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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagttgttttccctagaatacataaatatatagcagcaatgccactatgacacatctgaaatgtttttttttcctgaatgcagATTTCTGTGATAACATGGGGAATTGGTTCGTTTATCGTTGTCATCAACACCTACTTCCTGATAACAAGCTTTGTCAAGCTGCTTCTCCACAACGGTCTAT

Basic information

species Oryza sativa
transcript LOC_Os06g46310.3
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g46310.3 (Oryza sativa), 3'ss of exon 12
lower sequence: GRMZM2G069198_T02 (Zea mays), 3'ss of exon 13
gtaagttgttttccc-tagaatacataaatatatagcagcaatgccactatgacacatctgaaatgtttttttttcctgaatgcagATTTCTGTGATAACATGGGGAATTGGTTCGTTTATCGTTGTCATCAACACCTACTTCCTGATAACAAGCTTTGTCAAGCTGCTTCTCCACAACGGTCTAT
|| |||  ||||  |  |||||  | |   ||      | | |  ||     || ||||| |       ||  ||    |||||||| | ||||| | ||||||   || || |||||||| |||||||||||||||||||| ||||||||||||||||| ||  ||||  |||| | ||| ||  
gtgagtcattttgtcacagaatcgacagtaattaccttgaatttgcatagcaactcatctaa------cttgattgtcaaatgcagACTGCTGTGCTGACATGGATGATCGGCTCGTTTATTGTTGTCATCAACACCTACTTTCTGATAACAAGCTTTGTGAAATTGCTCGTCCAGAGCGGGCTGA
















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|27921051|gb|CB096859.1|CB096859
EST:     GGGGCAGCACACAAATTCAAAAGCC                         ATTTCTGTGATAACATGGGGAATTGGTTCGTTTATCGTTGTCATCAACACC
genomic: GGGGCAGCACACAAATTCAAAAGCCgtaagttgtt ... ctgaatgcagATTTCTGTGATAACATGGGGAATTGGTTCGTTTATCGTTGTCATCAACACC
EST: gi|218490953|gb|FG953072.1|FG953072
EST:     AATTCACAAGCAGCAGGACAAAAATGGGGCAGCACACAAATTCAAAAGCC                         ATTTCTGTGATAACATGGGGAATTGGTTCGTTTATCGTTGTCATCAACACC
genomic: AATTCACAAGCAGCAGGACAAAAATGGGGCAGCACACAAATTCAAAAGCCgtaagttgtt ... ctgaatgcagATTTCTGTGATAACATGGGGAATTGGTTCGTTTATCGTTGTCATCAACACC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatagcagcaatgccactatgacacatctgaaatgtttttttttcctgaatgcagATTTCTGTGATAACATGGGGAATTGGTTCGTTTATCGTTGTCATCAACACCTACTTCCTGATAACAAGCTTTGTCAAGCTGCTTCTCCACAACGGTCTAT
                                 tgtttttttttcct  CT-rich tract
                            tgaaatgttttttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagttgttttccctagaatacataaatatatagcagcaatgccactatgacacatctgaaatgtttttttttcctgaatgcagATTTCTGTGATAACATGGGGAATTGGTTCGTTTATCGTTGTCATCAACACCTACTTCCTGATAACAAGCTTTGTCAAGCTGCTTCTCCACAACGGTCTAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT