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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...caatctcaatctcgccacccaaaccaccaacctcgaaatttctgtagtgataacatactaaaatcatctctcatgacaaattatctttcatgtcatgcagGGCATCAGCAAAGGTGTGGTTGTGGACAACCTCTTGTCATCCATGGTGAGCCGAGGGAAGGCGCCCGATTTCGTGCTGTGCATTGGGGACGACCGGTCGG

Basic information

species Oryza sativa
transcript LOC_Os02g54820.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g54820.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G312521_T01 (Zea mays), 3'ss of exon 2
caatctcaatctcgccacccaaaccaccaacctcgaaatttctgtagtgataacatactaaaatcatctctcatgacaaattatctt--tcatgtcatgcagGGCATCAGCAAAGGTGTGGTTGTGGACAACCTCTTGTCATCCATGGTGAGCCGAGGGAAGGCGCCCGATTTCGTGCTGTGCATTGGGGACGACCGGTCGG
   ||||  | ||  || |||       |     |  |||   |  | |        | || | || |   |   | ||| ||||||  |  |||  ||||||||||||||||||| ||||| ||||||| |||  |||| |||||||||||    |||||| |||| || |||||||||||||| || |||||||||||||
ttgtctcgttgtccgcaaccacttggaaatttctgggatta--gcggcggaggagagcaaataacaacgggctcaaaaaaatatcttggtgctgtggtgcagGGCATCAGCAAAGGCGTGGTGGTGGACAGCCTGCTGTCGTCCATGGTGAGGACGGGGAAGCCGCCGGACTTCGTGCTGTGCATCGGCGACGACCGGTCGG

upper sequence: LOC_Os02g54820.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G122231_T01 (Zea mays), 3'ss of exon 2
--caatctcaatctcgccacccaaaccaccaacctcgaaatttctgtagtgataacatactaaaatcatctctcatgacaaattatctttcatgtcatgcagGGCATCAGCAAAGGTGTGGTTGTGGACAACCTCTTGTCATCCATGGTGAGCCGAGGGAAGGCGCCCGATTTCGTGCTGTGCATTGGGGACGACCGGTCGG
  ||||| ||||   |  |  |     ||   |   || |       ||    || ||   | ||  | | | | ||| ||  | ||  |  |||| ||||||||||||||||||| ||||| ||||||| |||| |||| || ||||||||    |||||| |||| || |||||||||||||| || |||||||||||||
cgcaatcacaattgggaaattcctgggactggcga-gagagggggagagcagcaa-atggcataaataacacgcgtgaaaatatctccgtgctgtcgtgcagGGCATCAGCAAAGGCGTGGTAGTGGACAGCCTCCTGTCGTCGATGGTGAGGACGGGGAAGCCGCCGGACTTCGTGCTGTGCATCGGCGACGACCGGTCGG
















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|88690012|gb|CI734091.1|CI734091
EST:     AACCAGTCGTTGTTAAGAGGGGCCAGCATATCGTCGAAGTAAATCCACAG                         GGCATCAGCAAAGGTGTGGTTGTGGACAACCTCTTGTCATCCATGGTGAGC
genomic: AACCAGTCGTTGTTAAGAGGGGCCAGCATATCGTCGAAGTAAATCCACAGgtaagcgcct ... tgtcatgcagGGCATCAGCAAAGGTGTGGTTGTGGACAACCTCTTGTCATCCATGGTGAGC
EST: gi|88691952|gb|CI735527.1|CI735527
EST:     AACCAGTCGTTGTTAAGAGGGGCCAGCATATCGTCGAAGTAAATCCACAG                         GGCATCAGCAAAGGTGTGGTTGTGGACAACCTCTTGTCATCCATGGTGAGC
genomic: AACCAGTCGTTGTTAAGAGGGGCCAGCATATCGTCGAAGTAAATCCACAGgtaagcgcct ... tgtcatgcagGGCATCAGCAAAGGTGTGGTTGTGGACAACCTCTTGTCATCCATGGTGAGC
EST: gi|88688734|gb|CI732310.1|CI732310
EST:     AACCAGTCGTTGTTAAGAGGGGCCAGCATATCGTCGAAGTAAATCCACAG                         GGCATCAGCAAAGGTGTGGTTGTGGACAACCTCTTGTCATCCATGGTGAGC
genomic: AACCAGTCGTTGTTAAGAGGGGCCAGCATATCGTCGAAGTAAATCCACAGgtaagcgcct ... tgtcatgcagGGCATCAGCAAAGGTGTGGTTGTGGACAACCTCTTGTCATCCATGGTGAGC
EST: gi|33681830|gb|CF310069.1|CF310069
EST:     AACCAGTCGTTGTTAAGAGGGGCCAGCATATCGTCGAAGTAAATCCACAG                         GGCATCAGCAAAGGTGGGTGGTTGTGGACAANCCTCTTGTCATCCATGGTG
genomic: AACCAGTCGTTGTTAAGAGGGGCCAGCATATCGTCGAAGTAAATCCACAGgtaagcgcct ... tgtcatgcagGGCATCAGCAAAGGTG--TGGTTGTGGACAA-CCTCTTGTCATCCATGGTG
EST: gi|29646548|gb|CB651555.1|CB651555
EST:     AACCAGTCGTTGTTAAGAGGGGCCAGCATATCGTCGAAGTAAATCCACAG                         GGCATCAGCAAAGGTGTGGTTGTGGACAACCTCTTGTCATCCATGGTGAGC
genomic: AACCAGTCGTTGTTAAGAGGGGCCAGCATATCGTCGAAGTAAATCCACAGgtaagcgcct ... tgtcatgcagGGCATCAGCAAAGGTGTGGTTGTGGACAACCTCTTGTCATCCATGGTGAGC
EST: gi|88689077|gb|CI732653.1|CI732653
EST:     AACCAGTCGTTGTTAAGAGGGGCCAGCATATCGTCGAAGTAAATCCACAG                         GGCATCAGCAAAGGTGTGGTTGTGGACAACCTCTTGTCATCCATGGTGAGC
genomic: AACCAGTCGTTGTTAAGAGGGGCCAGCATATCGTCGAAGTAAATCCACAGgtaagcgcct ... tgtcatgcagGGCATCAGCAAAGGTGTGGTTGTGGACAACCTCTTGTCATCCATGGTGAGC
EST: gi|33683659|gb|CF311898.1|CF311898
EST:     AACCAGTCGTTGTTAAGAGGGGCCAGCATATCGTCGAAGTAAATCCACAG                         GGCATCAGCAAAGGTGGTGGTNTGTGGACAANCCTCTTGTCATCCATGGTG
genomic: AACCAGTCGTTGTTAAGAGGGGCCAGCATATCGTCGAAGTAAATCCACAGgtaagcgcct ... tgtcatgcagGGCATCAGCAAAGGTG-TGGT-TGTGGACAA-CCTCTTGTCATCCATGGTG
EST: gi|29658934|gb|CB655209.1|CB655209
EST:     AACCAGTCGTTGTTAAGAGGGGCCAGCATATCGTCGAAGTAAATCCACAG                         GGCATCAGCAAAGGTGTGGTTGTGGACAACCTCTTGTCATCCATGGTGAGC
genomic: AACCAGTCGTTGTTAAGAGGGGCCAGCATATCGTCGAAGTAAATCCACAGgtaagcgcct ... tgtcatgcagGGCATCAGCAAAGGTGTGGTTGTGGACAACCTCTTGTCATCCATGGTGAGC
EST: gi|86891979|gb|CI310115.1|CI310115
EST:     AACCAGTCGTTGTTAAGAGGGGCCAACATATCGTCGAAGTAAATCCACAG                         GGCATCAGCAAAGGTGTGGTTGTGGACAACCTCTTGTCATCCATGGTGAGC
genomic: AACCAGTCGTTGTTAAGAGGGGCCAGCATATCGTCGAAGTAAATCCACAGgtaagcgcct ... tgtcatgcagGGCATCAGCAAAGGTGTGGTTGTGGACAACCTCTTGTCATCCATGGTGAGC
EST: gi|58595542|gb|CK006070.1|CK006070
EST:     AACCAGTCGTTGTTAAGAGGGGCCAGCATATCGTCGAAGTAAATCCACAG                         GGCATCAGCAAAGGTGTGGTTGTGGACAACCTCTTGTCATCCATGGTGAGC
genomic: AACCAGTCGTTGTTAAGAGGGGCCAGCATATCGTCGAAGTAAATCCACAGgtaagcgcct ... tgtcatgcagGGCATCAGCAAAGGTGTGGTTGTGGACAACCTCTTGTCATCCATGGTGAGC
EST: gi|9884518|gb|BE607351.1|BE607351
EST:     AACCAGTCGTTGTTAAGAGGGGCCAGCATATCGTCGAAGTAAATCCACAG                         GGCATCAGCAAAGGTGTGGTTGTGGACAACCTCTTGTCATCCATGGTGAGC
genomic: AACCAGTCGTTGTTAAGAGGGGCCAGCATATCGTCGAAGTAAATCCACAGgtaagcgcct ... tgtcatgcagGGCATCAGCAAAGGTGTGGTTGTGGACAACCTCTTGTCATCCATGGTGAGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agtgataacatactaaaatcatctctcatgacaaattatctttcatgtcatgcagGGCATCAGCAAAGGTGTGGTTGTGGACAACCTCTTGTCATCCATGGTGAGCCGAGGGAAGGCGCCCGATTTCGTGCTGTGCATTGGGGACGACCGGTCGG
          tactaaa  putative branch site (score: 1)
                                      tctttcat  putative PPT
     taacatactaaaat  TA-rich tract