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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagataggtttttcttatctgccccaatggctggtgtatgagtagtctaaatgcttttgttttgttaacacagCTTCTTCACGAAAGCATATACCGAACATTTCTTGATCAACTTGTTGAGGTTTATAAACAAGTCCGAATTGGGGATCCTTTGGAGAATGGTACGTTACTGG

Basic information

species Oryza sativa
transcript LOC_Os09g26880.4
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os09g26880.4 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G130440_T02 (Zea mays), 3'ss of exon 9
gtaagataggtttttcttatctgcccc--------aatggctggtgtatgagtagtctaaatgcttttgttttgttaacacagCTTCTTCACGAAAGCATATACCGAACATTTCTTGATCAACTTGTTGAGGTTTATAAACAAGTCCGAATTGGGGATCCTTTGGAGAATGGTACGTTACTGG
||| | ||  ||| | || | |  |          | ||| | || |   | | || ||| ||  |||    | |||  |||| ||||||| || | |||||| | ||| || |||||||| ||||||||||| || ||||||||||||||||||||||| |||||||| || || |||||||
gtatggtatttttcttttgtttctcttttccgtatagtggttcgttttcaatttgtttaattgtctttcccatcttattacagATTCTTCATGAGAACATATATCAAACCTTCCTTGATCAGCTTGTTGAGGTATACAAACAAGTCCGAATTGGGGATCCGTTGGAGAAAGGCACCTTACTGG

upper sequence: LOC_Os09g26880.4 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM5G820733_T01 (Zea mays), 3'ss of exon 1
gtaagataggtttttcttatctgcccc--------aatggctggtgtatgagtagtctaaatgcttttgttttgttaacacagCTTCTTCACGAAAGCATATACCGAACATTTCTTGATCAACTTGTTGAGGTTTATAAACAAGTCCGAATTGGGGATCCTTTGGAGAATGGTACGTTACTGG
||| | ||  ||| | || | |  |          | ||| | || |   | | || ||| ||  |||    | |||  |||| ||||||| || |  ||||| | ||| || |||||||| ||||||||||| || ||||||||||||||||||||||| |||||||| || || |||||||
gtatggtatttttcttttgtttctcttttccgtatagtggttcgttttcaatttgtttaattgtctttcccattttattacagATTCTTCATGAGAATATATATCAAACCTTCCTTGATCAGCTTGTTGAGGTATACAAACAAGTCCGAATTGGGGATCCGTTGGAGAAAGGCACCTTACTGG
















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|33364555|gb|BP432941.1|BP432941
EST:     TTGCTGCTGTTGGAACAGCAGGACAACGCTGCACTACATGTCGTAGGCTG                         CTTCTTCACGAAAGCATATACCGAACATTTCTTGATCAACTTGTTGAGGTT
genomic: TTGCTGCTGTTGGAACAGCAGGACAACGCTGCACTACATGTCGTAGGCTGgtaagatagg ... gttaacacagCTTCTTCACGAAAGCATATACCGAACATTTCTTGATCAACTTGTTGAGGTT
EST: gi|58591281|gb|CF989589.1|CF989589
EST:     TTGCTGCTGTTGGAACAGCAGGACAACGCTGCACTACATGTCGTAGGCTG                         CTTCTTCACGAAAGCATATACCGAACATTTCTTGATCAACTTGTTGAGGTT
genomic: TTGCTGCTGTTGGAACAGCAGGACAACGCTGCACTACATGTCGTAGGCTGgtaagatagg ... gttaacacagCTTCTTCACGAAAGCATATACCGAACATTTCTTGATCAACTTGTTGAGGTT
EST: gi|29668604|gb|CB664879.1|CB664879
EST:     TTGCTGCTGTTGGAACAGCAGGACAACGCTGCACTACATGTCGTAGGCTG                         CTTCTTCACGAAAGCATATACCGAACATTTCTTGATCAACTTGTTGAGGTT
genomic: TTGCTGCTGTTGGAACAGCAGGACAACGCTGCACTACATGTCGTAGGCTGgtaagatagg ... gttaacacagCTTCTTCACGAAAGCATATACCGAACATTTCTTGATCAACTTGTTGAGGTT
EST: gi|58695697|gb|CK084384.1|CK084384
EST:     TTGCTGCTGTTGGAACAGCAGGACAACGCTGCACTACATGTCGTAGGCTG                         CTTCTTCACGAAAGCATATACCGAACATTTCTTGATCAACTTGTTGAGGTT
genomic: TTGCTGCTGTTGGAACAGCAGGACAACGCTGCACTACATGTCGTAGGCTGgtaagatagg ... gttaacacagCTTCTTCACGAAAGCATATACCGAACATTTCTTGATCAACTTGTTGAGGTT
EST: gi|59930115|gb|AB178657.1|AB178657
EST:     TTGCTGCTGTTGGAACAGCAGGACAACGCTGCACTACATGTCGTAGGCTG                         CTTCTTCACGAAAGCATATACCGAACATTTCTTGATCAACTTGTTGAGGTT
genomic: TTGCTGCTGTTGGAACAGCAGGACAACGCTGCACTACATGTCGTAGGCTGgtaagatagg ... gttaacacagCTTCTTCACGAAAGCATATACCGAACATTTCTTGATCAACTTGTTGAGGTT
EST: gi|29663938|gb|CB660213.1|CB660213
EST:     TTGCTGCTGTTGGAACAGCAGGACAACGCTGCACTACATGTCGTAGGCTG                         CTTCTTCACGAAAGCATATACCGAACATTTCTTGATCAACTTGTTGAGGTT
genomic: TTGCTGCTGTTGGAACAGCAGGACAACGCTGCACTACATGTCGTAGGCTGgtaagatagg ... gttaacacagCTTCTTCACGAAAGCATATACCGAACATTTCTTGATCAACTTGTTGAGGTT
EST: gi|88571108|gb|CI662481.1|CI662481
EST:     TTGCTGCTGTTGGAACAGCAGGACAACGCTGCACTACATGTCGTAGGCTG                         CTTCTTCACGAAAGCGTATACCGAACATTTCTTGATCAACTTGTTGAGGTT
genomic: TTGCTGCTGTTGGAACAGCAGGACAACGCTGCACTACATGTCGTAGGCTGgtaagatagg ... gttaacacagCTTCTTCACGAAAGCATATACCGAACATTTCTTGATCAACTTGTTGAGGTT
EST: gi|29673829|gb|CB670104.1|CB670104
EST:     TTGCTGCTGTTGGAACAGCAGGACAACGCTGCACTACATGTCGTAAGCTG                         CTTCTTCACGAGAGCATATACCGAACATTTCTTGATCAACTTGTTGAGGTT
genomic: TTGCTGCTGTTGGAACAGCAGGACAACGCTGCACTACATGTCGTAGGCTGgtaagatagg ... gttaacacagCTTCTTCACGAAAGCATATACCGAACATTTCTTGATCAACTTGTTGAGGTT
EST: gi|29663977|gb|CB660252.1|CB660252
EST:     TTGCTGCTGTTGGAACAGCAGGACAACGCTGCACTACATGTCGTATGCTG                         CTTCTTCACGAAAGCATATACCGAACATTTCTTGATCAACTTGTTGAGGTT
genomic: TTGCTGCTGTTGGAACAGCAGGACAACGCTGCACTACATGTCGTAGGCTGgtaagatagg ... gttaacacagCTTCTTCACGAAAGCATATACCGAACATTTCTTGATCAACTTGTTGAGGTT
EST: gi|29668613|gb|CB664888.1|CB664888
EST:     TTGCTGCTGTTGGAACAGCAGGACAACGCTGCACTACATGTCGTAGGCTG                         CTTCTTCACGAAAGCATATACCGAACATTTCTTGATCAACTTGTTGAGGTT
genomic: TTGCTGCTGTTGGAACAGCAGGACAACGCTGCACTACATGTCGTAGGCTGgtaagatagg ... gttaacacagCTTCTTCACGAAAGCATATACCGAACATTTCTTGATCAACTTGTTGAGGTT
EST: gi|66920685|gb|CX107533.1|CX107533
EST:     TTGCTGCTGTTGGAACAGCAGGACAACGCTGCACTACATGTCGTAGGCTG                         CTTCTTCACGAAAGCATATACCGAACATTTCTTGATCAACTTGTTGAGGTT
genomic: TTGCTGCTGTTGGAACAGCAGGACAACGCTGCACTACATGTCGTAGGCTGgtaagatagg ... gttaacacagCTTCTTCACGAAAGCATATACCGAACATTTCTTGATCAACTTGTTGAGGTT
EST: gi|59930145|gb|AB178687.1|AB178687
EST:     TTGCTGCTGTTGGAACAGCAGGACAACGCTGCACTGCATGTCGTAGGCTG                         CTTCTTCACGAAAGCATATACCGAACATTTCTTGATCAACTTGTTGAGGTT
genomic: TTGCTGCTGTTGGAACAGCAGGACAACGCTGCACTACATGTCGTAGGCTGgtaagatagg ... gttaacacagCTTCTTCACGAAAGCATATACCGAACATTTCTTGATCAACTTGTTGAGGTT
EST: gi|29668647|gb|CB664922.1|CB664922
EST:     TTGCTGCTGTTGGAACAGCAGGACAACGCTGCACTACATGTCGTAGGCTG                         CTTCTTCACGAAAGCATATACCGAACATTTCTTGATCAACTTGTTGAGGTT
genomic: TTGCTGCTGTTGGAACAGCAGGACAACGCTGCACTACATGTCGTAGGCTGgtaagatagg ... gttaacacagCTTCTTCACGAAAGCATATACCGAACATTTCTTGATCAACTTGTTGAGGTT
EST: gi|58592388|gb|CF990696.1|CF990696
EST:     TTGCTGCTGTTGGAACAGCAGGACAACGCTGCACTACATGTCGTAGGCTG                         CTTCTTCACGGGAGCATATACCGAACATTTCTTGATCAACTTGTTGAGGTT
genomic: TTGCTGCTGTTGGAACAGCAGGACAACGCTGCACTACATGTCGTAGGCTGgtaagatagg ... gttaacacagCTTCTTCACGAAAGCATATACCGAACATTTCTTGATCAACTTGTTGAGGTT
EST: gi|29668563|gb|CB664838.1|CB664838
EST:     TTGCTGCTGTTGGAACAGCAGGACAACGCTGCACTACATGTCGTAGGCTG                         CTTCTTCACGAAAGCATATACCGAACATTTCTTGATCAACTTGTTGAGGTT
genomic: TTGCTGCTGTTGGAACAGCAGGACAACGCTGCACTACATGTCGTAGGCTGgtaagatagg ... gttaacacagCTTCTTCACGAAAGCATATACCGAACATTTCTTGATCAACTTGTTGAGGTT
EST: gi|29633228|gb|CB638237.1|CB638237
EST:     TTGCTGCTGTTGGAACAGCAGGACAACGCTGCACTACATGTCGTAGGCTG                         CTTCTTCACGAAAGCATATACCGAACATTTCTTGATCAACTTGTTGAGGTT
genomic: TTGCTGCTGTTGGAACAGCAGGACAACGCTGCACTACATGTCGTAGGCTGgtaagatagg ... gttaacacagCTTCTTCACGAAAGCATATACCGAACATTTCTTGATCAACTTGTTGAGGTT
EST: gi|88307624|gb|CI644660.1|CI644660
EST:     TTGCTGCTGTTGGAACAGCAGGACAACGCTGCACTACATGTCGTAGGCTG                         CTTCTTCACGAAAGCGTATACCGAACATTTCTTGATCAACTTGTTGAGGTT
genomic: TTGCTGCTGTTGGAACAGCAGGACAACGCTGCACTACATGTCGTAGGCTGgtaagatagg ... gttaacacagCTTCTTCACGAAAGCATATACCGAACATTTCTTGATCAACTTGTTGAGGTT
EST: gi|59930143|gb|AB178685.1|AB178685
EST:     TTGCTGCTGTTGGAACAGCAGGACAACGCTGCACTACATGTCGTAGGCTG                         CTTCTTCACGAAAGCATATACCGAACATTTCTTGATCAACTTGTTGAGGTT
genomic: TTGCTGCTGTTGGAACAGCAGGACAACGCTGCACTACATGTCGTAGGCTGgtaagatagg ... gttaacacagCTTCTTCACGAAAGCATATACCGAACATTTCTTGATCAACTTGTTGAGGTT
EST: gi|58604471|gb|CK014999.1|CK014999
EST:     TTGCTGCTGTTGGAACAGCAGGACAACGCTGCACTACATGTCGTAGGCTG                         CTTCTTCACGAAAGCATATACCGAACATTTCTTGATCAACTTGTTGAGGTT
genomic: TTGCTGCTGTTGGAACAGCAGGACAACGCTGCACTACATGTCGTAGGCTGgtaagatagg ... gttaacacagCTTCTTCACGAAAGCATATACCGAACATTTCTTGATCAACTTGTTGAGGTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctgccccaatggctggtgtatgagtagtctaaatgcttttgttttgttaacacagCTTCTTCACGAAAGCATATACCGAACATTTCTTGATCAACTTGTTGAGGTTTATAAACAAGTCCGAATTGGGGATCCTTTGGAGAATGGTACGTTACTGG
                                            tgttaac  putative branch site (score: 2)
                                         ttttgtt  CT-rich tract
                                    ttttgttttgttaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagataggtttttcttatctgccccaatggctggtgtatgagtagtctaaatgcttttgttttgttaacacagCTTCTTCACGAAAGCATATACCGAACATTTCTTGATCAACTTGTTGAGGTTTATAAACAAGTCCGAATTGGGGATCCTTTGGAGAATGGTACGTTACTGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA