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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...catcaataatgtttcaagctgttcttctattttaatttctcaggaactaatatcttcttgtactgtgcatggatggaattcatggacggacgacgtacagATCTTGAGCAACTCGATGTACAAGAGCGTGGAGCACCGCGTGATCGTGAACGCCGAGGAGGAGCGCATCTCGCTCGCACTCTTCTACAACCCGAGAGGCG

Basic information

species Oryza sativa
transcript LOC_Os01g61610.3
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g61610.3 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G058024_T02 (Zea mays), 3'ss of exon 3
catcaataatgtttcaagctgttcttctatt--ttaatttctca--ggaactaatatcttcttgtactgtgcatggatggaattcatggacggacgacgtacagATCTTGAGCAACTCGATGTACAAGAGCGTGGAGCACCGCGTGATCGTGAACGCCGAGGAGGAGCGCATCTCGCTCGCACTCTTCTACAACCCGAGAGGCG
    ||| || | |  |  | |    |   |  ||| || |  |    | ||||    | ||  |  ||  | || ||    | ||  |||  ||     ||||||  ||||||||||  |||||||||||||||||||||| ||| |||||||||||||||||||||||||||| ||||| |||||||||||||| |  ||||
-tcaaatgatttctagaagtctagaaccggtcattagttgcctactatagctaaaggttgctgatgatgatcttgcatt---tccactgactcaccgacgacagATACTGAGCAACTCCGTGTACAAGAGCGTGGAGCACCGGGTGGTCGTGAACGCCGAGGAGGAGCGCATCTCCCTCGCGCTCTTCTACAACCCCAAGGGCG

upper sequence: LOC_Os01g61610.3 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G122280_T02 (Zea mays), 3'ss of exon 3
catcaataatgtttcaagctgttcttctattttaatttctcaggaactaatatcttcttgtactgtgcatggatgga--attcatggacggacg-acgtacagATCTTGAGCAACTCGATGTACAAGAGCGTGGAGCACCGCGTGATCGTGAACGCCGAGGAGGAGCGCATCTCGCTCGCACTCTTCTACAACCCGAGAGGCG
  |||   |||  || |      ||     |   || |  |   || |||||    |    |   ||  || ||     |||||   | | | | | | ||||||  ||||||||||  |||||||||||||||||||||| ||| ||||||||||||||||||||||||| || |||||  ||||||||||||| |  ||||
gttcatgcatgcatcgaaaaaacctc--gctcatatatagctataattaatactgacactgagaatgt-tgaattatttattcactcatgcatgcatggacagATAATGAGCAACTCCGTGTACAAGAGCGTGGAGCACCGGGTGGTCGTGAACGCCGAGGAGGAGCGCATATCCCTCGCCATCTTCTACAACCCCAAGGGCG
















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|58692632|gb|CK081319.1|CK081319
EST:     TGCAGCCCCTCCCCGACGCCTTCATCGTCAACGTCGGCGACCAGATTGAG                         ATCTTGAGCAACTCGATGTACAAGAGCGTGGAGCACCGCGTGATCGTGAAC
genomic: TGCAGCCCCTCCCCGACGCCTTCATCGTCAACGTCGGCGACCAGATTGAGgtacacatat ... cgacgtacagATCTTGAGCAACTCGATGTACAAGAGCGTGGAGCACCGCGTGATCGTGAAC
EST: gi|58689249|gb|CK077936.1|CK077936
EST:     TGCAGCCCCTCCCCGACGCCTTCATCGTCAACGTCGGCGACCAGATTGAG                         ATCTTGAGCAACTCGATGTACAAGAGCGTGGAGCACCGCGTGATCGTGAAC
genomic: TGCAGCCCCTCCCCGACGCCTTCATCGTCAACGTCGGCGACCAGATTGAGgtacacatat ... cgacgtacagATCTTGAGCAACTCGATGTACAAGAGCGTGGAGCACCGCGTGATCGTGAAC
EST: gi|88220933|gb|CI218784.1|CI218784
EST:     CGTCAACGTCGGCGACCAGATTGAG                         ATCTTGAGCAACTCGATGTACAAGAGCGTGGAGCACCGCGTGATCGTGAAC
genomic: CGTCAACGTCGGCGACCAGATTGAGgtacacatat ... cgacgtacagATCTTGAGCAACTCGATGTACAAGAGCGTGGAGCACCGCGTGATCGTGAAC
EST: gi|58687312|gb|CK075999.1|CK075999
EST:     TGCAGCCCCTCCCCGACGCCTTCATCGTCAACGTCGGCGACCAGATTGAG                         ATCTTGAGCAACTCGATGTACAAGAGCGTGGAGCACCGCGTGATCGTGAAC
genomic: TGCAGCCCCTCCCCGACGCCTTCATCGTCAACGTCGGCGACCAGATTGAGgtacacatat ... cgacgtacagATCTTGAGCAACTCGATGTACAAGAGCGTGGAGCACCGCGTGATCGTGAAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

actaatatcttcttgtactgtgcatggatggaattcatggacggacgacgtacagATCTTGAGCAACTCGATGTACAAGAGCGTGGAGCACCGCGTGATCGTGAACGCCGAGGAGGAGCGCATCTCGCTCGCACTCTTCTACAACCCGAGAGGCG
 aactaat  putative branch site (score: 2)
                               aattcat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
catcaataatgtttcaagctgttcttctattttaatttctcaggaactaatatcttcttgtactgtgcatggatggaattcatggacggacgacgtacagATCTTGAGCAACTCGATGTACAAGAGCGTGGAGCACCGCGTGATCGTGAACGCCGAGGAGGAGCGCATCTCGCTCGCACTCTTCTACAACCCGAGAGGCG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG