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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGTGAAGGTTCCATGGCCAGTTTCGGAGAGAGAAGCTCTTCTTCACTACTTCGAATTAGAGTATCTTAAAGAAGATCTTGTCATTGTAATCATGAAAACTgtgcgtatgctgaattttctgggctatttattttttatgaaccttgatccacagacttcattgtccatgcctccagttcatttatttctgcttattgcgttgttgcag

Basic information

species Oryza sativa
transcript LOC_Os11g36070.3
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os11g36070.2 (Oryza sativa), 5'ss of exon 7
lower sequence: GRMZM2G104449_T02 (Zea mays), 5'ss of exon 7
GGTGAAGGTTCCATGGCCAGTTTCGGAGAGAGAAGCTCTTCTTCACTACTTCGAATTAGAGTATCTTAAAGAAGATCTTGTCATTGTAATCATGAAAACTgtgcgtatgctgaattttctgggctat---ttattttttatgaacct-----tgatccacagacttcattgt--ccatgc-ctccagttcatttatttctgcttattgcgttgtt-gcag
|||||||||||||||||| ||||| |||||||| ||| |||| ||||| || ||| | || ||||||||||||||| | || ||||| || |||||||||||||||| || | ||||| | | || |||| | ||| || | || | | | ||||| |||| | | |||| || | ||||||||| ||||| ||||
GGTGAAGGTTCCATGGCCGGTTTCAGAGAGAGAGGCTATTCTACACTATTTTGAACTGGAATATCTTAAAGAAGATGTCGTAATTGTGATAATGAAAACTgtgcgta--cttcttcttctgcattttaagttcttttctgggaaactctccgtcattgtgataatgaattgttgccatatgccctagtttatc---gtgtgcttattggcttgtttgcag
















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|29623258|gb|CB628269.1|CB628269
EST:     TCGAATTAGAGTATCTTAAAGAAGATCTTGTCATTGTAATCATGAAAACT                         ATATCGGATATGGACAATATAAATATAGAGACACATGGATTTAGTAGGGAT
genomic: TCGAATTAGAGTATCTTAAAGAAGATCTTGTCATTGTAATCATGAAAACTgtgcgtatgc ... gttgttgcagATATCGGATACGGACAATATAAATATAGAGACACATGGATTTAGTAGGGAT
EST: gi|58606537|gb|CK034570.1|CK034570
EST:     TGGAATTAGAGTATCTTAAAGAAGATCTTGTCATTGTAATCATGAAAACT                         ATATCGGATACGGACAATATAAATATAGAGACACATGGATTTAGTAGGGAT
genomic: TCGAATTAGAGTATCTTAAAGAAGATCTTGTCATTGTAATCATGAAAACTgtgcgtatgc ... gttgttgcagATATCGGATACGGACAATATAAATATAGAGACACATGGATTTAGTAGGGAT
EST: gi|29626153|gb|CB631164.1|CB631164
EST:     TCGAATTAGAGTATCTTANAGAAGATCTTGTCATTGTAATCATGANAACT                         ATATCGGATATGGACAATATAAATATAGAGACACATGGATTTAGTAGGGAT
genomic: TCGAATTAGAGTATCTTAAAGAAGATCTTGTCATTGTAATCATGAAAACTgtgcgtatgc ... gttgttgcagATATCGGATACGGACAATATAAATATAGAGACACATGGATTTAGTAGGGAT
EST: gi|29665385|gb|CB661660.1|CB661660
EST:     TCGAATTAGAGTATCTTAAAGAAGATCTTGTCATTGTAATCATGAAAACT                         ATATCGGATACGGACAATATAAATATAGAGACACATGGATTTAGTAGGGAT
genomic: TCGAATTAGAGTATCTTAAAGAAGATCTTGTCATTGTAATCATGAAAACTgtgcgtatgc ... gttgttgcagATATCGGATACGGACAATATAAATATAGAGACACATGGATTTAGTAGGGAT
EST: gi|88273561|gb|CI393967.1|CI393967
EST:     TCGAATTAGAGTATCTTAAAGAAGATCTTGTCATTGTAATCATGAAAACT                         ATATCGGATACGGACAATATAAATATAGAGACACATGGATTTAGTAGGGAT
genomic: TCGAATTAGAGTATCTTAAAGAAGATCTTGTCATTGTAATCATGAAAACTgtgcgtatgc ... gttgttgcagATATCGGATACGGACAATATAAATATAGAGACACATGGATTTAGTAGGGAT
EST: gi|27576960|gb|CA999654.1|CA999654
EST:     CTTAAAGAAGATCTTGTCATTGTAATCATGAAAACT                         ATATCGGATACGGACAATATAAATATAGAGACACATGGATTTAGTAGGGAT
genomic: CTTAAAGAAGATCTTGTCATTGTAATCATGAAAACTgtgcgtatgc ... gttgttgcagATATCGGATACGGACAATATAAATATAGAGACACATGGATTTAGTAGGGAT
EST: gi|29626975|gb|CB631986.1|CB631986
EST:     TCGAATTAGAGTATCTTAAAGAAGATCTTGTCATTGTAATCATGAAAACT                         ATATCGGATATGGACAATATAAATATAGAGACACATGGATTTAGTA
genomic: TCGAATTAGAGTATCTTAAAGAAGATCTTGTCATTGTAATCATGAAAACTgtgcgtatgc ... gttgttgcagATATCGGATACGGACAATATAAATATAGAGACACATGGATTTAGTA
EST: gi|29672693|gb|CB668968.1|CB668968
EST:     TCGAATTAGAGTATCTTAAAGAAGATCTTGTCATTGTAATCATGAAAACT                         ATATCGGATACGGACAATATAAATATAGAGACACATGGATTTAGTAGGGAT
genomic: TCGAATTAGAGTATCTTAAAGAAGATCTTGTCATTGTAATCATGAAAACTgtgcgtatgc ... gttgttgcagATATCGGATACGGACAATATAAATATAGAGACACATGGATTTAGTAGGGAT
EST: gi|29623293|gb|CB628304.1|CB628304
EST:     TCGAATTAGAGTATCTTAAAGAAGATCTTGTCATTGTAATCATGAAAACT                         ATATCGGATATGGACAATATAAATATAGAGA
genomic: TCGAATTAGAGTATCTTAAAGAAGATCTTGTCATTGTAATCATGAAAACTgtgcgtatgc ... gttgttgcagATATCGGATACGGACAATATAAATATAGAGA
EST: gi|27578183|gb|CB000878.1|CB000878
EST:     CTTAAAGAAGATCTTGTCATTGTAATCATGAAAACT                         ATATCGGATACGGACAATATAAATATAGAGACACATGGATTTAGTAGGGAT
genomic: CTTAAAGAAGATCTTGTCATTGTAATCATGAAAACTgtgcgtatgc ... gttgttgcagATATCGGATACGGACAATATAAATATAGAGACACATGGATTTAGTAGGGAT
EST: gi|25778077|gb|CA752829.1|CA752829
EST:     TCGAATTAGAGTATCTTAAAGAAGATCTTGTCATTGTAATCATGAAAACT                         ATATCGGATACGGACAATATAAATATAGAGACACATGGATTTAGTAGGGAT
genomic: TCGAATTAGAGTATCTTAAAGAAGATCTTGTCATTGTAATCATGAAAACTgtgcgtatgc ... gttgttgcagATATCGGATACGGACAATATAAATATAGAGACACATGGATTTAGTAGGGAT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGTGAAGGTTCCATGGCCAGTTTCGGAGAGAGAAGCTCTTCTTCACTACTTCGAATTAGAGTATCTTAAAGAAGATCTTGTCATTGTAATCATGAAAACTgtgcgtatgctgaattttctgggctatttattttttatgaaccttgatccacagacttcattgtccatgcctccagttcatttatttctgcttattgcgttgttgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG