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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatcgtatgaatttttttctggcgacatttaaattctgcatatcctcttcttcagtaaccacaaccattgttctattgcagGCTGAATTGAAGGAATCAAATGAACAAGGTGCTGAGATTGGAGAGGCTGAGAGTACAATCACAGAAGTTGAAGCTGTCGTCAAGCCAACAGAAGATTGAA

Basic information

species Oryza sativa
transcript LOC_Os02g57150.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g57150.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G143627_T02 (Zea mays), 3'ss of exon 3
gtatcgtatgaatttt---tttctggcgacatttaaattctgcat-atcctcttcttcagtaaccacaaccattgttctattgcagGCTGAATTGAAGGAATCAAATGAACAAGGTGCTGAGATTGGAGAGGCTGAGAGTACAATCACAGAAGTTGAAGCTGTCGTCAAGCCAACAGAAGATTGAA
|||| | || ||  ||   |||| |    | |  |  ||||||||  |  ||||| |      |  |||    ||     | |||||||||| ||||||| |||||||| |||||||| ||||||||||| ||||||||||||||| ||||||||||||| || ||||||||| ||||||||| ||
gtatggcataaaagttccgtttccgtttccttaaatgttctgcattgttttcttcgtggcccgcttcaatggctgcatcgtcgcagGCTGAACTGAAGGAGTCAAATGAGCAAGGTGCCGAGATTGGAGAAGCTGAGAGTACAATCGCAGAAGTTGAAGCAGTTGTCAAGCCAGCAGAAGATTAAA
















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|29687350|gb|CB683625.1|CB683625
EST:     ACTGCCATAAGCGACTTGAAACTGCACTGGCAGACTTGAAAGCAACTCTG                         GCTGAATTGAAGGAATCAAATGAACAAGGTGCTGAGATTGGAGAGGCTGAG
genomic: ACTGCCATAAGCGACTTGAAACTGCACTGGCAGACTTGAAAGCAACTCTGgtatcgtatg ... tctattgcagGCTGAATTGAAGGAATCAAATGAACAAGGTGCTGAGATTGGAGAGGCTGAG
EST: gi|38468410|gb|CF952541.1|CF952541
EST:     ACTGCCATAAGCGACTTGAAACTGCACTGGCAGACTTGAAAGCAACTCTG                         GCTGAATTGAAGGAATCAAATGAACAAGGTGCTGAGATTGGAGAGGCTGAG
genomic: ACTGCCATAAGCGACTTGAAACTGCACTGGCAGACTTGAAAGCAACTCTGgtatcgtatg ... tctattgcagGCTGAATTGAAGGAATCAAATGAACAAGGTGCTGAGATTGGAGAGGCTGAG
EST: gi|88552750|gb|CI482788.1|CI482788
EST:     ACTGCCATAAGCGACTTGAAACTGCACTGGCAGACTTGAAAGCAACTCTG                         GCTGAATTGAAGGAATCAAATGAACAAGGTGCTGAGATTGGAGAGGCTGAG
genomic: ACTGCCATAAGCGACTTGAAACTGCACTGGCAGACTTGAAAGCAACTCTGgtatcgtatg ... tctattgcagGCTGAATTGAAGGAATCAAATGAACAAGGTGCTGAGATTGGAGAGGCTGAG
EST: gi|163926431|gb|EG711893.1|EG711893
EST:     ACTGCCATAAGCGACTTGAAACTGCACTGGCAGACTTGAAAGCAACTCTG                         GCTGAATTGAAGGAATCAAATGAACAAGGTGCTGAGATTGGAGAGGCTGAG
genomic: ACTGCCATAAGCGACTTGAAACTGCACTGGCAGACTTGAAAGCAACTCTGgtatcgtatg ... tctattgcagGCTGAATTGAAGGAATCAAATGAACAAGGTGCTGAGATTGGAGAGGCTGAG
EST: gi|88554104|gb|CI484264.1|CI484264
EST:     ACTGCCATAAGCGACTTGAAACTGCACTGGCAGACTTGAAAGCAACTCTG                         GCTGAATTGAAGGAATCAAATGAACAAGGTGCTGAGATTGGAGAGGCTGAG
genomic: ACTGCCATAAGCGACTTGAAACTGCACTGGCAGACTTGAAAGCAACTCTGgtatcgtatg ... tctattgcagGCTGAATTGAAGGAATCAAATGAACAAGGTGCTGAGATTGGAGAGGCTGAG
EST: gi|88541694|gb|CI470980.1|CI470980
EST:     ACTGCCATAAGCGACTTGAAACTGCACTGGCAGACTTGAAAGCAACTCTG                         GCTGAATTGAAGGAATCAAATGAACAAGGTGCTGAGATTGGAGAGGCTGAG
genomic: ACTGCCATAAGCGACTTGAAACTGCACTGGCAGACTTGAAAGCAACTCTGgtatcgtatg ... tctattgcagGCTGAATTGAAGGAATCAAATGAACAAGGTGCTGAGATTGGAGAGGCTGAG
EST: gi|88378742|gb|CI681558.1|CI681558
EST:     ACTGCCATAAGCGACTTGAAACTGCACTGGCAGACTTGAAAGCAACTCTG                         GCTGAATTGAAGGAATCAAATGAACAAGGTGCTGAGATTGGAGAGGCTGAG
genomic: ACTGCCATAAGCGACTTGAAACTGCACTGGCAGACTTGAAAGCAACTCTGgtatcgtatg ... tctattgcagGCTGAATTGAAGGAATCAAATGAACAAGGTGCTGAGATTGGAGAGGCTGAG
EST: gi|88335167|gb|CI658174.1|CI658174
EST:     ACTGCCATAAGCGACTTGAAACTGCACTGGCAGACTTGAAAGCAACTCTG                         GCTGAATTGAAGGAATCAAATGAACAAGGTGCTGAGATTGGA
genomic: ACTGCCATAAGCGACTTGAAACTGCACTGGCAGACTTGAAAGCAACTCTGgtatcgtatg ... tctattgcagGCTGAATTGAAGGAATCAAATGAACAAGGTGCTGAGATTGGA
EST: gi|88487783|gb|CI425054.1|CI425054
EST:     ACTGCCATAAGCGACTTGAAACTGCACTGGCAGACTTGAAAGCAACTCTG                         GCTGAATTGAAGGAATCAAATGAACAAGGTGCTGAGATTGGAGAGGCTGAG
genomic: ACTGCCATAAGCGACTTGAAACTGCACTGGCAGACTTGAAAGCAACTCTGgtatcgtatg ... tctattgcagGCTGAATTGAAGGAATCAAATGAACAAGGTGCTGAGATTGGAGAGGCTGAG
EST: gi|88297278|gb|CI545368.1|CI545368
EST:     ACTGCCATAAGCGACTTGAAACTGCACTGGCAGACTTGAAAGCAACTCTG                         GCTGAATTGAAGGAATCAAATGAACAAGGTGCTGAGATTGGAGAGGCTGAG
genomic: ACTGCCATAAGCGACTTGAAACTGCACTGGCAGACTTGAAAGCAACTCTGgtatcgtatg ... tctattgcagGCTGAATTGAAGGAATCAAATGAACAAGGTGCTGAGATTGGAGAGGCTGAG
EST: gi|88444509|gb|CI557810.1|CI557810
EST:     ACTGCCATAAGCGACTTGAAACTGCACTGGCAGACTTGAAAGCAACTCTG                         GCTGAATTGAAGGAATCAAATGAACAAGGTGCTGAGATTGGAGAGGCTGAG
genomic: ACTGCCATAAGCGACTTGAAACTGCACTGGCAGACTTGAAAGCAACTCTGgtatcgtatg ... tctattgcagGCTGAATTGAAGGAATCAAATGAACAAGGTGCTGAGATTGGAGAGGCTGAG
EST: gi|88541160|gb|CI468412.1|CI468412
EST:     ACTGCCATAAGCGACTTGAAACTGCACTGGCAGACTTGAAAGCAACTCTG                         GCTGAATTGAAGGAATCAAATGAACAAGGTGCTGAGATTGGAGAGGCTGAG
genomic: ACTGCCATAAGCGACTTGAAACTGCACTGGCAGACTTGAAAGCAACTCTGgtatcgtatg ... tctattgcagGCTGAATTGAAGGAATCAAATGAACAAGGTGCTGAGATTGGAGAGGCTGAG
EST: gi|88552603|gb|CI482626.1|CI482626
EST:     ACTGCCATAAGCGACTTGAAACTGCACTGGCAGACTTGAAAGCAACTCTG                         GCTGAATTGAAGGAATCAAATGAACAAGGTGCTGAGATTGGAGAGGCTGAG
genomic: ACTGCCATAAGCGACTTGAAACTGCACTGGCAGACTTGAAAGCAACTCTGgtatcgtatg ... tctattgcagGCTGAATTGAAGGAATCAAATGAACAAGGTGCTGAGATTGGAGAGGCTGAG
EST: gi|88578844|gb|CI687799.1|CI687799
EST:     ACTGCCATAAGCGACTTGAAACTGCACTGGCAGACTTGAAAGCAACTCTG                         GCTGAATTGAAGGAATCAAATGAACAAGGTGCTGAGATTGGAGAGGCTGAG
genomic: ACTGCCATAAGCGACTTGAAACTGCACTGGCAGACTTGAAAGCAACTCTGgtatcgtatg ... tctattgcagGCTGAATTGAAGGAATCAAATGAACAAGGTGCTGAGATTGGAGAGGCTGAG
EST: gi|88329844|gb|CI651516.1|CI651516
EST:     ACTGCCATAAGCGACTTGAAACTGCACTGGCAGACTTGAAAGCAACTCTG                         GCTGAATTGAAGGAATCAAATGAACAAGGTGCTGAGATTGGAG
genomic: ACTGCCATAAGCGACTTGAAACTGCACTGGCAGACTTGAAAGCAACTCTGgtatcgtatg ... tctattgcagGCTGAATTGAAGGAATCAAATGAACAAGGTGCTGAGATTGGAG
EST: gi|117237837|gb|CT861936.1|CT861936
EST:     ACTGCCATAAGCGACTTGAAACTGCACTGGCAGACTTGAAAGCAACTCTG                         GCTGAATTGAAGGAATCAAATGAACAAGGTGCTGAGATTGGAGAGGCTGAG
genomic: ACTGCCATAAGCGACTTGAAACTGCACTGGCAGACTTGAAAGCAACTCTGgtatcgtatg ... tctattgcagGCTGAATTGAAGGAATCAAATGAACAAGGTGCTGAGATTGGAGAGGCTGAG
EST: gi|88505968|gb|CI433474.1|CI433474
EST:     ACTGCCATAAGCGACTTGAAACTGCACTGGCAGACTTGAAAGCAACTCTG                         GCTGAATTGAAGGAATCAAATGAACAAGGTGCTGAGATTGGAGAGGCTGAG
genomic: ACTGCCATAAGCGACTTGAAACTGCACTGGCAGACTTGAAAGCAACTCTGgtatcgtatg ... tctattgcagGCTGAATTGAAGGAATCAAATGAACAAGGTGCTGAGATTGGAGAGGCTGAG
EST: gi|88579760|gb|CI691745.1|CI691745
EST:     ACTGCCATAAGCGACTTGAAACTGCACTGGCAGACTTGAAAGCAACTCTG                         GCTGAATTGAAGGAATCAAATGAACAAGGTGCTGAGAT
genomic: ACTGCCATAAGCGACTTGAAACTGCACTGGCAGACTTGAAAGCAACTCTGgtatcgtatg ... tctattgcagGCTGAATTGAAGGAATCAAATGAACAAGGTGCTGAGAT
EST: gi|95101340|gb|CI693086.1|CI693086
EST:     ACTGCCATAAGCGACTTGAAACTGCACTGGCAGACTTGAAAGCAACTCTG                         GCTGAATTGAAGGAATCAAATGAACAAGGTGCTGAG
genomic: ACTGCCATAAGCGACTTGAAACTGCACTGGCAGACTTGAAAGCAACTCTGgtatcgtatg ... tctattgcagGCTGAATTGAAGGAATCAAATGAACAAGGTGCTGAG
EST: gi|88554291|gb|CI484460.1|CI484460
EST:     ACTGCCATAAGCGACTTGAAACTGCACTGGCAGACTTGAAAGCAACTCTG                         GCTGAATTGAAGGAATCAAATGAACAAGGTGCTGAGATTGGAGAGGCTGAG
genomic: ACTGCCATAAGCGACTTGAAACTGCACTGGCAGACTTGAAAGCAACTCTGgtatcgtatg ... tctattgcagGCTGAATTGAAGGAATCAAATGAACAAGGTGCTGAGATTGGAGAGGCTGAG
EST: gi|38475684|gb|CF959817.1|CF959817
EST:     ACTGCCATAAGCGACTTGAAACTGCACTGGCAGACTTGAAAGCAACTCTG                         GCTGAATTGAAGGAATCAAATGAACAAGGTGCTGAGATTGGAGAGGCTGAG
genomic: ACTGCCATAAGCGACTTGAAACTGCACTGGCAGACTTGAAAGCAACTCTGgtatcgtatg ... tctattgcagGCTGAATTGAAGGAATCAAATGAACAAGGTGCTGAGATTGGAGAGGCTGAG
EST: gi|88544850|gb|CI472375.1|CI472375
EST:     ACTGCCATAAGCGACTTGAAACTGCACTGGCAGACTTGAAAGCAACTCTG                         GCTGAATTGAAGGAATCAAATGAACAAGGTGCTGAGATTGGAGAGGCTGAG
genomic: ACTGCCATAAGCGACTTGAAACTGCACTGGCAGACTTGAAAGCAACTCTGgtatcgtatg ... tctattgcagGCTGAATTGAAGGAATCAAATGAACAAGGTGCTGAGATTGGAGAGGCTGAG
EST: gi|88528705|gb|CI456962.1|CI456962
EST:     ACTGCCATAAGCGACTTGAAACTGCACTGCCAGACTTGAAAGCAACTCTG                         GCTGAATTGAAGGAATCAAATGAACAAGGTGCTGAGATTGGAGAGGCTGAG
genomic: ACTGCCATAAGCGACTTGAAACTGCACTGGCAGACTTGAAAGCAACTCTGgtatcgtatg ... tctattgcagGCTGAATTGAAGGAATCAAATGAACAAGGTGCTGAGATTGGAGAGGCTGAG
EST: gi|88531318|gb|CI459787.1|CI459787
EST:     ACTGCCATAAGCGACTTGAAACTGCACTGGCAGACTTGAAAGCAACTCTG                         GCTGAATTGAAGGAATCAAATGAACAAGGTGCTGAGATTGGAGAGGCTGAG
genomic: ACTGCCATAAGCGACTTGAAACTGCACTGGCAGACTTGAAAGCAACTCTGgtatcgtatg ... tctattgcagGCTGAATTGAAGGAATCAAATGAACAAGGTGCTGAGATTGGAGAGGCTGAG
EST: gi|88365970|gb|CI548217.1|CI548217
EST:     ACTGCCATAAGCGACTTGAAACTGCACTGGCAGACTTGAAAGCAACTCTG                         GCTGAATTGAAGGAATCAAATGAACAAGGTGCTGAGATTGGAGAGGCTGAG
genomic: ACTGCCATAAGCGACTTGAAACTGCACTGGCAGACTTGAAAGCAACTCTGgtatcgtatg ... tctattgcagGCTGAATTGAAGGAATCAAATGAACAAGGTGCTGAGATTGGAGAGGCTGAG
EST: gi|88266009|gb|CI376911.1|CI376911
EST:     ACTGCCATAAGCGACTTGAAACTGCACTGGCAGACTTGAAAGCAACTCTG                         GCTGAATTGAAGGAATCAAATGAACAAGGTGCTGAGATTGGAGAGGCTGAG
genomic: ACTGCCATAAGCGACTTGAAACTGCACTGGCAGACTTGAAAGCAACTCTGgtatcgtatg ... tctattgcagGCTGAATTGAAGGAATCAAATGAACAAGGTGCTGAGATTGGAGAGGCTGAG
EST: gi|88587701|gb|CI704413.1|CI704413
EST:     ACTGCCATAAGCGACTTGAAACTGCACTGGCAGACTTGAAAGCAACTCTG                         GCTGAATTGAAGGAAT
genomic: ACTGCCATAAGCGACTTGAAACTGCACTGGCAGACTTGAAAGCAACTCTGgtatcgtatg ... tctattgcagGCTGAATTGAAGGAAT

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: 74 (upstream exon), 72 (downstream exon)
Score: 40

GAGAATGTTTTAGCCGAGTCAAGGATGATGGTCCCAGACTGCCATAAGCGACTTGAAACTGCACTGGCAGACTTGAAAGCAACTCTGgtatcgtatg ... tctattgcagGCTGAATTGAAGGAATCAAATGAACAAGGTGCTGAGATTGGAGAGGCTGAGAGTACAATCACAGAAGTTGAAGCTGTCGTCAAGCCAACAGAAGATTGAA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atttaaattctgcatatcctcttcttcagtaaccacaaccattgttctattgcagGCTGAATTGAAGGAATCAAATGAACAAGGTGCTGAGATTGGAGAGGCTGAGAGTACAATCACAGAAGTTGAAGCTGTCGTCAAGCCAACAGAAGATTGAA
                          cagtaac  putative branch site (score: 40)
                                         ttgttct  putative PPT
                                            ttctatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatcgtatgaatttttttctggcgacatttaaattctgcatatcctcttcttcagtaaccacaaccattgttctattgcagGCTGAATTGAAGGAATCAAATGAACAAGGTGCTGAGATTGGAGAGGCTGAGAGTACAATCACAGAAGTTGAAGCTGTCGTCAAGCCAACAGAAGATTGAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG