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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtgccacaaacaaaaagactggtgctattatgttttgctacagttgcattgttattcattattcaatctaacggaggttctgatggatgaacaattgcagGCTGGTGCTTTAGTGCAAGTTTACACTGATGGAACTGTCCTTGTAACGCATGGTGGGGTTGAAATGGGGCAGGGTTTACACACAAAGGTAGCCCAAGTTG

Basic information

species Oryza sativa
transcript LOC_Os03g31550.1
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g31550.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM2G050984_T01 (Zea mays), 3'ss of exon 5
-gtgccacaaacaaaaagactggtgctattatgttttgctacagttgcattgttattcattattcaatctaacggaggttctgatggatgaacaattgcagGCTGGTGCTTTAGTGCAAGTTTACACTGATGGAACTGTCCTTGTAACGCATGGTGGGGTTGAAATGGGGCAGGGTTTACACACAAAGGTAGCCCAAGTTG
  |   | || ||  ||    |     |   ||  ||       | |  |  | || | |||||||||||||   | |||  | | ||||||  | |||||||||| ||| | |||||||||||||||||||| |||||||| ||||| ||||| ||||| || ||||| |||||||| ||||||||||||||||||||||
tatcaaagaagcagtaaattagacatgacattgacttatgttcttagtttcatcatcc-ttattcaatctaagataagtttcggtcgatgaaataatgcagGCTGGCGCTCTTGTGCAAGTTTACACTGATGGCACTGTCCTGGTAACACATGGCGGGGTCGAGATGGGACAGGGTTTGCACACAAAGGTAGCCCAAGTTG

upper sequence: LOC_Os03g31550.1 (Oryza sativa), 3'ss of exon 9
lower sequence: EFJ27160 (Selaginella moellendorffii), 3'ss of exon 9
gtgccacaaacaaaaagactggtgctattatgttttgctacagttgcattgttattcattattcaa--tctaacggaggttctgatgga-tgaacaattgcagGCTGGTGCTTTAGTGCAAGTTTACACTGATGGAACTGTCCTTGTAACGCATGGTGGGGTTGAAATGGGGCAGGGTTTACACACAAAGGTAGCCCAAGTTG
                                            || || |||  | || |  ||   | | | || ||   ||| ||| |   |   | ||||| ||||| || || |||||||| || || || || || || || || |||||||| ||||||||||| || ||||||||||||||  | || || || |
-------------------------------------------gtgaatggtt--taatcaggcagcttttgatggtggaaatgacggaattttctcgtccagGCAGGTGCATTGGTCCAAGTTTATACAGACGGTACAGTTCTAGTGACACATGGTGGAGTTGAAATGGGACAAGGTTTACACACAAAAATCGCACAGGTCG

upper sequence: LOC_Os03g31550.1 (Oryza sativa), 3'ss of exon 9
lower sequence: EFJ33495 (Selaginella moellendorffii), 3'ss of exon 9
gtgccacaaacaaaaagactggtgctattatgttttgctacagttgcattgttattcattattcaatct--aacggaggttctgatgga-tgaacaattgcagGCTGGTGCTTTAGTGCAAGTTTACACTGATGGAACTGTCCTTGTAACGCATGGTGGGGTTGAAATGGGGCAGGGTTTACACACAAAGGTAGCCCAAGTTG
                                            || || |||  | || |  ||  ||   | || ||   ||| ||| |   |   | ||||| ||||| || || |||||||| || || || || || || || || |||||||| ||||||||||| || ||||||||||||||  | || || || |
-------------------------------------------gtgaatggtt--taatcaggcagcctttgatggtggaaatgacggaattttctcgtccagGCAGGTGCATTGGTCCAAGTTTATACAGACGGTACAGTTCTAGTGACACATGGTGGAGTTGAAATGGGACAAGGTTTACACACAAAAATCGCACAGGTCG

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|58682426|gb|CK071113.1|CK071113
EST:     TGGTTCCCACCAAGTTTGGGATATCCTTCACTACAAAATTCATGAATCAG                         GCTGGTGCTTTAGTGCAAGTTTACACTGATGGAACTGTCCTTGTAACACAT
genomic: TGGTTCCCACCAAGTTTGGGATATCCTTCACTACAAAATTCATGAATCAGgtgaataggg ... acaattgcagGCTGGTGCTTTAGTGCAAGTTTACACTGATGGAACTGTCCTTGTAACGCAT
EST: gi|58695695|gb|CK084382.1|CK084382
EST:     TGGTTCCCACCAAGTTTGGGATATCCTTCACTACAAAATTCATGAATCAG                         GCTGGTGCTTTAGTGCAAGTTTACACTGATGGAACTGTCCTTGTAACACAT
genomic: TGGTTCCCACCAAGTTTGGGATATCCTTCACTACAAAATTCATGAATCAGgtgaataggg ... acaattgcagGCTGGTGCTTTAGTGCAAGTTTACACTGATGGAACTGTCCTTGTAACGCAT
EST: gi|218495632|gb|FG967039.1|FG967039
EST:     TGGTTCCCACCAAGTTTGGGATATCCTTCACTACAAAATTCATGAATCAG                         GCTGGTGCTTTAGTGCAAGTTTACACTGATGGAACTGTCCTTGTAACACAT
genomic: TGGTTCCCACCAAGTTTGGGATATCCTTCACTACAAAATTCATGAATCAGgtgaataggg ... acaattgcagGCTGGTGCTTTAGTGCAAGTTTACACTGATGGAACTGTCCTTGTAACGCAT
EST: gi|29675056|gb|CB671331.1|CB671331
EST:     TGGTTCCCACCAAGTTTGGGATATCCTTCACTACAAAATTCATGAATCAG                         GCTGGTGCTTTAGTGCAAGTTTACACTGATGGAACTGTCCTTGTAACGCAT
genomic: TGGTTCCCACCAAGTTTGGGATATCCTTCACTACAAAATTCATGAATCAGgtgaataggg ... acaattgcagGCTGGTGCTTTAGTGCAAGTTTACACTGATGGAACTGTCCTTGTAACGCAT
EST: gi|58683895|gb|CK072582.1|CK072582
EST:     TGGTTCCCACCAAGTTTGGGATATCCTTCACTACAAAATTCATGAATCAG                         GCTGGTGCTTTAGTGCAAGTTTACACTGATGGAACTGTCCTTGTAACACAT
genomic: TGGTTCCCACCAAGTTTGGGATATCCTTCACTACAAAATTCATGAATCAGgtgaataggg ... acaattgcagGCTGGTGCTTTAGTGCAAGTTTACACTGATGGAACTGTCCTTGTAACGCAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcattgttattcattattcaatctaacggaggttctgatggatgaacaattgcagGCTGGTGCTTTAGTGCAAGTTTACACTGATGGAACTGTCCTTGTAACGCATGGTGGGGTTGAAATGGGGCAGGGTTTACACACAAAGGTAGCCCAAGTTG
      ttattcattattcaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgccacaaacaaaaagactggtgctattatgttttgctacagttgcattgttattcattattcaatctaacggaggttctgatggatgaacaattgcagGCTGGTGCTTTAGTGCAAGTTTACACTGATGGAACTGTCCTTGTAACGCATGGTGGGGTTGAAATGGGGCAGGGTTTACACACAAAGGTAGCCCAAGTTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG