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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTGCAGACTTTGGTGTTTCTGCGCAGCTGACTAAAACAATGTCAAGGAGAAAGgtgcgatcttaaccatgattcttcaatgtcaagttactcgatattgctgtatatgtgcaccaggaacctagtgactcatctacaatcatattttggctat...

Basic information

species Oryza sativa
transcript LOC_Os07g32400.2
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os07g32400.2 (Oryza sativa), 5'ss of exon 7
lower sequence: GRMZM2G027756_T02 (Zea mays), 5'ss of exon 4
GTTGCAGACTTTGGTGTTTCTGCGCAGCTGACTAAAACAATGTCAAGGAGAAAGgtgcgatcttaaccatgattcttcaatgtcaagttactcgatattgctg------tatatgtgcaccaggaacctagtga--ctcatctacaatcatattttggctat
||||| ||||||||||||||||| |||||||||||||||||||| ||||| |||||   | |||| ||||  ||||   | ||||  || ||   | || |||      |  |  ||||  ||||||||| | |  || | |||||    ||          
GTTGCGGACTTTGGTGTTTCTGCACAGCTGACTAAAACAATGTCTAGGAGGAAGgtataaccttagccattcttctgttacgtcagattgcttagtgtttctggctttctgaacatgcattaggaacctattaagccttaactacacatctacc--------
















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|33796053|gb|CF323894.1|CF323894
EST:     GTCAAGGAGAAAG                         ACATTTGTTGGAACTCCCTTTTGGATGGCACCTGAGGTTATTCAAAACTCT
genomic: GTCAAGGAGAAAGgtgcgatctt ... aattgtgtagACATTTGTTGGAACTCCCTTTTGGATGGCACCTGAGGTTATTCAAAACTCT
EST: gi|25799236|gb|CA755197.1|CA755197
EST:     CAGACTTTGGTGTTTCTGCGCAGCTGACTAATACAATGTCAAGGAGAAAG                         ACATTTGTTGGAACTCCCTTTTGGATGGCACCTGAGGTTATTCAAAACTCT
genomic: CAGACTTTGGTGTTTCTGCGCAGCTGACTAAAACAATGTCAAGGAGAAAGgtgcgatctt ... aattgtgtagACATTTGTTGGAACTCCCTTTTGGATGGCACCTGAGGTTATTCAAAACTCT
EST: gi|58665909|gb|CK054595.1|CK054595
EST:     CAGACTTTGGTGTTTCTGCGCAGCTGACTAAAACAATGTCAAGGAGAAAG                         ACATTTGTTGGAACTCCCTTTTGGATGGCACCTGAGGTTATTCAAAACTCT
genomic: CAGACTTTGGTGTTTCTGCGCAGCTGACTAAAACAATGTCAAGGAGAAAGgtgcgatctt ... aattgtgtagACATTTGTTGGAACTCCCTTTTGGATGGCACCTGAGGTTATTCAAAACTCT
EST: gi|33796927|gb|CF324327.1|CF324327
EST:     CAGACTTTGGTGTTTCTGCGCAGCTGACTAAAACAATGTCAAGGAGAAAG                         ACATTTGTTGGAACTCCC
genomic: CAGACTTTGGTGTTTCTGCGCAGCTGACTAAAACAATGTCAAGGAGAAAGgtgcgatctt ... aattgtgtagACATTTGTTGGAACTCCC
EST: gi|58669013|gb|CK057699.1|CK057699
EST:     CAGACTTTGGTGTTTCTGCGCAGCTGACTAAAACAATGTCAAGGAGAAAG                         ACATTTGTTGGAACTCCCTTTTGGATGGCACCTGAGGTTATTCAAAACTCT
genomic: CAGACTTTGGTGTTTCTGCGCAGCTGACTAAAACAATGTCAAGGAGAAAGgtgcgatctt ... aattgtgtagACATTTGTTGGAACTCCCTTTTGGATGGCACCTGAGGTTATTCAAAACTCT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTTGCAGACTTTGGTGTTTCTGCGCAGCTGACTAAAACAATGTCAAGGAGAAAGgtgcgatcttaaccatgattcttcaatgtcaagttactcgatattgctgtatatgtgcaccaggaacctagtgactcatctacaatcatattttggctat

- - - - - - - - - - -  GCAGCT
- - - - - - - - - - - - CAGCTG
- - - - - - - - - - - -  AGCTGA
- - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - -  AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - GGAGAA