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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtcataaccatctgacatacctgtgctaattatgatgttgcatataatacagatttactgacaataaataagatttaattgtggtcttatctcctttcagGTTCATGCAGATAACCCTGATGGGCTATTTAGAATTCTCTCATCAACCTTCCGCATCGAGGCTACCATAAGAGGGATGCAGAATTGAGGTGCAGAAGCCC

Basic information

species Oryza sativa
transcript LOC_Os01g66240.1
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g66240.1 (Oryza sativa), 3'ss of exon 12
lower sequence: GRMZM2G007160_T02 (Zea mays), 3'ss of exon 12
gtcataaccatctgacatacctgtgctaattatgatgttgcatataatacagatttactgacaataaataagatttaattgtggtcttatctcctttcagGTTCATGCAGATAACCCTGATGGGCTATTTAGAATTCTCTCATCAACCTTCCGCATCGAGGCTACCATAAGAGGGATGCAGAATTGAGGTGCAGAAGCCC
          | || |  ||| |   |  || |  | ||   || |||| ||     |||  ||  || || |||| ||| |   | | | ||||| |||||||||||||| ||||| || || || ||||||||||| || |||||||| || |||||  |||| |||||||| |||||| | |||||  || |     
------gtattttggc--acccgccttttttttctttttttttacaataaag-----ctgcaaaccaa-aatatttgattatttgcatgtttccttccagGTTCATGCAGACAACCCAGACGGTCTCTTTAGAATTCTTTCGTCAACCTTTCGAATCGAAACTACTATAAGAGGAATGCAGGACTGAGGATCAAACCTTT
















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|88847776|gb|CI018467.1|CI018467
EST:     ATGAGGCTGGAGGAGTTGAAATGCACGTGCTTGAAGATGCTGGACATTGG                         GTTCATGCAGGATAACCCTGATGGGCTATTTAGAATTCTCTCATCAACCTT
genomic: ATGAGGGTGGAGGAGTTGAAATGCACGTGCTTGAAGATGCTGGACATTGGgtatgcttac ... ctcctttcagGTTCATGCA-GATAACCCTGATGGGCTATTTAGAATTCTCTCATCAACCTT
EST: gi|86828316|gb|CI276890.1|CI276890
EST:     ATGAGGGTGGAGGAGTTGAAATGCACGTGCTTGAAGATGCTGGACATTGG                         GTTCATGCAGATAACCCTGATGGGCTATTTAGAATTCTCTCATCAACCTTC
genomic: ATGAGGGTGGAGGAGTTGAAATGCACGTGCTTGAAGATGCTGGACATTGGgtatgcttac ... ctcctttcagGTTCATGCAGATAACCCTGATGGGCTATTTAGAATTCTCTCATCAACCTTC
EST: gi|88506156|gb|CI433662.1|CI433662
EST:     ATGAGGGTGGAGGAGTTGAAATGCACNTGCTTGAAGATGCTGGACATTTG                         GTTCATGCAGATAACCCTGATGGGCTATTTAGAATTCTCTCATCAACCTTC
genomic: ATGAGGGTGGAGGAGTTGAAATGCACGTGCTTGAAGATGCTGGACATTGGgtatgcttac ... ctcctttcagGTTCATGCAGATAACCCTGATGGGCTATTTAGAATTCTCTCATCAACCTTC
EST: gi|33800785|gb|CF326264.1|CF326264
EST:     ATGAGGGTGGAGGAGTTGAAATGCACGTGCTTGAAGATGCTGGACATTGG                         GTTCATGCAGATAACCCTGATGGGCTATTTAGAATTCTCTCATCAACCTTC
genomic: ATGAGGGTGGAGGAGTTGAAATGCACGTGCTTGAAGATGCTGGACATTGGgtatgcttac ... ctcctttcagGTTCATGCAGATAACCCTGATGGGCTATTTAGAATTCTCTCATCAACCTTC
EST: gi|88849992|gb|CI091287.1|CI091287
EST:     ATGAGGGTGGAGGAGTTGAAATGCACGTGCTTGAGGATGCTGGACATTGG                         GTTCATGCAGATAACCCTGATGGGCTATTTAGAATTCTCTCATCAACCTTC
genomic: ATGAGGGTGGAGGAGTTGAAATGCACGTGCTTGAAGATGCTGGACATTGGgtatgcttac ... ctcctttcagGTTCATGCAGATAACCCTGATGGGCTATTTAGAATTCTCTCATCAACCTTC
EST: gi|27921004|gb|CB096812.1|CB096812
EST:     ATGAGGGTGGAGGAGTTGAAATGCACGTGCTTGAAGATGCTGGACATTGG                         GTTCATGCAGATAACCCTGATGGGCTCTTTAGAATTCTCTCATCAACCTTC
genomic: ATGAGGGTGGAGGAGTTGAAATGCACGTGCTTGAAGATGCTGGACATTGGgtatgcttac ... ctcctttcagGTTCATGCAGATAACCCTGATGGGCTATTTAGAATTCTCTCATCAACCTTC
EST: gi|88477707|gb|CI414978.1|CI414978
EST:     ATGAGGGTGGAGGAGTTGAAATGCACGTGCTTGAAGATGCTGGACATTGG                         GTTCATGCAGATAACCCTGATGGGCTATTTAGAATTCTCTCATCAACCTTC
genomic: ATGAGGGTGGAGGAGTTGAAATGCACGTGCTTGAAGATGCTGGACATTGGgtatgcttac ... ctcctttcagGTTCATGCAGATAACCCTGATGGGCTATTTAGAATTCTCTCATCAACCTTC
EST: gi|88504626|gb|CI432132.1|CI432132
EST:     ATGCACGTGCTTGAAGATGCTGGACATTGG                         GTTCATGCAGATAACCCTGATGGGCTATTTAGAATTCTCTCATCAACCTTC
genomic: ATGCACGTGCTTGAAGATGCTGGACATTGGgtatgcttac ... ctcctttcagGTTCATGCAGATAACCCTGATGGGCTATTTAGAATTCTCTCATCAACCTTC
EST: gi|88524625|gb|CI453463.1|CI453463
EST:     GCTTGAAGATGCTGGACATTGG                         GTTCATGCAGATAACCCTGATGGGCTATTTAGAATTCTCTCATCAACCTTC
genomic: GCTTGAAGATGCTGGACATTGGgtatgcttac ... ctcctttcagGTTCATGCAGATAACCCTGATGGGCTATTTAGAATTCTCTCATCAACCTTC
EST: gi|88513871|gb|CI441377.1|CI441377
EST:     ATGAGGGTGGAGGAGTTGAAATGCACGTGCTTGAAGATGCTGGACATTGGG                         GTTCATNCAGATAACCCTGATGGGCTATTTAGAATTCTCTCATCAACCTT
genomic: ATGAGGGTGGAGGAGTTGAAATGCACGTGCTTGAAGATGCTGGACATT-GGgtatgcttac ... ctcctttcagGTTCATGCAGATAACCCTGATGGGCTATTTAGAATTCTCTCATCAACCTT
EST: gi|88491392|gb|CI428664.1|CI428664
EST:     GGGTGGAGGAGTTGAAATGCACGTGCTTGAAGATGCTGGACATTGG                         GTTCATGCAGATAACCCTGATGGGCTATTTAGAATTCTCTCATCAACCTTC
genomic: GGGTGGAGGAGTTGAAATGCACGTGCTTGAAGATGCTGGACATTGGgtatgcttac ... ctcctttcagGTTCATGCAGATAACCCTGATGGGCTATTTAGAATTCTCTCATCAACCTTC
EST: gi|25803855|gb|CA759816.1|CA759816
EST:     ATGAGGGTGGAGGAGTTGAAATGCACCTGCTTGAAGATGCTGGACATTGG                         GTTCATGCAGATAACCCTGATGGGCTATTTAGAATTCTTTCATCAACCTTC
genomic: ATGAGGGTGGAGGAGTTGAAATGCACGTGCTTGAAGATGCTGGACATTGGgtatgcttac ... ctcctttcagGTTCATGCAGATAACCCTGATGGGCTATTTAGAATTCTCTCATCAACCTTC
EST: gi|29678812|gb|CB675087.1|CB675087
EST:     ATGAGGGTGGAGGAGTTGAAATGCACGTGCTTGAAGATGCTGGACATTGG                         GTTCATGCAGATAACCCTGATGGGCTATTTAGAATTTTTTCATCAACCTTC
genomic: ATGAGGGTGGAGGAGTTGAAATGCACGTGCTTGAAGATGCTGGACATTGGgtatgcttac ... ctcctttcagGTTCATGCAGATAACCCTGATGGGCTATTTAGAATTCTCTCATCAACCTTC
EST: gi|88249323|gb|CI249172.1|CI249172
EST:     AAATGCACGTGCTTGAAGATGCTGGACATTGG                         GTTCATGCAGATAACCCTGATGGGCTATTTAGAATTCTCTCATCAACCTTC
genomic: AAATGCACGTGCTTGAAGATGCTGGACATTGGgtatgcttac ... ctcctttcagGTTCATGCAGATAACCCTGATGGGCTATTTAGAATTCTCTCATCAACCTTC
EST: gi|89188496|gb|CI115745.1|CI115745
EST:     ATGAGGGTGGAGGAGTTGAAATGCACGTGCTTGAAGATGCTGGACATTGG                         GTTCATGCAGATAACCCTGATGGGCTATTTAGAATTCTCTCATCAACCTTC
genomic: ATGAGGGTGGAGGAGTTGAAATGCACGTGCTTGAAGATGCTGGACATTGGgtatgcttac ... ctcctttcagGTTCATGCAGATAACCCTGATGGGCTATTTAGAATTCTCTCATCAACCTTC
EST: gi|88504689|gb|CI432195.1|CI432195
EST:     ACGTGCTTGAAGATGCTGGACATTGG                         GTTCATGCAGATAACCCTGATGGGCTATTTAGAATTCTCTCATCAACCTTC
genomic: ACGTGCTTGAAGATGCTGGACATTGGgtatgcttac ... ctcctttcagGTTCATGCAGATAACCCTGATGGGCTATTTAGAATTCTCTCATCAACCTTC
EST: gi|88223989|gb|CI223838.1|CI223838
EST:     ATGAGGGTGGAGGAGTTGAAATGCACGTGCTTGAAGATGCTGGACATTGG                         GTTCATGCAGATAACCCTGATGGGCTATTTAGAATTCTCTCATCAACCTTC
genomic: ATGAGGGTGGAGGAGTTGAAATGCACGTGCTTGAAGATGCTGGACATTGGgtatgcttac ... ctcctttcagGTTCATGCAGATAACCCTGATGGGCTATTTAGAATTCTCTCATCAACCTTC
EST: gi|3767332|gb|AU031442.1|AU031442
EST:     ATGAGGGTGGAGGAGTTGAAATGCACGTGCTTGAAGATGCTGGACATTGG                         GTTCATGCAGATAACCCTGATGGGCTATTTAGAATTCTCTCATCAACCTTC
genomic: ATGAGGGTGGAGGAGTTGAAATGCACGTGCTTGAAGATGCTGGACATTGGgtatgcttac ... ctcctttcagGTTCATGCAGATAACCCTGATGGGCTATTTAGAATTCTCTCATCAACCTTC
EST: gi|88511417|gb|CI438923.1|CI438923
EST:     GCTGGACATTGG                         GTTCATGCAGATAACCCTGATGGGCTATTTAGAATTCTCTCATCAACCTTC
genomic: GCTGGACATTGGgtatgcttac ... ctcctttcagGTTCATGCAGATAACCCTGATGGGCTATTTAGAATTCTCTCATCAACCTTC
EST: gi|8858056|gb|AU095374.1|AU095374
EST:     ATGAGGGTGGAGGAGTTNAAATGCACGTGCTTGAAGATGCTGGACATTGG                         GGTTCATGGCAGGATAACCCTGGATGGGGCTATTTAGAATTCTCTCATCAA
genomic: ATGAGGGTGGAGGAGTTGAAATGCACGTGCTTGAAGATGCTGGACATTGGgtatgcttac ... ctcctttcagG-TTCATG-CAG-ATAACCCTG-ATGGG-CTATTTAGAATTCTCTCATCAA
EST: gi|88505067|gb|CI432573.1|CI432573
EST:     TGGAGGAGTTGAAATGCACGTGCTTGAAGATGCTGGACATTGG                         GTTCATCCAGATAACCCTGATGGGCTATTTAGAATTCTCTCATCAACCTTC
genomic: TGGAGGAGTTGAAATGCACGTGCTTGAAGATGCTGGACATTGGgtatgcttac ... ctcctttcagGTTCATGCAGATAACCCTGATGGGCTATTTAGAATTCTCTCATCAACCTTC
EST: gi|88851353|gb|CI404405.1|CI404405
EST:     ATGAGGGTGGAGGAGTTGAAATGCACGTGCTTGAAGATGCTGGACATTGG                         GTTCATGCAGATAACCCTGATGGGCTATTTAGAATTCTCTCATCAACCTTC
genomic: ATGAGGGTGGAGGAGTTGAAATGCACGTGCTTGAAGATGCTGGACATTGGgtatgcttac ... ctcctttcagGTTCATGCAGATAACCCTGATGGGCTATTTAGAATTCTCTCATCAACCTTC
EST: gi|88510082|gb|CI437588.1|CI437588
EST:     GGGTGGAGGAGTTGAAATGCACGTGCTTGAAGATGCTGGACATTGG                         GTTCATGCAGATAACCCTGATGGGCTATTTAGAATTCTCTCATCAACCTTC
genomic: GGGTGGAGGAGTTGAAATGCACGTGCTTGAAGATGCTGGACATTGGgtatgcttac ... ctcctttcagGTTCATGCAGATAACCCTGATGGGCTATTTAGAATTCTCTCATCAACCTTC
EST: gi|88980867|gb|CI022557.1|CI022557
EST:     ATGAGGGTGGAGGAGTTGAAATGCACGTGCTTGAAGATGCTGGACATTGG                         GTTCATGCAGATAACCCTGATGGGCTATTTAGAATTCTCTCATCAACCTTC
genomic: ATGAGGGTGGAGGAGTTGAAATGCACGTGCTTGAAGATGCTGGACATTGGgtatgcttac ... ctcctttcagGTTCATGCAGATAACCCTGATGGGCTATTTAGAATTCTCTCATCAACCTTC

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: 64 (upstream exon), 75 (downstream exon)
Score: 24

GGCTCTTGATGATCTCCAGAGAATTCATACTGCTGAGGAACTGGCTGCAGATGAGGGTGGAGGAGTTGAAATGCACGTGCTTGAAGATGCTGGACATTGGgtatgcttac ... ctcctttcagGTTCATGCAGATAACCCTGATGGGCTATTTAGAATTCTCTCATCAACCTTCCGCATCGAGGCTACCATAAGAGGGATGCAGAATTGAGGTGCAGAAGCCC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aatacagatttactgacaataaataagatttaattgtggtcttatctcctttcagGTTCATGCAGATAACCCTGATGGGCTATTTAGAATTCTCTCATCAACCTTCCGCATCGAGGCTACCATAAGAGGGATGCAGAATTGAGGTGCAGAAGCCC
                                       tcttatctcctttc  CT-rich tract
       atttactgacaataaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtcataaccatctgacatacctgtgctaattatgatgttgcatataatacagatttactgacaataaataagatttaattgtggtcttatctcctttcagGTTCATGCAGATAACCCTGATGGGCTATTTAGAATTCTCTCATCAACCTTCCGCATCGAGGCTACCATAAGAGGGATGCAGAATTGAGGTGCAGAAGCCC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - catctga
- - - - - - - - - -cctgtgc
- - - - - - - - - - - - - - - - - atgttgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - ttactga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -caataaa