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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCGTGAGTCATGTATATTCTCTGAGGGTTGCTATACAAAGGATCTGACAATTCTTGGAGTTGACCTGGCAAAAGTTGTAATAGTTGACAATACTCCACAGgtagcatgcctttttccgaatactgtatatgctttatatggacagatggaaatgtttccatttctatagttctagacttagacttggttgctagaaatat...

Basic information

species Oryza sativa
transcript LOC_Os01g43870.1
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g43870.1 (Oryza sativa), 5'ss of exon 6
lower sequence: GRMZM2G162347_T02 (Zea mays), 5'ss of exon 6
TCGTGAGTCATGTATATTCTCTGAGGGTTGCTATACAAAGGATCTGACAATTCTTGGAGTTGACCTGGCAAAAGTTGTAATAGTTGACAATACTCCACAGgtagcatgcctttttccgaatactgtatatgctttatatggacagatggaaatgtttccatttctatagttctagacttagacttggttgctaga--aatat
|||||| || ||| |||||||||| ||||||||||||||||| ||||||||||| ||  | ||| |||||||||||| ||||||||||||||||||||||||| ||  || ||| |   ||     |  |  | |  ||||||  ||     |  |  | ||| | | | |||    | || || |    ||||   |  | 
TCGTGAATCTTGTGTATTCTCTGACGGTTGCTATACAAAGGACCTGACAATTCTGGGGATCGACTTGGCAAAAGTTGCAATAGTTGACAATACTCCACAGgta-caatccctttccaatatgtaaaaactattctg-atggacgcatttcccttgtcacttttatcttgatctctggtaagtctagtactctagtctagcac

upper sequence: LOC_Os01g43870.1 (Oryza sativa), 5'ss of exon 6
lower sequence: GRMZM2G068690_T03 (Zea mays), 5'ss of exon 6
TCGTGAGTCATGTATATTCTCTGAGGGTTGCTATACAAAGGATCTGACAATTCTTGGAGTTGACCTGGCAAAAGTTGTAATAGTTGACAATACTCCACAGgtagcatgcctttttc-cgaatactgtatatgctttatatggacagatggaaatgtt---tccatttctatagttctagacttagacttggttgctagaaatat
|||||| || |||||||||||||| ||||||||||||||||||||||||||  | ||  | ||| |||| ||||||| |||||||||||||||||||||||||| || |||||     | ||||    | ||   | ||| ||      |   ||     | ||||||  | |||      |    |||| |  || | ||   
TCGTGAATCTTGTATATTCTCTGACGGTTGCTATACAAAGGATCTGACAATCTTGGGGATCGACTTGGCGAAAGTTGCAATAGTTGACAATACTCCACAGgtagaatccctttccaatgtatacaaagtttgtgctttatcgattatctgttctggcagatgcatttcccttgtt---acttctatcttgatctctggtaagt-

upper sequence: LOC_Os01g43870.1 (Oryza sativa), 5'ss of exon 6
lower sequence: GLYMA04G15970.1 (Glycine max), 5'ss of exon 7
TCGTGAGTCATGTATATTCTCTGAGGGTTGCTATACAAAGGATCTGACAATTCTTGGAGTTGACCTGGCAAAAGTTGTAATAGTTGACAATACTCCACAGgtagcatgcctttttccgaatactgtatatgctttatatggacagatggaaatgtttccatttctatagttctagacttagacttggttgctagaaatat
 || || ||||| |  |     ||  |  |||     |||||| ||||| |||||||| ||||||||||||||||    ||| | ||||| |||||| |||||  ||  | ||   |   |  || |  |  |   |              |||   | || | | | ||  || |   ||   ||  |  ||| |||| 
CCGAGAATCATGCACCTGGAAAGATCGCCGCTGCGTCAAGGATTTGACAGTTCTTGGAATTGACCTGGCAAAAGTATGCATAATCGACAACACTCCAGAGgtattatttccttggtcttttgttgcaggttttcagttcattgtttcttccatgaaacaatatttttggtgttatatcaagtactgtattgtaggaatac

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|33680628|gb|CF308867.1|CF308867
EST:     TTCTTGGAGTTGACCTGGCAAAAGTTGTAATAGTTGACAATACTCCACAG                         GTTTTCCAGTTGCAAGTGGACAATGGTATACCAATAAAGAGCTGGTTTGAT
genomic: TTCTTGGAGTTGACCTGGCAAAAGTTGTAATAGTTGACAATACTCCACAGgtagcatgcc ... tttttttcagGTTTTCCAGTTGCAAGTGGACAATGGTATACCAATAAAGAGCTGGTTTGAT
EST: gi|29667801|gb|CB664076.1|CB664076
EST:     TTCTTGGAGTTGACCTGGCAAAAGTTGTAATAGTTGACAATACTCCACAG                         GTTTTCCAGTTGCAAGTGGACAATGGTATACCAATAAAGAGCTGGTTTGAT
genomic: TTCTTGGAGTTGACCTGGCAAAAGTTGTAATAGTTGACAATACTCCACAGgtagcatgcc ... tttttttcagGTTTTCCAGTTGCAAGTGGACAATGGTATACCAATAAAGAGCTGGTTTGAT
EST: gi|300216153|gb|HO087938.1|HO087938
EST:     TTCTTGGAGTTGACCTGGCAAAAGTTGTAATAGTTGACAATACTCCACAG                         GTTTTCCAGTTGCAAGTGGACAATGGTATACCAATAAAGAGCTGGTTTGAT
genomic: TTCTTGGAGTTGACCTGGCAAAAGTTGTAATAGTTGACAATACTCCACAGgtagcatgcc ... tttttttcagGTTTTCCAGTTGCAAGTGGACAATGGTATACCAATAAAGAGCTGGTTTGAT
EST: gi|23322156|gb|BU572401.1|BU572401
EST:     TTCTTGGAGTTGACCTGGCAAAAGTTGTAATAGTTGACAATACTCCACAG                         GTTTTCCAGTTGCAAGTGGACAATGGTATACCAATAAAGAGCTGGTTTGAT
genomic: TTCTTGGAGTTGACCTGGCAAAAGTTGTAATAGTTGACAATACTCCACAGgtagcatgcc ... tttttttcagGTTTTCCAGTTGCAAGTGGACAATGGTATACCAATAAAGAGCTGGTTTGAT
EST: gi|88667374|gb|CI722113.1|CI722113
EST:     TCTTGGAGTTGACCTGGCAAAAGTTGTAATAGTTGACCAATACTCCACAG                         GTTTTCCAGTTGCCAGTGGACAATGGTATACCAATAAAGAGCTGGTTTGAT
genomic: TCTTGGAGTTGACCTGGCAAAAGTTGTAATAGTTGAC-AATACTCCACAGgtagcatgcc ... tttttttcagGTTTTCCAGTTGCAAGTGGACAATGGTATACCAATAAAGAGCTGGTTTGAT
EST: gi|87004417|gb|CI298949.1|CI298949
EST:     TTCTTGGAGTTGACCTGGCAAAAGTTGTAATAGTTGACAATACTCCACAG                         GTTTTCCAGTTGCAAGTGGACAATGGTATACCAATAAAGAGCTGGTTTGAT
genomic: TTCTTGGAGTTGACCTGGCAAAAGTTGTAATAGTTGACAATACTCCACAGgtagcatgcc ... tttttttcagGTTTTCCAGTTGCAAGTGGACAATGGTATACCAATAAAGAGCTGGTTTGAT
EST: gi|300215929|gb|HO088555.1|HO088555
EST:     TTCTTGGAGTTGACCTGGCAAAAGTTGTAATAGTTGACAATACTCCACAG                         GTTTTCCAGTTGCAAGTGGACAATGGTATACCAATAAAGAGCTGGTTTGAT
genomic: TTCTTGGAGTTGACCTGGCAAAAGTTGTAATAGTTGACAATACTCCACAGgtagcatgcc ... tttttttcagGTTTTCCAGTTGCAAGTGGACAATGGTATACCAATAAAGAGCTGGTTTGAT
EST: gi|88992694|gb|CI035700.1|CI035700
EST:     TTCTTGGAGTTGACCTGGCAAAAGTTGTAATAGTTGACAATACTCCACAG                         GTTTTCCAGTTGCAAGTGGACAATGGTATACCAATAAAGAGCTGGTTTGAT
genomic: TTCTTGGAGTTGACCTGGCAAAAGTTGTAATAGTTGACAATACTCCACAGgtagcatgcc ... tttttttcagGTTTTCCAGTTGCAAGTGGACAATGGTATACCAATAAAGAGCTGGTTTGAT
EST: gi|88837692|gb|CI079052.1|CI079052
EST:     TTCTNGGAGTTGACCTGGCAAAAGTTGTAATAGTTGACAATACTCCACAG                         GTTTTCCAGTTGCAAGTGGACAATGGTATACCAATAAAGAGCTGGTTTGAT
genomic: TTCTTGGAGTTGACCTGGCAAAAGTTGTAATAGTTGACAATACTCCACAGgtagcatgcc ... tttttttcagGTTTTCCAGTTGCAAGTGGACAATGGTATACCAATAAAGAGCTGGTTTGAT
EST: gi|86846123|gb|CI339752.1|CI339752
EST:     TTGACAATACTCCACAG                         GTTTTCCAGTTGCAAGTGGACAATGGTATACCAATAAAGAGCTGGTTTGAT
genomic: TTGACAATACTCCACAGgtagcatgcc ... tttttttcagGTTTTCCAGTTGCAAGTGGACAATGGTATACCAATAAAGAGCTGGTTTGAT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TCGTGAGTCATGTATATTCTCTGAGGGTTGCTATACAAAGGATCTGACAATTCTTGGAGTTGACCTGGCAAAAGTTGTAATAGTTGACAATACTCCACAGgtagcatgcctttttccgaatactgtatatgctttatatggacagatggaaatgtttccatttctatagttctagacttagacttggttgctagaaatat

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