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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaactgcactttcttttcagtgtttcaagaattttttatgtttaaatcgcaattattctgaaagtgtgtttactcttatggcatcagAAAACAGGGGAGGACCATGTTGACATTATCACTTTCTACAACGAAGTATTTATTCCTACTGTGAAACCTTTGCTGGTTGAGCTAGGGTCTGGTACTAGTC

Basic information

species Oryza sativa
transcript LOC_Os08g42600.1
intron # 14
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os08g42600.2 (Oryza sativa), 3'ss of exon 14
lower sequence: GRMZM2G016997_T01 (Zea mays), 3'ss of exon 14
-gtaactgcactttcttttcagtgtttcaagaattttttatgtttaaatcgcaattattctgaaagtgtgtttactcttatggcatcagAAAACAGGGGAGGACCATGTTGACATTATCACTTTCTACAACGAAGTATTTATTCCTACTGTGAAACCTTTGCTGGTTGAGCTAGGGTCTGGTACTAGTC
  ||  |     || |||| ||  ||| ||||||||     | | |  | | | ||  | |||        | | |  |||     ||||||||||| || || |||||||| ||||||||||||||||| ||||||||||||||| |||| || |||||| | || ||| | ||  ||||| ||||||
gttagttctgtcttgtttttagc-ttttaagaatttc--gcgatgagttggaagtttatatga-------ctgaattatatcctgccagAAAACAGGAGAAGATCATGTTGATATTATCACTTTCTACAATGAAGTATTTATTCCTGCTGTCAAGCCTTTGTTAGTGGAGGTTGGACCTGGTGCTAGTC

upper sequence: LOC_Os08g42600.2 (Oryza sativa), 3'ss of exon 14
lower sequence: GRMZM2G033828_T02 (Zea mays), 3'ss of exon 15
gtaactgcactttcttttcagtgtttcaagaattttttatgtttaaatcgcaattattctgaaagtgtgtttactcttatggcatc-----agAAAACAGGGGAGGACCATGTTGACATTATCACTTTCTACAACGAAGTATTTATTCCTACTGTGAAACCTTTGCTGGTTGAGCTAGGGTCTGGTACTAGTC
      | |  ||| | ||    ||||||     || |||    |  | | ||| | || |||||| | | |  ||  || | |||     |||||||||| || ||||| || ||||| ||||||||||||||||||||||| |||||| | || ||  | ||| |||| ||| ||||| ||||  | ||  
------gtaagttcctatcttgttttcaa----cttatataagaattttggaatgagtc-gaaagtctatctgatcaaattgtatcctgccagAAAACAGGAGAAGACCACGTCGACATCATCACTTTCTACAACGAAGTATTCATTCCTGCCGTCAAGTCCTTGTTGGTGGAGGTAGGGCCTGGCGCCAGCG

upper sequence: LOC_Os08g42600.2 (Oryza sativa), 3'ss of exon 14
lower sequence: AT3G12280.2 (Arabidopsis thaliana), 3'ss of exon 14
gtaactgcactttcttttcagtgtttcaagaattttttatgtttaaatcgcaattattctgaaagtgtgtttactcttatggcatcagAAAACAGGGGAGGACCATGTTGACATTATCACTTTCTACAACGAAGTATTTATTCCTACTGTGAAACCTTTGCTGGTTGAGCTAGGGTCTGGTACTAGTC
|||  |  ||  ||||  |  | |    | || ||| | |  |    | |  |  |  || ||  ||||   ||  | |    | |||| || ||||   || ||||||||||| ||||| |||||||| ||| ||||||||||| | || || ||  ||||||| ||||||||  |||  |  |   
gtatatatacactcttaaccttatgctgaaaagtttctttactcgg-tggaga--agactaaatttgtg---acaatgacttgaacagAGAATAGGGCCAGATCATGTTGACATCATCACATTCTACAATGAAATATTTATTCCTGCCGTAAAGCCGCTGCTGGTGGAGCTAGGTCCTGTAAGAAACG

upper sequence: LOC_Os08g42600.2 (Oryza sativa), 3'ss of exon 14
lower sequence: Vv04s0008g02780.t01 (Vitis vinifera), 3'ss of exon 14
gtaactgcactttcttttcagtgtttcaagaattttttatgtttaaatcgcaattattctgaaagtgtgtttactcttatggcatcagAAAACAGGGGAGGACCATGTTGACATTATCACTTTCTACAACGAAGTATTTATTCCTACTGTGAAACCTTTGCTGGTTGAGCTAGGGTCTGGTACTAGTC
|||  |   |||  | |  | | | | |    |   || ||||  |   | |||        |||  | |  |||  | | | | |||||||||||| |||| |||||||| |||||||| || ||||| ||| | ||||||||  |||| || ||  || |  | ||| | ||| |||||  | |  
gtatgt-tgcttaatctctattctcttagtgttagcttctgttctatgggaaatct------aagcctttcaactgattttg-aacagAAAACAGGGAAGGAACATGTTGATATTATCACATTTTACAATGAAATTTTTATTCCGGCTGTAAAGCCGCTGTTAATGGAGATTGGGCCTGGTGGTGGAA

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|58675166|gb|CK063853.1|CK063853
EST:     AAGTTTTCCGTAGTGTTTATGTTCATTGGGCATCACGAAGCCGCAATGGG                         AAAACAGGGGAGGACCATGTTGACATTATCACTTTCTACAACGAAGTATTT
genomic: AAGTTTTCCGTAGTGTTTATGTTCATTGGGCATCACGAAGCCGCAATGGGgtaactgcac ... atggcatcagAAAACAGGGGAGGACCATGTTGACATTATCACTTTCTACAACGAAGTATTT
EST: gi|58602114|gb|CK012642.1|CK012642
EST:     AGTTTTCCCGTAGTGTTTATGTTCATTGGGCATCACGAAGCCGCAATGGG                         AAAACAGGGGAGGACCATGTTGACATTATCACTTTCTACAACGAAGTATTT
genomic: AGTTTT-CCGTAGTGTTTATGTTCATTGGGCATCACGAAGCCGCAATGGGgtaactgcac ... atggcatcagAAAACAGGGGAGGACCATGTTGACATTATCACTTTCTACAACGAAGTATTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttttatgtttaaatcgcaattattctgaaagtgtgtttactcttatggcatcagAAAACAGGGGAGGACCATGTTGACATTATCACTTTCTACAACGAAGTATTTATTCCTACTGTGAAACCTTTGCTGGTTGAGCTAGGGTCTGGTACTAGTC
                                        ctcttat  CT-rich tract
     atgtttaaat  TA-rich tract