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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacggtgaactgatattttggccactgtaaattatcatttcttcaggattcatgccttgacattgttgatatatcttgtgcattgcagCTGAGTTGGCCACTAACCAACCTCTTTTCGCTGGAGATTCCGAGGTTCAGCAGCTTCTGCACATTTTCAA

Basic information

species Oryza sativa
transcript LOC_Os08g40170.1
intron # 3
splice site 3'
intron type U2

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|29663133|gb|CB659408.1|CB659408
EST:     GGCACACTACTCCACTCCGGTTGACATCTGGTCTGTGGGCTGCATTTTTG                         CTGAGTTGGCCACTAACCAACCTCTTTTCGCTGGAGATTCCGAGGTTCAGC
genomic: GGCACACTACTCCACTCCGGTTGACATCTGGTCTGTGGGCTGCATTTTTGgtacggtgaa ... tgcattgcagCTGAGTTGGCCACTAACCAACCTCTTTTCGCTGGAGATTCCGAGGTTCAGC
EST: gi|29663132|gb|CB659407.1|CB659407
EST:     GGCACACTACTCCACTCCGGTTGACATCTGGTCTGTGGGCTGCATTTTTG                         CTGAGTTGGCCACTAACCAACCTCTTTTCGCTGGAGATTCCGAGGTTCAGC
genomic: GGCACACTACTCCACTCCGGTTGACATCTGGTCTGTGGGCTGCATTTTTGgtacggtgaa ... tgcattgcagCTGAGTTGGCCACTAACCAACCTCTTTTCGCTGGAGATTCCGAGGTTCAGC
EST: gi|58604123|gb|CK014651.1|CK014651
EST:     GGCACACTACTCCACTCCGGTTGACATCTGGTCTGTGGGCTGCATTTTTG                         CTGAGTTGGCCACTAACCAACCTCTTTTCGCTGGAGATTCCGAGGTTCAGC
genomic: GGCACACTACTCCACTCCGGTTGACATCTGGTCTGTGGGCTGCATTTTTGgtacggtgaa ... tgcattgcagCTGAGTTGGCCACTAACCAACCTCTTTTCGCTGGAGATTCCGAGGTTCAGC
EST: gi|58676453|gb|CK065140.1|CK065140
EST:     GGCACACTACTCCACTCCGGTTGACATCTGGTCTGTGGGCTGCATTTTTG                         CTGAGTTGGCCACTAACCAAACTCTTTTCGCTGGAGATTCCGAGGTTCAGC
genomic: GGCACACTACTCCACTCCGGTTGACATCTGGTCTGTGGGCTGCATTTTTGgtacggtgaa ... tgcattgcagCTGAGTTGGCCACTAACCAACCTCTTTTCGCTGGAGATTCCGAGGTTCAGC
EST: gi|33801905|gb|CF326824.1|CF326824
EST:     GGCACACTACTCCACTCCGGTTGACATCTGGTCTGTGGGCTGCATTTTTG                         CTGAGTTGGCCACTAACCAACCTCTTTTCGCTGGAGATTCCGAGGTTCAGC
genomic: GGCACACTACTCCACTCCGGTTGACATCTGGTCTGTGGGCTGCATTTTTGgtacggtgaa ... tgcattgcagCTGAGTTGGCCACTAACCAACCTCTTTTCGCTGGAGATTCCGAGGTTCAGC
EST: gi|89175978|gb|CI042999.1|CI042999
EST:     GGCACACTACTCCACTCCGGTTGACATCTGGTCTGTGGGCTGCATTTTTG                         CTGAGTTGGCCACTAACCAACCTCTTTTCGCTGGAGATTCCGAGGTTCAGC
genomic: GGCACACTACTCCACTCCGGTTGACATCTGGTCTGTGGGCTGCATTTTTGgtacggtgaa ... tgcattgcagCTGAGTTGGCCACTAACCAACCTCTTTTCGCTGGAGATTCCGAGGTTCAGC
EST: gi|88962742|gb|CI023842.1|CI023842
EST:     ACATCTGGTCTGTGGGCTGCATTTTTG                         CTGAGTTGGCCACTAACCAACCTCTTTTCGCTGGAGATTCCGAGGTTCAGC
genomic: ACATCTGGTCTGTGGGCTGCATTTTTGgtacggtgaa ... tgcattgcagCTGAGTTGGCCACTAACCAACCTCTTTTCGCTGGAGATTCCGAGGTTCAGC
EST: gi|86496840|gb|CI139473.1|CI139473
EST:     GGCACACTACTCCACTCCGGTTGACATCTGGTCTGTGGGCTGCATTTTTG                         CTGAGTTGGCCACTAACCAACCTCTTTTCGCTGGAGATTCCGAGGTTCAGC
genomic: GGCACACTACTCCACTCCGGTTGACATCTGGTCTGTGGGCTGCATTTTTGgtacggtgaa ... tgcattgcagCTGAGTTGGCCACTAACCAACCTCTTTTCGCTGGAGATTCCGAGGTTCAGC
EST: gi|86593618|gb|CI264497.1|CI264497
EST:     GGCACACTACTCCACTCCGGTTGACATCTGGTCTGTGGGCTGCATTTTTG                         CTGAGTTGGCCACTAACCAACCTCTTTTCGCTGGAGATTCCGAGGTTCAGC
genomic: GGCACACTACTCCACTCCGGTTGACATCTGGTCTGTGGGCTGCATTTTTGgtacggtgaa ... tgcattgcagCTGAGTTGGCCACTAACCAACCTCTTTTCGCTGGAGATTCCGAGGTTCAGC
EST: gi|88850591|gb|CI094856.1|CI094856
EST:     TCTGGTCTGTGGGCTGCATTTTTG                         CTGAGTTGGCCACTAACCAACCTCTTTTCGCTGGAGATTCCGAGGTTCAGC
genomic: TCTGGTCTGTGGGCTGCATTTTTGgtacggtgaa ... tgcattgcagCTGAGTTGGCCACTAACCAACCTCTTTTCGCTGGAGATTCCGAGGTTCAGC
EST: gi|58603848|gb|CK014376.1|CK014376
EST:     GGCACACTACTCCACTCCGGTTGACATCTGGTCTGTGGGCTGCATTTTTG                         CTGAGTTGGCCACTAACCAACCTCTTTTCGCTGGAGATTCCGAGGTTCAGC
genomic: GGCACACTACTCCACTCCGGTTGACATCTGGTCTGTGGGCTGCATTTTTGgtacggtgaa ... tgcattgcagCTGAGTTGGCCACTAACCAACCTCTTTTCGCTGGAGATTCCGAGGTTCAGC
EST: gi|3768776|gb|AU032803.1|AU032803
EST:     GCACACTACTTCACTNCGGTTGACATCTGGTCTGTGGGGCTGCATTTTTG                         CTGAGTTGGNCACTAACCAACCT
genomic: GCACACTACTCCACTCCGGTTGACATCTGGTCTGTGGG-CTGCATTTTTGgtacggtgaa ... tgcattgcagCTGAGTTGGCCACTAACCAACCT
EST: gi|88975465|gb|CI023716.1|CI023716
EST:     ACTACTCCACTCCGGTTGACATCTGGTCTGTGGGCTGCATTTTTG                         CTGAGTTGGCCACTAACCAACCTCTTTTCGCTGGAGATTCCGAGGTTCAGC
genomic: ACTACTCCACTCCGGTTGACATCTGGTCTGTGGGCTGCATTTTTGgtacggtgaa ... tgcattgcagCTGAGTTGGCCACTAACCAACCTCTTTTCGCTGGAGATTCCGAGGTTCAGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atcatttcttcaggattcatgccttgacattgttgatatatcttgtgcattgcagCTGAGTTGGCCACTAACCAACCTCTTTTCGCTGGAGATTCCGAGGTTCAGCAGCTTCTGCACATTTTCAA
                              tgttgat  putative branch site (score: 4)
                                ttgatatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacggtgaactgatattttggccactgtaaattatcatttcttcaggattcatgccttgacattgttgatatatcttgtgcattgcagCTGAGTTGGCCACTAACCAACCTCTTTTCGCTGGAGATTCCGAGGTTCAGCAGCTTCTGCACATTTTCAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT