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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tcgctttggttcgagattgcattttttttttaaaatcagattatttgtggcgtttgctttggaagtatgggtgagtgctcatgtgtttgtgctattgtagGCTAATACGCTGCGATTGTATCTCACTTGCATAAGGAACACTCTGGAGGCTGCCATGTGCCTGCAG

Basic information

species Oryza sativa
transcript LOC_Os03g63090.2
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g63090.2 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G112015_T01 (Zea mays), 3'ss of exon 1
tcgctttggttcgagattgcattttttttttaaaatcagattatttgtggcgtttgctttggaagtatgggt----gagtgctcatgtgtttgtgctatt-gtagGCTAATACGCTGCGATTGTATCTCACTTGCATAAGGAACACTCTGGAGGCTGCCATGTGCCTGCAG
  || |         | | || | | |    ||||  |  ||  ||  ||||| ||||    |  |     |     |  | | | | |    |  | || | |||| ||||||||||| ||||| ||||| |||||  |||||||||||||||| || |||||||| |||
--gcctg---ctataacttcagtatctggcaaaaactatcttcgtttcggcgtgtgctagacacatcgacatctcaaaacgttaacgagcgactctttttcgcagGCCAATACGCTGCGGTTGTACCTCACCTGCATCCGGAACACTCTGGAGGCGGCGATGTGCCTCCAG

upper sequence: LOC_Os03g63090.2 (Oryza sativa), 3'ss of exon 1
lower sequence: Vv05s0029g01310.t01 (Vitis vinifera), 3'ss of exon 1
tcgctttggttcgagattgcattttttttttaaaatcagattatttgtggcgtttgctttggaagtatgggtgagtgctcatgtgtttgtgctattgt-agGCTAATACGCTGCGATTGTATCTCACTTGCATAAGGAACACTCTGGAGGCTGCCATGTGCCTGCAG
  | |    || |   | |  ||   |||      ||||    |      |  || ||       ||   || |||   |     ||| |  |||| | |||| || ||    ||||||||| ||||||||||| |||||||||| || ||||||||||||||||||
-tgttcaattttgttgtagttttgggtttggctgctcagtgcgtagagttctatttctgcccccttaccagtaagtttactcagttttttaatattttcagGCAAACACATCTCGATTGTATTTCACTTGCATACGGAACACTCTTGAAGCTGCCATGTGCCTGCAG
















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|218490476|gb|FG964035.1|FG964035
EST:     TACCTCTCCGACCCCCGGCGGGCGCCACCGCCGCCGCCGCGCCTACCATG                         GCTAATACGCTGCGATTGTATCTCACTTGCATAAGGAACACTCTGGAGGCT
genomic: TACCTCTCCGACCCCCGGCGGGCGCCGCCGCCGCCGCCGCGCCTACCATGgtaacctcct ... gctattgtagGCTAATACGCTGCGATTGTATCTCACTTGCATAAGGAACACTCTGGAGGCT
EST: gi|33683666|gb|CF311905.1|CF311905
EST:     CCGCCGCCGCGCCTACCATG                         GCTAATACGCTGCGATTGTATCTCACTTGCATAAGGAACACTCTGGAGGCT
genomic: CCGCCGCCGCGCCTACCATGgtaacctcct ... gctattgtagGCTAATACGCTGCGATTGTATCTCACTTGCATAAGGAACACTCTGGAGGCT
EST: gi|117226003|gb|CT845644.1|CT845644
EST:     TACCTCTCCGACCCCCGGCGGGCGCCACCGCCGCCGCCGCGCCTACCATG                         GCTAATACGCTGCGATTGTATCTCACTTGCATAAGGAACACTCTGGAGGCT
genomic: TACCTCTCCGACCCCCGGCGGGCGCCGCCGCCGCCGCCGCGCCTACCATGgtaacctcct ... gctattgtagGCTAATACGCTGCGATTGTATCTCACTTGCATAAGGAACACTCTGGAGGCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtggcgtttgctttggaagtatgggtgagtgctcatgtgtttgtgctattgtagGCTAATACGCTGCGATTGTATCTCACTTGCATAAGGAACACTCTGGAGGCTGCCATGTGCCTGCAG
                                               tattgta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tcgctttggttcgagattgcattttttttttaaaatcagattatttgtggcgtttgctttggaagtatgggtgagtgctcatgtgtttgtgctattgtagGCTAATACGCTGCGATTGTATCTCACTTGCATAAGGAACACTCTGGAGGCTGCCATGTGCCTGCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG
- - - - - - - - ttgcatt
- - - - - - - - - - - - - - - -aaaatcag
- - - - - - - - - - - - - - - - - - - - - - -tgtggcg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgagtgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -catgtgt