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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtataacctcttcatcccatgtcccatgtgtattgaacttcacgggtcgatcaataatagaaacaaataattaaattattatgttgctctatttattatggcagACAGATAATATTCTTGCACCTATGATCACCCACGGCATATACTCTACCGTTGTGCTTTGCCATGGGTTGTGGAAAATACACGACCACAGGAGAAGGCTAC

Basic information

species Oryza sativa
transcript LOC_Os03g01014.1
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g01014.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G005859_T02 (Zea mays), 3'ss of exon 8
--------gtataacctcttcatcccatgtcccatgt-gtattgaacttcacgggtcgatcaataatagaaacaaataattaaattattatgttgctctatttattatggcagACAGATAATATTCTTGCACCTATGATCACCCACGGCATATACTCTACCGTTGTGCTTTGCCATGGGTTGTGGAAAATACACGACCACAGGAGAAGGCTAC
         |||| |   | || ||||||    || |   ||| || ||||  |   | |  |||    |  ||   ||  || | |  ||||   |||   |    |||||||| || ||||| || ||||||||||||||||||||||||||||| |||||||| ||| |||||||| | ||||| || ||||||||| ||||||||||||
gtacgcatatatagcaggtccagcccatgcatgatatcagatttaagttcatcgtcaggtgtatatataattcatgcaacaaattgacaatgtatatctgcgtg---tggcagACCGACAATATCCTGGCACCTATGATCACCCACGGCATATACTCCACCGTTGTTCTTGGCCATGGGCTCTGGAAGATCCACGACCACCGGAGAAGGCTAC
















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|86889444|gb|CI317244.1|CI317244
EST:     CTCTTCTTGAAGGAATCTTGGCTTTCTACCTTGGCTTTGAGTGGATCCAG                         ACAGATAATATTCTTGCACCTATGATCACCCACGGCATATACTCTACCGTT
genomic: CTCTTCTTGAAGGAATCTTGGCTTTCTACCTTGGCTTTGAGTGGATCCAGgtataacctc ... attatggcagACAGATAATATTCTTGCACCTATGATCACCCACGGCATATACTCTACCGTT
EST: gi|86840112|gb|CI332743.1|CI332743
EST:     TCTTCTTGAAGGAATCTTGGCTTTCTACCTTGGCTTTGAGTGGATCCAG                         ACAGATAATATTCTTGCACCTATGATCACCCACGGCATATACTCTACCGTT
genomic: TCTTCTTGAAGGAATCTTGGCTTTCTACCTTGGCTTTGAGTGGATCCAGgtataacctc ... attatggcagACAGATAATATTCTTGCACCTATGATCACCCACGGCATATACTCTACCGTT
EST: gi|86502916|gb|CI145549.1|CI145549
EST:     CTCTTCTTGAAGGAATCTTGGCTTTCTACCTTGGCTTTGAGTGGATCCAG                         ACAGATAATATTCTTGCACCTATGATCACCCACGGCATATACTCTACCGTT
genomic: CTCTTCTTGAAGGAATCTTGGCTTTCTACCTTGGCTTTGAGTGGATCCAGgtataacctc ... attatggcagACAGATAATATTCTTGCACCTATGATCACCCACGGCATATACTCTACCGTT
EST: gi|88538054|gb|CI467050.1|CI467050
EST:     TTCTACCTTGGCTTTGAGTGGATCCAG                         ACAGATAATATTCTTGCACCTATGATCACCCACGGCATATACTCTACCNTT
genomic: TTCTACCTTGGCTTTGAGTGGATCCAGgtataacctc ... attatggcagACAGATAATATTCTTGCACCTATGATCACCCACGGCATATACTCTACCGTT
EST: gi|88480386|gb|CI417657.1|CI417657
EST:     AATCTTGGCTTTCTACCTTGGGCTTTGAGTGGATCCAG                         ACANATAATATTCTTGCACCTATGATCACCCACGGCATATACTCTACCGTT
genomic: AATCTTGGCTTTCTACCTT-GGCTTTGAGTGGATCCAGgtataacctc ... attatggcagACAGATAATATTCTTGCACCTATGATCACCCACGGCATATACTCTACCGTT
EST: gi|86834968|gb|CI346052.1|CI346052
EST:     CTCTTCTTGAAGGAATCTTGGCTTTCTACCTTGGCTTTGAGTGGATCCAG                         ACAGATAATATTCTTGCACCTATGATCACCCACGGCATATACTCTACCGTT
genomic: CTCTTCTTGAAGGAATCTTGGCTTTCTACCTTGGCTTTGAGTGGATCCAGgtataacctc ... attatggcagACAGATAATATTCTTGCACCTATGATCACCCACGGCATATACTCTACCGTT
EST: gi|88540705|gb|CI468771.1|CI468771
EST:     TTTCTACCTTGGGCTTTGAGTGGATCCAG                         ACAGATAATATTCTTGCACCTATGATCACCCACGGCATATACTCTACCGTT
genomic: TTTCTACCTT-GGCTTTGAGTGGATCCAGgtataacctc ... attatggcagACAGATAATATTCTTGCACCTATGATCACCCACGGCATATACTCTACCGTT
EST: gi|88504888|gb|CI432394.1|CI432394
EST:     CTCTTCTTGAAGGAATCTTGGCTTTCTACCTTGGCTTTGAGTGGATCCAG                         ACAGATAATATTCTTGCACCTATGATCACCCACGGCATATACTCTACCGTT
genomic: CTCTTCTTGAAGGAATCTTGGCTTTCTACCTTGGCTTTGAGTGGATCCAGgtataacctc ... attatggcagACAGATAATATTCTTGCACCTATGATCACCCACGGCATATACTCTACCGTT
EST: gi|88284834|gb|CI406280.1|CI406280
EST:     TTTGAGTGGATCCAG                         ACAGATAATATTCTTGCACCTATGATCACCCACGGCATATACTCTACCGTT
genomic: TTTGAGTGGATCCAGgtataacctc ... attatggcagACAGATAATATTCTTGCACCTATGATCACCCACGGCATATACTCTACCGTT
EST: gi|87015730|gb|CI277688.1|CI277688
EST:     CTCTTCTTGAAGGAATCTTGGCTTTCTACCTTGGCTTTGAGTGGATCCAG                         ACAGATAATATTCTTGCACCTATGATCACCCACGGCATATACTCTACCGTT
genomic: CTCTTCTTGAAGGAATCTTGGCTTTCTACCTTGGCTTTGAGTGGATCCAGgtataacctc ... attatggcagACAGATAATATTCTTGCACCTATGATCACCCACGGCATATACTCTACCGTT
EST: gi|88261574|gb|CI365150.1|CI365150
EST:     TCTTCTTGAAGGAATCTTCGCTTTCTACCTTGGCTTTGAGTGGATCCAG                         ACAGATAATATTCTTGCACCTATGATCACCCACGGCATATACTCTACCGTT
genomic: TCTTCTTGAAGGAATCTTGGCTTTCTACCTTGGCTTTGAGTGGATCCAGgtataacctc ... attatggcagACAGATAATATTCTTGCACCTATGATCACCCACGGCATATACTCTACCGTT
EST: gi|66931443|gb|CX118291.1|CX118291
EST:     CTCTTCTTGAAGGAATCTTGGCTTTCTACCTTGGCTTTGAGTGGATCCAG                         ACAGATAATATTCTTGCACCTATGATCACCCACGGCATATACTCTACCGTT
genomic: CTCTTCTTGAAGGAATCTTGGCTTTCTACCTTGGCTTTGAGTGGATCCAGgtataacctc ... attatggcagACAGATAATATTCTTGCACCTATGATCACCCACGGCATATACTCTACCGTT
EST: gi|86501807|gb|CI144440.1|CI144440
EST:     CTCTTCTTGAAGGAATCTTGGCTTTCTACCTTGGCTTTGAGTGGATCCAG                         ACAGATAATATTCTTGCACCTATGATCACCCACGGCATATACTCTACCGTT
genomic: CTCTTCTTGAAGGAATCTTGGCTTTCTACCTTGGCTTTGAGTGGATCCAGgtataacctc ... attatggcagACAGATAATATTCTTGCACCTATGATCACCCACGGCATATACTCTACCGTT
EST: gi|38477321|gb|CF961454.1|CF961454
EST:     GCTTTGAGTGGATCCAG                         ACAGATAATATTCTTGCACCTATGATCACCCACGGCATATACTCTACCGTT
genomic: GCTTTGAGTGGATCCAGgtataacctc ... attatggcagACAGATAATATTCTTGCACCTATGATCACCCACGGCATATACTCTACCGTT
EST: gi|58693667|gb|CK082354.1|CK082354
EST:     CTCTTCTTGAAGGAATCTTGGCTTTCTACCTTGGCTTTGAGTGGATCCAG                         ACAGATAATATTCTTGCACCTATGATCACCCACGGCATATACTCTACCGTT
genomic: CTCTTCTTGAAGGAATCTTGGCTTTCTACCTTGGCTTTGAGTGGATCCAGgtataacctc ... attatggcagACAGATAATATTCTTGCACCTATGATCACCCACGGCATATACTCTACCGTT
EST: gi|88522964|gb|CI450762.1|CI450762
EST:     TGAAGGAATCTTGGCTTTCTACCTTGGCTTTGAGTGGATCCAG                         ACAGATAATATTCTTGCACCTATGATCACCCACGGCATATACTCTACCGTT
genomic: TGAAGGAATCTTGGCTTTCTACCTTGGCTTTGAGTGGATCCAGgtataacctc ... attatggcagACAGATAATATTCTTGCACCTATGATCACCCACGGCATATACTCTACCGTT
EST: gi|33679461|gb|CF307700.1|CF307700
EST:     CTTTGAGTGGATCCAG                         ACAGATAATATTCTTGCACCTATGATCACCCACGGCATATACTCTACCGTT
genomic: CTTTGAGTGGATCCAGgtataacctc ... attatggcagACAGATAATATTCTTGCACCTATGATCACCCACGGCATATACTCTACCGTT
EST: gi|29615143|gb|CB620156.1|CB620156
EST:     CTCTTCTTGAAGGAATCTTGGCTTTCTACCTTGGCTTTGAGTGGATCCAG                         ACAGATAATATTCTTGCACCTATGATCACCCACGGCATATACTCTACCGTT
genomic: CTCTTCTTGAAGGAATCTTGGCTTTCTACCTTGGCTTTGAGTGGATCCAGgtataacctc ... attatggcagACAGATAATATTCTTGCACCTATGATCACCCACGGCATATACTCTACCGTT
EST: gi|29684278|gb|CB680553.1|CB680553
EST:     CTCTTCTTGAAGGAATCTTGGCTTTCTACCTTGGCTTTGAGTGGATCCAG                         ACAGATAATATTCTTGCACCTATGATCACCCACGGCATATACTCTACCGTT
genomic: CTCTTCTTGAAGGAATCTTGGCTTTCTACCTTGGCTTTGAGTGGATCCAGgtataacctc ... attatggcagACAGATAATATTCTTGCACCTATGATCACCCACGGCATATACTCTACCGTT
EST: gi|88542145|gb|CI471454.1|CI471454
EST:     TTGGCTTTGAGTGGATCCAG                         ACAGATAATATTCTTGCACCTATGATCACCCACGGCATATACTCTACCGTT
genomic: TTGGCTTTGAGTGGATCCAGgtataacctc ... attatggcagACAGATAATATTCTTGCACCTATGATCACCCACGGCATATACTCTACCGTT
EST: gi|86870634|gb|CI323510.1|CI323510
EST:     CTCTTCTTGAA-GAATCTTGCCTTTCTACCTTGGCTTTGAGTGGATCCAG                         ACAGATAATATTCTTGCACCTATGATCACCCAC-GCATATACTCTACCATT
genomic: CTCTTCTTGAAGGAATCTTGGCTTTCTACCTTGGCTTTGAGTGGATCCAGgtataacctc ... attatggcagACAGATAATATTCTTGCACCTATGATCACCCACGGCATATACTCTACCGTT
EST: gi|29642142|gb|CB647149.1|CB647149
EST:     CTCTTCTTGAAGGAATCTTGGCTTTCTACCTTGGCTTTGAGTGGATCCAG                         ACAGATAATATTCTTGCACCTATGATCACCCACGGCATATACTCTACCGTT
genomic: CTCTTCTTGAAGGAATCTTGGCTTTCTACCTTGGCTTTGAGTGGATCCAGgtataacctc ... attatggcagACAGATAATATTCTTGCACCTATGATCACCCACGGCATATACTCTACCGTT
EST: gi|88958690|gb|CI096205.1|CI096205
EST:     CTCTTCTTGAAGGAATCTTGGCTTTCTACCTTGGCTTTGAGTGGATCCAG                         ACAGATAATATTCTTGCACCTATGATCACCCACGGCATATACTCTACCGTT
genomic: CTCTTCTTGAAGGAATCTTGGCTTTCTACCTTGGCTTTGAGTGGATCCAGgtataacctc ... attatggcagACAGATAATATTCTTGCACCTATGATCACCCACGGCATATACTCTACCGTT
EST: gi|29685648|gb|CB681923.1|CB681923
EST:     CTCTTCTTGAAGGAATCTTGGCTTTCTACCTTGGCTTTGAGTGGATCCAG                         ACAGATAATATTCTTGCACCTATGATCACCCACGGCATATACTCTACCGTT
genomic: CTCTTCTTGAAGGAATCTTGGCTTTCTACCTTGGCTTTGAGTGGATCCAGgtataacctc ... attatggcagACAGATAATATTCTTGCACCTATGATCACCCACGGCATATACTCTACCGTT
EST: gi|88381478|gb|CI528458.1|CI528458
EST:     TTGGCTTTGAGTGGATCCAG                         ACAGATAATATTCTTGCACCTATGATCACCCACGGCATATACTCTACCGTT
genomic: TTGGCTTTGAGTGGATCCAGgtataacctc ... attatggcagACAGATAATATTCTTGCACCTATGATCACCCACGGCATATACTCTACCGTT
EST: gi|29684277|gb|CB680552.1|CB680552
EST:     CTCTTCTTGAAGGAATCTTGGCTTTCTACCTTGGCTTTGAGTGGATCCAG                         ACAGATAATATTCTTGCACCTATGATCACCCACGGCATATACTCTACCGTT
genomic: CTCTTCTTGAAGGAATCTTGGCTTTCTACCTTGGCTTTGAGTGGATCCAGgtataacctc ... attatggcagACAGATAATATTCTTGCACCTATGATCACCCACGGCATATACTCTACCGTT
EST: gi|88276793|gb|CI395956.1|CI395956
EST:     ATCTTGGCTTTCTACCTTGGCTTTGAGTGGATCCAG                         ACAGATAATATTCTTGCACCTATGATCACCCACGGCATATACTCTACCGTT
genomic: ATCTTGGCTTTCTACCTTGGCTTTGAGTGGATCCAGgtataacctc ... attatggcagACAGATAATATTCTTGCACCTATGATCACCCACGGCATATACTCTACCGTT
EST: gi|88502577|gb|CI430083.1|CI430083
EST:     TGAGTGGATCCAG                         ACAGATAATATTCTTGCACCTATGATCACCCACGGCATATACTCTACCGTT
genomic: TGAGTGGATCCAGgtataacctc ... attatggcagACAGATAATATTCTTGCACCTATGATCACCCACGGCATATACTCTACCGTT
EST: gi|87009421|gb|CI313894.1|CI313894
EST:     CTCTTCTTGAAGG-ATCTTGGCTTTCTACCTTGGCTTTGAGT-GATCCAG                         ACAGATAATATTCTTGCACCTATGATCACCCACGGCATATACTCTACCGTT
genomic: CTCTTCTTGAAGGAATCTTGGCTTTCTACCTTGGCTTTGAGTGGATCCAGgtataacctc ... attatggcagACAGATAATATTCTTGCACCTATGATCACCCACGGCATATACTCTACCGTT
EST: gi|13420794|gb|AU174884.1|AU174884
EST:     TTGGCTTTCTACCTTGGCTTTGAGTGGATCCAG                         ACAGATAATATTCTTGCACCTATGATCACCCACGGCATATACTCTACCGTT
genomic: TTGGCTTTCTACCTTGGCTTTGAGTGGATCCAGgtataacctc ... attatggcagACAGATAATATTCTTGCACCTATGATCACCCACGGCATATACTCTACCGTT
EST: gi|88542949|gb|CI472309.1|CI472309
EST:     GGAATCTTGGCTTTCTACCTTGGCTTTGAGTGGATCCAG                         ACAGATAATATTCTTGCACCTATGATCACCCACGGCATATACTCTACCGTT
genomic: GGAATCTTGGCTTTCTACCTTGGCTTTGAGTGGATCCAGgtataacctc ... attatggcagACAGATAATATTCTTGCACCTATGATCACCCACGGCATATACTCTACCGTT
EST: gi|88484274|gb|CI421545.1|CI421545
EST:     GAAGGAATCTTGGCTTTCTACCTTGGCTTTGAGTGGATCCAG                         ACAGATAATATTCTTGCACCTATGATCACCCACGGCATATACTCTACCGTT
genomic: GAAGGAATCTTGGCTTTCTACCTTGGCTTTGAGTGGATCCAGgtataacctc ... attatggcagACAGATAATATTCTTGCACCTATGATCACCCACGGCATATACTCTACCGTT
EST: gi|88977251|gb|CI024988.1|CI024988
EST:     CTCTTCTTGAAGGAATCTTGGCTTTCTACCTTGGCTTTGAGTGGATCCAG                         ACAGATAATATTCTTGCACCTATGATCACCCACGGCATATACTCTACCGTT
genomic: CTCTTCTTGAAGGAATCTTGGCTTTCTACCTTGGCTTTGAGTGGATCCAGgtataacctc ... attatggcagACAGATAATATTCTTGCACCTATGATCACCCACGGCATATACTCTACCGTT
EST: gi|29669725|gb|CB666000.1|CB666000
EST:     CTCTTCTTGAAGGAATCTTGGCTTTCTACCTTGGCTTTGAGTGGATCCAG                         ACAGATAATATTCTTGCACCTATGATCACCCACGGCATATACTCTACCGTT
genomic: CTCTTCTTGAAGGAATCTTGGCTTTCTACCTTGGCTTTGAGTGGATCCAGgtataacctc ... attatggcagACAGATAATATTCTTGCACCTATGATCACCCACGGCATATACTCTACCGTT
EST: gi|29668135|gb|CB664410.1|CB664410
EST:     CTCTTCTTGAAGGAATATTGGCTTTATACCTTGGCTTTGAGTGGATCCAG                         ACAGATAATATTCTTGCACCTATGATCACCCACGGCATATACTTTACCGTT
genomic: CTCTTCTTGAAGGAATCTTGGCTTTCTACCTTGGCTTTGAGTGGATCCAGgtataacctc ... attatggcagACAGATAATATTCTTGCACCTATGATCACCCACGGCATATACTCTACCGTT
EST: gi|88523827|gb|CI451685.1|CI451685
EST:     TGGCTTTCTACCTTGGCTTTGAGTGGATCCAG                         ACAGATAATATTCTTGCACCTATGATCACCCACGGCATATACTCTACCGTT
genomic: TGGCTTTCTACCTTGGCTTTGAGTGGATCCAGgtataacctc ... attatggcagACAGATAATATTCTTGCACCTATGATCACCCACGGCATATACTCTACCGTT
EST: gi|86842186|gb|CI338515.1|CI338515
EST:     CTCTTCTTGAAGGAATCTTGGCTTTCTACCTTGGCTTTGAGTGGATCCAG                         ACAGATAATATTCTTGCACCTATGATCACCCACGGCATATACTCTACCCTT
genomic: CTCTTCTTGAAGGAATCTTGGCTTTCTACCTTGGCTTTGAGTGGATCCAGgtataacctc ... attatggcagACAGATAATATTCTTGCACCTATGATCACCCACGGCATATACTCTACCGTT
EST: gi|88522633|gb|CI449459.1|CI449459
EST:     TTGGCTTTCTACCTTGGCTTTGAGTGGATCCAG                         ACAGATAATATTCTTGCACCTATGATCACCCACGGCATATACTCTACCGTT
genomic: TTGGCTTTCTACCTTGGCTTTGAGTGGATCCAGgtataacctc ... attatggcagACAGATAATATTCTTGCACCTATGATCACCCACGGCATATACTCTACCGTT
EST: gi|88523904|gb|CI451770.1|CI451770
EST:     TCTACCTGGGCTTTGAGTGGATCCAG                         ACAGATAATATTCTTGCACCTATGATCACCCACGGCATATACTCTACCGTT
genomic: TCTACCTTGGCTTTGAGTGGATCCAGgtataacctc ... attatggcagACAGATAATATTCTTGCACCTATGATCACCCACGGCATATACTCTACCGTT

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 1 RNA-Seqlibrary.


Block sizes: 75 (upstream exon), 73 (downstream exon)
Score: 73

CATGGTATGAAAGGCGGCAAATGAGGAAGATATATTCCCCTCTTCTTGAAGGAATCTTGGCTTTCTACCTTGGCTTTGAGTGGATCCAGgtataacctc ... attatggcagACAGATAATATTCTTGCACCTATGATCACCCACGGCATATACTCTACCGTTGTGCTTTGCCATGGGTTGTGGAAAATACACGACCACAGGAGAAGGCTAC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atcaataatagaaacaaataattaaattattatgttgctctatttattatggcagACAGATAATATTCTTGCACCTATGATCACCCACGGCATATACTCTACCGTTGTGCTTTGCCATGGGTTGTGGAAAATACACGACCACAGGAGAAGGCTAC
           aaacaaataattaaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtataacctcttcatcccatgtcccatgtgtattgaacttcacgggtcgatcaataatagaaacaaataattaaattattatgttgctctatttattatggcagACAGATAATATTCTTGCACCTATGATCACCCACGGCATATACTCTACCGTTGTGCTTTGCCATGGGTTGTGGAAAATACACGACCACAGGAGAAGGCTAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA