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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaatatctaaataaatatttgtaccttgaactaaatatgcctaaaattaatttcttgtgtaaagttagattaatgttcttaatctttttcagAAGATTGGAGGCATGTTCCAAGAAGCCCTTGCAATGCCTAATCCAGTACTGAACCAATCAAGCCCAGCTCCATCTCAAGCTATCATGGACACAACCTCAA

Basic information

species Oryza sativa
transcript LOC_Os08g42470.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os08g42470.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM5G882527_T03 (Zea mays), 3'ss of exon 5
gtaaatatctaaataaatatttgtaccttgaactaaatatgcctaaaattaatttcttgtgtaaagttagatt----aatgttcttaatctttttcagAAGATTGGAGGCATGTTCCAAGAAGCCCTTGCAATGCCTAATCCAGTACTGAACCAATCAAGCCCAGC---TCCATCTCAAGCTATCATGGACACAACCTCAA
|||   | |   | ||  |||| |    | | ||||| || |    ||| ||  |  ||| ||||  |  | |    |||     | || | ||||||||||| |||| ||||||||| ||||||||||||||| |   |||||| |||| |||| | ||||||||   ||||||| |||| ||||||||||| |||    
gtatggaacagcaaaatcattttt-ttgtcagctaaaaatacggtcaat-aagctgatgtttaaatgtgaactgtaaaattgcgctgatgtgtttcagAAGATGGGAGTCATGTTCCAGGAAGCCCTTGCAATGGCAGGTCCAGTGCTGAGCCAAGCCAGCCCAGCAGCTCCATCTGAAGCCATCATGGACACCACCA---

upper sequence: LOC_Os08g42470.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM5G882527_T02 (Zea mays), 3'ss of exon 5
gtaaatatctaaataaatatttgtaccttgaactaaatatgcctaaaattaatttcttgtgtaaagttagatt----aatgttcttaatctttttcagAAGATTGGAGGCATGTTCCAAGAAGCCCTTGCAATGCCTAATCCAGTACTGAACCAATCAAGCCCAGC---TCCATCTCAAGCTATCATGGACACAACCTCAA
|||   | |   | ||  |||| |    | | ||||| || |    ||| ||  |  ||| ||||  |  | |    |||     | || | ||||||||||| |||| ||||||||| ||||||||||||||| |   |||||| |||| |||| | ||||||||   ||||||| |||| ||||||||||| ||| || 
gtatggaacagcaaaatcattttt-ttgtcagctaaaaatacggtcaat-aagctgatgtttaaatgtgaactgtaaaattgcgctgatgtgtttcagaagATGGGAGTCATGTTCCAGGAAGCCCTTGCAATGGCAGGTCCAGTGCTGAGCCAAGCCAGCCCAGCAGCTCCATCTGAAGCCATCATGGACACCACCACAC
















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|58669636|gb|CK058322.1|CK058322
EST:     GATGGCCTCCATGACCAA                         AAGATTGGAGGCATGTTCCAAGAAGCCCTTGCAATGCCTAATCCAGTACTG
genomic: GATGGCCTCCATGACCAAgtaaatatct ... tctttttcagAAGATTGGAGGCATGTTCCAAGAAGCCCTTGCAATGCCTAATCCAGTACTG
EST: gi|15852981|gb|BI805777.1|BI805777
EST:     CTTTGGAATGGACAGCGATGGCCTCCANGACC-A                         AAGATTGGAGGCATGTTCCTAGAAGCCCTTGC-ATGCCTAATCCAGTACTG
genomic: CTTTGGAATGGACAGCGATGGCCTCCATGACCAAgtaaatatct ... tctttttcagAAGATTGGAGGCATGTTCCAAGAAGCCCTTGCAATGCCTAATCCAGTACTG
EST: gi|163926679|gb|EG713695.1|EG713695
EST:     GCCCAGTGTTGTATGGCTTTGGAATGGACAGCGATGGCCTCCATGACCAA                         AAGATTGGAGGCATGTTCCAAGAAGCCCT
genomic: GCCCAGTGTTGTATGGCTTTGGAATGGACAGCGATGGCCTCCATGACCAAgtaaatatct ... tctttttcagAAGATTGGAGGCATGTTCCAAGAAGCCCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgcctaaaattaatttcttgtgtaaagttagattaatgttcttaatctttttcagAAGATTGGAGGCATGTTCCAAGAAGCCCTTGCAATGCCTAATCCAGTACTGAACCAATCAAGCCCAGCTCCATCTCAAGCTATCATGGACACAACCTCAA
                                       tcttaat  putative branch site (score: 3)
                                      ttcttaatctttttc  CT-rich tract
     aaaattaatttcttgt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaatatctaaataaatatttgtaccttgaactaaatatgcctaaaattaatttcttgtgtaaagttagattaatgttcttaatctttttcagAAGATTGGAGGCATGTTCCAAGAAGCCCTTGCAATGCCTAATCCAGTACTGAACCAATCAAGCCCAGCTCCATCTCAAGCTATCATGGACACAACCTCAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CATGGA