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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gcaatgtccaatgaatcatttctgttcttttgacatgttccttcacagtcctttcctgttccattttggttttaatgcgcggtatgtttgttcctcccagATTGTGGAATTCATCTCTGTTTTGCTGACGATTGGTAGTGAAACTGCGGAACAGGAGCTAATCAACCAATCTGCAGTAAAACGTTCCATTGATTTGTTCT

Basic information

species Oryza sativa
transcript LOC_Os05g51490.1
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g51490.1 (Oryza sativa), 3'ss of exon 11
lower sequence: GRMZM5G812498_T01 (Zea mays), 3'ss of exon 1
gcaatgtccaatgaatcatttctgttcttttgacatgttccttcacagtcctttcctgttccattttggttttaatgcgcggta--tgtttgttcctcccagATTGTGGAATTCATCTCTGTTTTGCTGACGATTGGTAGTGAAACTGCGGAACAGGAGCTAATCAACCAATCTGCAGTAAAACGTTCCATTGATTTGTTCT
  || ||||||| |||  ||||  ||| ||  || |||  ||||| | ||||||||| ||   |||| ||||||||      |   ||||| ||  |  |||||||| |||||||||||||||||||| || |||||||| ||||  || ||  || ||||||| | |||||| |   |||| | || ||||||||| || |
-gaaggtccaattaattgtttcc-ttcattcaacgtgtctcttcagaatcctttcctatttattttttgttttaataaattattcttgtttttttttttcagATTGTAGAATTCATCTCTGTTTTGCTAACAATTGGTAGCGAAATAGCTGAGAAGAAGCTAATAAGCCAATCAGTGATAAAGCATTGCATTGATTTATTTT
















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|58611996|gb|CK039708.1|CK039708
EST:     CTACAACATATGGGTGTTTGCAGCCCCCTCTTGGAAAACACCGCTTGAAG                         ATTGTGGAATTCATCTCTGTTTTGCTGACGATTGGTAGTGAAACTGCGGAA
genomic: CTACAACATATGGATGTTTGCAGCCCCCTCTTGGAAAACACCGCTTGAAGgtatggcttc ... ttcctcccagATTGTGGAATTCATCTCTGTTTTGCTGACGATTGGTAGTGAAACTGCGGAA
EST: gi|58611304|gb|CK039016.1|CK039016
EST:     CTACAACATATGGATGTTTGCAGCCCCCTCTTGGAAAACACCGCTTGAAG                         ATTGTGGAATTCATCTCTGTTTTGCTGACGATTGGTGGTGAAACTGCGGAA
genomic: CTACAACATATGGATGTTTGCAGCCCCCTCTTGGAAAACACCGCTTGAAGgtatggcttc ... ttcctcccagATTGTGGAATTCATCTCTGTTTTGCTGACGATTGGTAGTGAAACTGCGGAA
EST: gi|58689163|gb|CK077850.1|CK077850
EST:     CTACAACATATGGATGTTTGCAGCCCCCTCTTGGAAAACACCGCTTGAAG                         ATTGTGGAATTCATCTCTGTTTTGCTGACGATTGGTAGTGAAACTGCGGAA
genomic: CTACAACATATGGATGTTTGCAGCCCCCTCTTGGAAAACACCGCTTGAAGgtatggcttc ... ttcctcccagATTGTGGAATTCATCTCTGTTTTGCTGACGATTGGTAGTGAAACTGCGGAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cagtcctttcctgttccattttggttttaatgcgcggtatgtttgttcctcccagATTGTGGAATTCATCTCTGTTTTGCTGACGATTGGTAGTGAAACTGCGGAACAGGAGCTAATCAACCAATCTGCAGTAAAACGTTCCATTGATTTGTTCT
                        ttttaat  putative branch site (score: 3)
                                       tgtttgttcctccc  putative PPT
                 attttggttttaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gcaatgtccaatgaatcatttctgttcttttgacatgttccttcacagtcctttcctgttccattttggttttaatgcgcggtatgtttgttcctcccagATTGTGGAATTCATCTCTGTTTTGCTGACGATTGGTAGTGAAACTGCGGAACAGGAGCTAATCAACCAATCTGCAGTAAAACGTTCCATTGATTTGTTCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG