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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtcagtgctagcttgtactgtatttttagcagcttaatcagaccttaaaaattcaattcattggactcacatactacatataaatctttcttgcttggatcagGCATTGTCAGCTATTCCCTTCCTGGATATTTATTTCTTGGGAGTACCCATGGTCAGCATGCTTCTTTATGTCTGGAGCAGAGAATATCCGAATTCTCAGA

Basic information

species Oryza sativa
transcript LOC_Os05g09550.2
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g09550.3 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G117388_T04 (Zea mays), 3'ss of exon 4
----gtcagtgctagcttgtac-tgtatttttagcagcttaatcagaccttaaaa-attcaattcattggactcacatactacatataaatctttcttgcttggatcagGCATTGTCAGCTATTCCCTTCCTGGATATTTATTTCTTGGGAGTACCCATGGTCAGCATGCTTCTTTATGTCTGGAGCAGAGAATATCCGAATTCTCAGA
    || | |  ||  || | | | ||   ||   |  || | || |||     | |||| |    ||  ||| |  |  |  ||| || ||| | ||||||| ||||||  |||||   ||||||| |  |  ||  || |||||| ||| |||| |||||||||||||| ||||||||||||||| ||||  |||| ||| ||||||
gtcagttatttttactttttgcatttacaatttcaaatttgaccaaaccaagggacattctagaacttttactaaact--tgtatacaactctgtattgcttgaatcagGTGTTGTCTATTATTCCCCTATTCAATTCTTTTTTCTTAGGAATACCTATGGTCAGCATGCTCCTTTATGTCTGGAGCCGAGAGAATCCAAATGCTCAGA

upper sequence: LOC_Os05g09550.3 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G143817_T01 (Zea mays), 3'ss of exon 4
gtcagtgctagcttgtactgtatttttag---cagcttaatcagaccttaaaaattcaattcattggactcacatactacatataaatctttcttgcttggatcagGCATTGTCAGCTATTCCCTTCCTGGATATTTATTTCTTGGGAGTACCCATGGTCAGCATGCTTCTTTATGTCTGGAGCAGAGAATATCCGAATTCTCAGA
||||||| ||| |  | ||  | |   |    ||| |||  |  | |  | | |     || |       |  |   | | ||| | ||| | ||||||| ||||||  ||||| | |||||||    || ||| |||| |||||||| |||| ||||||||||||||| |||||||||||||| ||||  |||| ||| | ||||
gtcagtggtagttctttctacaatcagaatttcagattaggcgaaaccaagagacattcttgaacttctacttaacttgcgtatgactctgtattgcttgaatcagGTGTTGTCTGTTATTCCCCAATTGAATACTTATGTCTTGGGATTACCTATGGTCAGCATGCTTGTTTATGTCTGGAGCCGAGAGAATCCAAATGCCCAGA
















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|218492921|gb|FG948483.1|FG948483
EST:     GCACAGCTGATTTCTTGTGGATGATGATATTTGGTGCCATATCACTGCTG                         GCATTGTCAGCTATTCCCTTCCTGGATATTTATTTCTTGGGAGTACCCATG
genomic: GCACAGCTGATTTCTTGTGGATGATGATATTTGGTGCCATATCACTGCTGgtcagtgcta ... cttggatcagGCATTGTCAGCTATTCCCTTCCTGGATATTTATTTCTTGGGAGTACCCATG
EST: gi|157651306|gb|EX450940.1|EX450940
EST:     GCACAGCTGATTTCTTGTGGATGATGATATTTGGTGCCATATCACTGCTG                         GCATTGTCAACTATTCCCTTCCTGGATATTTATTTCTTGGGAGTACC
genomic: GCACAGCTGATTTCTTGTGGATGATGATATTTGGTGCCATATCACTGCTGgtcagtgcta ... cttggatcagGCATTGTCAGCTATTCCCTTCCTGGATATTTATTTCTTGGGAGTACC
EST: gi|27554498|gb|CA998398.1|CA998398
EST:     GCACAGCTGATTTCTTGTGGATGATGATATTTGGTGCCATATCACTGCTG                         GCATTGTCAGCTATTCCCTTCCTGGATATTTATTTCTTGGGAGTACCCATG
genomic: GCACAGCTGATTTCTTGTGGATGATGATATTTGGTGCCATATCACTGCTGgtcagtgcta ... cttggatcagGCATTGTCAGCTATTCCCTTCCTGGATATTTATTTCTTGGGAGTACCCATG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaattcaattcattggactcacatactacatataaatctttcttgcttggatcagGCATTGTCAGCTATTCCCTTCCTGGATATTTATTTCTTGGGAGTACCCATGGTCAGCATGCTTCTTTATGTCTGGAGCAGAGAATATCCGAATTCTCAGA
               gactcac  putative branch site (score: 2)
                                    tctttcttgctt  putative PPT
                      atactacatataaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtcagtgctagcttgtactgtatttttagcagcttaatcagaccttaaaaattcaattcattggactcacatactacatataaatctttcttgcttggatcagGCATTGTCAGCTATTCCCTTCCTGGATATTTATTTCTTGGGAGTACCCATGGTCAGCATGCTTCTTTATGTCTGGAGCAGAGAATATCCGAATTCTCAGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCAG