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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agtcctgacattagagtagcttctcacttagcatatctataggtcagggtgcatgttgtaatgttcttccgatttaacaactctcttgtattctctgcagGATTTCAGCTCATCATGGGATATCCGCGCAACGCCGACCTTTTTCTTCATAAAAAACGAGAAGCAGGTCGACAAGCTTGTGGGCGCCAACAAACCTGAGC

Basic information

species Oryza sativa
transcript LOC_Os05g07690.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g07690.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G066612_T01 (Zea mays), 3'ss of exon 2
agtcctgacattagagtagcttctcacttagcatatctataggtcagggtgcatgttgtaatgttcttccgatttaacaactctcttg--tattc-tctgcagGATTTCAGCTCATCATGGGATATCCGCGCAACGCCGACCTTTTTCTTCATAAAAAACGAGAAGCAGGTCGACAAGCTTGTGGGCGCCAACAAACCTGAGC
    |  |    |  |||     |   ||  ||| || ||||||| | |    | |  |      ||    |||       | || ||  ||||| ||| ||||| |||||||| |||||||| ||||| ||||| ||||| || |||||| | || |||| | ||||| |||||||||| |||||||| |||||||||||||
---tcaaatcaaatggtattaagtatatttccatctcgataggtctgtgctgctttcatctaaccctattcattgcgttgttttcgtgactattcatctccagGACTTCAGCTCTTCATGGGACATCCGTGCAACCCCGACATTCTTCTTCCTCAAGAACGGGCAGCAGATCGACAAGCTCGTGGGCGCGAACAAACCTGAGC

upper sequence: LOC_Os05g07690.1 (Oryza sativa), 3'ss of exon 4
lower sequence: Vv08s0040g00020.t01 (Vitis vinifera), 3'ss of exon 4
agtcctgacattagagt-agcttctcacttagcatatctataggtcagggtgcatgttgtaatgttcttccgatttaac-----aactctcttgtattctc-tgcagGATTTCAGCTCATCATGGGATATCCGCGCAACGCCGACCTTTTTCTTCATAAAAAACGAGAAGCAGGTCGACAAGCTTGTGGGCGCCAACAAACCTGAGC
        ||  | | | | | |  |    |  | ||  |      | |    || |        | |   ||   ||      || |   || |  | |   |||||| ||||| || ||||||||||||   || || || |||||||||||| | | | | | | | ||||| |||||||||||||| || |||||||||||||
-------gcagcataatcaacatgccctggaaaagataaaagaaaaatgaaaaatatcaaccaaatatctagaaaaaaatattgaaatggtttatggtataacgcagGAATTCAGTTCTTCATGGGATATCAAAGCCACTCCAACCTTTTTCTTCCTCAGAGATGGGCAACAGGTAGACAAGCTTGTGGGGGCGAACAAACCTGAGC
















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|38473602|gb|CF957734.1|CF957734
EST:     AGACTTATCCTCAACTCATGTTCTTGACAATAGATGTTGATGACCTAATG                         GATTTCAGCTCATCATGGGATATCCGCGCAACGCCGACCTTTTTCTTCATA
genomic: AGACTTATCCTCAACTCATGTTCTTGACAATAGATGTTGATGACCTAATGgtaattctaa ... ttctctgcagGATTTCAGCTCATCATGGGATATCCGCGCAACGCCGACCTTTTTCTTCATA
EST: gi|88691222|gb|CI735301.1|CI735301
EST:     AGACTTATCCTCAACTCATGTTCTTGACAATAGATGTTGATGACCTAATG                         GATTTCAGCTCATCATGGGATATCCGCGCAACGCCGACCTTTTTCTTCATA
genomic: AGACTTATCCTCAACTCATGTTCTTGACAATAGATGTTGATGACCTAATGgtaattctaa ... ttctctgcagGATTTCAGCTCATCATGGGATATCCGCGCAACGCCGACCTTTTTCTTCATA
EST: gi|88688210|gb|CI731786.1|CI731786
EST:     AGACTTATCCTCAACTCATGTTCTTGACAATAGATGTTGATGACCTAATG                         GATTTCAGCTCATCATGGGATATCCGCGCAACGCCGACCTTTTTCTTCATA
genomic: AGACTTATCCTCAACTCATGTTCTTGACAATAGATGTTGATGACCTAATGgtaattctaa ... ttctctgcagGATTTCAGCTCATCATGGGATATCCGCGCAACGCCGACCTTTTTCTTCATA
EST: gi|58596706|gb|CK007234.1|CK007234
EST:     AGACTTATCCTCAACTCATGTTCTTGACAATAGATGTTGATGACCTAATG                         GATTTCAGCTCATCATGGGATATCCGCGCAACGCCGACCTTTTTCTTCATA
genomic: AGACTTATCCTCAACTCATGTTCTTGACAATAGATGTTGATGACCTAATGgtaattctaa ... ttctctgcagGATTTCAGCTCATCATGGGATATCCGCGCAACGCCGACCTTTTTCTTCATA
EST: gi|88844283|gb|CI005656.1|CI005656
EST:     AGACTTATCCTCAACTCATGTTCTTGACAATAGATGTTGATGACCTAATG                         GATTTCAGCTCATCATGGGATATCCGCGCAACGCCGACCTTTTTCTTCATA
genomic: AGACTTATCCTCAACTCATGTTCTTGACAATAGATGTTGATGACCTAATGgtaattctaa ... ttctctgcagGATTTCAGCTCATCATGGGATATCCGCGCAACGCCGACCTTTTTCTTCATA
EST: gi|88263215|gb|CI366989.1|CI366989
EST:     TCATGTTCTTGACAATAGATGTTGATGACCTAATG                         GATTTCAGCTCATCATGGGATATCCGCGCAACGCCGACCTTTTTCTTCATA
genomic: TCATGTTCTTGACAATAGATGTTGATGACCTAATGgtaattctaa ... ttctctgcagGATTTCAGCTCATCATGGGATATCCGCGCAACGCCGACCTTTTTCTTCATA
EST: gi|88237719|gb|CI237568.1|CI237568
EST:     AGACTTATCCTCAACTCATGTTCTTGACAATAGATGTTGATGACCTAATG                         GATTTCAGCTCGTCATGGGATATCCGCGCAACGCCGACCTTTTTCTTCATA
genomic: AGACTTATCCTCAACTCATGTTCTTGACAATAGATGTTGATGACCTAATGgtaattctaa ... ttctctgcagGATTTCAGCTCATCATGGGATATCCGCGCAACGCCGACCTTTTTCTTCATA
EST: gi|218480992|gb|FG958013.1|FG958013
EST:     AGACTTATCCTCAACTCATGTTCTTGACAATAGATGTTGATGACCTAATG                         GATTTCAGCTCATCATGGGATATCCGCGCAACGCCGACCTTTTTCTTCATA
genomic: AGACTTATCCTCAACTCATGTTCTTGACAATAGATGTTGATGACCTAATGgtaattctaa ... ttctctgcagGATTTCAGCTCATCATGGGATATCCGCGCAACGCCGACCTTTTTCTTCATA
EST: gi|88957526|gb|CI011455.1|CI011455
EST:     AGACTTATCCTCAACTCATGTTCTTGACAATAGATGTTGATGACCTAATG                         GATTTCAGCTCATCATGGGATATCCGCGCAACGCCGACCTTTTTCTTCATA
genomic: AGACTTATCCTCAACTCATGTTCTTGACAATAGATGTTGATGACCTAATGgtaattctaa ... ttctctgcagGATTTCAGCTCATCATGGGATATCCGCGCAACGCCGACCTTTTTCTTCATA
EST: gi|88847816|gb|CI006002.1|CI006002
EST:     AGACTTATCCTCAACTCATGTTCTTGACAATAGATGTTGATGACCTAATG                         GATTTCAGCTCATCATGGGATATCCGCGCAACGCCGACCTTTTTCTTCATA
genomic: AGACTTATCCTCAACTCATGTTCTTGACAATAGATGTTGATGACCTAATGgtaattctaa ... ttctctgcagGATTTCAGCTCATCATGGGATATCCGCGCAACGCCGACCTTTTTCTTCATA
EST: gi|86527391|gb|CI167597.1|CI167597
EST:     AGACTTATCCTCAACTCATGTTCTTGACAATAGATGTTGATGACCTAATG                         GATTTCAGCTCATCATGGGATATCCGCGCAACGCCGACCTTTTTCTTCATA
genomic: AGACTTATCCTCAACTCATGTTCTTGACAATAGATGTTGATGACCTAATGgtaattctaa ... ttctctgcagGATTTCAGCTCATCATGGGATATCCGCGCAACGCCGACCTTTTTCTTCATA
EST: gi|88693751|gb|CI735404.1|CI735404
EST:     AGACTTATCCTCAACTCATGTTCTTGACAATAGATGTTGATGACCTAATG                         GATTTCAGCTCATCATGGGATATCCGCGCAACGCCGACCTTTTTCTTCATA
genomic: AGACTTATCCTCAACTCATGTTCTTGACAATAGATGTTGATGACCTAATGgtaattctaa ... ttctctgcagGATTTCAGCTCATCATGGGATATCCGCGCAACGCCGACCTTTTTCTTCATA
EST: gi|89199020|gb|CI253094.1|CI253094
EST:     AGACTTATCCTCAACTCATGTTCTTGACAATAGATGTTGATGACCTAATG                         GATTTCAGCTCATCATGGGATATCCGCGCAACGCCGACCTTTTTCTTCATA
genomic: AGACTTATCCTCAACTCATGTTCTTGACAATAGATGTTGATGACCTAATGgtaattctaa ... ttctctgcagGATTTCAGCTCATCATGGGATATCCGCGCAACGCCGACCTTTTTCTTCATA
EST: gi|88469849|gb|CI407120.1|CI407120
EST:     TAGATGTTGATGACCTAATG                         GATTTCAGCTCATCATGGGATATCCGCGCAACGCCGACCTTTTTCTTCATA
genomic: TAGATGTTGATGACCTAATGgtaattctaa ... ttctctgcagGATTTCAGCTCATCATGGGATATCCGCGCAACGCCGACCTTTTTCTTCATA
EST: gi|58683882|gb|CK072569.1|CK072569
EST:     AGACTTATCCTCAACTCATGTTCTTGACAATAGATGTTGATGACCTAATG                         GATTTCAGCTCATCATGGGATATCCGCGCAACGCCGACCTTTTTCTTCATA
genomic: AGACTTATCCTCAACTCATGTTCTTGACAATAGATGTTGATGACCTAATGgtaattctaa ... ttctctgcagGATTTCAGCTCATCATGGGATATCCGCGCAACGCCGACCTTTTTCTTCATA
EST: gi|88836925|gb|CI008361.1|CI008361
EST:     AGACTTATCCTCAACTCATGTTCTTGACAATAGATGTTGATGACCTAATG                         GATTTCAGCTCATCATGGGATATCCGCGCAACGCCGACCTTTTTCTTCATA
genomic: AGACTTATCCTCAACTCATGTTCTTGACAATAGATGTTGATGACCTAATGgtaattctaa ... ttctctgcagGATTTCAGCTCATCATGGGATATCCGCGCAACGCCGACCTTTTTCTTCATA
EST: gi|33661687|gb|CF292654.1|CF292654
EST:     AGACTTATCCTCAACTCATGTTCTTGTCAATAGATGTTGATGACCTAATG                         GATTTCAGCTCATCATGGGATATCCGCGCAACGCCGACCTTTTTCTTCATA
genomic: AGACTTATCCTCAACTCATGTTCTTGACAATAGATGTTGATGACCTAATGgtaattctaa ... ttctctgcagGATTTCAGCTCATCATGGGATATCCGCGCAACGCCGACCTTTTTCTTCATA
EST: gi|88205100|gb|CI204949.1|CI204949
EST:     AGACTTATCCTCAACTCATGTTCTTGACAATAGATGTTGATGACCTAATG                         GATTTCAGCTCATCATGGGATATCCGCGCAACGCCGACCTTTTTCTTCATA
genomic: AGACTTATCCTCAACTCATGTTCTTGACAATAGATGTTGATGACCTAATGgtaattctaa ... ttctctgcagGATTTCAGCTCATCATGGGATATCCGCGCAACGCCGACCTTTTTCTTCATA
EST: gi|33821282|gb|CF336453.1|CF336453
EST:     AGACTTATCCTCAACTCATGTTCTTGACAATAGATGTTGATGACCTAATG                         GATTTCAGCTCATCATGGGATATCCGCGCAACGCCGACCTTTTTCTTCATA
genomic: AGACTTATCCTCAACTCATGTTCTTGACAATAGATGTTGATGACCTAATGgtaattctaa ... ttctctgcagGATTTCAGCTCATCATGGGATATCCGCGCAACGCCGACCTTTTTCTTCATA
EST: gi|88321921|gb|CI673069.1|CI673069
EST:     AGACTTATCCTCAACTCATGTTCTTGACAATAGATGTTGATGACCTAATG                         GATTTCAGCTCATCATGGGATATCCGCGCAACGCCGACC
genomic: AGACTTATCCTCAACTCATGTTCTTGACAATAGATGTTGATGACCTAATGgtaattctaa ... ttctctgcagGATTTCAGCTCATCATGGGATATCCGCGCAACGCCGACC
EST: gi|88689728|gb|CI733304.1|CI733304
EST:     AGACTTATCCTCAACTCATGTTCTTGACAATAGATGTTGATGACCTAATG                         GATTTCAGCTCATCATGGGATATCCGCGCAACGCCGACCTTTTTCTTCATA
genomic: AGACTTATCCTCAACTCATGTTCTTGACAATAGATGTTGATGACCTAATGgtaattctaa ... ttctctgcagGATTTCAGCTCATCATGGGATATCCGCGCAACGCCGACCTTTTTCTTCATA
EST: gi|38480845|gb|CF964934.1|CF964934
EST:     AGACTTATCCTCAACTCATGTTCTTGACAATAGATGTTGATGACCTAATG                         GATTTCAGCTCATCATGGGATATCCGCGCAACGCCGACCTTTTTCTTCATA
genomic: AGACTTATCCTCAACTCATGTTCTTGACAATAGATGTTGATGACCTAATGgtaattctaa ... ttctctgcagGATTTCAGCTCATCATGGGATATCCGCGCAACGCCGACCTTTTTCTTCATA
EST: gi|86593727|gb|CI266407.1|CI266407
EST:     AGACTTATCCTCAACTCATGTTCTTGACAATAGATGTTGATGACCTAATG                         GATTTCAGCTCATCATGGGATATCCGCGCAACGCCGACCTTTTTCTTCATA
genomic: AGACTTATCCTCAACTCATGTTCTTGACAATAGATGTTGATGACCTAATGgtaattctaa ... ttctctgcagGATTTCAGCTCATCATGGGATATCCGCGCAACGCCGACCTTTTTCTTCATA
EST: gi|87028600|gb|CI265999.1|CI265999
EST:     AGACTTATCCTCAACTCATGTTCTTGACAATAGATGTTGATGACCTAATG                         GATTTCAGCTCATCATGGGATATCCGCGCAACGCCGACCTTTTTCTTCATA
genomic: AGACTTATCCTCAACTCATGTTCTTGACAATAGATGTTGATGACCTAATGgtaattctaa ... ttctctgcagGATTTCAGCTCATCATGGGATATCCGCGCAACGCCGACCTTTTTCTTCATA
EST: gi|88691439|gb|CI733517.1|CI733517
EST:     AGACTTATCCTCAACTCATGTTCTTGACAATAGATGTTGATGACCTAATG                         GATTTCAGCTCATCATGGGATATCCGCGCAACGCCGACCTTTTTCTTCATA
genomic: AGACTTATCCTCAACTCATGTTCTTGACAATAGATGTTGATGACCTAATGgtaattctaa ... ttctctgcagGATTTCAGCTCATCATGGGATATCCGCGCAACGCCGACCTTTTTCTTCATA
EST: gi|89186360|gb|CI262192.1|CI262192
EST:     AGACTTATCCTCAACTCATGTTCTTGACAATAGATGTTGATGACCTAATG                         GATTTCAGCTCATCATGGGATATCCGCGCAACGCCGACCTTTTTCTTCATA
genomic: AGACTTATCCTCAACTCATGTTCTTGACAATAGATGTTGATGACCTAATGgtaattctaa ... ttctctgcagGATTTCAGCTCATCATGGGATATCCGCGCAACGCCGACCTTTTTCTTCATA
EST: gi|33814147|gb|CF332955.1|CF332955
EST:     AGACTTATCCTCAACTCATGTTCTTGACAATAGATGTTGATGACCTAATG                         GATTTCAGCTCATCATGGGATATCCGCGCAACGCCGACCTTTTTCTTCATA
genomic: AGACTTATCCTCAACTCATGTTCTTGACAATAGATGTTGATGACCTAATGgtaattctaa ... ttctctgcagGATTTCAGCTCATCATGGGATATCCGCGCAACGCCGACCTTTTTCTTCATA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agggtgcatgttgtaatgttcttccgatttaacaactctcttgtattctctgcagGATTTCAGCTCATCATGGGATATCCGCGCAACGCCGACCTTTTTCTTCATAAAAAACGAGAAGCAGGTCGACAAGCTTGTGGGCGCCAACAAACCTGAGC
                          atttaac  putative branch site (score: 3)
                                   ctctcttgtattctct  putative PPT
                          atttaacaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
agtcctgacattagagtagcttctcacttagcatatctataggtcagggtgcatgttgtaatgttcttccgatttaacaactctcttgtattctctgcagGATTTCAGCTCATCATGGGATATCCGCGCAACGCCGACCTTTTTCTTCATAAAAAACGAGAAGCAGGTCGACAAGCTTGTGGGCGCCAACAAACCTGAGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAAGCT