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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTGGTTAAGAAGCTTGCAAAGAAATATCACGCTTTCCTTGCATCTGAGGCCATCATTAAGCAGATTCCTCGACTTCTTGGACCTGGTCTTAACAAGGCAGgcaagtatcttgttccatctattgcactaccatgatagctgttggacttgagttgttggcaatcatagacagctggctaacttctgctgatatgttctca...

Basic information

species Oryza sativa
transcript LOC_Os01g64090.1
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g64090.1 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM2G023748_T02 (Zea mays), 5'ss of exon 4
CTGGTTAAGAAGCTTGCAAAGAAATATCACGCTTTCCTTGCATCTGAGGCCATCATTAAGCAGATTCCTCGACTTCTTGGACCTGGTCTTAACAAGGCAGgcaagtatcttgttccatctattgcactaccatgatagctgttggacttgagttgttggcaatcatagacagctggctaacttctgctgatatgttctca-----
|| || |||||||| |||||||| || || |||||||||||||||||||| ||||||||||| |||||||| |||||||| |||||||||||||||||||||||| | ||  | |  |    | |  |      |||     ||   ||  |||  ||    | || ||     |  |||| ||| |   ||| |    |     
CTAGTGAAGAAGCTGGCAAAGAAGTACCATGCTTTCCTTGCATCTGAGGCTATCATTAAGCAAATTCCTCGTCTTCTTGGTCCTGGTCTTAACAAGGCAGgcaaggacctcttccttttctgtactttgggtcaatatagtctgttgttatgttactgttttttattga-----gcttaacctctacatttatctgtgtagatgt

upper sequence: LOC_Os01g64090.1 (Oryza sativa), 5'ss of exon 4
lower sequence: AT2G27530.1 (Arabidopsis thaliana), 5'ss of exon 4
CTGGTTAAGAAGCTTGCAAAGAAATATCACGCTTTCCTTGCATCTGAGGCCATCATTAAGCAGATTCCTCGACTTCTTGGACCTGGTCTTAACAAGGCAGgcaagtatcttgttccatctattgcact-accatgatagctgttggac-ttgagtt--gttggcaatcatagacagctggctaacttctgctgatatgttctca------
|| |||||||||||||| |||   || || |||||| | || |||||| |  ||||||||||||||||||| |||||||| ||||||||||||||||||||| ||| ||||     | || |   |||    ||  ||  || |   | || ||||  |||  ||| | |  |   |||      |||| ||  | || |          
CTTGTTAAGAAGCTTGCTAAGTCTTACCATGCTTTCTTGGCTTCTGAGTCTGTCATTAAGCAGATTCCTCGTCTTCTTGGTCCTGGTCTTAACAAGGCAGgcgagtttctt-caataactttgatacttggtatattatatggtcatcatttagtttcgttttcaagc-tctatgtctga--ggtttctacttgtttgattgatgaacag

upper sequence: LOC_Os01g64090.1 (Oryza sativa), 5'ss of exon 4
lower sequence: AT1G08360.1 (Arabidopsis thaliana), 5'ss of exon 4
CTGGTTAAGAAGCTTGCAAAGAAATATCACGCTTTCCTTGCATCTGAGGCCATCATTAAGCAGATTCCTCGACTTCTTGGACCTGGTCTTAACAAGGCAGgcaagtatcttgttccatctattgcactaccatgatagct---gttggacttgagttgttggcaatcatagacagctggctaacttctgctgatatgttctca----------------------------------------------------------------------------------
|| || |||||||||||||||||||| || |||||| | || |||||| |  ||||||||||||||||||| |||||||| ||||||||||||||||||||||||| ||| | | || ||| |   | |   |  |   |    |  |  |||| || | |  |    |    ||     |  ||| ||   || | || |                                                                                    
CTCGTCAAGAAGCTTGCAAAGAAATACCATGCTTTCTTGGCCTCTGAGTCTGTCATTAAGCAGATTCCTCGTCTTCTTGGTCCTGGTCTTAACAAGGCAGgcaagt-tctggctacagctaatattccattgttcttctttacatccgttttga-ttttggataggttttagtagtctattt-cttttgtcaatgtctttttgatacaatgccaatcctttatcctgtgagattatgcttctttgatgattcttaagtaacattcctttgctttactttacacag

upper sequence: LOC_Os01g64090.1 (Oryza sativa), 5'ss of exon 4
lower sequence: AT5G22440.1 (Arabidopsis thaliana), 5'ss of exon 4
CTGGTTAAGAAGCTTGCAAAGAAATATCACGCTTTCCTTGCATCTGAGGCCATCATTAAGCAGATTCCTCGACTTCTTGGACCTGGTCTTAACAAGGCAGgcaagtatcttgttccatctattgcactaccatgatagctgttggacttgagttgttggcaatcatagacagctggctaacttctgctgatatgttctca-
|| |||||||||||||| |||||||  || ||||||||||| |||||  |  ||||||||||||||||||| |||||||| |||||||| ||||||||||||| || |||      | |||    |           | | ||| |       | |     ||  || |        | |||  |    | |  |   || 
CTTGTTAAGAAGCTTGCTAAGAAATTCCATGCTTTCCTTGCTTCTGAATCTGTCATTAAGCAGATTCCTCGTCTTCTTGGTCCTGGTCTCAACAAGGCAGgcatgtctctaaccttaccta----atctttgcatatgttcttgtatcctctctat--atgatgctacattaaatcttgactcttatgaaca-atgaacag

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|86855006|gb|CI263073.1|CI263073
EST:     CATCATTAAGCAGATTCCTCGACTTCTTGGACCTGGTCTTAACAAGGCAG                         GCAAATTCCCAACGTTGGTGACTCACCAGGAATCACTTGAGTCCAAGGTTA
genomic: CATCATTAAGCAGATTCCTCGACTTCTTGGACCTGGTCTTAACAAGGCAGgcaagtatct ... tctactgcagGCAAATTCCCAACGTTGGTGACTCACCAGGAATCACTTGAGTCCAAGGTTA
EST: gi|86543712|gb|CI183918.1|CI183918
EST:     CATCATTAAGCAGATTCCTCGACTTCTTGGACCTGGTCTTAACAAGGCAG                         GCAAATTCCCAACGTTGGTGACTCACCAGGAATCACTTGAGTCCAAGGTTA
genomic: CATCATTAAGCAGATTCCTCGACTTCTTGGACCTGGTCTTAACAAGGCAGgcaagtatct ... tctactgcagGCAAATTCCCAACGTTGGTGACTCACCAGGAATCACTTGAGTCCAAGGTTA
EST: gi|38479924|gb|CF964013.1|CF964013
EST:     CATCATTAAGCAGATTCCTCGACTTCTTGGACCTGGTCTTAACAAGGCAG                         GCAAATTCCCA
genomic: CATCATTAAGCAGATTCCTCGACTTCTTGGACCTGGTCTTAACAAGGCAGgcaagtatct ... tctactgcagGCAAATTCCCA
EST: gi|27920704|gb|CB096512.1|CB096512
EST:     CATCATTAAGCAGATTCCTCGACTTCTTGGACCTGGTCTTAACAAGGCAG                         GCAAATTCCCAACGTTGGTGACTCACCAGGAATCACTTGAGTCCAAGGTTA
genomic: CATCATTAAGCAGATTCCTCGACTTCTTGGACCTGGTCTTAACAAGGCAGgcaagtatct ... tctactgcagGCAAATTCCCAACGTTGGTGACTCACCAGGAATCACTTGAGTCCAAGGTTA
EST: gi|86543033|gb|CI183239.1|CI183239
EST:     CATCATTAAGCAGATTCCTCGACTTCTTGGACCTGGTCTTAACAAGGCAG                         GCAAATTCCCAACGTTGGTGACTCACCAGGAATCACTTGAGTCCAAGGTTA
genomic: CATCATTAAGCAGATTCCTCGACTTCTTGGACCTGGTCTTAACAAGGCAGgcaagtatct ... tctactgcagGCAAATTCCCAACGTTGGTGACTCACCAGGAATCACTTGAGTCCAAGGTTA
EST: gi|87034170|gb|CI188794.1|CI188794
EST:     CATCATTAAGCAGATTCCTCGACTTCTTGGACCTGGTCTTAACAAGGCAG                         GCAAATTCCCAACGTTGGTGACTCACCAGGAATCACTTGAGTCCAAGGTTA
genomic: CATCATTAAGCAGATTCCTCGACTTCTTGGACCTGGTCTTAACAAGGCAGgcaagtatct ... tctactgcagGCAAATTCCCAACGTTGGTGACTCACCAGGAATCACTTGAGTCCAAGGTTA
EST: gi|88969139|gb|CI382688.1|CI382688
EST:     GACCTGGTCTTAACAAGGCAG                         GCAAATTCCCAACGTTGGTGACTCACCAGGAATCACTTGAGTCCAAGGTTA
genomic: GACCTGGTCTTAACAAGGCAGgcaagtatct ... tctactgcagGCAAATTCCCAACGTTGGTGACTCACCAGGAATCACTTGAGTCCAAGGTTA
EST: gi|86498451|gb|CI141084.1|CI141084
EST:     CATCATTAAGCAGATTCCTCGACTTCTTGGACCTGGTCTTAACAAGGCAG                         GCAAATTCCCAACGTTGGTGACTCACCAGGAATCACTTGAGTCCAAGGTTA
genomic: CATCATTAAGCAGATTCCTCGACTTCTTGGACCTGGTCTTAACAAGGCAGgcaagtatct ... tctactgcagGCAAATTCCCAACGTTGGTGACTCACCAGGAATCACTTGAGTCCAAGGTTA
EST: gi|86526191|gb|CI166397.1|CI166397
EST:     CATCATTAAGCAGATTCCTCGACTTCTTGGACCTGGTCTTAACAAGGCAG                         GCAAATTCCCAACGTTGGTGACTCACCAGGAATCACTTGAGTCCAAGGTTA
genomic: CATCATTAAGCAGATTCCTCGACTTCTTGGACCTGGTCTTAACAAGGCAGgcaagtatct ... tctactgcagGCAAATTCCCAACGTTGGTGACTCACCAGGAATCACTTGAGTCCAAGGTTA
EST: gi|86546888|gb|CI187094.1|CI187094
EST:     CATTAAGCAGATTCCTCGACTTCTTGGACCTGGTCTTAACAAGGCAG                         GCAAATTCCCAACGTTGGTGACTCACCAGGAATCACTTGAGTCCAAGGTTA
genomic: CATTAAGCAGATTCCTCGACTTCTTGGACCTGGTCTTAACAAGGCAGgcaagtatct ... tctactgcagGCAAATTCCCAACGTTGGTGACTCACCAGGAATCACTTGAGTCCAAGGTTA
EST: gi|86543087|gb|CI183293.1|CI183293
EST:     CATCATTAAGCAGATTCCTCGACTTCTTGGACCTGGTCTTAACAAGGCAG                         GCAAATTCCCAACGTTGGTGACTCACCAGGAATCACTTGAGTCCAAGGTTA
genomic: CATCATTAAGCAGATTCCTCGACTTCTTGGACCTGGTCTTAACAAGGCAGgcaagtatct ... tctactgcagGCAAATTCCCAACGTTGGTGACTCACCAGGAATCACTTGAGTCCAAGGTTA
EST: gi|218503115|gb|FG965410.1|FG965410
EST:     CATCATTAAGCAGATTCCTCGACTTCTTGGACCTGGTCTTAACAAGGCAG                         GCAAATTCCCAACGTTGGTGACTCACCAGGAATCACTTGAGTCCAAGGTTA
genomic: CATCATTAAGCAGATTCCTCGACTTCTTGGACCTGGTCTTAACAAGGCAGgcaagtatct ... tctactgcagGCAAATTCCCAACGTTGGTGACTCACCAGGAATCACTTGAGTCCAAGGTTA
EST: gi|88216033|gb|CI215882.1|CI215882
EST:     CATCATTAAGCAGATTCCTCGACTTCTTGGACCTGGTCTTAACAAGGCAG                         GCAAATTCCCAACGTTGGTGACTCACCAGGAATCACTTGAGTCCAAGGTTA
genomic: CATCATTAAGCAGATTCCTCGACTTCTTGGACCTGGTCTTAACAAGGCAGgcaagtatct ... tctactgcagGCAAATTCCCAACGTTGGTGACTCACCAGGAATCACTTGAGTCCAAGGTTA
EST: gi|87020293|gb|CI261157.1|CI261157
EST:     CCTGGTCTTAACAAGGCAG                         GCAAATTCCCAACGTTGGTGACTCACCAGGAATCACTTGAGTCCAAGGTTA
genomic: CCTGGTCTTAACAAGGCAGgcaagtatct ... tctactgcagGCAAATTCCCAACGTTGGTGACTCACCAGGAATCACTTGAGTCCAAGGTTA
EST: gi|86529462|gb|CI169668.1|CI169668
EST:     CATCATTAAGCAGATTCCTCGACTTCTTGGACCTGGTCTTAACAAGGCAG                         GCAAATTCCCAACGTTGGTGACTCACCAGGAATCACTTGAGTCCAAGGTTA
genomic: CATCATTAAGCAGATTCCTCGACTTCTTGGACCTGGTCTTAACAAGGCAGgcaagtatct ... tctactgcagGCAAATTCCCAACGTTGGTGACTCACCAGGAATCACTTGAGTCCAAGGTTA
EST: gi|88509604|gb|CI437110.1|CI437110
EST:     TAAGCAGATTCCTCGACTTCTTGGACCTGGTCTTAACAAGGCAG                         GCAAATTCCCAACGTTGGTGACTCACCAGGAATCACTTGAGTCCAAGGTTA
genomic: TAAGCAGATTCCTCGACTTCTTGGACCTGGTCTTAACAAGGCAGgcaagtatct ... tctactgcagGCAAATTCCCAACGTTGGTGACTCACCAGGAATCACTTGAGTCCAAGGTTA
EST: gi|88199182|gb|CI199032.1|CI199032
EST:     ATTCCTCGACTTCTTGGACCTGGTCTTAACAAGGCAG                         GCAAATTCCCAACGTTGGTGACTCACCAGGAATCACTTGAGTCCAAGGTTA
genomic: ATTCCTCGACTTCTTGGACCTGGTCTTAACAAGGCAGgcaagtatct ... tctactgcagGCAAATTCCCAACGTTGGTGACTCACCAGGAATCACTTGAGTCCAAGGTTA
EST: gi|33683413|gb|CF311652.1|CF311652
EST:     CATCATTAAGCAGATTCCTCGACTTCTTGGACCTGGTCTTAACAAGGCAG                         GCAAATTCCCAACGTTGGTGACTCACCAGGAATCACTTGAGTCCAAGGTTA
genomic: CATCATTAAGCAGATTCCTCGACTTCTTGGACCTGGTCTTAACAAGGCAGgcaagtatct ... tctactgcagGCAAATTCCCAACGTTGGTGACTCACCAGGAATCACTTGAGTCCAAGGTTA
EST: gi|88202396|gb|CI201258.1|CI201258
EST:     CATCATTAAGCAGATTCCTCGACTTCTTGGACCTGGTCTTAACAAGGCAG                         GCAAATTCCCAACGTTGGTGACTCACCAGGAATCACTTGAGTCCAAGGTTA
genomic: CATCATTAAGCAGATTCCTCGACTTCTTGGACCTGGTCTTAACAAGGCAGgcaagtatct ... tctactgcagGCAAATTCCCAACGTTGGTGACTCACCAGGAATCACTTGAGTCCAAGGTTA
EST: gi|88199507|gb|CI199357.1|CI199357
EST:     GATTCCTCGACTTCTTGGACCTGGTCTTAACAAGGCAG                         GCAAATTCCCAACGTTGGTGACTCACCAGGAATCACTTGAGTCCAAGGTTA
genomic: GATTCCTCGACTTCTTGGACCTGGTCTTAACAAGGCAGgcaagtatct ... tctactgcagGCAAATTCCCAACGTTGGTGACTCACCAGGAATCACTTGAGTCCAAGGTTA
EST: gi|86544876|gb|CI185082.1|CI185082
EST:     ATTAAGCAGATTCCTCGACTTCTTGGACCTGGTCTTAACAAGGCAG                         GCAAATTCCCAACGTTGGTGACTCACCAGGAATCACTTGAGTCCAAGGTTA
genomic: ATTAAGCAGATTCCTCGACTTCTTGGACCTGGTCTTAACAAGGCAGgcaagtatct ... tctactgcagGCAAATTCCCAACGTTGGTGACTCACCAGGAATCACTTGAGTCCAAGGTTA
EST: gi|88965837|gb|CI006671.1|CI006671
EST:     CATCATTAAGCAGATTCCTCGACTTCTTGGACCTGGTCTTAACAAGGCAG                         GCAAATTCCCAACGTTGGTGACTCACCAGGAATCACTTGAGTCCAAGGTTA
genomic: CATCATTAAGCAGATTCCTCGACTTCTTGGACCTGGTCTTAACAAGGCAGgcaagtatct ... tctactgcagGCAAATTCCCAACGTTGGTGACTCACCAGGAATCACTTGAGTCCAAGGTTA
EST: gi|86529199|gb|CI169405.1|CI169405
EST:     CATCATTAAGCAGATTCCTCGACTTCTTGGACCTGGTCTTAACAAGGCAG                         GCAAATTCCCAACGTTGGTGACTCACCAGGAATCACTTGAGTCCAAGGTTA
genomic: CATCATTAAGCAGATTCCTCGACTTCTTGGACCTGGTCTTAACAAGGCAGgcaagtatct ... tctactgcagGCAAATTCCCAACGTTGGTGACTCACCAGGAATCACTTGAGTCCAAGGTTA
EST: gi|88237903|gb|CI237752.1|CI237752
EST:     CATCATTAAGCAGATTCCTCGACTTCTTGGACCTGGTCTTAACAAGGCAG                         GCAAATTCCCAACGTTGGTGACTCACCAGGAATCACTTGAGTCCAAGGTTA
genomic: CATCATTAAGCAGATTCCTCGACTTCTTGGACCTGGTCTTAACAAGGCAGgcaagtatct ... tctactgcagGCAAATTCCCAACGTTGGTGACTCACCAGGAATCACTTGAGTCCAAGGTTA
EST: gi|86542550|gb|CI182756.1|CI182756
EST:     CATCATTAAGCAGATTCCTCGACTTCTTGGACCTGGTCTTAACAAGGCAG                         GCAAATTCCCAACGTTGGTGACTCACCAGGAATCACTTGAGTCCAAGGTTA
genomic: CATCATTAAGCAGATTCCTCGACTTCTTGGACCTGGTCTTAACAAGGCAGgcaagtatct ... tctactgcagGCAAATTCCCAACGTTGGTGACTCACCAGGAATCACTTGAGTCCAAGGTTA
EST: gi|87033326|gb|CI187950.1|CI187950
EST:     CATTAAGCAGATTCCTCGACTTCTTGGACCTGGTCTTAACAAGGCAG                         GCAAATTCCCAACGTTGGTGACTCACCAGGAATCACTTGAGTCCAAGGTTA
genomic: CATTAAGCAGATTCCTCGACTTCTTGGACCTGGTCTTAACAAGGCAGgcaagtatct ... tctactgcagGCAAATTCCCAACGTTGGTGACTCACCAGGAATCACTTGAGTCCAAGGTTA
EST: gi|86543029|gb|CI183235.1|CI183235
EST:     CATCATTAAGCAGATTCCTCGACTTCTTGGACCTGGTCTTAACAAGGCAG                         GCAAATTCCCAACGTTGGTGACTCACCAGGAATCACTTGAGTCCAAGGTTA
genomic: CATCATTAAGCAGATTCCTCGACTTCTTGGACCTGGTCTTAACAAGGCAGgcaagtatct ... tctactgcagGCAAATTCCCAACGTTGGTGACTCACCAGGAATCACTTGAGTCCAAGGTTA

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: 71 (upstream exon), 63 (downstream exon)
Score: 52

CTGGTTAAGAAGCTTGCAAAGAAATATCACGCTTTCCTTGCATCTGAGGCCATCATTAAGCAGATTCCTCGACTTCTTGGACCTGGTCTTAACAAGGCAGgcaagtatct ... tctactgcagGCAAATTCCCAACGTTGGTGACTCACCAGGAATCACTTGAGTCCAAGGTTAACGAGACTAAGGCTACAGTGAAGTTCCAACTGAAAAAGGTTCTTTGCAT




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTGGTTAAGAAGCTTGCAAAGAAATATCACGCTTTCCTTGCATCTGAGGCCATCATTAAGCAGATTCCTCGACTTCTTGGACCTGGTCTTAACAAGGCAGgcaagtatcttgttccatctattgcactaccatgatagctgttggacttgagttgttggcaatcatagacagctggctaacttctgctgatatgttctca

- - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGAT