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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tttccctccagactggacttccttctttgtgttctttcttgttggctgcattggctgttgggaaacttatgatgtataagacgtctatggcaatatgcagGATGCTGTTGATTGCCCGGAATGGGTTGTTCCATTCCATCTCTTCAAATTGCTGGCAGAGGAG

Basic information

species Oryza sativa
transcript LOC_Os08g08200.1
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os08g08200.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM2G042398_T01 (Zea mays), 3'ss of exon 10
tttccctccagactggacttccttctttgtgttctttcttgttggctgcattggctgttgggaaactta-tgatgtataagacgtctatggcaatatgcagGATGCTGTTGATTGCCCGGAATGGGTTGTTCCATTCCATCTCTTCAAATTGCTGGCAGAGGAG
|      ||||| |||  ||| ||    || |  ||| |   |   |  |    |||   | |||   | || || || | |  |||   |||| ||||||||||||||||||||||| ||||||||||||||||||||||||||||||||  |||||||||||
tagtttcccagattggctttcttttggagtttcttttgtctgtatttataaattctgaaagaaaaacaagtggtgaattaaat-tcttctgcaacatgcagGATGCTGTTGATTGCCCAGAATGGGTTGTTCCATTCCATCTCTTCAAATTATTGGCAGAGGAG

upper sequence: LOC_Os08g08200.1 (Oryza sativa), 3'ss of exon 9
lower sequence: Vv19s0014g04740.t01 (Vitis vinifera), 3'ss of exon 9
tttccctccagactggacttccttctttgtgttctttcttgttggctgcattggctgttgggaaacttatgatgtataagacgtctatggcaatat-gcagGATGCTGTTGATTGCCCGGAATGGGTTGTTCCATTCCATCTCTTCAAATTGCTGGCAGAGGAG
||    ||| |          || | |||  | |||   |    |   ||     |  |    |    || || | | ||| |     |    | | |||||||||||||||||| || |||||| |||| ||||| ||| |||||||||   ||||||| |||
ttatgatcctgctgctcagctctaccttgattccttaagttacagaaccacacaatcctacccataaaataatat-tgagaagaaagagcttttgttgcagGATGCTGTTGATTGTCCTGAATGGATTGTCCCATTTCATGTCTTCAAATCATTGGCAGAAGAG
















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|86477891|gb|CI120524.1|CI120524
EST:     AAGTCCCCGCATCCAGACCTTTCGGTATCAAATACAAGTTTCACTTAGAG                         GATGCTGTTGATTGCCCGGAATGGGTTGTTCCATTCCATCTCTTCAAATTG
genomic: AATTCCCCGCATCCAGACCTTTCGGTATCAAATACAAGTTTCACTTAGAGgtaagggatt ... caatatgcagGATGCTGTTGATTGCCCGGAATGGGTTGTTCCATTCCATCTCTTCAAATTG
EST: gi|58687919|gb|CK076606.1|CK076606
EST:     AATTCCCCGCATCCAGACCTTTCGGTATCAAATACAAGTTTCACTTAGAG                         GATGCTGTTGATTGCCCGGAATGGGTTGTTCCATTCCATCTCTTCAAATTG
genomic: AATTCCCCGCATCCAGACCTTTCGGTATCAAATACAAGTTTCACTTAGAGgtaagggatt ... caatatgcagGATGCTGTTGATTGCCCGGAATGGGTTGTTCCATTCCATCTCTTCAAATTG
EST: gi|89175372|gb|CI042393.1|CI042393
EST:     TCGGTATCAAATACAAGTTTCACTTAGAG                         GATGCTGTTGATTGCCCGGAATGGGTTGTTCCATTCCATCTCTTCAAATTG
genomic: TCGGTATCAAATACAAGTTTCACTTAGAGgtaagggatt ... caatatgcagGATGCTGTTGATTGCCCGGAATGGGTTGTTCCATTCCATCTCTTCAAATTG
EST: gi|87027891|gb|CI276247.1|CI276247
EST:     CGGTATCAAATACAAGTTTCACTTAGAG                         GATGCTGTTGATTGCCCGGAATGGGTTGTTCCATTCCATCTCTTCAAATTG
genomic: CGGTATCAAATACAAGTTTCACTTAGAGgtaagggatt ... caatatgcagGATGCTGTTGATTGCCCGGAATGGGTTGTTCCATTCCATCTCTTCAAATTG
EST: gi|58693212|gb|CK081899.1|CK081899
EST:     AATTCCCCGCATCCAGACCTTTCGGTATCAAATACAAGTTTCACTTAGAG                         GATGCTGTTGATTGCCCGGAATGGGTTGTTCCATTCCATCTCTTCAAATTG
genomic: AATTCCCCGCATCCAGACCTTTCGGTATCAAATACAAGTTTCACTTAGAGgtaagggatt ... caatatgcagGATGCTGTTGATTGCCCGGAATGGGTTGTTCCATTCCATCTCTTCAAATTG
EST: gi|29689085|gb|CB685360.1|CB685360
EST:     AATTCCCCGCATCCAGACCTTTCGGTATCAAATACAAGTTTCACTTAGAG                         GATGCTGTTGATTGCCCGGAATGGGTTGTTCCATTCCATCTCTTCAAATTG
genomic: AATTCCCCGCATCCAGACCTTTCGGTATCAAATACAAGTTTCACTTAGAGgtaagggatt ... caatatgcagGATGCTGTTGATTGCCCGGAATGGGTTGTTCCATTCCATCTCTTCAAATTG
EST: gi|86854764|gb|CI259050.1|CI259050
EST:     AATTCCCCGCATCCAGACCTTTCGGTATCAAATACAAGTTTCACTTAGAG                         GATGCTGTTGATTGCCCGGAATGGGTTGTTCCATTCCATCTCTTCAAATTG
genomic: AATTCCCCGCATCCAGACCTTTCGGTATCAAATACAAGTTTCACTTAGAGgtaagggatt ... caatatgcagGATGCTGTTGATTGCCCGGAATGGGTTGTTCCATTCCATCTCTTCAAATTG
EST: gi|25801957|gb|CA757918.1|CA757918
EST:     AATTCCCTGCATCCAGACCTTTCGGTATCAAATACAAGTTTCACTTAGAG                         GATGCTGTTGATTGCCCGGAATGGGTTGTTCCATTCCATCTCTTCAAATTG
genomic: AATTCCCCGCATCCAGACCTTTCGGTATCAAATACAAGTTTCACTTAGAGgtaagggatt ... caatatgcagGATGCTGTTGATTGCCCGGAATGGGTTGTTCCATTCCATCTCTTCAAATTG

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: 68 (upstream exon), 69 (downstream exon)
Score: 12

AAATTCCCCGCATCCAGACCTTTCGGTATCAAATACAAGTTTCACTTAGAGgtaagggatt ... caatatgcagGATGCTGTTGATTGCCCGGAATGGGTTGTTCCATTCCATCTCTTCAAATTGCTGGCAGAGGAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctgcattggctgttgggaaacttatgatgtataagacgtctatggcaatatgcagGATGCTGTTGATTGCCCGGAATGGGTTGTTCCATTCCATCTCTTCAAATTGCTGGCAGAGGAG
                 aaacttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tttccctccagactggacttccttctttgtgttctttcttgttggctgcattggctgttgggaaacttatgatgtataagacgtctatggcaatatgcagGATGCTGTTGATTGCCCGGAATGGGTTGTTCCATTCCATCTCTTCAAATTGCTGGCAGAGGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG
- -ccctcca
- - - - - - - - - - - - - ttgtgtt
- - - - - - - - - - - - - - - - - - -cttgttg
- - - - - - - - - - - - - - - - - - - - - - - tgcattg
- - - - - - - - - - - - - - - - - - - - - - - - - - -gctgttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - atgatgt