGTTTGAACCTTTGATTCAGAAGCCATATAGCATTGTCTATTTCCATTCT
EST: gi|25803039|gb|CA759000.1|CA759000
EST:     CGGTTTGTTCTACATGTAGTAAAG                         GAGTTTGAACCTTTGATTCAGAAGCCATATAGCATTGTCTATTTCCATTTT
genomic: CGGTTTGTTCTACATGTAGTAAAGgtaattgtcc ... ctctttgcagGAGTTTGAACCTTTGATTCAGAAGCCATATAGCATTGTCTATTTCCATTCT
EST: gi|86828186|gb|CI276799.1|CI276799
EST:     GTTTGTTCTACATGTAGTAAAG                         GAGTGTGAACCTTTGATTCAGAAGCCATATAGCATTGTCTATTTCCATTCT
genomic: GTTTGTTCTACATGTAGTAAAGgtaattgtcc ... ctctttgcagGAGTTTGAACCTTTGATTCAGAAGCCATATAGCATTGTCTATTTCCATTCT
EST: gi|33800827|gb|CF326285.1|CF326285
EST:     TTCTTCTTCGCTGCTTGGATCTTGAACGGTTTGTTCTACATGTAGTAAAG                         GAGTTTGAACCTTTGATTCAGAAGCCATATAGCATTGTCTATTTCCATTCT
genomic: TTCTTCTTCGCTGCTTGGATCTTGAACGGTTTGTTCTACATGTAGTAAAGgtaattgtcc ... ctctttgcagGAGTTTGAACCTTTGATTCAGAAGCCATATAGCATTGTCTATTTCCATTCT
EST: gi|218487094|gb|FG954412.1|FG954412
EST:     TTCTTCTTCGCTGCTTGGATCTTGAACGGTTTGTTCTACATGTAGTAAAG                         GAGTTTGAACCTTTGATTCAGAAGCCATATAGCATTGTCTATTTCCATTCT
genomic: TTCTTCTTCGCTGCTTGGATCTTGAACGGTTTGTTCTACATGTAGTAAAGgtaattgtcc ... ctctttgcagGAGTTTGAACCTTTGATTCAGAAGCCATATAGCATTGTCTATTTCCATTCT

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: 64 (upstream exon), 68 (downstream exon)
Score: 25

TGGAGTTGACAGTGAAGGACGCCCGGTTATGGTTGTTGTTGGTGCACACTTTCTTCTTCGCTGCTTGGATCTTGAACGGTTTGTTCTACATGTAGTAAAGgtaattgtcc ... ctctttgcagGAGTTTGAACCTTTGATTCAGAAGCCATATAGCATTGTCTATTTCCATTCTGCTGCATCATTACAACC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttttggctgttagcaatttaatgctgaaaacatcacgttatttactctttgcagGAGTTTGAACCTTTGATTCAGAAGCCATATAGCATTGTCTATTTCCATTCTGCTGCATCATTACAACC
                atttaat  putative branch site (score: 25)
                                         tttactcttt  putative PPT
               aatttaat  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
agatagttagattagcttaaccaaaatctgcttctgccataccctgttttggctgttagcaatttaatgctgaaaacatcacgttatttactctttgcagGAGTTTGAACCTTTGATTCAGAAGCCATATAGCATTGTCTATTTCCATTCTGCTGCATCATTACAACC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - -taaccaa
- - - - - - - - - - - - aatctgc
- - - - - - - - - - - - - - - -ttctgcc
- - - - - - - - - - - - - - - - - - - - - - - - - ggctgtt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgctgaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aacatca