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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTTGTGAAGCTACCTCGGTCCCCCACGGTCGATGATATTCTAAAGAAGTACTTGGAGCACCGGACAAAGAAGGATAACAAgtaagcattctatataaacataaattctgatttattggcatatctttgacacagcaagttataaacagtacgggattcggaattctactgtaggtattga...

Basic information

species Oryza sativa
transcript LOC_Os11g34300.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os11g34300.2 (Oryza sativa), 5'ss of exon 8
lower sequence: GRMZM2G484880_T01 (Zea mays), 5'ss of exon 8
CTTGTGAAGCTACCTCGGTCCCCCACGGTCGATGATATTCTAAAGAAGTACTTGGAGCACCGGACAAAGAAGGATAACAAgtaagcattctat-ataaacataaattc-tgatttattggcatatct-ttgacacagcaagttataaacagtacgggattcggaattctactgtaggtattga
|||||||||||||| || || || || || |||||||||||||||||||||||||| |||||| |||||||||||  ||||| || |||||||     ||||  |||| |  | |||  |||| |    |          |  |  | |  |||  ||  |   |  ||  | |   ||    
CTTGTGAAGCTACCACGATCACCTACTGTTGATGATATTCTAAAGAAGTACTTGGAACACCGGGCAAAGAAGGATGGCAAgtgagtattctattgctgacatggattcattttctatatgcattttcgctcttggtcttgggcaatagccttacctgaaccatgagcctcttttgtatac---
















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|58679417|gb|CK068104.1|CK068104
EST:     GATGATATTCTAAAGAAGTACTTGGAGCACCGGACAAAGAAGGATAACAA                         GATAAATGACTCTTACGCTGAGATTTTGAAAGGATTGCGATGCTACTTTGA
genomic: GATGATATTCTAAAGAAGTACTTGGAGCACCGGACAAAGAAGGATAACAAgtaagcattc ... tgtactgaagGATAAATGACTCTTACGCTGAGATTTTGAAAGGATTGCGATGCTACTTTGA
EST: gi|86539094|gb|CI179300.1|CI179300
EST:     GATGATATTCTAAAGAAGTACTTGGAGCACCGGACAAAGAAGGATAACAA                         GATAAATGACTCTTACGCTGAGATTTTGAAAGGATTGCGATGCTACTTTGA
genomic: GATGATATTCTAAAGAAGTACTTGGAGCACCGGACAAAGAAGGATAACAAgtaagcattc ... tgtactgaagGATAAATGACTCTTACGCTGAGATTTTGAAAGGATTGCGATGCTACTTTGA
EST: gi|88415243|gb|CI584066.1|CI584066
EST:     GATGATATTCTAAAGAAGTACTTGGAGCACCGGACAAAGAAGGATAACAA                         GATAAATGACTCTTACGCTGAGATTTTGAAAGGATTGC
genomic: GATGATATTCTAAAGAAGTACTTGGAGCACCGGACAAAGAAGGATAACAAgtaagcattc ... tgtactgaagGATAAATGACTCTTACGCTGAGATTTTGAAAGGATTGC
EST: gi|88983252|gb|CI020816.1|CI020816
EST:     GATGATATTCTAAAGAAGTACTTGGAGCACCGGACAAAGAAGGATAACAA                         GATAAATGACTCTTACGCTGAGATTTTGAAAGGATTGCGATGCTACTTTGA
genomic: GATGATATTCTAAAGAAGTACTTGGAGCACCGGACAAAGAAGGATAACAAgtaagcattc ... tgtactgaagGATAAATGACTCTTACGCTGAGATTTTGAAAGGATTGCGATGCTACTTTGA
EST: gi|86870999|gb|CI326818.1|CI326818
EST:     TGGAGCACCGGACAAAGAAGGATAACAA                         GATAAATGACTCTTACGCTGAGATTTTGAAAGGATTGCGATGCTACTTTGA
genomic: TGGAGCACCGGACAAAGAAGGATAACAAgtaagcattc ... tgtactgaagGATAAATGACTCTTACGCTGAGATTTTGAAAGGATTGCGATGCTACTTTGA
EST: gi|89173985|gb|CI041878.1|CI041878
EST:     GATGATATTCTAAAGAAGTACTTGGAGCACCGGACAAAGAAGGATAACAA                         GATAAATGACTCTTACGCTGAGATTTTGAAAGGATTGCGATGCTACTTTGA
genomic: GATGATATTCTAAAGAAGTACTTGGAGCACCGGACAAAGAAGGATAACAAgtaagcattc ... tgtactgaagGATAAATGACTCTTACGCTGAGATTTTGAAAGGATTGCGATGCTACTTTGA
EST: gi|13165184|gb|AU173981.1|AU173981
EST:     GAAGGATANCAA                         GATAAATGACTCTTACGCTGAGATTTTGAAAGGATTGCGATGCTACTTTGA
genomic: GAAGGATAACAAgtaagcattc ... tgtactgaagGATAAATGACTCTTACGCTGAGATTTTGAAAGGATTGCGATGCTACTTTGA
EST: gi|88415227|gb|CI584050.1|CI584050
EST:     GATGATATTCTAAAGAAGTACTTGGAGCACCGGACAAAGAAGGATAACAA                         GATAAATGACTCTTACGCTGAGATTTTGAAAG
genomic: GATGATATTCTAAAGAAGTACTTGGAGCACCGGACAAAGAAGGATAACAAgtaagcattc ... tgtactgaagGATAAATGACTCTTACGCTGAGATTTTGAAAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTTGTGAAGCTACCTCGGTCCCCCACGGTCGATGATATTCTAAAGAAGTACTTGGAGCACCGGACAAAGAAGGATAACAAgtaagcattctatataaacataaattctgatttattggcatatctttgacacagcaagttataaacagtacgggattcggaattctactgtaggtattga

- - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - -  AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG