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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTGCTTGTATCTTCAACTTCTCTATCGGCACACAGATAATTTGTCAAAGAAAGATGTTCCAGAAATTTTTATGAAGAAGAAAGTGAAAAGgtaggtttgaaaatgttaatcattttttattatcaatcttttgccctcactttgtcattaattgtccctatatatgtgacaatgctag

Basic information

species Oryza sativa
transcript LOC_Os03g20640.1
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g20640.1 (Oryza sativa), 5'ss of exon 7
lower sequence: GRMZM2G060842_T01 (Zea mays), 5'ss of exon 7
TTGCTTGTATCTTCAACTTCTCTATCGGCACACAGATAATTTGTCAAAGAAAGATGTTCCAGAAATTTTTATGAAGAAGAAAGTGAAAAGgtaggtttgaaaatgttaatcattttttattatcaatcttttg--ccctcactttgtcattaattgtccctatata------tgtgacaatgctag
||||||||||||||||||||| ||||  ||  | |||||  | |||||| ||||| |||||||| ||||| | |||||||||||||| | |||||||| || ||   |       | | |   | ||  ||||   |||||| || | |||  ||      ||||       | ||  ||||||||
TTGCTTGTATCTTCAACTTCTGTATCAACATGCTGATAACCTATCAAAGGAAGATATTCCAGAAGTTTTTCTAAAGAAGAAAGTGAAGAAgtaggtttcaatattccacctgcagtctgtatcccattatttggttcctcacattttgattgtttaagtaaatatgactatttatgcaaatgctag
















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|88330013|gb|CI652403.1|CI652403
EST:     TTGTCAAAGAAAGATGTTCCAGAAATTTTTATGAAGAAGAAAGTGAAAAG                         AATCGGCATAAGAAGCGAGGATTTGAAGAATACAATAGAGAAGGTGTTGGG
genomic: TTGTCAAAGAAAGATGTTCCAGAAATTTTTATGAAGAAGAAAGTGAAAAGgtaggtttga ... acaatgctagAATCGGCATAAGAAGCGAGGATTTGAAGAATACAATAGAGAAGGTGTTGGG
EST: gi|88571218|gb|CI662591.1|CI662591
EST:     TTGTCAAAGAAAGATGTTCCAGAAATTTTTATGAAGAAGAAAGTGAAAAG                         AATCGGCATAAGAAGCGAGGATTTGAAGAATACAATAGAGAAGGTGTTGGG
genomic: TTGTCAAAGAAAGATGTTCCAGAAATTTTTATGAAGAAGAAAGTGAAAAGgtaggtttga ... acaatgctagAATCGGCATAAGAAGCGAGGATTTGAAGAATACAATAGAGAAGGTGTTGGG
EST: gi|29663267|gb|CB659542.1|CB659542
EST:     TTGTCAAAGAAAGATGTTCCAGAAATTTTTATGAAGAAGAAAGTGAAAAG                         AATCGGCATAAGAAGCGAGGATTTGAAGAATACAATAGAGAAGGTGTTGGG
genomic: TTGTCAAAGAAAGATGTTCCAGAAATTTTTATGAAGAAGAAAGTGAAAAGgtaggtttga ... acaatgctagAATCGGCATAAGAAGCGAGGATTTGAAGAATACAATAGAGAAGGTGTTGGG
EST: gi|88209249|gb|CI208675.1|CI208675
EST:     TTGTCAAAGAAAGATGTTCCAG-AATTTTTATGAAGAAGAAAGTGAAAAG                         AATCGGCATAAGAAGCGAGGATTTGAAGAATACAATAGAGAAGGTGTTGGG
genomic: TTGTCAAAGAAAGATGTTCCAGAAATTTTTATGAAGAAGAAAGTGAAAAGgtaggtttga ... acaatgctagAATCGGCATAAGAAGCGAGGATTTGAAGAATACAATAGAGAAGGTGTTGGG
EST: gi|88477015|gb|CI414286.1|CI414286
EST:     TTGTCAAAGAAAGATGTTCCAGAAATTTTTATGAAGAAGAAAGTGAAAAG                         AATCGGCATAAGAAGCGAGGATTTGAAGAATACAATAGAGAAGGTGTTGGG
genomic: TTGTCAAAGAAAGATGTTCCAGAAATTTTTATGAAGAAGAAAGTGAAAAGgtaggtttga ... acaatgctagAATCGGCATAAGAAGCGAGGATTTGAAGAATACAATAGAGAAGGTGTTGGG
EST: gi|86418084|gb|CI032293.1|CI032293
EST:     TTGTCAAAGAAAGATGTTCCAGAAATTTTTATGAAGAAGAAAGTGAAAAG                         AATCGGCATAAGAAGCGAGGATTTGAAGAATACAATAGAGAAGGTGTTGGG
genomic: TTGTCAAAGAAAGATGTTCCAGAAATTTTTATGAAGAAGAAAGTGAAAAGgtaggtttga ... acaatgctagAATCGGCATAAGAAGCGAGGATTTGAAGAATACAATAGAGAAGGTGTTGGG
EST: gi|88571155|gb|CI662528.1|CI662528
EST:     TTGTCAAAGAAAGATGTTCCAGAAATTTTTATGAAGAAGAAAGTGAAAAG                         AATCGGCATAAGAAGCGAGGATTTGAAGAATACAATAGAGAAGGTGTTGGG
genomic: TTGTCAAAGAAAGATGTTCCAGAAATTTTTATGAAGAAGAAAGTGAAAAGgtaggtttga ... acaatgctagAATCGGCATAAGAAGCGAGGATTTGAAGAATACAATAGAGAAGGTGTTGGG
EST: gi|88508429|gb|CI435935.1|CI435935
EST:     TTGTCAAAGAAAGATGTTCCAGGAATTTTTATGAAGAAGAAAGTGNAAAG                         AATCGGCATAAGAAGCCAGGATTTGAAGGATACAATAGAGAAGGTGTTGGG
genomic: TTGTCAAAGAAAGATGTTCCAGAAATTTTTATGAAGAAGAAAGTGAAAAGgtaggtttga ... acaatgctagAATCGGCATAAGAAGCGAGGATTTGAAGAATACAATAGAGAAGGTGTTGGG
EST: gi|88526125|gb|CI452504.1|CI452504
EST:     AGAAATTTTTATGAAGAAGAAAGTGAAAAG                         AATCGGCATAAGAAGCGAGGATTTGAAGAATACAATAGAGAAGGTGTTGGG
genomic: AGAAATTTTTATGAAGAAGAAAGTGAAAAGgtaggtttga ... acaatgctagAATCGGCATAAGAAGCGAGGATTTGAAGAATACAATAGAGAAGGTGTTGGG
EST: gi|89170010|gb|CI039287.1|CI039287
EST:     TTGTCAAAGAAAGATGTTCCAGAAATTTTTATGAAGAAGAAAGTGAAAAG                         AATCGGCATAAGAAGCGAGGATTTGAAGAATACCATAGAGAAGGTGTTGGG
genomic: TTGTCAAAGAAAGATGTTCCAGAAATTTTTATGAAGAAGAAAGTGAAAAGgtaggtttga ... acaatgctagAATCGGCATAAGAAGCGAGGATTTGAAGAATACAATAGAGAAGGTGTTGGG
EST: gi|88477016|gb|CI414287.1|CI414287
EST:     TTGTCAAAGAAAGATGTTCCAGAAATTTTTATGAAGAAGAAAGTGAAAAG                         AATCGGCATAAGAAGCGAGGATTTGAAGAATACAATAGAGAAGGTGTTGGG
genomic: TTGTCAAAGAAAGATGTTCCAGAAATTTTTATGAAGAAGAAAGTGAAAAGgtaggtttga ... acaatgctagAATCGGCATAAGAAGCGAGGATTTGAAGAATACAATAGAGAAGGTGTTGGG
EST: gi|88982477|gb|CI027950.1|CI027950
EST:     TTGTCAAAGAAAGATGTTCCAGAAATTTTTATGAAGAAGAAAGTGAAAAG                         AATCGGCATAAGAAGCGAGGATTTGAAGAATACAATAGAGAAGGTGTTGGG
genomic: TTGTCAAAGAAAGATGTTCCAGAAATTTTTATGAAGAAGAAAGTGAAAAGgtaggtttga ... acaatgctagAATCGGCATAAGAAGCGAGGATTTGAAGAATACAATAGAGAAGGTGTTGGG
EST: gi|86871982|gb|CI332154.1|CI332154
EST:     TTGTCAAAGAAAGATGTTCCAGAAATTTTTATGAAGAAGAAAGTGAAAAG                         AATCGGCATAAGAAGCGAGGATTTGAAGAATACAATAGAGAAGGTGTTGGG
genomic: TTGTCAAAGAAAGATGTTCCAGAAATTTTTATGAAGAAGAAAGTGAAAAGgtaggtttga ... acaatgctagAATCGGCATAAGAAGCGAGGATTTGAAGAATACAATAGAGAAGGTGTTGGG
EST: gi|14571326|gb|BI118694.1|BI118694
EST:     GTTCCAGAAATTTTTATGAAGAAGAAAGTGAAAAG                         AATCGGCATAAGAAGCGAGGATTTGAAGAATACAATAGAGAAGGTGTTGGG
genomic: GTTCCAGAAATTTTTATGAAGAAGAAAGTGAAAAGgtaggtttga ... acaatgctagAATCGGCATAAGAAGCGAGGATTTGAAGAATACAATAGAGAAGGTGTTGGG
EST: gi|88353819|gb|CI634610.1|CI634610
EST:     TTGTCAAAGAAAGATGTTCCAGAAATTTTTATGAAGAAGAAAGTGAAAAG                         AATCGGCATAAGAAGCGAGGATTTGAAGAATACAATAGAGAAGGTGTTGGG
genomic: TTGTCAAAGAAAGATGTTCCAGAAATTTTTATGAAGAAGAAAGTGAAAAGgtaggtttga ... acaatgctagAATCGGCATAAGAAGCGAGGATTTGAAGAATACAATAGAGAAGGTGTTGGG

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), 72 (downstream exon)
Score: 54

TTGCTTGTATCTTCAACTTCTCTATCGGCACACAGATAATTTGTCAAAGAAAGATGTTCCAGAAATTTTTATGAAGAAGAAAGTGAAAAGgtaggtttga ... acaatgctagAATCGGCATAAGAAGCGAGGATTTGAAGAATACAATAGAGAAGGTGTTGGGTGGTATTTCAGTAGCTCTTTCGTCTCCAAGGCTTGTGATACCCGCTATA




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTGCTTGTATCTTCAACTTCTCTATCGGCACACAGATAATTTGTCAAAGAAAGATGTTCCAGAAATTTTTATGAAGAAGAAAGTGAAAAGgtaggtttgaaaatgttaatcattttttattatcaatcttttgccctcactttgtcattaattgtccctatatatgtgacaatgctag

- - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA