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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCTCGAGCTGTGTTAATTAATGCTGGACAAGCAAATGCAGCAACAgtaagtgtttctgacaaccgtatccgttccgctggctctgtactgtattcgaaaacaccgtggctagtattgatatacttatctaaataatttatctcag

Basic information

species Oryza sativa
transcript LOC_Os03g17120.1
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g17120.1 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM2G044237_T02 (Zea mays), 5'ss of exon 4
GCTCGAGCTGTGTTAATTAATGCTGGACAAGCAAATGCAGCAACAgtaagtgtttctgacaaccgtatccgttccgctggct-ctgtactgtattcgaaaac-accgtggctagtattgatatacttatctaaataatttatctcag
| ||| |||||||||||||||||||||||||||||||| ||||| |||||||||| | |  ||| | ||     |    |   | ||  || | ||    ||     |   | | | || ||  || |    |  | || | |    
GGTCGTGCTGTGTTAATTAATGCTGGACAAGCAAATGCTGCAACTgtaagtgtttataagcaccatgtcatagtcatcagtagcagttatgaactcagtgactgatatttgttgaagtgttaggctgactccagcagttcaccca--

upper sequence: LOC_Os03g17120.1 (Oryza sativa), 5'ss of exon 4
lower sequence: Vv08s0040g03320.t01 (Vitis vinifera), 5'ss of exon 5
GCTCGAGCTGTGTTAATTAATGCTGGACAAGCAAATGCAGCAACAgtaag-tgtttctgacaaccgtatccgttccgctggctctgtactgtattcgaaaacaccgtggctagtattgatatacttatctaaataatttatctcag--
|| || || |||||||| |||||||| ||||| ||||||||||| ||||| ||| |  ||  | | ||   |||    |  ||         ||||  || |   ||| ||  |   ||| |  |    |  ||    |  || ||  
GCGCGTGCAGTGTTAATAAATGCTGGTCAAGCCAATGCAGCAACGgtaagatgtgttagaatagc-tagatgtttt-ttttcttgacttctcattcagaagctatgtg-cttttcaagattttgtctcatggattccattgcttagct
















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|88433054|gb|CI569723.1|CI569723
EST:     GCTCGAGCTGTGTTACTTAATGCTGGACAAGCAA-TGCAGCAATA                         GGTGATG-AGGATATTAGGATTCAGTGG
genomic: GCTCGAGCTGTGTTAATTAATGCTGGACAAGCAAATGCAGCAACAgtaagtgttt ... tttatctcagGGTGATGCAGGATATCAGGATACAGTGG
EST: gi|88358225|gb|CI605150.1|CI605150
EST:     GCTCGAGCTGTGTTAATTAATGCTGGACAAGCAAATGCAGCAACA                         GGTGATGCAGGATATCAGGATNCAGTGGATAAGTGCTAATGCTGTTGCCAA
genomic: GCTCGAGCTGTGTTAATTAATGCTGGACAAGCAAATGCAGCAACAgtaagtgttt ... tttatctcagGGTGATGCAGGATATCAGGATACAGTGGATA-GTGCTGATGCTGTTGCCAA
EST: gi|29613226|gb|CB618239.1|CB618239
EST:     GCTCGAGCTGTGTTAATTAATGCTGGACAAGCAAATGCAGCAACA                         GGTGATGCAGGATATCAGGATACAGTGGATAGTGCTGATGCTGTTGCCAAG
genomic: GCTCGAGCTGTGTTAATTAATGCTGGACAAGCAAATGCAGCAACAgtaagtgttt ... tttatctcagGGTGATGCAGGATATCAGGATACAGTGGATAGTGCTGATGCTGTTGCCAAG
EST: gi|218494800|gb|FG943469.1|FG943469
EST:     GCTCGAGCTGTGTTAATTAATGCTGGACAAGCAAATGCAGCAACA                         GGTGATGCAGGATATCAGGATACAGTGGGTAGTGCTGATGCTGTTGCCAAG
genomic: GCTCGAGCTGTGTTAATTAATGCTGGACAAGCAAATGCAGCAACAgtaagtgttt ... tttatctcagGGTGATGCAGGATATCAGGATACAGTGGATAGTGCTGATGCTGTTGCCAAG
EST: gi|29670993|gb|CB667268.1|CB667268
EST:     GCTCCCTCTGTGTTAATTAATGCTGGACAAGCAAATGCAGCAACA                         GGTGATGCAGGATATCAGGATACAGTGGATAGTGCTGATGCTGTTGCCAAG
genomic: GCTCGAGCTGTGTTAATTAATGCTGGACAAGCAAATGCAGCAACAgtaagtgttt ... tttatctcagGGTGATGCAGGATATCAGGATACAGTGGATAGTGCTGATGCTGTTGCCAAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCTCGAGCTGTGTTAATTAATGCTGGACAAGCAAATGCAGCAACAgtaagtgtttctgacaaccgtatccgttccgctggctctgtactgtattcgaaaacaccgtggctagtattgatatacttatctaaataatttatctcag

- - - - - - - - -  ATGCTG
- - - - - - - - - -  GCTGGA
- - - - - - - - - - - - - - AAGCAA