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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATTATTTCGAGAATTCGAAGAGCATGATTTCGCCAGGACAGGAAGTATTGCGACAGAAACGgtattcaagttatcctttctatttatgtacctctgttcatggcttgttttctcagtaaacaatctagaatgaccatgcttatcgagatttatgctgacgt...

Basic information

species Oryza sativa
transcript LOC_Os12g01430.2
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os12g01430.2 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM2G155437_T01 (Zea mays), 5'ss of exon 5
ATTATTTCGAGAATTCGAAGAGCATGATTTCGCCAGGACAGGAAGTATTGCGACAGAAACGgtattcaagttatcctttct-atttatgtacctctgttcatggctt---gttttctcagtaaacaatctagaatgac-catgcttatcg-agatttatgctgacgt-------------------------------------------------------------------------
  | ||||||||||| || ||||||||||| || ||||||||||||| |||| |||| |||||||||  ||| | |||| | || ||| | |||   ||  |  |||    ||  |||| ||   | |  | |||||  | |  ||   | || |   |  || | |                                                                         
GATGTTTCGAGAATTTGAGGAGCATGATTTTGCAAGGACAGGAAGTACTGCGGCAGATACGgtattctggttttgctttttcatgtatatccctggtttggtttcttcaaattgactcactaggaagttgacaatgaaacttatttgcagtagctccttagtgccatttttggtttcttgtataatgtgtttcaccaaatttacaacctttttttataatttttttttacaattcctcag

upper sequence: LOC_Os12g01430.2 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM2G477632_T01 (Zea mays), 5'ss of exon 4
ATTATTTCGAGAATTCGAAGAGCATGATTTCGCCAGGACAGGAAGTATTGCGACAGAAACGgtattcaagttatcctttct-atttatgtacctctgttcatggctt---gttttctcagtaaacaatctagaatgac-catgcttatcg-agatttatgctgacgt-----------------------------------------------------------------------
  | ||||||||||| || ||||||||||| || ||||||||| ||| |||| |||| |||||||||  ||| | |||| | |||||| | |||   ||  |  |||    |   |||| ||   | |  | |||||  | |  ||   | || |   |  || | |                                                                       
GATGTTTCGAGAATTTGAGGAGCATGATTTTGCAAGGACAGGATGTACTGCGGCAGATACGgtattctggttttgctttttcatttatatccctggtttggtttcttcaaatagactcactaggaagttgacaatgaaacttatttgcggtagctccttagtgccatttttggtttcctgtataatgtgtttcgccaaatttacagaaccttttaaaaaaacatttacaattcctcag

upper sequence: LOC_Os12g01430.2 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM2G109133_T01 (Zea mays), 5'ss of exon 3
ATTATTTCGAGAATTCGAAGAGCATGATTTCGCCAGGACAGGAAGTATTGCGACAGAAACGgtattcaagttatcctttct-atttatgtacctctgttcatggctt---gttttctcagtaaacaatctagaatgac-catgcttatcg-agatttatgctgacgt-----------------------------------------------------------------------
  | ||||||||||| || ||||||||||| || ||||||||| ||| ||||  ||| |||||||||  ||| | |||| | |||||| | |||   ||  |  |||    |   |||| ||   | |  | |||||  | |  ||   | || |   |  || | |                                                                       
GATGTTTCGAGAATTTGAGGAGCATGATTTTGCAAGGACAGGATGTACTGCGGTAGATACGgtattctggttttgctttttcatttatatccctggtttggtttcttcaaatagactcactaggaagttgacaatgaaacttatttgcggtagctccttagtgccatttttggtttcctgtataatgtgtttcgccaaatatacaaaaccttttaaaaaaacatttacaattcctcag

upper sequence: LOC_Os12g01430.2 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM2G467086_T01 (Zea mays), 5'ss of exon 5
ATTATTTCGAGAATTCGAAGAGCATGATTTCGCCAGGACAGGAAGTATTGCGACAGAAACGgtattcaagttatcctttctatttatgtacctctgttcatggcttgttttctcagtaaacaatctagaatgaccatgcttatcgagatttatgctgacgt-------
  | |||||||||||||| ||||||||||| || ||||||||||||| ||| |  || ||||||||| |||| | ||||  ||   | || | ||| || ||| || ||     | || ||   |||| |  |||||| || |   ||   |||   |  |       
GATGTTTCGAGAATTCGAGGAGCATGATTTTGCAAGGACAGGAAGTACTGCTATCGATACGgtattctagttttgcttttcat--gtatatccctggtc-tggtttcttca---aatagactggctaggaaaaccatg-ttctgctgaccaatgtcaagtttaggctc

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|218485998|gb|FG965622.1|FG965622
EST:     AATTCGAAGAGCATGATTTCGCCAGGACAGGAAGTATTGCGACAGAAACG                         GTGGAGCTTAAGGAAGGCCCCTTAGAACAGTTTACACATGAAATGGAACCC
genomic: AATTCGAAGAGCATGATTTCGCCAGGACAGGAAGTATTGCGACAGAAACGgtattcaagt ... gatatgtcagGTGGAGCTTAAGGAAGGCCCCTTAGAACAGTTTACACATGAAATGGAACCC
EST: gi|33686640|gb|CF314879.1|CF314879
EST:     AATTCGAAGAGCATGATTTCGCCAGGACAGGAAGTATTGCGACAGAAACG                         GTGGAGCTTAAGGAAGGCCCCTTAGAACAGTTTACACATGAAATGGAACCC
genomic: AATTCGAAGAGCATGATTTCGCCAGGACAGGAAGTATTGCGACAGAAACGgtattcaagt ... gatatgtcagGTGGAGCTTAAGGAAGGCCCCTTAGAACAGTTTACACATGAAATGGAACCC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATTATTTCGAGAATTCGAAGAGCATGATTTCGCCAGGACAGGAAGTATTGCGACAGAAACGgtattcaagttatcctttctatttatgtacctctgttcatggcttgttttctcagtaaacaatctagaatgaccatgcttatcgagatttatgctgacgt

- - - - - - -  CGAAGA
- - - - - - - - - AGAGCA