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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttcggatccatctgatctcttccggccgcattctggttgcccagatccatgccactttcctcgttcatgttaacgaggagattttcggttcgttttgcagATGAACAAGGAGAGGCTTATGAAGATGGCCGGCGCCGTCCGCACCGGCGGGAAAGGCACCGTGCGCAG

Basic information

species Oryza sativa
transcript LOC_Os03g63400.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g63400.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G023242_T03 (Zea mays), 3'ss of exon 1
ttcggatccatctgatctcttccggccgcattctggttgcccagatccatgccactttcctcgttcatgttaacgaggagat---tttcggttcgttttgcagATGAACAAGGAGAGGCTTATGAAGATGGCCGGCGCCGTCCGCACCGGCGGGAAAGGCACCGTGCGCAG
            ||  ||      |   | |||||       |||||  |||  | |    ||||      |  |    | |   || || |  |||  ||||||||||||||||||||| |||||||||||||||||||||||||||||||| || |||||| |||||||
-----------gtgcgctagaatcgattcgttctgacgat--agatctgtgctccatgtgccgtttgaccgactggttggttccgttccgttctgttccgcagATGAACAAGGAGAGGCTCATGAAGATGGCCGGCGCCGTCCGCACCGGCGGCAAGGGCACCATGCGCAG

upper sequence: LOC_Os03g63400.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G023242_T05 (Zea mays), 3'ss of exon 1
-----------------------------------------------------------ttcggat-ccatctgatctcttccggccgcattctggttgcccagatccatgccactttcctcgttcatgttaacgaggagat---tttcggttcgttttgcagATGAACAAGGAGAGGCTTATGAAGATGGCCGGCGCCGTCCGCACCGGCGGGAAAGGCACCGTGCGCAG
                                                             ||| | |    ||  ||      |   | |||||       |||||  |||  | |    ||||      |  |    | |   || || |  |||  ||||||||||||||||||||| |||||||||||||||||||||||||||||||| || |||||| |||||||
gtcagtcatttcttccgctccccaatctgacgtcaccgtaccaaatcggagcgcgccgccccggttgctgggtgcgctagaatcgattcgttctgacgat--agatctgtgctccatgtgccgtttgaccgactggttggttccgttccgttctgttccgcagATGAACAAGGAGAGGCTCATGAAGATGGCCGGCGCCGTCCGCACCGGCGGCAAGGGCACCATGCGCAG
















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|38477612|gb|CF961745.1|CF961745
EST:     GCTGCCGGCCGCGCTTCGCGAAG                         ATGAACAAGGAGAGGCTTATGAAGATGGCCGGCGCCGTCCGCACCGGCGGG
genomic: GCTGCCGGCCGCGCTTCGCCAAGgtgagactcc ... cgttttgcagATGAACAAGGAGAGGCTTATGAAGATGGCCGGCGCCGTCCGCACCGGCGGG
EST: gi|55409416|gb|CV721792.1|CV721792
EST:     CCCGCATCTCCCTCCTCGCCTCTCGCTGCCGGCCGCGCTTCGCCAAG                         ATGAACAAGGAGAGGCTTATGAAGATGGCCGGCGCCGTCCGCACCGGCGGG
genomic: CCCGCATCTCCCTCCTCGCCTCTCGCTGCCGGCCGCGCTTCGCCAAGgtgagactcc ... cgttttgcagATGAACAAGGAGAGGCTTATGAAGATGGCCGGCGCCGTCCGCACCGGCGGG
EST: gi|425823|gb|D22501.1|D22501
EST:     CCTCCCGCATCTCCCTCCTCGCCTCTCGCTGCCGGCCGCGCTTCGCCAAG                         ATGAACAAGGAGAGGCTTATGAAGATGGCCGGCGCCGTCCGCACCGGCGGG
genomic: CCTCCCGCATCTCCCTCCTCGCCTCTCGCTGCCGGCCGCGCTTCGCCAAGgtgagactcc ... cgttttgcagATGAACAAGGAGAGGCTTATGAAGATGGCCGGCGCCGTCCGCACCGGCGGG
EST: gi|426706|gb|D22776.1|D22776
EST:     CGCCTCTCGCTGCCGGCCGCGCTTCGCCAAG                         ATGAACAAGGAGAGGCTTATGAAGATGGCCGGCGCCGTCCGCACCGGCGGG
genomic: CGCCTCTCGCTGCCGGCCGCGCTTCGCCAAGgtgagactcc ... cgttttgcagATGAACAAGGAGAGGCTTATGAAGATGGCCGGCGCCGTCCGCACCGGCGGG
EST: gi|3760604|gb|C97858.1|C97858
EST:     TCCCGGATCTCCTTCTTCGCNTCTCGTTGCCGGCC-CGCNTTCGCCAAG                         ATGAACAAGGAGAGGCTTATGAAGATGGCCGGCGCCGTCCGCACCGGCGG
genomic: TCCCGCATCTCCCTCCTCGCCTCTCGCTGCCGGCCGCGC-TTCGCCAAGgtgagactcc ... cgttttgcagATGAACAAGGAGAGGCTTATGAAGATGGCCGGCGCCGTCCGCACCGGCGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tccatgccactttcctcgttcatgttaacgaggagattttcggttcgttttgcagATGAACAAGGAGAGGCTTATGAAGATGGCCGGCGCCGTCCGCACCGGCGGGAAAGGCACCGTGCGCAG
                      tgttaac  putative branch site (score: 2)
                                           ttcgtttt  putative PPT
                     atgttaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttcggatccatctgatctcttccggccgcattctggttgcccagatccatgccactttcctcgttcatgttaacgaggagattttcggttcgttttgcagATGAACAAGGAGAGGCTTATGAAGATGGCCGGCGCCGTCCGCACCGGCGGGAAAGGCACCGTGCGCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG
- - - - catctga
- - - - - - - - - - - cggccgc
- - - - - - - - - - - - - - - - -tggttgc
- - - - - - - - - - - - - - - - - - - - - - atccatg