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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATTTTGAAGGGAAAACTGATGATAAAATCAAGACCATGGAAGTGGTGGAAGAATTAAGATCTAAAAGGGCTGACATGCAGgtattattttgaaagcttgaatatatgtgctctcgattctcatagtttgtgtataccagcacatgtaactaatagtaaataaagttttaatcctactggcatttttcttctttgttgcag

Basic information

species Oryza sativa
transcript LOC_Os03g62640.4
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g62640.4 (Oryza sativa), 5'ss of exon 5
lower sequence: GRMZM2G118014_T02 (Zea mays), 5'ss of exon 5
ATTTTGAAGGGAAAACTGATGATAAAATCAAGACCATGGAAGTGGTGGAAGAATTAAGATCTAAAAGGGCTGACATGCAGgtattattttgaaagcttgaata-tatgtgctctcgattctcata---gtttgtgtataccagcacatgtaact--aatagta--aataaagttttaatcctactggcatttttctt-ctttgttgcag
|||||||||||| ||||||||||||||| ||| ||  |||||| ||||||||| | ||| ||||||| ||||| |||||||||||| |||||    ||||  | |||||  | ||  |||| |||    | |   | | ||||||||  | | |  ||| |||  | |  |||||| ||          |||||| |  |||| | |||
ATTTTGAAGGGAGAACTGATGATAAAATAAAGGCCCAGGAAGTAGTGGAAGAACTCAGAACTAAAAGAGCTGATATGCAGgtattaatttgattctttgagaagtatgttttttcatttcttatattgatcttattgttccagcacaaattattcaaattgtagtactttagttttgatttggtaattgtttttcctattttgctccag

upper sequence: LOC_Os03g62640.4 (Oryza sativa), 5'ss of exon 5
lower sequence: GRMZM2G069916_T04 (Zea mays), 5'ss of exon 5
ATTTTGAAGGGAAAACTGATGATAAAATCAAGACCATGGAAGTGGTGGAAGAATTAAGATCTAAAAGGGCTGACATGCAGgtattattttgaaagcttgaatatatgtgctctcgattctcatagtttgtgt-ataccagcacatgtaacta--atagtaaa--taaagttttaatcctactggcatttttctt-ctttgttgcag
|||||||||||| ||||||||| ||||| ||| ||  |||||| ||||||||  ||||| ||||||| ||||| |||||||||||| ||  |    |||||    | |  |     || |  |  ||||| |  | ||||||||  | | ||  || |||    |   ||||| ||          |||||  |  |||  |||||
ATTTTGAAGGGAGAACTGATGACAAAATAAAGGCCCAGGAAGTAGTGGAAGAGCTAAGAGCTAAAAGAGCTGATATGCAGgtattaattcaattttttgaaagagtatttttattcttatattgatttgtattgttccagcacaaattattataattgtagtgctttggttttgatgtggtaattgttttttctattttcctgcag
















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|29623140|gb|CB628151.1|CB628151
EST:     AGACCATGGAAGTGGTGGAAGAATTAAGATCTAAAAGGGCTGACATGCAG                         GCTACCCTTCTGCTTGATGCCTTTAACAAGGACAGAGCTTCATTACCTCAG
genomic: AGACCATGGAAGTGGTGGAAGAATTAAGATCTAAAAGGGCTGACATGCAGgtattatttt ... tttgttgcagGCTACCCTTCTGCTTGATGCCTTTAACAAGGACAGAGCTTCATTACCTCAG
EST: gi|29623911|gb|CB628922.1|CB628922
EST:     AGACCATGGAAGTGGTGGAAGAATTAAGATCTAAAAGGGCTGACATGCAG                         GCTACCCTTCTGCTTGATGCCTTTAACAAGGACAGAGCTTCATTACCTCAG
genomic: AGACCATGGAAGTGGTGGAAGAATTAAGATCTAAAAGGGCTGACATGCAGgtattatttt ... tttgttgcagGCTACCCTTCTGCTTGATGCCTTTAACAAGGACAGAGCTTCATTACCTCAG
EST: gi|29661287|gb|CB657562.1|CB657562
EST:     AGACCATGGAAGTGGTGGAAGAATTAAGATCTAAAAGGGCTGACATGCAG                         GCTACCCTTCTGCTTGATGCCTTTAACAAGGACAGAGCTTCATTACCTCAG
genomic: AGACCATGGAAGTGGTGGAAGAATTAAGATCTAAAAGGGCTGACATGCAGgtattatttt ... tttgttgcagGCTACCCTTCTGCTTGATGCCTTTAACAAGGACAGAGCTTCATTACCTCAG
EST: gi|29630312|gb|CB635321.1|CB635321
EST:     AGACCATGGAAGTGGTGGAAGAATTAAGATCTAAAAGGGCTGACATGCAG                         GCTACCCTTCTGCTTGATGCCTTTAACAAGGACAGAGCTTCATTACCTCAG
genomic: AGACCATGGAAGTGGTGGAAGAATTAAGATCTAAAAGGGCTGACATGCAGgtattatttt ... tttgttgcagGCTACCCTTCTGCTTGATGCCTTTAACAAGGACAGAGCTTCATTACCTCAG
EST: gi|29624088|gb|CB629099.1|CB629099
EST:     AGACCATGGAAGTGGTGGAAGAATTAAGATCTAAAAGGGCTGACATGCAG                         GCTACCCTTCTGCTTGATGCCTTTAACAAGGACAGAGCTTCATTACCTCAA
genomic: AGACCATGGAAGTGGTGGAAGAATTAAGATCTAAAAGGGCTGACATGCAGgtattatttt ... tttgttgcagGCTACCCTTCTGCTTGATGCCTTTAACAAGGACAGAGCTTCATTACCTCAG
EST: gi|29681987|gb|CB678262.1|CB678262
EST:     AGACCATGGAAGTGGTGGAAGAATTAAGATCTAAAAGGGCTGACATGCAT                         GCTACCCTTCTGCTTGATGCCTTTAACAAGGACAGAGCTTCATTACCTCAG
genomic: AGACCATGGAAGTGGTGGAAGAATTAAGATCTAAAAGGGCTGACATGCAGgtattatttt ... tttgttgcagGCTACCCTTCTGCTTGATGCCTTTAACAAGGACAGAGCTTCATTACCTCAG
EST: gi|29672226|gb|CB668501.1|CB668501
EST:     AGACCATGGAAGTGGTGGAAGAATTAAGATCTAAAAGGGCTGACATGCAG                         GCTACCCTTCTGCTTGATGCCTTTAACAAGGACAGAGCTTCATTACCTCAG
genomic: AGACCATGGAAGTGGTGGAAGAATTAAGATCTAAAAGGGCTGACATGCAGgtattatttt ... tttgttgcagGCTACCCTTCTGCTTGATGCCTTTAACAAGGACAGAGCTTCATTACCTCAG
EST: gi|29679242|gb|CB675517.1|CB675517
EST:     AGACCATGGAAGTGGTGGAAGAATTAAGATCTAAAAGGGCTGACATGCAG                         GCTACCCTTCTGCTTGATGCCTTTAACAAGGACAGAGCTTCATTACCTCAG
genomic: AGACCATGGAAGTGGTGGAAGAATTAAGATCTAAAAGGGCTGACATGCAGgtattatttt ... tttgttgcagGCTACCCTTCTGCTTGATGCCTTTAACAAGGACAGAGCTTCATTACCTCAG
EST: gi|88689613|gb|CI733189.1|CI733189
EST:     AGACCATGGAAGTGGTGGAAGAATTAAGATCTAAAAGGGCTGACATGCAG                         GCTACCCTTCTGCTTGATGCCTTTAACAAGGACAGAGCTTCATTACCT
genomic: AGACCATGGAAGTGGTGGAAGAATTAAGATCTAAAAGGGCTGACATGCAGgtattatttt ... tttgttgcagGCTACCCTTCTGCTTGATGCCTTTAACAAGGACAGAGCTTCATTACCT
EST: gi|29627005|gb|CB632016.1|CB632016
EST:     AGACCATGGAAGTGGTGGAAGAATTAAGATCTAAAAGGGCTGACGTGCAG                         GCTACCCTTCTGCTTGATGCCTTTCACAAGGACAGAGCTTCATTACCTCAG
genomic: AGACCATGGAAGTGGTGGAAGAATTAAGATCTAAAAGGGCTGACATGCAGgtattatttt ... tttgttgcagGCTACCCTTCTGCTTGATGCCTTTAACAAGGACAGAGCTTCATTACCTCAG
EST: gi|29681845|gb|CB678120.1|CB678120
EST:     AGACCATGGAAGTGGTGGAAGAATTAAGATCTAAAAGGGCTGACATGCAG                         GCTACCCTTCTGCTTGATGCCTTTAACAAGGACAGAGCTTCATTACCTCAG
genomic: AGACCATGGAAGTGGTGGAAGAATTAAGATCTAAAAGGGCTGACATGCAGgtattatttt ... tttgttgcagGCTACCCTTCTGCTTGATGCCTTTAACAAGGACAGAGCTTCATTACCTCAG
EST: gi|29681724|gb|CB677999.1|CB677999
EST:     AGACCATGGAAGTGGTGGAAGAATTAAGATCTAAAAGGGCTGACATGCAG                         GCTACCCTTCTGCTTGATGCCTTTAACAAGGACAGAGCTTCATTACCTCAG
genomic: AGACCATGGAAGTGGTGGAAGAATTAAGATCTAAAAGGGCTGACATGCAGgtattatttt ... tttgttgcagGCTACCCTTCTGCTTGATGCCTTTAACAAGGACAGAGCTTCATTACCTCAG
EST: gi|29678406|gb|CB674681.1|CB674681
EST:     AGACCATGGAAGTGGTGGAAGAATTAAGATCTAAAAGGGCTGACATGCAG                         GCTACCCTTCTGCTTGATGCCTTTAACAAGGACAGAGCTTCATTACCTCAG
genomic: AGACCATGGAAGTGGTGGAAGAATTAAGATCTAAAAGGGCTGACATGCAGgtattatttt ... tttgttgcagGCTACCCTTCTGCTTGATGCCTTTAACAAGGACAGAGCTTCATTACCTCAG
EST: gi|29629756|gb|CB634765.1|CB634765
EST:     AGACCATGGAAGTGGTGGAAGAATTAAGATCTAAAAGGGCTGACATGCAG                         GCTACCCTTCTGCTTGATGCCTTTAACAAGGACAGAGCTTCATTACCTCAG
genomic: AGACCATGGAAGTGGTGGAAGAATTAAGATCTAAAAGGGCTGACATGCAGgtattatttt ... tttgttgcagGCTACCCTTCTGCTTGATGCCTTTAACAAGGACAGAGCTTCATTACCTCAG
EST: gi|29680593|gb|CB676868.1|CB676868
EST:     AGACCATGGAAGTGGTGGAAGAATTAAGATCTAAAAGGGCTGACATGCAG                         GCTACCCTTCTGCTTGATGCCTTTAACAAGGACAGAGCTTCATTACCTCAG
genomic: AGACCATGGAAGTGGTGGAAGAATTAAGATCTAAAAGGGCTGACATGCAGgtattatttt ... tttgttgcagGCTACCCTTCTGCTTGATGCCTTTAACAAGGACAGAGCTTCATTACCTCAG
EST: gi|29674493|gb|CB670768.1|CB670768
EST:     AGACCATGGAAGTGGTGGAAGAATTAAGATCTAAAAGGGCTGACATGCAG                         GCTACCCTTCTGCTTGATGCCTTTAACAAGGACAGAGCTTCATTACCTCAG
genomic: AGACCATGGAAGTGGTGGAAGAATTAAGATCTAAAAGGGCTGACATGCAGgtattatttt ... tttgttgcagGCTACCCTTCTGCTTGATGCCTTTAACAAGGACAGAGCTTCATTACCTCAG
EST: gi|29664072|gb|CB660347.1|CB660347
EST:     AGACCATGGAAGTGGTGGAAGAATTAAGATCTAAAAGGGCTGACATGCAG                         GCTACCCTTCTGCTTGATGCCTTTAACAAGGACAGAGCTTCATTACCTCAG
genomic: AGACCATGGAAGTGGTGGAAGAATTAAGATCTAAAAGGGCTGACATGCAGgtattatttt ... tttgttgcagGCTACCCTTCTGCTTGATGCCTTTAACAAGGACAGAGCTTCATTACCTCAG
EST: gi|29660244|gb|CB656519.1|CB656519
EST:     AGACCATGGAAGTGGTGGAAGAATTAAGATCTAAAAGGGCTGACATGCAG                         GCTACCCTTCTGCTTGATGCCTTTAACAAGGACAGAGCTTCATTACCTCAG
genomic: AGACCATGGAAGTGGTGGAAGAATTAAGATCTAAAAGGGCTGACATGCAGgtattatttt ... tttgttgcagGCTACCCTTCTGCTTGATGCCTTTAACAAGGACAGAGCTTCATTACCTCAG
EST: gi|29621718|gb|CB626729.1|CB626729
EST:     AGACCATGGAAGTGGTGGAAGAATTAAGATCTAAAAGGGCTGACATGCAG                         GCTACCCTTCTGCTTGATGCCTTTAACAAGGACAGAGCTTCATTACCTCAG
genomic: AGACCATGGAAGTGGTGGAAGAATTAAGATCTAAAAGGGCTGACATGCAGgtattatttt ... tttgttgcagGCTACCCTTCTGCTTGATGCCTTTAACAAGGACAGAGCTTCATTACCTCAG
EST: gi|29639321|gb|CB644330.1|CB644330
EST:     AGACCATGGAAGTGGTGGAAGAATTAAGATCTAAAAGGGCTGACATGCAG                         GCTACCCTTCTGCTTGATGCCTTTAACAAGGACAGAGCTTCATTACCTCAG
genomic: AGACCATGGAAGTGGTGGAAGAATTAAGATCTAAAAGGGCTGACATGCAGgtattatttt ... tttgttgcagGCTACCCTTCTGCTTGATGCCTTTAACAAGGACAGAGCTTCATTACCTCAG
EST: gi|29629579|gb|CB634588.1|CB634588
EST:     AGACCATGGAAGTGGTGGAAGAATTAAGATCTAAAAGGGCTGACATGCAG                         GCTACCCTTCTGCTTGATGCCTTTAACAAGGACAGAGCTTCATTACCTCAG
genomic: AGACCATGGAAGTGGTGGAAGAATTAAGATCTAAAAGGGCTGACATGCAGgtattatttt ... tttgttgcagGCTACCCTTCTGCTTGATGCCTTTAACAAGGACAGAGCTTCATTACCTCAG
EST: gi|29617712|gb|CB622724.1|CB622724
EST:     AGACCATGGAAGTGGTGGAAGAATTAAGATCTAAAAGGGCTGACATGCAG                         GCTACCCTTCTGCTTGATGCCTTTAACAAGGACAGAGCTTCATTACCTCAG
genomic: AGACCATGGAAGTGGTGGAAGAATTAAGATCTAAAAGGGCTGACATGCAGgtattatttt ... tttgttgcagGCTACCCTTCTGCTTGATGCCTTTAACAAGGACAGAGCTTCATTACCTCAG
EST: gi|29665628|gb|CB661903.1|CB661903
EST:     AGACCATGGAAGTGGTGGAAGAATTAAGATCTAAAAGGGCTGACATGCAG                         GCTACCCTTCTGCTTGATGCCTTTAACAAGGACAGAGCTTCATTACCTCAG
genomic: AGACCATGGAAGTGGTGGAAGAATTAAGATCTAAAAGGGCTGACATGCAGgtattatttt ... tttgttgcagGCTACCCTTCTGCTTGATGCCTTTAACAAGGACAGAGCTTCATTACCTCAG
EST: gi|38480710|gb|CF964799.1|CF964799
EST:     TGGTGGAAGAATTAAGATCTAAAAGGGCTGACATGCAG                         GCTACCCTTCTGCTTGATGCCTTTAACAAGGACAGAGCTTCATTACCTCAG
genomic: TGGTGGAAGAATTAAGATCTAAAAGGGCTGACATGCAGgtattatttt ... tttgttgcagGCTACCCTTCTGCTTGATGCCTTTAACAAGGACAGAGCTTCATTACCTCAG
EST: gi|29629757|gb|CB634766.1|CB634766
EST:     AGACCATGGAAGTGGTGGAAGAATTAAGATCTAAAAGGGCTGACATGCAG                         GCTACCCTTCTGCTTGATGCCTTTAACAAGGACAGAGCTTCATTACCTCAG
genomic: AGACCATGGAAGTGGTGGAAGAATTAAGATCTAAAAGGGCTGACATGCAGgtattatttt ... tttgttgcagGCTACCCTTCTGCTTGATGCCTTTAACAAGGACAGAGCTTCATTACCTCAG
EST: gi|29674744|gb|CB671019.1|CB671019
EST:     AGACCATGGAAGTGGTGGAAGAATTAAGATCTAAAAGGGCTGACATGCAG                         GCTACCCTTCTGCTTGATGCCTTTAACAAGGACAGAGCTTCATTACCTCAG
genomic: AGACCATGGAAGTGGTGGAAGAATTAAGATCTAAAAGGGCTGACATGCAGgtattatttt ... tttgttgcagGCTACCCTTCTGCTTGATGCCTTTAACAAGGACAGAGCTTCATTACCTCAG
EST: gi|29678347|gb|CB674622.1|CB674622
EST:     AGACCATGGAAGTGGTGGAAGAATTAAGATCTAAAAGGGCTGACATGCAG                         GCTACCCTTCTGCTTGATGCCTTTAACAAGGACAGAGCTTCATTACCTCAG
genomic: AGACCATGGAAGTGGTGGAAGAATTAAGATCTAAAAGGGCTGACATGCAGgtattatttt ... tttgttgcagGCTACCCTTCTGCTTGATGCCTTTAACAAGGACAGAGCTTCATTACCTCAG
EST: gi|29626366|gb|CB631377.1|CB631377
EST:     AGACCATGGAAGTGGTGGAAGAATTAAGATCTAAAAGGGCTGACATGCAG                         GCTACCCTTCTGCTTGATGCCTTTAACAAGGACAGAGCTTCATTACCTCAG
genomic: AGACCATGGAAGTGGTGGAAGAATTAAGATCTAAAAGGGCTGACATGCAGgtattatttt ... tttgttgcagGCTACCCTTCTGCTTGATGCCTTTAACAAGGACAGAGCTTCATTACCTCAG
EST: gi|88367212|gb|CI563976.1|CI563976
EST:     GACCATGGAAGTGGTGGAAGAAATTA-GATCTANNAGGGCTGACATGCAN                         GCTACCCTTCTGCTTGA
genomic: GACCATGGAAGTGGTGGAAGAA-TTAAGATCTAAAAGGGCTGACATGCAGgtattatttt ... tttgttgcagGCTACCCTTCTGCTTGA
EST: gi|29656040|gb|CB652315.1|CB652315
EST:     ACACCATGGAAGTGGTGGAAGAATTAAGATCTACAAGGGCTGACATGCAG                         GCTACCCTTCTGCTTGATGCC
genomic: AGACCATGGAAGTGGTGGAAGAATTAAGATCTAAAAGGGCTGACATGCAGgtattatttt ... tttgttgcagGCTACCCTTCTGCTTGATGCC

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: 59 (upstream exon), 63 (downstream exon)
Score: 53

ATTTTGAAGGGAAAACTGATGATAAAATCAAGACCATGGAAGTGGTGGAAGAATTAAGATCTAAAAGGGCTGACATGCAGgtattatttt ... tttgttgcagGCTACCCTTCTGCTTGATGCCTTTAACAAGGACAGAGCTTCATTACCTCAGCCTACTCCAACACCTCAAATGGCATCAGTACCAGCACCTGCTCCCCCTG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATTTTGAAGGGAAAACTGATGATAAAATCAAGACCATGGAAGTGGTGGAAGAATTAAGATCTAAAAGGGCTGACATGCAGgtattattttgaaagcttgaatatatgtgctctcgattctcatagtttgtgtataccagcacatgtaactaatagtaaataaagttttaatcctactggcatttttcttctttgttgcag

- - - - - - - - - - - - - - - - - CATGGA
- - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - -  GGTGGA
- - - - - - - - - - - - - - - - - - - - - -  TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - GGAAGA