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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATTGAGACCGACTGTGAAGTCGACTTTGCTCCACCACTTGACTATAAAGAACCTGAGCGACAAAAAGCTGCTGTTCCTCCAAGTACAGCGCCTACTGCTGgtagatttctctttatgccccgttattgatcttgatctcttccctcagattctcttgctgttcattactttaagatttattcgttttgcag

Basic information

species Oryza sativa
transcript LOC_Os02g08480.1
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g08480.1 (Oryza sativa), 5'ss of exon 8
lower sequence: GRMZM2G037185_T01 (Zea mays), 5'ss of exon 7
ATTGAGACCGACTGTGAAGTCGACTTTGCTCCACCACTTGACTATAAAGAACCTGAGCGACAAAAAGCTGCTGTTCCTCCAAGTACAGCGCCTACTGCTGgtagatttctctttatgccccgttattgatcttgatctcttccctcagattctcttgctgttcattactttaagatttattcgttttgcag
||||||||||| ||||| || ||||||||||||||||||||||| ||||||||||||| |  |||| ||||||||||| |||| || | ||||  | | ||||    | |  |  |      ||| || ||          |||  |   | | ||  ||  ||||| ||| |   |||||  ||  |   
ATTGAGACCGATTGTGAGGTTGACTTTGCTCCACCACTTGACTACAAAGAACCTGAGCCAGTAAAACCTGCTGTTCCTGCAAGCACGGAGCCTGGTACCGgtaagactattgtcctatgtgattactgttc----------cccatatggttttttcatgcacattatttttatgattattttttcag---
















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|27921103|gb|CB096911.1|CB096911
EST:     ACCTGAGCGACAAAAAGCTGCCGTTCCTCCAAGTACAGCGCCTACTGCTG                         AAGAGGCAGCTGAAGAAGAACCAAAGTTCATCCCCTTTACTGGACCTGGGA
genomic: ACCTGAGCGACAAAAAGCTGCTGTTCCTCCAAGTACAGCGCCTACTGCTGgtagatttct ... cgttttgcagAAGAGGCAGCTGAAGAAGAACCAAAGTTCATCCCCTTTACTGGACCTGGGA
EST: gi|29641787|gb|CB646794.1|CB646794
EST:     ACCTGAGCGACAAAAAGCTGCTGTTCCTCCAAGTACAGCGCCTACTGCTG                         AAGAGGCAGCTGAAGAAGAACCAAAGTTCATCCCCTTTACTGGACCTGGGA
genomic: ACCTGAGCGACAAAAAGCTGCTGTTCCTCCAAGTACAGCGCCTACTGCTGgtagatttct ... cgttttgcagAAGAGGCAGCTGAAGAAGAACCAAAGTTCATCCCCTTTACTGGACCTGGGA
EST: gi|58599220|gb|CK009748.1|CK009748
EST:     ACCTGAGCGACAAAAAGCTGCTGTTCCTCCAAGTACAGCGCCTACTGCTG                         AAGAGGCAGCTGAAGAAGAACCAAAGTTCATCCCCTTTACTGGACCTGGGA
genomic: ACCTGAGCGACAAAAAGCTGCTGTTCCTCCAAGTACAGCGCCTACTGCTGgtagatttct ... cgttttgcagAAGAGGCAGCTGAAGAAGAACCAAAGTTCATCCCCTTTACTGGACCTGGGA
EST: gi|29641788|gb|CB646795.1|CB646795
EST:     ACCTGAGCGACAAAAAGCTGCTGTTCCTCCAAGTACAGCGCCTACTGCTG                         AAGAGGCAGCTGAAGAAGAACCAAAGTTCATCCCCTTTACTGGACCTGGGA
genomic: ACCTGAGCGACAAAAAGCTGCTGTTCCTCCAAGTACAGCGCCTACTGCTGgtagatttct ... cgttttgcagAAGAGGCAGCTGAAGAAGAACCAAAGTTCATCCCCTTTACTGGACCTGGGA
EST: gi|87018863|gb|CI256748.1|CI256748
EST:     ACCTGAGCGACAAAAAGCTGCTGTTCCTCCAAGTACAGCGCCTACTGCTG                         AAGAGGCAGCTGAAGAAGAACCAAAGTTCATCCCCTTTACTGGACCTGGGA
genomic: ACCTGAGCGACAAAAAGCTGCTGTTCCTCCAAGTACAGCGCCTACTGCTGgtagatttct ... cgttttgcagAAGAGGCAGCTGAAGAAGAACCAAAGTTCATCCCCTTTACTGGACCTGGGA
EST: gi|86527163|gb|CI167369.1|CI167369
EST:     CTGTTCCTCCAAGTACAGCGCCTACTGCTG                         AAGAGGCAGCTGAAGAAGAACCAAAGTTCATCCCCTTTACTGGACCTGGGA
genomic: CTGTTCCTCCAAGTACAGCGCCTACTGCTGgtagatttct ... cgttttgcagAAGAGGCAGCTGAAGAAGAACCAAAGTTCATCCCCTTTACTGGACCTGGGA
EST: gi|33793328|gb|CF322545.1|CF322545
EST:     ACCTGAGCGACAAAAAGCTGCTGTTCCTCCAAGTACAGCGCCTACTGCTG                         AAGAGGCAGCTGAAGAAGAACCAAAGTTCATCCCCTTTACTGGACCTGGGA
genomic: ACCTGAGCGACAAAAAGCTGCTGTTCCTCCAAGTACAGCGCCTACTGCTGgtagatttct ... cgttttgcagAAGAGGCAGCTGAAGAAGAACCAAAGTTCATCCCCTTTACTGGACCTGGGA
EST: gi|29663476|gb|CB659751.1|CB659751
EST:     ACCTGAGCGACAAAAAGCTGCTGTTCCTCCAAGTACAGCGCCTACTGCTG                         AAGAGGCAGCTGAAGAAGAACCAAAGTTCATCCCCTTTACTGGACCTGGGA
genomic: ACCTGAGCGACAAAAAGCTGCTGTTCCTCCAAGTACAGCGCCTACTGCTGgtagatttct ... cgttttgcagAAGAGGCAGCTGAAGAAGAACCAAAGTTCATCCCCTTTACTGGACCTGGGA
EST: gi|87018867|gb|CI256752.1|CI256752
EST:     ACCTGAGCGACAAAAAGCTGCTGTTCCTCCAAGTACAGCGCCTACTGCTG                         AAGAGGCAGCTGAAGAAGAACCAAAGTTCATCCCCTTTACTGGACCTGGGA
genomic: ACCTGAGCGACAAAAAGCTGCTGTTCCTCCAAGTACAGCGCCTACTGCTGgtagatttct ... cgttttgcagAAGAGGCAGCTGAAGAAGAACCAAAGTTCATCCCCTTTACTGGACCTGGGA

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: 28

ATTGAGACCGACTGTGAAGTCGACTTTGCTCCACCACTTGACTATAAAGAACCTGAGCGACAAAAAGCTGCTGTTCCTCCAAGTACAGCGCCTACTGCTGgtagatttct ... cgttttgcagAAGAGGCAGCTGAAGAAGAACCAAAGTTCATCCCCTTTACTGGACCTGGGAGGCGTCTGGATGGGAAGGCTCCTAAAGATAAGGATGTATCAGCTTCATC




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATTGAGACCGACTGTGAAGTCGACTTTGCTCCACCACTTGACTATAAAGAACCTGAGCGACAAAAAGCTGCTGTTCCTCCAAGTACAGCGCCTACTGCTGgtagatttctctttatgccccgttattgatcttgatctcttccctcagattctcttgctgttcattactttaagatttattcgttttgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGTT