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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...caattggcattgtacttttcttcaattatgttgctcaagcatttgctctatacttaacttcaacactggtggttttttaacagtaggttgtcttatacagAAACGGCGCTAAAGCTTGACAGTTTTGTCGGCGACGTAGAAGATGCTGTTTCATCTTCTGTGACCGGAAAACTTAAATCTCGTGCAGAAAGTTCACTG

Basic information

species Oryza sativa
transcript LOC_Os02g51330.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g51330.2 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G036418_T02 (Zea mays), 3'ss of exon 2
--------caattggcattgtacttttcttcaattatgtt--gctcaagcatttgc-----tctatacttaacttcaacactggtggttttttaacagtaggttgtcttatacagAAACGGCGCTAAAGCTTGACAGTTTTGTCGGCGACGTAGAAGATGCTGTTTCATCTTCTGTGACCGGAAAACTTAAATCTCGTGCAGAAAGTTCACTG
          |||  |||   | || ||||   || | ||    | |||  | |||     | |||  |||||||    | |||||  || ||| | |||||||||| |||||||||| ||| || || ||||||||||| || || ||  |||||||||| ||||| |||||||| || ||||||||||||||||||| |            
cattatttacatttacatccca-ttctcttggcttgtttttgagtgaagtttctgcagtactttatttttaactttgcaattggtgtgttcttaccggtagGTTGTCCTATACAGAAATGGCTCTCAAACTTGACAGTTTGGTGGGTGATATAGAAGATGCAGTTTCTTCTTCTGTTACTGGAAAACTTAAATCTCGTGTA------------

upper sequence: LOC_Os02g51330.2 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G036418_T01 (Zea mays), 3'ss of exon 2
-----caattggcattgtacttttcttcaattatgttgctcaagcatttgctctatacttaacttcaacactggtggttttttaacagtaggttgtcttatacagAAACGGCGCTAAAGCTTGACAGTTTTGTCGGCGACGTAGAAGATGCTGTTTCATCTTCTGTGACCGGAAAACTTAAATCTCGTGCAGAAAGTTCACTG
     | |||  | |||   | || || | | | ||| ||  || | ||    |||  |||||||    | |||||  || ||| | |||||||||| |||||||||| ||| || || ||||||||||| || || ||  |||||||||| ||||| |||||||| || ||||||||||||||||||| ||| | |||   |
acatcccattctc-ttggcttgtttttgagtgaagtttctgcagtactt----tatttttaactttgcaattggtgtgttcttaccggtaggttgtcctatacagAAATGGCTCTCAAACTTGACAGTTTGGTGGGTGATATAGAAGATGCAGTTTCTTCTTCTGTTACTGGAAAACTTAAATCTCGTGTAGACAATTCGGAG
















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|58605796|gb|CK033829.1|CK033829
EST:     TTCTCTGGCCAAAGAGGTGGCGAGAGTGGAGTTGGTCAGGGATTACGCCG                         AAACGGCGCTAAAGCTTGACAGTTTTGTCGGCGACGTAGAAGATGCTGTTT
genomic: TTCTCTGGCCAAAGAGGTGGCGAGAGTGGAGTTGGTCAGGGATTACGCCGgtgagtgtga ... tcttatacagAAACGGCGCTAAAGCTTGACAGTTTTGTCGGCGACGTAGAAGATGCTGTTT






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctctatacttaacttcaacactggtggttttttaacagtaggttgtcttatacagAAACGGCGCTAAAGCTTGACAGTTTTGTCGGCGACGTAGAAGATGCTGTTTCATCTTCTGTGACCGGAAAACTTAAATCTCGTGCAGAAAGTTCACTG
                             ttttaac  putative branch site (score: 2)
                                          ttgtctt  putative PPT
                           ttttttaaca  TA-rich tract