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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTGAACTCTCATCTTACACCTCGACCTATTTTGCTTACAAGGCATGGTGAGAGTTTACACAATGTCAGAGGAAGAGTTGGTGGTGACACGGTCCTGAGgtttgcttttactttttttttcctttactaccttccaatgtggcacaccttcagattatatatttctactctgatatctcattttgagttatggaagtta...

Basic information

species Oryza sativa
transcript LOC_Os05g07130.2
intron # 16
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g07130.1 (Oryza sativa), 5'ss of exon 16
lower sequence: GRMZM2G021846_T02 (Zea mays), 5'ss of exon 16
GTGAACTCTCATCTTACACCTCGACCTATTTTGCTTACAAGGCATGGTGAGAGTTTACACAATGTCAGAGGAAGAGTTGGTGGTGACACGGTCCTGAGgtttgcttttactttttttttcctttactaccttccaatgtggcacaccttcagattatatatttctactctgatatctcattt--tgagttatggaagtta---
|||||||||||||||||||| ||||||||||||||||| |||||||||||||||||||| ||||| ||||||||||| |||||||| || || || |||||||||||  | |   ||||| | ||  ||||||  |||    | || ||| |    ||   | | | | |||  | | | ||  | |   |||   | ||   
GTGAACTCTCATCTTACACCACGACCTATTTTGCTTACCAGGCATGGTGAGAGTTTACATAATGTTAGAGGAAGAGTCGGTGGTGATACAGTTCTAAGgtttgctttc-cctaagttttcatctaacaccttcagatg----atacattctgcacttagtatgccattttgagttgtgagttatttaaacatgacggctagag
















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|29616012|gb|CB621024.1|CB621024
EST:     GAGAGTTTACACAATGTCAGAGGAAGAGTTGGTGGTGACACGGTCCTGAG                         TGAAGATGGAGAGCTTTACTCGAAGAAATTAGCCAACTTCATAGAAAAGAG
genomic: GAGAGTTTACACAATGTCAGAGGAAGAGTTGGTGGTGACACGGTCCTGAGgtttgctttt ... tggtgcacagTGAAGATGGAGAGCTTTACTCGAAGAAATTAGCCAACTTCATAGAAAAGAG
EST: gi|29612782|gb|CB617795.1|CB617795
EST:     GAGAGTTTACACAATGTCAGAGGAAGAGTTGGTGGTGACACGGTCCTGAG                         TGAAGATGGAGAGCTTTACTCGAAGAAATTAGCCAACTTCATAGAAAAGAG
genomic: GAGAGTTTACACAATGTCAGAGGAAGAGTTGGTGGTGACACGGTCCTGAGgtttgctttt ... tggtgcacagTGAAGATGGAGAGCTTTACTCGAAGAAATTAGCCAACTTCATAGAAAAGAG
EST: gi|29615977|gb|CB620989.1|CB620989
EST:     GAGAGTTTACACAATGTCAGAGGAAGAGTTGGTGGTGACACGGTCCTGAG                         TGAAGATGGAGAGCTTTACTCGAAGAAATTAGCCAACTTCATAGAAAAGAG
genomic: GAGAGTTTACACAATGTCAGAGGAAGAGTTGGTGGTGACACGGTCCTGAGgtttgctttt ... tggtgcacagTGAAGATGGAGAGCTTTACTCGAAGAAATTAGCCAACTTCATAGAAAAGAG
EST: gi|29615975|gb|CB620987.1|CB620987
EST:     GAGAGTTTACACAATGTCAGAGGAAGAGTTGGTGGTGACACGGTCCTGAG                         TGAAGATGGAGAGCTTTACTCGAAGAAATTAGCCAACTTCATAGAAAAGAG
genomic: GAGAGTTTACACAATGTCAGAGGAAGAGTTGGTGGTGACACGGTCCTGAGgtttgctttt ... tggtgcacagTGAAGATGGAGAGCTTTACTCGAAGAAATTAGCCAACTTCATAGAAAAGAG
EST: gi|29616052|gb|CB621064.1|CB621064
EST:     GAGAGTTTACACAATGTCAGAGGAAGAGTTGGTGGTGACACGGTCCTGAG                         TGAAGATGGAGAGCTTTACTCGAAGAAATTAGCCAACTTCATAGAAAAGAG
genomic: GAGAGTTTACACAATGTCAGAGGAAGAGTTGGTGGTGACACGGTCCTGAGgtttgctttt ... tggtgcacagTGAAGATGGAGAGCTTTACTCGAAGAAATTAGCCAACTTCATAGAAAAGAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTGAACTCTCATCTTACACCTCGACCTATTTTGCTTACAAGGCATGGTGAGAGTTTACACAATGTCAGAGGAAGAGTTGGTGGTGACACGGTCCTGAGgtttgcttttactttttttttcctttactaccttccaatgtggcacaccttcagattatatatttctactctgatatctcattttgagttatggaagtta

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG