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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agccaactctcaaacgtcaacgtatttcttgtagacagtaccaaattcttatccctgcataggtgtagagatacttatttgctcaattttgactacgcagGCACGACCAATTTTACGAGATAAAGATACGCTAGAAGAACTAGCTGATCCCAAGCTTGGTGGCCAGTATCCAAAAGATGATTTTGTGCGAGTATGCACAA

Basic information

species Oryza sativa
transcript LOC_Os01g14932.3
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g14932.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G180065_T03 (Zea mays), 3'ss of exon 6
agccaactctcaaacgtcaacgtatttcttgtagacagtaccaaattcttatccctgcataggtg---------tagagatacttatttgctcaattttgactacgcagGCACGACCAATTTTACGAGATAAAGATACGCTAGAAGAACTAGCTGATCCCAAGCTTGGTGGCCAGTATCCAAAAGATGATTTTGTGCGAGTATGCACAA
     |     | |  |  |  |||   |  | | |  |  |    | |  | | || | |||||         |  ||| | |  |||||||  | ||| ||  ||||||||| |||||| | |||||  ||||||   ||| ||| ||||||||||||| |||||| |||||||| || ||||||||||||||||| || |||||||
----tatatatatatatatatatatgattatttgtccct-tcgtggtgtggtgcatgaagaggtgatatcacactcaagacattcttttgctc--tgttggct--gcagGCACGGCCAATTCTCCGAGACCAAGATAGATTAGGAGAGCTAGCTGATCCCAGGCTTGGCGGCCAGTACCCGAAAGATGATTTTGTGCGGGTGTGCACAA
















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|29625207|gb|CB630218.1|CB630218
EST:     GGCCTGTGGATATGTCACAACCTTCTGGCCAGGAAAATCTAGTGACATGG                         GCACGACCAATTTTACGAGATAAAGATACGCTAGAAGAACTAGCTGATCCC
genomic: GGCCTGTGGATATGTCACAACCTTCTGGCCAGGAAAATCTAGTGACATGGgttagatttc ... gactacgcagGCACGACCAATTTTACGAGATAAAGATACGCTAGAAGAACTAGCTGATCCC
EST: gi|88902229|gb|CI374837.1|CI374837
EST:     GGCCTGTGGATATGTCACAACCTTCTGGCCAGGAAAATCTAGTGACATGG                         GCACGACCAATTTTACGAGATAAAGATACGCTAGAAGAACTAGCTGATCCC
genomic: GGCCTGTGGATATGTCACAACCTTCTGGCCAGGAAAATCTAGTGACATGGgttagatttc ... gactacgcagGCACGACCAATTTTACGAGATAAAGATACGCTAGAAGAACTAGCTGATCCC
EST: gi|88198013|gb|CI197863.1|CI197863
EST:     GGCCTGTGGATATGCCACAACCTTCTGGCCAGGAAAATCTAGTGACATGG                         GCACGACCAATTTTACGAGATAAAGGTACGCTAGAAGAACTAGCTGATCCC
genomic: GGCCTGTGGATATGTCACAACCTTCTGGCCAGGAAAATCTAGTGACATGGgttagatttc ... gactacgcagGCACGACCAATTTTACGAGATAAAGATACGCTAGAAGAACTAGCTGATCCC
EST: gi|88198766|gb|CI198616.1|CI198616
EST:     GCCCTGTGAATATGTCACAACCTTCTGGCCAGGAAAATCTAGTGACATGG                         GCACGACCAATTTTACGAGATAAAGATACGCTAGAAGAACTAGCTGATCCC
genomic: GGCCTGTGGATATGTCACAACCTTCTGGCCAGGAAAATCTAGTGACATGGgttagatttc ... gactacgcagGCACGACCAATTTTACGAGATAAAGATACGCTAGAAGAACTAGCTGATCCC
EST: gi|29619813|gb|CB624825.1|CB624825
EST:     GGCCTGTGGATATGTCACAACCTTCTGGCCAGGAAAATCTAGTGACATGG                         GCACGACCAATTTTACGAGATAAAGATACGCTAGAAGAACTAGCTGATCCC
genomic: GGCCTGTGGATATGTCACAACCTTCTGGCCAGGAAAATCTAGTGACATGGgttagatttc ... gactacgcagGCACGACCAATTTTACGAGATAAAGATACGCTAGAAGAACTAGCTGATCCC
EST: gi|29628587|gb|CB633598.1|CB633598
EST:     GGCCTGTGGATATGTCACAACCTTCTGGCCAGGAAAATCTAGTGACATGG                         GCACGACCAATTTTACGAGATAAAGATACGCTAGAAGAACTAGCTGATCCC
genomic: GGCCTGTGGATATGTCACAACCTTCTGGCCAGGAAAATCTAGTGACATGGgttagatttc ... gactacgcagGCACGACCAATTTTACGAGATAAAGATACGCTAGAAGAACTAGCTGATCCC
EST: gi|3763865|gb|AU030604.1|AU030604
EST:     GCCCTGTGGATATGTCACACCCTTCTGGCCAGGAAAATCTAGTGACATGG                         GCCACGCCCAATTTTACGAGATAAAGATACGCTAGAAGAACTAGCTGATCC
genomic: GGCCTGTGGATATGTCACAACCTTCTGGCCAGGAAAATCTAGTGACATGGgttagatttc ... gactacgcagG-CACGACCAATTTTACGAGATAAAGATACGCTAGAAGAACTAGCTGAT-C


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcttatccctgcataggtgtagagatacttatttgctcaattttgactacgcagGCACGACCAATTTTACGAGATAAAGATACGCTAGAAGAACTAGCTGATCCCAAGCTTGGTGGCCAGTATCCAAAAGATGATTTTGTGCGAGTATGCACAA
                                         ttttgac  putative branch site (score: 3)
                         atacttattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
agccaactctcaaacgtcaacgtatttcttgtagacagtaccaaattcttatccctgcataggtgtagagatacttatttgctcaattttgactacgcagGCACGACCAATTTTACGAGATAAAGATACGCTAGAAGAACTAGCTGATCCCAAGCTTGGTGGCCAGTATCCAAAAGATGATTTTGTGCGAGTATGCACAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG