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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGCAGGGCTACAGTGCTGTACTCCCTGAGAAGTTGCAAACTGGAAAGTGGAATGTGTACAGgtaggttatttagtagtatatgttatactgcatttgcttatgtcatggctcaaaatttctgtttccatcttgcag

Basic information

species Oryza sativa
transcript LOC_Os12g04990.3
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os12g04990.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GLYMA20G28200.1 (Glycine max), 5'ss of exon 2
TGCAGGGCTACAGTGCTGTACTCCCTGAGAAGTTGCAAACTGGAAAGTGGAATGTGTACAGgtaggttatttagtagtatatgttatactgcatttgcttatg--tcatggctcaaaatttctgtttccatcttgcag-----------------
  || || || |||| ||||||||| ||||| || ||||| ||||||||||| || ||||||||      ||   | | |   | ||  ||  |||    ||   ||| ||  |||| ||     |    | |||                    
AACAAGGGTATAGTGTTGTACTCCCAGAGAAATTACAAACAGGAAAGTGGAACGTTTACAGgtatacctcttc-caatgttcttgatcttgattttttacatcattcaggggccaaatttctgagtatggtattgtttttaattctttctggcag

upper sequence: LOC_Os12g04990.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GLYMA10G39540.1 (Glycine max), 5'ss of exon 2
TGCAGGGCTACAGTGCTGTACTCCCTGAGAAGTTGCAAACTGGAAAGTGGAATGTGTACAGgtaggt-----------tatttagtagtatatgttatactgcattt----gcttatgtcatggctcaaa----atttctgtttccatcttgcag
  || || || |||| ||||||||| ||||| || ||||| ||||||||||| || ||||||||              |  ||  |  |   | ||||||  ||||     ||| |  | |||  |   |    |||| |  |||  ||| ||||
AACAAGGGTATAGTGTTGTACTCCCAGAGAAATTACAAACAGGAAAGTGGAACGTTTACAGgtatacctcttccaatgttcttgatcttgatttttatacatcattctggggctaaatttatgagtatgatattatttttaattctttctggcag
















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|88307649|gb|CI644685.1|CI644685
EST:     AGTGCTGTACTCCCTGAGAAGTGGCAAACTGGAAAGTGGAATGTGTACAG                         ATCCGCAAAGTCACCTCTTAAGTTAATAAATAGATTCCCTGATAACCCAGA
genomic: AGTGCTGTACTCCCTGAGAAGTTGCAAACTGGAAAGTGGAATGTGTACAGgtaggttatt ... catcttgcagATCCGCAAAGTCACCTCTTAAGTTAATAAATAGATTCCCTGATAACCCAGA
EST: gi|33675569|gb|CF303808.1|CF303808
EST:     AGTGCTGTACTCCCTGAGAAGTTGCAAACTGGAAAGTGGAATGTGTACAG                         ATCCGCAAAGTCACCTCTTAAGTTAATAAATAGATTCCCTGATAACCCAGA
genomic: AGTGCTGTACTCCCTGAGAAGTTGCAAACTGGAAAGTGGAATGTGTACAGgtaggttatt ... catcttgcagATCCGCAAAGTCACCTCTTAAGTTAATAAATAGATTCCCTGATAACCCAGA
EST: gi|88294822|gb|CI604694.1|CI604694
EST:     AGTGCTGTACTCCCTGAGAAGTTGCAAACTGGAAAGTGGAATGTGTACAG                         ATCCGCAAAGTCACCTCTTAAGTTAATAAATAGATTCCCTGATAACCCAGA
genomic: AGTGCTGTACTCCCTGAGAAGTTGCAAACTGGAAAGTGGAATGTGTACAGgtaggttatt ... catcttgcagATCCGCAAAGTCACCTCTTAAGTTAATAAATAGATTCCCTGATAACCCAGA
EST: gi|87009029|gb|CI304972.1|CI304972
EST:     AGTGCTGTACTCCCTGAGAAGTTGCAAACTGGAAAGTGGAATGTGTACAG                         ATCCGCAAAGTCACCTCTTAAGTTAATANATAGATTCCCTGATAACCCAGA
genomic: AGTGCTGTACTCCCTGAGAAGTTGCAAACTGGAAAGTGGAATGTGTACAGgtaggttatt ... catcttgcagATCCGCAAAGTCACCTCTTAAGTTAATAAATAGATTCCCTGATAACCCAGA
EST: gi|88574980|gb|CI666749.1|CI666749
EST:     AGTGCTGTACTCCCTGAGAAGTTGCAAACTGGAAAGTGGAATGTGTACAG                         ATCCGCAAAGTCACCTCTTAAGTTAATAAATAGATTCCCTGATAACCCAGA
genomic: AGTGCTGTACTCCCTGAGAAGTTGCAAACTGGAAAGTGGAATGTGTACAGgtaggttatt ... catcttgcagATCCGCAAAGTCACCTCTTAAGTTAATAAATAGATTCCCTGATAACCCAGA
EST: gi|88307728|gb|CI644768.1|CI644768
EST:     AGTGCTGTACTCCCTGAGAAGTTGCAAACTGGAAAGTGGAATGTGTACAG                         ATCCGCAAAGTCACCTCTTAAGTTAATAAATAGATTCCCTGATAACCCAGA
genomic: AGTGCTGTACTCCCTGAGAAGTTGCAAACTGGAAAGTGGAATGTGTACAGgtaggttatt ... catcttgcagATCCGCAAAGTCACCTCTTAAGTTAATAAATAGATTCCCTGATAACCCAGA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGCAGGGCTACAGTGCTGTACTCCCTGAGAAGTTGCAAACTGGAAAGTGGAATGTGTACAGgtaggttatttagtagtatatgttatactgcatttgcttatgtcatggctcaaaatttctgtttccatcttgcag

- - - - - - - - - - - - -  AGAAGT
- - - - - - - - - - - - - - - - - - - - - -  AGTGGA