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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...actgaatgcttctcatgattgtgaacttaacatttttgtcatcatgatatggctgcattttgctgcacatattgacctgattgttttacactggtcccagGTGCTGCCCATATTTCCAAGACTAGTTGATCTCCCACCTGATAGATTCCAAGATGCACTTGCTCGGATATTGCAG

Basic information

species Oryza sativa
transcript LOC_Os01g49940.2
intron # 19
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g49940.1 (Oryza sativa), 3'ss of exon 19
lower sequence: GRMZM2G466139_T01 (Zea mays), 3'ss of exon 16
actgaatgcttctcatgattgtgaacttaacatttttgtcatca-tgatatggctg------cattttgctgcacatattgacctgattgttttacactggtcccagGTGCTGCCCATATTTCCAAGACTAGTTGATCTCCCACCTGATAGATTCCAAGATGCACTTGCTCGGATATTGCAG
       | ||||||| | |    | || |   | || |  | | ||||||   ||        ||||  ||||| ||   |  |  || || || ||||| | |||||  |||| |||||||| || |||||||||||||| | ||| ||||||||||| | |||||||||||||||||||
----tgcggttctcatcaatacagatttcaatctgttttggttaatgatataattgacaagatcttttattgcacttaacaattt--ttcttatatactgg-ctcagGTATTGCCTATATTTCCTAGGCTAGTTGATCTCCCGCTTGAGAGATTCCAAGACGTACTTGCTCGGATATTGCAG
















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|29644685|gb|CB649692.1|CB649692
EST:     GATGCATCTATTCTCATTCCGTTGTTATCCTCATTTCCAAAGGAAGAG                         GTGCTGCCCATATTTCCAAGACTAGTTGATCTCCCACCTGATAGATTCCAA
genomic: GATGCATCTATTCTCATTCCGTTGTTATCCTCATTTCCAAAGGAAGAGgtagtggtct ... ctggtcccagGTGCTGCCCATATTTCCAAGACTAGTTGATCTCCCACCTGATAGATTCCAA
EST: gi|58610716|gb|CK038428.1|CK038428
EST:     GATGCATCTATTCTCATTCCGTTGTTATCTTCATTTCCAAAGGAAGAG                         GTGCTGCCCATATTTCCAAGACTAGTTGATCTCCCAACTGATAGATTCCAA
genomic: GATGCATCTATTCTCATTCCGTTGTTATCCTCATTTCCAAAGGAAGAGgtagtggtct ... ctggtcccagGTGCTGCCCATATTTCCAAGACTAGTTGATCTCCCACCTGATAGATTCCAA
EST: gi|33794819|gb|CF323289.1|CF323289
EST:     GATGCATCTATTCTCATTCCGTTGTTATCCTCATTTCCAAAGGAAGAG                         GTGCTGCCCATATTTCCAAGACTAGTTGATCTCCCACCTGATAGATTCCAA
genomic: GATGCATCTATTCTCATTCCGTTGTTATCCTCATTTCCAAAGGAAGAGgtagtggtct ... ctggtcccagGTGCTGCCCATATTTCCAAGACTAGTTGATCTCCCACCTGATAGATTCCAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gatatggctgcattttgctgcacatattgacctgattgttttacactggtcccagGTGCTGCCCATATTTCCAAGACTAGTTGATCTCCCACCTGATAGATTCCAAGATGCACTTGCTCGGATATTGCAG
                                  attgtttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
actgaatgcttctcatgattgtgaacttaacatttttgtcatcatgatatggctgcattttgctgcacatattgacctgattgttttacactggtcccagGTGCTGCCCATATTTCCAAGACTAGTTGATCTCCCACCTGATAGATTCCAAGATGCACTTGCTCGGATATTGCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG