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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagcaattaagcatgaagttattatatatgttatattttaatgggcacaatttgcagtatccaataatatcctcaatttctgctcatccaacaatacctttcatttctgtagACAAGCTTGTGGTCTCGACTTCCTGCTCACTCATGCACACCGCTGTGGATCTTGTAAATGAGACCAAGCTCGATAGCGAGATTAAGTCATGGCTTGCTTT

Basic information

species Oryza sativa
transcript LOC_Os12g42884.3
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os12g42884.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G149751_T02 (Zea mays), 3'ss of exon 6
gtaagcaattaagcatgaagttattatatatgttatattttaatgggcacaatttgcagtatccaataatatcctcaatttctgctcatccaacaatacctttcatttctgtagACAAGCTTGTGGTCTCGACTTCCTGCTCACTCATGCACACCGCTGTGGATCTTGTAAATGAGACCAAGCTCGATAGCGAGATTAAGTCATGGCTTGCTTT
    | ||| | || || | ||||| | | |  || | ||  ||        || |    | |    ||||||                   | ||| |||  ||| | |  |||||||||||| || || ||||||||||| |||||||||||||||||||||||||| || ||||| ||||| || |||||||||||||| |||||||||||
----gtaatcatgcttgcacttattgtctgtcataaaattggat--------ttagttacagctggcaatatct-----------------gataatgcctaccatctgttcagACAAGCTTGTCGTATCAACTTCCTGCTCGCTCATGCACACCGCTGTGGATCTTGTGAACGAGACTAAGCTTGACAGCGAGATTAAGTCTTGGCTTGCTTT
















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|300215517|gb|HO088143.1|HO088143
EST:     CGCCGCATCTCTCACCACCCTCGAGTCTCTTGAGGCTATTGTTGGAAAGG                         ACAAGCTTGTGGTCTCGACTTCCTGCTCACTCATGCACACCGCTGTGGATC
genomic: CGCCGCATCTCTCACCACCCTCGAGTCTCTTGAGGCTATTGTTGGAAAGGgtaagcaatt ... atttctgtagACAAGCTTGTGGTCTCGACTTCCTGCTCACTCATGCACACCGCTGTGGATC
EST: gi|300216253|gb|HO088038.1|HO088038
EST:     TTGTTGG-AAGG                         ACAAGCTTGTGGTCTCGACTTCCTGCTCACTCATGCACACCGCTGTGGATC
genomic: TTGTTGGAAAGGgtaagcaatt ... atttctgtagACAAGCTTGTGGTCTCGACTTCCTGCTCACTCATGCACACCGCTGTGGATC
EST: gi|29620902|gb|CB625913.1|CB625913
EST:     CGCCGCATCTCTCACCACCCTCGAGTCTCTTGAGGCTATTGTTGGAAAGG                         ACAAGCTTGTGGTCTCGACTTCCTGCTCACTCATGCACACCGCTGTGGATC
genomic: CGCCGCATCTCTCACCACCCTCGAGTCTCTTGAGGCTATTGTTGGAAAGGgtaagcaatt ... atttctgtagACAAGCTTGTGGTCTCGACTTCCTGCTCACTCATGCACACCGCTGTGGATC
EST: gi|29637650|gb|CB642659.1|CB642659
EST:     TGAGGTTACTTGCTGGAAAGG                         ACTAGCTTGTGGACTCGACTTCCTGCTCGCTCATGCACGCCGCTGTGGATC
genomic: TGAGGCTA-TTGTTGGAAAGGgtaagcaatt ... atttctgtagACAAGCTTGTGGTCTCGACTTCCTGCTCACTCATGCACACCGCTGTGGATC
EST: gi|2443164|gb|C74935.1|C74935
EST:     CGCCGCATCTCTCACCANCCTCGAGTCTCTTGAGGCTATTGTTGGAAAGG                         ACAAGCTTGTGGTCTCGACTTCCTGCTCANTCATGCACACCGCTGTGGATC
genomic: CGCCGCATCTCTCACCACCCTCGAGTCTCTTGAGGCTATTGTTGGAAAGGgtaagcaatt ... atttctgtagACAAGCTTGTGGTCTCGACTTCCTGCTCACTCATGCACACCGCTGTGGATC
EST: gi|428283|gb|D24431.1|D24431
EST:     CGCCGCATCTCTCACCACCCTCGAGTCTCTTGAGGCTATTGTTGGAAAGG                         ACAAGCTTGTGGTCTCGACTTCCTGCTCACTCATGCACACCGCTGTGGATC
genomic: CGCCGCATCTCTCACCACCCTCGAGTCTCTTGAGGCTATTGTTGGAAAGGgtaagcaatt ... atttctgtagACAAGCTTGTGGTCTCGACTTCCTGCTCACTCATGCACACCGCTGTGGATC
EST: gi|29615679|gb|CB620691.1|CB620691
EST:     CGCCGCATCTCTCACCACCCTCGAGTCTCTTGAGGCTATTGTTGGAAAGG                         ACAAGCTTGTGGTCTCGACTTCCTGCTCACTCATGCACACCGCTGTGGATC
genomic: CGCCGCATCTCTCACCACCCTCGAGTCTCTTGAGGCTATTGTTGGAAAGGgtaagcaatt ... atttctgtagACAAGCTTGTGGTCTCGACTTCCTGCTCACTCATGCACACCGCTGTGGATC
EST: gi|29635138|gb|CB640147.1|CB640147
EST:     CGCCGCATCTCTCACCACCCTCGAGTCTCTTGAGGCTATTGTTGGAAAGG                         ACAAGCTTGTGGTCTCGACTTCCTGCTCACTCATGCACACCGCTGTGGATC
genomic: CGCCGCATCTCTCACCACCCTCGAGTCTCTTGAGGCTATTGTTGGAAAGGgtaagcaatt ... atttctgtagACAAGCTTGTGGTCTCGACTTCCTGCTCACTCATGCACACCGCTGTGGATC
EST: gi|4881161|gb|AU065460.1|AU065460
EST:     CGCCGCATCTCTCACCACCCTCGAGTCTCTTGAGGCTATTGTTGGAAAGG                         ACAAGCTTGTGGTCTCGACTTCCTGCTCACTCATGCACACCGCTGTGGATC
genomic: CGCCGCATCTCTCACCACCCTCGAGTCTCTTGAGGCTATTGTTGGAAAGGgtaagcaatt ... atttctgtagACAAGCTTGTGGTCTCGACTTCCTGCTCACTCATGCACACCGCTGTGGATC
EST: gi|3766872|gb|AU030982.1|AU030982
EST:     GCCGCATCTCTCACCANCCNCGAGTCTCTTGAGGCTATTGTTGGGAAAGG                         ACA-GCTTGTGGTCTCGACTTCCTGCTCACTNCATGCACACCGCTGTGGA
genomic: GCCGCATCTCTCACCACCCTCGAGTCTCTTGAGGCTATTGTTGG-AAAGGgtaagcaatt ... atttctgtagACAAGCTTGTGGTCTCGACTTCCTGCTCACT-CATGCACACCGCTGTGGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatccaataatatcctcaatttctgctcatccaacaatacctttcatttctgtagACAAGCTTGTGGTCTCGACTTCCTGCTCACTCATGCACACCGCTGTGGATCTTGTAAATGAGACCAAGCTCGATAGCGAGATTAAGTCATGGCTTGCTTT
                                     tacctttcatttct  CT-rich tract
     aataatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagcaattaagcatgaagttattatatatgttatattttaatgggcacaatttgcagtatccaataatatcctcaatttctgctcatccaacaatacctttcatttctgtagACAAGCTTGTGGTCTCGACTTCCTGCTCACTCATGCACACCGCTGTGGATCTTGTAAATGAGACCAAGCTCGATAGCGAGATTAAGTCATGGCTTGCTTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT