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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtccctattttctgtttccactctcttttttactaccttgtttctcttattactttcagccattcattcagcagttattctgaaaggaatccttttgtatcctcagGTCAGGGTTATGATCATGTCACTGAAAGCAGGTAATCTTGGTCTCAATATGGTTGCTGCTTGCCATGTAATTCTCCTTGATCTTTGGTGGAATCCTTATG

Basic information

species Oryza sativa
transcript LOC_Os08g08220.2
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os08g08220.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM2G449355_T02 (Zea mays), 3'ss of exon 9
gtccctattttctgtttccactctcttttttactaccttgtttctcttattactttcagccattcattcagcagttattctgaaaggaatccttttgtatcctcagGTCAGGGTTATGATCATGTCACTGAAAGCAGGTAATCTTGGTCTCAATATGGTTGCTGCTTGCCATGTAATTCTCCTTGATCTTTGGTGGAATCCTTATG
       |  | ||||     |   ||||| |   | |||||||| |||    || ||| |||  | | || || | || |           |||| | || |||||| || |||||||| |||||||||||||| ||||||||||||||||| |||||| |||||||||||||||||||||||||||| |||||||| |||||||
------gtcatatgttat-gtttgttttttcatgcctttgtttcttttacagtttccagacat--actaagaagatttttt-----------ttttctttcttcagGTTAGAGTTATGATTATGTCACTGAAAGCTGGTAATCTTGGTCTCAACATGGTTTCTGCTTGCCATGTAATTCTCCTTGATCTCTGGTGGAACCCTTATG

upper sequence: LOC_Os08g08220.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GLYMA20G23390.1 (Glycine max), 3'ss of exon 8
gtccctattttctgtttccactctcttttttactaccttgtttctcttattactttcagcc--attcattcagcagttattctgaaaggaatccttttgtatcctcagGTCAGGGTTATGATCATGTCACTGAAAGCAGGTAATCTTGGTCTCAATATGGTTGCTGCTTGCCATGTAATTCTCCTTGATCTTTGGTGGAATCCTTATG
 ||  ||| || |    |  ||     ||  | |  ||  | | |  || |   || | |    |  | |  |  ||    || |  | |||   |||       ||| | |  |||||| | |||||||| |||||||| || |||||| | |||||||||||||| || ||||| |||||  | |||||||||||||||||     
-tcagtatgttttccaactccttgaacttgaattttctactgtgttctagtgtcttaaccttggtagactttggtgtctgactaattgaaatttgttt-------cagATAACTGTTATGCTGATGTCACTAAAAGCAGGAAACCTTGGTTTGAATATGGTTGCTGCATGTCATGTTATTCTTTTGGATCTTTGGTGGAATCCGACAA

upper sequence: LOC_Os08g08220.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GLYMA10G43430.1 (Glycine max), 3'ss of exon 10
gtccctattttctgtttccactctcttttttactaccttgtttctcttattactttcagccattca--ttcagcag---ttattctgaaaggaatccttttgtatcctcagGTCAGGGTTATGATCATGTCACTGAAAGCAGGTAATCTTGGTCTCAATATGGTTGCTGCTTGCCATGTAATTCTCCTTGATCTTTGGTGGAATCCTTATG
       |||||    |||  |     ||  | || ||  | | |  ||  | ||  ||    |||   || | ||   ||  | |   |  | |     | | |  |||| |    |||||| | |||||||| |||||||| || |||||| | |||||||||||||| || ||||| || ||  | |||||||||||||||||     
-------ttttccaactcc--ttgaacttgcattatctactgtgttctac-agttctagtgtctcaacctcggtagactttggtgtctgactagttgaaatttgtt-tcagATTGCTGTTATGCTGATGTCACTAAAAGCAGGAAACCTTGGTTTGAATATGGTTGCTGCATGTCATGTTATACTTTTGGATCTTTGGTGGAATCCAACAA

upper sequence: LOC_Os08g08220.1 (Oryza sativa), 3'ss of exon 9
lower sequence: AT1G50410.1 (Arabidopsis thaliana), 3'ss of exon 9
gtccctattttctgtttccactctcttttttactaccttgtttctcttattactttcagccattcattcagcagttattctgaaaggaatccttttgtatcct-cagGTCAGGGTTATGATCATGTCACTGAAAGCAGGTAATCTTGGTCTCAATATGGTTGCTGCTTGCCATGTAATTCTCCTTGATCTTTGGTGGAATCCTTATG
||   |  | |   | ||     || ||||| |        || ||||| |  |       ||   |||     || || ||       |  |||||| |    ||||| |  || ||||| |||||  | ||||| || |||||||| || |||||| ||||||| || ||||| ||||| |||||||| |||||||||||   | 
gtaagtcgtatgcatatctgaaatcattttttcctaaacaattttcttagtggtggtg--tatgtgttccctcctttttttg-------tttttttgtcttaaacagGTAAAAGTGATGATAATGTCTTTAAAAGCTGGAAATCTTGGGCTGAATATGATTGCTGCATGTCATGTCATTCTTCTTGATCTATGGTGGAATCCAACTA

upper sequence: LOC_Os08g08220.1 (Oryza sativa), 3'ss of exon 9
lower sequence: AT3G20010.1 (Arabidopsis thaliana), 3'ss of exon 8
--------------------gtccctattttctgtttccactctcttttttactaccttgtttctcttattactttcagccattcattcagcagttattctgaaaggaatccttttgtatcctcagGTCAGGGTTATGATCATGTCACTGAAAGCAGGTAATCTTGGTCTCAATATGGTTGCTGCTTGCCATGTAATTCTCCTTGATCTTTGGTGGAATCCTTATG
                         | ||||||    | |    ||  |    |  ||    | |   ||     |     ||| || | | || |  ||| ||||           | |  | |||| | ||| ||| | ||||| || ||||| || || ||||| || |||||||| ||||| || ||||| |||||| | |||||||||||||||||   | 
gtaagtgatgtaaatatcttagatatgttttctaaaacaatatactaatcgtttctctgaaatatggaatgttcatggagtattgatcctgaagct-ctctaaaagcgcaaaaaaaattttattagGTAAAGGTGATGCTGATGTCGCTAAAAGCTGGAAACCTTGGGCTGAATATGGTAGCTGCATGTCATGTTATTCTCTTGGATCTTTGGTGGAATCCAACTA

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|29683404|gb|CB679679.1|CB679679
EST:     CCCTCAATTCAAGAGATAAAGCAGTGAAAGATTTTAACACAGACCCAGAG                         GTCAGGGTTATGATCATGTCACTGAAAGCAGGTAATCTTGGTCTCAATATG
genomic: CCCTCAATTCAAGAGATAAAGCAGTGAAAGATTTTAACACAGACCCAGAGgtccctattt ... gtatcctcagGTCAGGGTTATGATCATGTCACTGAAAGCAGGTAATCTTGGTCTCAATATG






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

actttcagccattcattcagcagttattctgaaaggaatccttttgtatcctcagGTCAGGGTTATGATCATGTCACTGAAAGCAGGTAATCTTGGTCTCAATATGGTTGCTGCTTGCCATGTAATTCTCCTTGATCTTTGGTGGAATCCTTATG
                                      tccttttgtatcctc  CT-rich tract
                                         ttttgtat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtccctattttctgtttccactctcttttttactaccttgtttctcttattactttcagccattcattcagcagttattctgaaaggaatccttttgtatcctcagGTCAGGGTTATGATCATGTCACTGAAAGCAGGTAATCTTGGTCTCAATATGGTTGCTGCTTGCCATGTAATTCTCCTTGATCTTTGGTGGAATCCTTATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGTGGA