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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgtgtttttatacattcactgatttaggtggtttcaccactgttgtgaactgttttaataaatacttaaaaagggtgtgattttttactttcaatgacagGTTACTGCTAATTCTGTTCGTCTGGTTAGTTGTACCTCTCGGGAGCTAGTGGATCAATGGAATGCACCAGAAGGATTTTCAGTCAATGTTGCATCAGCTA

Basic information

species Oryza sativa
transcript LOC_Os05g51480.2
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g51480.2 (Oryza sativa), 3'ss of exon 13
lower sequence: GRMZM2G430027_T01 (Zea mays), 3'ss of exon 1
---tgtgtttttatacattcactgatttaggtggtttcaccactgttgtgaactgttttaataaatacttaaaaagggtgtgattttttactttcaatgacagGTTACTGCTAATTCTGTTCGTCTGGTTAGTTGTACCTCTCGGGAGCTAGTGGATCAATGGAATGCACCAGAAGGATTTTCAGTCAATGTTGCATCAGCTA
   |   ||  | |   |||| |   ||   |  ||| | ||    |||||   ||| |  | |||     |  |  || | |  | ||  ||| | |||||||||||||||||||| |||||  | || ||||||||||| ||||||||||||||||| ||||||||||||| |||||| |||||||||||||| |||||||
gattagtttcctgtcacttcatt---tttcatcattttagcagctatgtgatgagttatgtttaatcaactatcaatgttttacctgttgttttgattgacagGTTACTGCTAATTCGGTTCGATTAGTCAGTTGTACCTCCCGGGAGCTAGTGGATCAGTGGAATGCACCAGCAGGATTCTCAGTCAATGTTGCTTCAGCTA

upper sequence: LOC_Os05g51480.2 (Oryza sativa), 3'ss of exon 13
lower sequence: GRMZM2G402002_T01 (Zea mays), 3'ss of exon 13
---tgtgtttttatacattcactgatttaggtggtttcaccactgttgtgaactgttttaataaatacttaaaaagggtgtgattttttactttcaatgacagGTTACTGCTAATTCTGTTCGTCTGGTTAGTTGTACCTCTCGGGAGCTAGTGGATCAATGGAATGCACCAGAAGGATTTTCAGTCAATGTTGCATCAGCTA
   |||   || ||   |||| | ||||  |  |||  |    || | |||    ||||||| ||   |   || |  |   |  | ||  ||| |||| |||||||||||||||||||||||  | || ||||| ||||| |||||| ||||| |||||||||||||||||| |||||| |||||||||||||| |||||||
tcctgtcagttaattttttca-tcattttagcagttatatg--tgatatgagtcattttaatcaacgttaccaatgttttacacctgttgttttgaatggcagGTTACTGCTAATTCTGTTCGGTTAGTCAGTTGCACCTCCCGGGAGTTAGTGAATCAATGGAATGCACCAGCAGGATTCTCAGTCAATGTTGCTTCAGCTA
















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|58668330|gb|CK057016.1|CK057016
EST:     AGACTCAGACTTNG-TTTGTCAAAATGCCATCAATGATCTGCTTATACAG                         GTTACTGCTAATTCTGTTCGTCTGGTTAGTTGTACCTCTCGGGAGCTAGTG
genomic: AGACTCAGACTTTGTTTTGTCAAAATGCCATCAATGATCTGCTTATACAGgtgccttttt ... tcaatgacagGTTACTGCTAATTCTGTTCGTCTGGTTAGTTGTACCTCTCGGGAGCTAGTG
EST: gi|29630334|gb|CB635343.1|CB635343
EST:     AGACTCAGACTTTGTTTTGTCAAAATGCCCCCAATGATCTGCTTATACAG                         GTTACTGCTAATTCTGTTCGTCTGGTTAGTTGTACCTCTCGGGAGCTAGTG
genomic: AGACTCAGACTTTGTTTTGTCAAAATGCCATCAATGATCTGCTTATACAGgtgccttttt ... tcaatgacagGTTACTGCTAATTCTGTTCGTCTGGTTAGTTGTACCTCTCGGGAGCTAGTG
EST: gi|29669278|gb|CB665553.1|CB665553
EST:     AGACTCAGACTTTGTTTTGTCAAAATGCCATCAATGATCTGCTTATACAG                         GTTACTGCTAATTCTGTTCGTCTGGTTAGTTGTACCTCTCGGGAGCTAGTG
genomic: AGACTCAGACTTTGTTTTGTCAAAATGCCATCAATGATCTGCTTATACAGgtgccttttt ... tcaatgacagGTTACTGCTAATTCTGTTCGTCTGGTTAGTTGTACCTCTCGGGAGCTAGTG
EST: gi|29634960|gb|CB639969.1|CB639969
EST:     AGACTCAGACTTTGTTTTGTCAAAATGCCATCAATGATCTGCTTATACAA                         GTTACTGCTAATTCTGTTCGTCTGGTTAGTTGTACCTCTCGGGAGCTAGTG
genomic: AGACTCAGACTTTGTTTTGTCAAAATGCCATCAATGATCTGCTTATACAGgtgccttttt ... tcaatgacagGTTACTGCTAATTCTGTTCGTCTGGTTAGTTGTACCTCTCGGGAGCTAGTG
EST: gi|29632887|gb|CB637896.1|CB637896
EST:     AGACTCAGACTTTGTTTTGTCAAAATGCCATCAATGATCTGCTTATACAG                         GTTACTGCTAATTCTGTTCGTCTGGTTAGTTGTACCTCTCGGGAGCTAGTG
genomic: AGACTCAGACTTTGTTTTGTCAAAATGCCATCAATGATCTGCTTATACAGgtgccttttt ... tcaatgacagGTTACTGCTAATTCTGTTCGTCTGGTTAGTTGTACCTCTCGGGAGCTAGTG
EST: gi|87009621|gb|CI309142.1|CI309142
EST:     AGACTCAGACTTTGTTTTGTCAAATTGCCATCAATGATCTGCTTATACAG                         GTTGCTGCTAATTCTGTTCGTCTGGTTAGTTGTACCTCTCGGGAGCTAGTG
genomic: AGACTCAGACTTTGTTTTGTCAAAATGCCATCAATGATCTGCTTATACAGgtgccttttt ... tcaatgacagGTTACTGCTAATTCTGTTCGTCTGGTTAGTTGTACCTCTCGGGAGCTAGTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgaactgttttaataaatacttaaaaagggtgtgattttttactttcaatgacagGTTACTGCTAATTCTGTTCGTCTGGTTAGTTGTACCTCTCGGGAGCTAGTGGATCAATGGAATGCACCAGAAGGATTTTCAGTCAATGTTGCATCAGCTA
       ttttaat  putative branch site (score: 3)
                                   ttttttactttc  putative PPT
     tgttttaataaatact  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgtgtttttatacattcactgatttaggtggtttcaccactgttgtgaactgttttaataaatacttaaaaagggtgtgattttttactttcaatgacagGTTACTGCTAATTCTGTTCGTCTGGTTAGTTGTACCTCTCGGGAGCTAGTGGATCAATGGAATGCACCAGAAGGATTTTCAGTCAATGTTGCATCAGCTA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TCAGCT