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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtagtgttgaattataatgcatgttttttcatggacctatcacagcatacatgcctatttaccttatggttgaacttgtctgtgatgacagCAAACATGTTTTTGGAATCAAAGGATGAAGCTCATGATTTTGCAAGCCTACGGCATGCGCTTCTGGAACAG

Basic information

species Oryza sativa
transcript LOC_Os03g08270.3
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g08270.6 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G017254_T02 (Zea mays), 3'ss of exon 4
gtagtgtt---gaattataatgcatgttttttcatggacctatcacagcatacatgcctatttaccttatggtt-gaacttgtctgtgatgacagCAAACATGTTTTTGGAATCAAAGGATGAAGCTCATGATTTTGCAAGCCTACGGCATGCGCTTCTGGAACAG
|||||| |   ||||||||||  |    |||| |||    |||   || | |  ||  | ||   ||||||||| | ||||||   | |||||||||||||  | |||||||||||||||||||| |||||||||||||||||| || |||||  |||| ||||||
gtagtgctcgggaattataatatac---tttttatga---tatgctagtaaatgtgtgtttt---cttatggtttggacttgttatttatgacagCAAACACATATTTGGAATCAAAGGATGAAGTTCATGATTTTGCAAGCCTGCGACATGCAGTTCTTGAACAG

upper sequence: LOC_Os03g08270.6 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM5G830874_T04 (Zea mays), 3'ss of exon 2
-------------------------------------------------------------------------------------gtagtgttgaatt-ataatgcatgttttttcatggacctatcacagcata---catgcctatttaccttatggtt-gaacttgtctgtgatgacagCAAACATGTTTTTGGAATCAAAGGATGAAGCTCATGATTTTGCAAGCCTACGGCATGCGCTTCTGGAACAG
                                                                                      ||     |||   |    | |  |||| | ||       | |     |    ||||| | |||  ||||||||| |||||||| |||||| | ||||| ||  | |||||||||||||||||||| |||||||||||||||||| || |||||  |||| ||||||
gtagtgctctcgaattacaatattactacatccgttctcgaatatttatcgtccgctagttcatttttgaactaaaacgtgacaaataaaaaagaacggagggagtactttttatgatatggtagtaaatatgtgtggcatgcatgttt-tcttatggtttgaacttgtttgtgataatagCAAGCACATATTTGGAATCAAAGGATGAAGTTCATGATTTTGCAAGCCTGCGACATGCAGTTCTTGAACAG
















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|38470462|gb|CF954593.1|CF954593
EST:     TATAGCTGGAGTTCAAACAGGACCTGCTTGGCTTGAAGCTGATACTGCAG                         CAAACATGTTTTTGGAATCAAAGGATGAAGCTCATGATTTTGCAAGCCTAC
genomic: TATAGCTGGAGTTCAAACAGGACCTGCTTGGCTTGAAGCTGATACTGCAGgtagtgttga ... gtgatgacagCAAACATGTTTTTGGAATCAAAGGATGAAGCTCATGATTTTGCAAGCCTAC
EST: gi|4715235|gb|AU056352.1|AU056352
EST:     TATAGCTGGAGTTCAAACAGGACCTGCTTGGCTTGAAGCTGATACTGCAG                         CAAACATGTTTTTGGAATCAAAGGATGAAGCTCATGATTTTGCAAGCCTAC
genomic: TATAGCTGGAGTTCAAACAGGACCTGCTTGGCTTGAAGCTGATACTGCAGgtagtgttga ... gtgatgacagCAAACATGTTTTTGGAATCAAAGGATGAAGCTCATGATTTTGCAAGCCTAC
EST: gi|88847048|gb|CI001320.1|CI001320
EST:     GCTTGAAGCTGATACTGCAG                         CAAACATGTTTTTGGAATCAAAGGATAAAGCTCATGATTTTGCAAGCCTAC
genomic: GCTTGAAGCTGATACTGCAGgtagtgttga ... gtgatgacagCAAACATGTTTTTGGAATCAAAGGATGAAGCTCATGATTTTGCAAGCCTAC
EST: gi|38476095|gb|CF960228.1|CF960228
EST:     TATAGCTGGAGTTCAAACAGGACCTGCTTGGCTTGAAGCTGATACTGCAG                         CAAACATGTTTTTGGAATCAAAGGATGAAGCTCATGATTTTGCAAGCCTAC
genomic: TATAGCTGGAGTTCAAACAGGACCTGCTTGGCTTGAAGCTGATACTGCAGgtagtgttga ... gtgatgacagCAAACATGTTTTTGGAATCAAAGGATGAAGCTCATGATTTTGCAAGCCTAC
EST: gi|66921841|gb|CX108689.1|CX108689
EST:     TATAGCTGGAGTTCAAACAGGACCTGCTTGGCTTGAAGCTGATACTGCAG                         CAAACATGTTTTTGGAATCAAAGGATGAAGCTCATGATTTTGCAAGCCTAC
genomic: TATAGCTGGAGTTCAAACAGGACCTGCTTGGCTTGAAGCTGATACTGCAGgtagtgttga ... gtgatgacagCAAACATGTTTTTGGAATCAAAGGATGAAGCTCATGATTTTGCAAGCCTAC
EST: gi|29615641|gb|CB620653.1|CB620653
EST:     TATAGCTGGAGTTCAAACAGGACCTGCTTGGCTTGAAGCTGATACTGCAG                         CAAACATGTTTTTGGAATCAAAGGATGAAGCTCATGATTTTGCAAGCCTAC
genomic: TATAGCTGGAGTTCAAACAGGACCTGCTTGGCTTGAAGCTGATACTGCAGgtagtgttga ... gtgatgacagCAAACATGTTTTTGGAATCAAAGGATGAAGCTCATGATTTTGCAAGCCTAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctatcacagcatacatgcctatttaccttatggttgaacttgtctgtgatgacagCAAACATGTTTTTGGAATCAAAGGATGAAGCTCATGATTTTGCAAGCCTACGGCATGCGCTTCTGGAACAG
                   tattta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtagtgttgaattataatgcatgttttttcatggacctatcacagcatacatgcctatttaccttatggttgaacttgtctgtgatgacagCAAACATGTTTTTGGAATCAAAGGATGAAGCTCATGATTTTGCAAGCCTACGGCATGCGCTTCTGGAACAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTCA