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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTGCTACAATAGCTTCAAAATCAGTTATTCCCTCCATGTTTGACACAGTTCTGAGAAATTTTACTCCAGATGTGCCAGCTGGAACAGCTTCTAGGCCAAGgtaaaagactgttaatgcattttttttaactattagttttacttgtgtgaaagtaactcatctagttgttaatgctgataatctgatgtttggtttgtcg...

Basic information

species Oryza sativa
transcript LOC_Os07g46660.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os07g46660.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G327635_T01 (Zea mays), 5'ss of exon 3
TTGCTACAATAGCTTCAAAATCAGTTATTCCCTCCATGTTTGACACAGTTCTGAGAAATTTTACTCCAGATGTGCCAGCTGGAACAGCTTCTAGGCCAAGgtaaaagactgttaatgcattttttttaactattagttttacttgtgtgaaagtaactcatctagttgttaatgctgat---aatctgatgtttggtttgtcg-
 | ||||  | ||| ||||  || ||| |||  ||||||||||    ||||| ||||| ||||| ||||||||||| ||||||| | || || |||||||||||  |  |||   |   || ||    |    |       |     | ||    ||||  | ||| ||  |   |||    |||       || |    |   
CTACTACTGTTGCTGCAAAGCCACTTAATCCTGCCATGTTTGATGATGTTCTCAGAAACTTTACACCAGATGTGCCGGCTGGAATAACTGCTCGGCCAAGgtaagtgcttgtggttctgttcttcggca----tgcccccccccccctaaataatactccacaagtcgtggactgtgaatcgaatgcagcaattaggcaattaa
















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|58672879|gb|CK061565.1|CK061565
EST:     CTGAGAAATTTTACTCCAGATGTGCCAGCTGGAACAGCTTCTAGTCCAAG                         GCAGGAAGATGCTCAAGAATTCTTAAGTTTTGCGATGGATAGAATGCATGA
genomic: CTGAGAAATTTTACTCCAGATGTGCCAGCTGGAACAGCTTCTAGGCCAAGgtaaaagact ... acttatgcagGCAGGAAGATGCTCAAGAATTCTTAAGTTTTGCGATGGATAGAATGCATGA
EST: gi|88372847|gb|CI640298.1|CI640298
EST:     CTGAGAAATTTTACTCCAGATGTGCCAGCTGGAACAGCTTCTAGGCCAAG                         GCAGGAAGATGCTCAAGAATTCTTAAGTTTTGCGATGGATAGAATGCATGA
genomic: CTGAGAAATTTTACTCCAGATGTGCCAGCTGGAACAGCTTCTAGGCCAAGgtaaaagact ... acttatgcagGCAGGAAGATGCTCAAGAATTCTTAAGTTTTGCGATGGATAGAATGCATGA
EST: gi|66919105|gb|CX105953.1|CX105953
EST:     CTGAGAAATTTTACTCCAGATGTGCCAGCTGGAACAGCTTCTAGGCCAAG                         GCAGGAAGATGCTCAAGAATTCTTAAGTTTTGCGATGGATAGAATGCATGA
genomic: CTGAGAAATTTTACTCCAGATGTGCCAGCTGGAACAGCTTCTAGGCCAAGgtaaaagact ... acttatgcagGCAGGAAGATGCTCAAGAATTCTTAAGTTTTGCGATGGATAGAATGCATGA
EST: gi|55410317|gb|CV722693.1|CV722693
EST:     CTGAGAAATTTTACTCCAGATGTGCCAGCTGGAACAGCTTCTAGGCCAAG                         GCAGGAAGATGCTCAAGAATTCTTAAGTTTTGCGATGGATAGAATGCATGA
genomic: CTGAGAAATTTTACTCCAGATGTGCCAGCTGGAACAGCTTCTAGGCCAAGgtaaaagact ... acttatgcagGCAGGAAGATGCTCAAGAATTCTTAAGTTTTGCGATGGATAGAATGCATGA
EST: gi|25798247|gb|CA754208.1|CA754208
EST:     TGAAGAA-TTTTACTCCAGATGTGCCAGCTGGAACAGCTTCTAGGCCAAG                         GCAGGAAGATGCTCAAGAATTCTTAAGTTTTGCGATGGATAGAATGCATGA
genomic: TGA-GAAATTTTACTCCAGATGTGCCAGCTGGAACAGCTTCTAGGCCAAGgtaaaagact ... acttatgcagGCAGGAAGATGCTCAAGAATTCTTAAGTTTTGCGATGGATAGAATGCATGA
EST: gi|33793582|gb|CF322675.1|CF322675
EST:     CTGAGAAATTTTACTCCAGATGTGCCAGCTGGAACAGCTTCTAGGCCAAG                         GCAGGAAGATGCTCAAGAATNCTTAAGTTTTGCGATGGATAGAATGCATGA
genomic: CTGAGAAATTTTACTCCAGATGTGCCAGCTGGAACAGCTTCTAGGCCAAGgtaaaagact ... acttatgcagGCAGGAAGATGCTCAAGAATTCTTAAGTTTTGCGATGGATAGAATGCATGA
EST: gi|58655563|gb|CK044243.1|CK044243
EST:     CTGAGAAATTTTACTCCAGATGTGCCAGCTGGAACAGCTTCTAGGCCAAG                         GCAGGAAGATGCTCAAGAATTCTTAAGTTTTGCGATGGATAGAATGCATGA
genomic: CTGAGAAATTTTACTCCAGATGTGCCAGCTGGAACAGCTTCTAGGCCAAGgtaaaagact ... acttatgcagGCAGGAAGATGCTCAAGAATTCTTAAGTTTTGCGATGGATAGAATGCATGA
EST: gi|33794187|gb|CF322984.1|CF322984
EST:     CTGAGAAATTTTACTCCAGATGTGCCAGCTGGAACAGCTTCTAGGCCAAG                         GCAGGAAGATGCTCAAGAATTCTTAAGTTTTGCGATGGATAGAATGCATGA
genomic: CTGAGAAATTTTACTCCAGATGTGCCAGCTGGAACAGCTTCTAGGCCAAGgtaaaagact ... acttatgcagGCAGGAAGATGCTCAAGAATTCTTAAGTTTTGCGATGGATAGAATGCATGA
EST: gi|58676223|gb|CK064910.1|CK064910
EST:     CTGAGAAATTTTACTCCAGATGTGCCAGCTGGAACAGCTTCTAGGCCAAG                         GCAGGAAGATGCTCAAGAATTCTTAAGTTTTGCGATGGATAGAATGCATGA
genomic: CTGAGAAATTTTACTCCAGATGTGCCAGCTGGAACAGCTTCTAGGCCAAGgtaaaagact ... acttatgcagGCAGGAAGATGCTCAAGAATTCTTAAGTTTTGCGATGGATAGAATGCATGA
EST: gi|88720901|gb|CI744200.1|CI744200
EST:     CTGAGAAATTTTACTCCAGATGTGCCAGCTGGAACAGCTTCTAGGCCAAG                         GCAGGAAGATGCTCAAGAATTCTTAAGTTTTGCGATGGATAGAATGCATGA
genomic: CTGAGAAATTTTACTCCAGATGTGCCAGCTGGAACAGCTTCTAGGCCAAGgtaaaagact ... acttatgcagGCAGGAAGATGCTCAAGAATTCTTAAGTTTTGCGATGGATAGAATGCATGA
EST: gi|4715803|gb|AU056919.1|AU056919
EST:     CTGAGAAATTTTACTCCAGATGTGCCAGCTGGAACAGCTTCTAGGCCAAG                         GCAGGAAGATGCTCAAGAATTCTTAAGTTTTGCGATGGATAGAATGCATGA
genomic: CTGAGAAATTTTACTCCAGATGTGCCAGCTGGAACAGCTTCTAGGCCAAGgtaaaagact ... acttatgcagGCAGGAAGATGCTCAAGAATTCTTAAGTTTTGCGATGGATAGAATGCATGA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTGCTACAATAGCTTCAAAATCAGTTATTCCCTCCATGTTTGACACAGTTCTGAGAAATTTTACTCCAGATGTGCCAGCTGGAACAGCTTCTAGGCCAAGgtaaaagactgttaatgcattttttttaactattagttttacttgtgtgaaagtaactcatctagttgttaatgctgataatctgatgtttggtttgtcg

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGGA