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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tacttgttggtggtttccagcatgtgtttttgttgttcataagaaactatcgcacttaaaacacttgatattgccctgatgttggttaaatctcctgcagGTGATAAAAAATTCCACATCATTAAAACGAAGAAGGTCACAAGAATTTCTCCCCCCAACATTTGTCTCAGAACCTTCCACTCCATCAAATTCATTTGTTG

Basic information

species Oryza sativa
transcript LOC_Os04g23890.4
intron # 17
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g23890.1 (Oryza sativa), 3'ss of exon 17
lower sequence: GRMZM2G032351_T01 (Zea mays), 3'ss of exon 16
tacttgttggtggtttccagcatgtgtttttgttgttcataagaaactatcg--cactt------aaaacacttgat--attgccctgatgttggttaa--atctcctgcagGTGATAAAAAATTCCACATCATTAAAACGAAGAAGGTCACAAGAATTTCTCCCCCCAACATTTGTCTCAGAACCTTCCACTCCATCAAATTCATTTGTTG---
               || | ||||| |  ||||| | ||| |||   | | |  |||||      ||| |  |   |  ||  || || |    | |||  || |  | |||||||||||  |||| ||||||   |  |||||||| ||  | || | ||| |||||||  ||||| ||||| ||| |||||||||||||||| |||||||   
------------tcctcaatcatgtatgcttgttttccatgagagcttcttgagcactttaatacaaagctataagtcaataaccatgctagctgctaatgatatatttcagGTGATAAAGCATTCTACATCA---AGGCGAAGAAGATCTAAGGAGTATCTGCCCCCAAGTTTTGTTTCAGATCCTGCCACTCCATCAAATTCTTTTGTTGGAA
















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|33799059|gb|CF325389.1|CF325389
EST:     TTGTACTGACTGATTTTGATCTTTCATTTTTGACGACTTCAAAACCCCAC                         GTGATAAAAAATTCCACATCATTAAAACGAAGAAGGTCACAAGAATTTCTC
genomic: TTGTACTGACTGATTTTGATCTTTCATTTTTGACGACTTCAAAACCCCACgtaagttgag ... tctcctgcagGTGATAAAAAATTCCACATCATTAAAACGAAGAAGGTCACAAGAATTTCTC
EST: gi|38470322|gb|CF954453.1|CF954453
EST:     TTGTACTGACTGATTTTGATCTTTCATTTTTGACGACTTCAAAACCCCAC                         GTGATAAAAAATTCCACATCATTAAAACGAAGAAGGTCACA-GAATTTCTC
genomic: TTGTACTGACTGATTTTGATCTTTCATTTTTGACGACTTCAAAACCCCACgtaagttgag ... tctcctgcagGTGATAAAAAATTCCACATCATTAAAACGAAGAAGGTCACAAGAATTTCTC
EST: gi|88306572|gb|CI671324.1|CI671324
EST:     TTGTACTGACTGATTTTGATCTTTCATTTTTGACGACTTCAAAACCCCAC                         GTGATAAAAAATTCCACATCATTAAAACGAAGAAGGTCACAAGAATTTCTC
genomic: TTGTACTGACTGATTTTGATCTTTCATTTTTGACGACTTCAAAACCCCACgtaagttgag ... tctcctgcagGTGATAAAAAATTCCACATCATTAAAACGAAGAAGGTCACAAGAATTTCTC
EST: gi|88578420|gb|CI687351.1|CI687351
EST:     TTGTACTGACTGATTTTGATCTTTCATTTTTGACGAATTCAAAACCCCAC                         GTGATAAAAAATTCCACATCATTAAAACGAACAAGGTCACAAGAATTTCTC
genomic: TTGTACTGACTGATTTTGATCTTTCATTTTTGACGACTTCAAAACCCCACgtaagttgag ... tctcctgcagGTGATAAAAAATTCCACATCATTAAAACGAAGAAGGTCACAAGAATTTCTC
EST: gi|88580457|gb|CI697388.1|CI697388
EST:     TTGTACTGACTGATTTTGATCTTTCATTTTTGACGACTTCAAAACCCCAC                         GTGATAAAAAATTCCACATCATTAAAACGAAGAAGGTCACAAGAATTTCTC
genomic: TTGTACTGACTGATTTTGATCTTTCATTTTTGACGACTTCAAAACCCCACgtaagttgag ... tctcctgcagGTGATAAAAAATTCCACATCATTAAAACGAAGAAGGTCACAAGAATTTCTC
EST: gi|29684157|gb|CB680432.1|CB680432
EST:     TTGTACTGACTGATTTTGATCTTTCATTTTTGACGACTTCAAAACCCCAC                         GTGATAAAAAATTCCACATCATTAAAACGAAGAAGGTCACAAGAATTTCTC
genomic: TTGTACTGACTGATTTTGATCTTTCATTTTTGACGACTTCAAAACCCCACgtaagttgag ... tctcctgcagGTGATAAAAAATTCCACATCATTAAAACGAAGAAGGTCACAAGAATTTCTC
EST: gi|33381050|gb|CF196393.1|CF196393
EST:     TTGTACTGACTGATTTTGATCTTTCATTTTTGACGACTTCAAAACCCCAC                         GTGATAAAAAATTCCACATCATTAAAACGAAGAAGGTCACAAGAATTTCTC
genomic: TTGTACTGACTGATTTTGATCTTTCATTTTTGACGACTTCAAAACCCCACgtaagttgag ... tctcctgcagGTGATAAAAAATTCCACATCATTAAAACGAAGAAGGTCACAAGAATTTCTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

actatcgcacttaaaacacttgatattgccctgatgttggttaaatctcctgcagGTGATAAAAAATTCCACATCATTAAAACGAAGAAGGTCACAAGAATTTCTCCCCCCAACATTTGTCTCAGAACCTTCCACTCCATCAAATTCATTTGTTG
                            ccctgat  putative branch site (score: 4)
                                             tctcctgc  putative PPT
        acttaaaa  TA-rich tract