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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATCTACGTAGTTGATTCCCTGGATAGAGAGAGGATTGGGAGAGCCAGAGCTGAATTTCAGgtttacatatatgtataaataatttattatgaggcagcaagtgtttgcttctgcactgacatttgttgccttgttgctctaacttactgtgtggtaatctgtctttcag

Basic information

species Oryza sativa
transcript LOC_Os10g42940.1
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os10g42940.1 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM2G011518_T01 (Zea mays), 5'ss of exon 4
ATCTACGTAGTTGATTCCCTGGATAGAGAGAGGATTGGGAGAGCCAGAGCTGAATTTCAGgtttacatatatgtataaataatttattatgaggcagcaagtgtttgcttctgcactgacatttgttgccttgt-tgctctaacttactgtgtggtaatc--tgtctttcag
|| ||||| |||||||| |||||||||||||| || ||||||||||| || || ||||||||||               || ||  || ||    |    |||  |  || ||||||||  ||   ||   | | | |||||||||  | ||   |  |   | ||||||||
ATTTACGTGGTTGATTCACTGGATAGAGAGAGAATCGGGAGAGCCAGGGCGGAGTTTCAGgtttg--------------tagttccttttgc--taattggtgcct--ttgtgcactgagcttctatgtaatatctactctaacttgttttgaaattttaaatctctttcag

upper sequence: LOC_Os10g42940.1 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM2G011518_T03 (Zea mays), 5'ss of exon 3
----------------------------------------ATCTACGTAGTTGATTCCCTGGATAGAGAGAGGATTGGGAGAGCCAGAGCTGAATTTCAGgtttacatatatgtataaataatttattatgaggcagcaagtgtttgcttctgcactgacatttgttgccttgt-tgctctaacttactgtgtggtaatc--tgtctttcag
                                        || ||||| |||||||| |||||||||||||| || ||||||||||| || || ||||||||||               || ||  || ||    |    |||  |  || ||||||||  ||   ||   | | | |||||||||  | ||   |  |   | ||||||||
TGAAATGTAAGATGTTCCCCATTATTTGCTGAACTTGCAGATTTACGTGGTTGATTCACTGGATAGAGAGAGAATCGGGAGAGCCAGGGCGGAGTTTCAGgtttg--------------tagttccttttgc--taattggtgcct--ttgtgcactgagcttctatgtaatatctactctaacttgttttgaaattttaaatctctttcag
















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|29641419|gb|CB646426.1|CB646426
EST:     TTGATTCCCTGGATAGAGAGAGGATTGGGAGAGCCAGAGCTGAATTTCAG                         GCCATTATTAATGACCCTTTTATGCTTAATAGTGTTCTATTGGTGTTTGCT
genomic: TTGATTCCCTGGATAGAGAGAGGATTGGGAGAGCCAGAGCTGAATTTCAGgtttacatat ... tgtctttcagGCCATTATTAATGACCCTTTTATGCTTAATAGTGTTCTATTGGTGTTTGCT
EST: gi|571720|gb|D41231.1|D41231
EST:     TTGATTCCCTGGATAGAGAGAGGATTGGGAGAGCCAGAGCTGAATTTCAG                         GCCATTATTAATGACCCTTTTATGCTTAATAGTGTTCTATTGGTGTTTGCT
genomic: TTGATTCCCTGGATAGAGAGAGGATTGGGAGAGCCAGAGCTGAATTTCAGgtttacatat ... tgtctttcagGCCATTATTAATGACCCTTTTATGCTTAATAGTGTTCTATTGGTGTTTGCT
EST: gi|66919127|gb|CX105975.1|CX105975
EST:     TTGATTCCCTGGATAGAGAGAGGATTGGGAGAGCCAGAGCTGAATTTCAG                         GCCATTATTAATGACCCTTTTATGCTTAATAGTGTTCTATTGGTGTTTGCT
genomic: TTGATTCCCTGGATAGAGAGAGGATTGGGAGAGCCAGAGCTGAATTTCAGgtttacatat ... tgtctttcagGCCATTATTAATGACCCTTTTATGCTTAATAGTGTTCTATTGGTGTTTGCT
EST: gi|325494682|gb|JG459206.1|JG459206
EST:     GGATAGAGAGAGGATTGGGAGAGCCAGAGCTGAATTTCAG                         GCCATTATTAATGACCCTTTTATGCTTAATAGTGTTCTATTGGTGTTTGCT
genomic: GGATAGAGAGAGGATTGGGAGAGCCAGAGCTGAATTTCAGgtttacatat ... tgtctttcagGCCATTATTAATGACCCTTTTATGCTTAATAGTGTTCTATTGGTGTTTGCT
EST: gi|88761917|gb|CI771473.1|CI771473
EST:     TTGATTCCCTGGATAGAGAGAGGATTGGGAGAGCCAGAGCTGAATTTCAG                         GCCATTATTAA
genomic: TTGATTCCCTGGATAGAGAGAGGATTGGGAGAGCCAGAGCTGAATTTCAGgtttacatat ... tgtctttcagGCCATTATTAA
EST: gi|33795688|gb|CF323714.1|CF323714
EST:     TTGATTCCCTGGATAGAGAGAGGATTGGGAGAGCCAGAGCTGAATTTCAG                         GCCATTATTAATGACCCTTTTATGCTTAATAGTGTTCTATTGGGTGTTTGC
genomic: TTGATTCCCTGGATAGAGAGAGGATTGGGAGAGCCAGAGCTGAATTTCAGgtttacatat ... tgtctttcagGCCATTATTAATGACCCTTTTATGCTTAATAGTGTTCTATTGG-TGTTTGC
EST: gi|218479871|gb|FG966995.1|FG966995
EST:     TTGATTCCCTGGATAGAGAGAGGATTGGGAGAGCCAGAGCTGAATTTCAG                         GCCATTATTAATGACCCTTTTATGCTTAATAGTGTTCTATAGGTGTATGCT
genomic: TTGATTCCCTGGATAGAGAGAGGATTGGGAGAGCCAGAGCTGAATTTCAGgtttacatat ... tgtctttcagGCCATTATTAATGACCCTTTTATGCTTAATAGTGTTCTATTGGTGTTTGCT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATCTACGTAGTTGATTCCCTGGATAGAGAGAGGATTGGGAGAGCCAGAGCTGAATTTCAGgtttacatatatgtataaataatttattatgaggcagcaagtgtttgcttctgcactgacatttgttgccttgttgctctaacttactgtgtggtaatctgtctttcag

- - - - - - - - - - - - -  GAGAGG
- - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - -  GAGGAT
- - - - - - - - - - - - - - - - - - - - - -  AGAGCT
- - - - - - - - - - - - - - - - - - - - - - -  AGCTGA