Skip to another splice site:
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 5'  3'   		2  
 5'  3'   		3  
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 5'  3'   		5  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtatatatcaaacatttgtaactataacttcatcagaaggaacataaatattgaagatccatactggcaatgtttagctgaaactatcatatctctaaccatataacttcatcacaaggaagattcagaagtttcttcatgaattaaattgcttcattttcattgttttaattttttttcccagTCAAGCGAGAGCATCGACGCAGCTATCGGTGATGTTTTATCGAAACCGTGGTTGCCTTTGCCTCTTGGACTGAAGCCACCTTCAGTGGACAGTGTGATGG

Basic information

species Oryza sativa
transcript LOC_Os06g24070.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g24070.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G026833_T02 (Zea mays), 3'ss of exon 5
gtaagtatatatcaaacatttgtaactataacttcatcagaaggaacataaatattgaagatccatactggcaatgtttagctgaaactatcatatctctaaccatataacttcatcacaaggaagattcagaagtttcttcatgaattaaattgcttcattttcattgttttaattttttttcccagTCAAGCGAGAGCATCGACGCAGCTATCGGTGATGTTTTATCGAAACCGTGGTTGCCTTTGCCTCTTGGACTGAAGCCACCTTCAGTGGACAGTGTGATGG
                                                                     |  | ||| |||||  | || |  |  |  | |   | |   |||||  |||  |  ||   | |  |||| ||  | |   |   |  |  ||   || |  |   | | |||  ||||||||||||||||| || ||||| || |||||||| ||| |||| |||||| ||||  |||| || ||||||||||| ||||| || |||||||| ||||
---------------------------------------------------------------------gtaagtgtatagct--agctgtagtgacattcat-gtttcttttcat-gcaacaacaatcatgta--ttctgcagcactctcaactcagcccttcttttttcctttctgtatttttcagTCAAGCGAGAGCATAGATGCAGCAATAGGTGATGTCTTAACGAAGCCGTGGCTGCCGCTGCCCCTCGGACTGAAGCCCCCTTCGGTAGACAGTGTCATGG

upper sequence: LOC_Os06g24070.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA13G37010.1 (Glycine max), 3'ss of exon 6
gtaagtatatatcaaacatttgtaactataacttcatcagaaggaacataaatattgaagatccatactggcaatgtttagctgaaactatcatatctctaaccatataacttcatcacaaggaagattcagaagtttcttcatg--aattaaattgcttcattttcattgttttaattttttttcccagTCAAGCGAGAGCATCGACGCAGCTATCGGTGATGTTTTATCGAAACCGTGGTTGCCTTTGCCTCTTGGACTGAAGCCACCTTCAGTGGACAGTGTGATGG
                                                                                         |  | | |   |   |||||  |  |  |  ||  ||| | |  | | |    | |  |||  ||    |   | |     ||  |   || ||||  |||||||  |||||||| |||||||||||  ||||||||||||| ||||| ||| ||||  | |||||||| || ||  | ||  || | ||  |||| ||||
----------------------------------------------------------------------------------------cacaaca-caagagagatatatttcgagaagtagctagaattaataatattgcaaggttaatctaacgtgtgtgtgtgtgg-gtcgtgtgttgttttgacagTCAAAGGAGAGCATAGACGCAGCTATTAGTGATGTTTTATCAAAACCATGGCTGCCACTACCTCTTGGCCTTAAAGCTCCAGCACTTGATGGTGTAATGG
















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|88557236|gb|CI487627.1|CI487627
EST:     AACTGCAGGTTCAACCA                         TCAAGGGAGAGCATGGACGCAGCTATCGGTGATGTTTTATCGAAACCGTGG
genomic: AACTCCAGGTTCAACCAgtaagtatat ... tttttcccagTCAAGCGAGAGCATCGACGCAGCTATCGGTGATGTTTTATCGAAACCGTGG
EST: gi|33669836|gb|CF298075.1|CF298075
EST:     TGGCGAGCAAGAATCAGCAGGAGGCGCAGCTTCAACTCCAGGTTCAACCA                         TCAAGCGAGAGCATCGACGCAGCTA
genomic: TGGCGAGCAAGAATCAGCAGGACGCACAGCTTCAACTCCAGGTTCAACCAgtaagtatat ... tttttcccagTCAAGCGAGAGCATCGACGCAGCTA
EST: gi|88534434|gb|CI463155.1|CI463155
EST:     TGGCGAGCAAGAATCAGCAGGACGCACAGCTTCAACTCCAGGTTCAACCA                         TCAAGCGAGAGCATCGACGCAGCTATCGGTGATGTTTTATCGAAACCGTGG
genomic: TGGCGAGCAAGAATCAGCAGGACGCACAGCTTCAACTCCAGGTTCAACCAgtaagtatat ... tttttcccagTCAAGCGAGAGCATCGACGCAGCTATCGGTGATGTTTTATCGAAACCGTGG
EST: gi|16577914|gb|BI812009.1|BI812009
EST:     TGACGAGCAAGAATCAGCAGGATGCACAGCTTCAACTCCAGGTTCAACCA                         TCAAGCGAGAGCATCGACGCAGCTATCGGTGATGTTTTATCGAAACCGTGG
genomic: TGGCGAGCAAGAATCAGCAGGACGCACAGCTTCAACTCCAGGTTCAACCAgtaagtatat ... tttttcccagTCAAGCGAGAGCATCGACGCAGCTATCGGTGATGTTTTATCGAAACCGTGG
EST: gi|109712581|gb|CI105189.1|CI105189
EST:     TGGCGAGCAAGAATCAGCAGGACGCACAGCTTCAACTCCAGGTTCAACCA                         TCAAGCGAGAGCATCGACGCAGCTATCGGTGATGTTTTATCGAAACCGTGG
genomic: TGGCGAGCAAGAATCAGCAGGACGCACAGCTTCAACTCCAGGTTCAACCAgtaagtatat ... tttttcccagTCAAGCGAGAGCATCGACGCAGCTATCGGTGATGTTTTATCGAAACCGTGG
EST: gi|86851181|gb|CI312582.1|CI312582
EST:     TGGCGAGCAAGAATCAGCAGGACGCACAGCTTCAACTCCAGGTTCAACCA                         TCAAGCGAGAGCATCGACGCAGCTATCGGTGATGTTTTATCGAAACCGTGG
genomic: TGGCGAGCAAGAATCAGCAGGACGCACAGCTTCAACTCCAGGTTCAACCAgtaagtatat ... tttttcccagTCAAGCGAGAGCATCGACGCAGCTATCGGTGATGTTTTATCGAAACCGTGG
EST: gi|29646518|gb|CB651525.1|CB651525
EST:     TGGCGAGCAAGAATCAGCAGGACGCACAGCTTCAACTCCAGGTTCAACCA                         TCAAGCGAGAGCATCGACGCAGCTATCGGTGATGTTTTATCGAAACCGTGG
genomic: TGGCGAGCAAGAATCAGCAGGACGCACAGCTTCAACTCCAGGTTCAACCAgtaagtatat ... tttttcccagTCAAGCGAGAGCATCGACGCAGCTATCGGTGATGTTTTATCGAAACCGTGG
EST: gi|88245126|gb|CI244975.1|CI244975
EST:     TGGCGAGCAAGAATCAGCAGGACGCACAGCTTCAACTCCAGGTTCAACCA                         TCAAGCGAGAGTATCGACGCAGCTATCGGTGATGTTTTATCGAAACCGTGG
genomic: TGGCGAGCAAGAATCAGCAGGACGCACAGCTTCAACTCCAGGTTCAACCAgtaagtatat ... tttttcccagTCAAGCGAGAGCATCGACGCAGCTATCGGTGATGTTTTATCGAAACCGTGG
EST: gi|88550395|gb|CI480364.1|CI480364
EST:     TGGCGAGCAAGAATCAGCAGGACGCACAGCTTCAACTCCAGGTTCAACCA                         TCAAGCGAGAGCATCGACGCAGCTATCGGTGATGTTTTATCGAAACCGTGG
genomic: TGGCGAGCAAGAATCAGCAGGACGCACAGCTTCAACTCCAGGTTCAACCAgtaagtatat ... tttttcccagTCAAGCGAGAGCATCGACGCAGCTATCGGTGATGTTTTATCGAAACCGTGG
EST: gi|58655623|gb|CK044303.1|CK044303
EST:     TGGCGAGCCAGAATCAGCAGGACGCACAGCTTCAACTCCAGGTTCAACCA                         TCAAGCGAGAGCATCGACGCAGCTATCGGTGATGTTTTATCGAAACCGTGG
genomic: TGGCGAGCAAGAATCAGCAGGACGCACAGCTTCAACTCCAGGTTCAACCAgtaagtatat ... tttttcccagTCAAGCGAGAGCATCGACGCAGCTATCGGTGATGTTTTATCGAAACCGTGG
EST: gi|29677764|gb|CB674039.1|CB674039
EST:     TGGCGAGCAAGAATCAGCAGGACGCACAGCTTCAACTCCAGGTTCAACCA                         TCAAGCGAGAGCATCGACGCAGCTATCGGTGATGTTTTATCGAAACCGTGG
genomic: TGGCGAGCAAGAATCAGCAGGACGCACAGCTTCAACTCCAGGTTCAACCAgtaagtatat ... tttttcccagTCAAGCGAGAGCATCGACGCAGCTATCGGTGATGTTTTATCGAAACCGTGG
EST: gi|87015668|gb|CI277626.1|CI277626
EST:     TGGCGAGCAAGAATCAGCAGGACGCACAGCTTCAACTCCAGGTTCAACCA                         TCAAGCGAGAGCATCGACGCAGCTATCGGTGATGTTTTATCGAAACCGTGG
genomic: TGGCGAGCAAGAATCAGCAGGACGCACAGCTTCAACTCCAGGTTCAACCAgtaagtatat ... tttttcccagTCAAGCGAGAGCATCGACGCAGCTATCGGTGATGTTTTATCGAAACCGTGG
EST: gi|88557964|gb|CI488413.1|CI488413
EST:     CAGGTTCAACCA                         TCAAGCGAGAGCATCGACGCAGCTATCGGTGATGTTTTATCGAAACCGTGG
genomic: CAGGTTCAACCAgtaagtatat ... tttttcccagTCAAGCGAGAGCATCGACGCAGCTATCGGTGATGTTTTATCGAAACCGTGG
EST: gi|86505799|gb|CI148432.1|CI148432
EST:     TGGCGAGCAAGAATCAGCAGGACGCACAGCTTCAACTCCAGGTTCAACCA                         TCAAGCGAGAGCATCGACGCAGCTATCGGTGATGTTTTATCGAAACCGTGG
genomic: TGGCGAGCAAGAATCAGCAGGACGCACAGCTTCAACTCCAGGTTCAACCAgtaagtatat ... tttttcccagTCAAGCGAGAGCATCGACGCAGCTATCGGTGATGTTTTATCGAAACCGTGG
EST: gi|88552687|gb|CI482718.1|CI482718
EST:     CTTCAACTCCAGGTTCAACCA                         TCAAGCGAGAGCATCGACGCAGCTATCGGTGATGTTTTATCGAAACCGTGG
genomic: CTTCAACTCCAGGTTCAACCAgtaagtatat ... tttttcccagTCAAGCGAGAGCATCGACGCAGCTATCGGTGATGTTTTATCGAAACCGTGG
EST: gi|88971522|gb|CI017836.1|CI017836
EST:     TGGCGAGCAAGAATCAGCAGGACGCACAGCTTCAACTCCAGGTTCAACCA                         TCAAGCGAGAGCATCGACGCAGCTATCGGTGATGTTTTATCGAAACCGTGG
genomic: TGGCGAGCAAGAATCAGCAGGACGCACAGCTTCAACTCCAGGTTCAACCAgtaagtatat ... tttttcccagTCAAGCGAGAGCATCGACGCAGCTATCGGTGATGTTTTATCGAAACCGTGG
EST: gi|89163861|gb|CI100751.1|CI100751
EST:     TGGCGAGCAAGAATCAGCAGGACGCACAGCTTCAACTCCAGGTTCAACCA                         TCAAGCGAGAGCATCGACGCAGCTATCGGTGATGTTTTATCGAAACCGTGG
genomic: TGGCGAGCAAGAATCAGCAGGACGCACAGCTTCAACTCCAGGTTCAACCAgtaagtatat ... tttttcccagTCAAGCGAGAGCATCGACGCAGCTATCGGTGATGTTTTATCGAAACCGTGG
EST: gi|29632770|gb|CB637779.1|CB637779
EST:     TGGCGAGCAAGAATCAGCAGGACGCACAGCTTCAACTCCAGGTTCAACCA                         TCAAGCGAGAGCATCGACGCAGCTATCGGTGATGTTTTATCGAAACCGTGG
genomic: TGGCGAGCAAGAATCAGCAGGACGCACAGCTTCAACTCCAGGTTCAACCAgtaagtatat ... tttttcccagTCAAGCGAGAGCATCGACGCAGCTATCGGTGATGTTTTATCGAAACCGTGG
EST: gi|33819905|gb|CF335766.1|CF335766
EST:     TGGCGAGCAAGAATCAGCAGGACGCACAGCTTCAACTCCAGGTTCAACCA                         TCAAGCGAGAGCATCGACGCAGCTATCGGTGATGTTTTATCGAAACCGTGG
genomic: TGGCGAGCAAGAATCAGCAGGACGCACAGCTTCAACTCCAGGTTCAACCAgtaagtatat ... tttttcccagTCAAGCGAGAGCATCGACGCAGCTATCGGTGATGTTTTATCGAAACCGTGG
EST: gi|88550323|gb|CI480287.1|CI480287
EST:     TGGCGAGCAAGAATCAGCAGGACGCACAGCTTCAACTCCAGGTTCAACCA                         TCAAGCGAGAGCATCGACGCAGCTATCGGTGATGTTTTATCGAAACCGTGG
genomic: TGGCGAGCAAGAATCAGCAGGACGCACAGCTTCAACTCCAGGTTCAACCAgtaagtatat ... tttttcccagTCAAGCGAGAGCATCGACGCAGCTATCGGTGATGTTTTATCGAAACCGTGG
EST: gi|38474383|gb|CF958515.1|CF958515
EST:     TGGCGAGCAAGAATGAGCAGGACGCACAGCTTCAACTCCAGGTTCAACCA                         TCAAGCGAGAGCATCGACGCAGCTATCGGTAATGTCTTATCGAAACCGTGG
genomic: TGGCGAGCAAGAATCAGCAGGACGCACAGCTTCAACTCCAGGTTCAACCAgtaagtatat ... tttttcccagTCAAGCGAGAGCATCGACGCAGCTATCGGTGATGTTTTATCGAAACCGTGG
EST: gi|87033461|gb|CI188085.1|CI188085
EST:     TGGCGAGCAAGAATCAGCAGGACGCACAGCTTCAACTCCAGGTTCAACCA                         TCAAGCGAGAGCATCGACGCAGCTATCGGTGATGTTTTATCGAAACCGTGG
genomic: TGGCGAGCAAGAATCAGCAGGACGCACAGCTTCAACTCCAGGTTCAACCAgtaagtatat ... tttttcccagTCAAGCGAGAGCATCGACGCAGCTATCGGTGATGTTTTATCGAAACCGTGG
EST: gi|89165913|gb|CI103003.1|CI103003
EST:     AACTCCAGGTTCAACCA                         TCAAGCGAGAGCATCGACGCAGCTATCGGTGATGTTTTATCGAAACCGTGG
genomic: AACTCCAGGTTCAACCAgtaagtatat ... tttttcccagTCAAGCGAGAGCATCGACGCAGCTATCGGTGATGTTTTATCGAAACCGTGG
EST: gi|58689120|gb|CK077807.1|CK077807
EST:     TGGCGAGCAAGAATCAGCAGGACGCACAGCTTCAACTCCAGGTTCAACCA                         TCAAGCGAGAGCATCGACGCAGCTATCGGTGATGTTTTATCGAAACCGTGG
genomic: TGGCGAGCAAGAATCAGCAGGACGCACAGCTTCAACTCCAGGTTCAACCAgtaagtatat ... tttttcccagTCAAGCGAGAGCATCGACGCAGCTATCGGTGATGTTTTATCGAAACCGTGG
EST: gi|88523247|gb|CI451055.1|CI451055
EST:     TGGCGAGCAAGAATCAGCAGGACGCACAGCTTCAACTCCAGGTTCAACCA                         TCAAGCGAGAGCATCGACGCAGCTATCGGTGATGTTTTATCGAAACCGTGG
genomic: TGGCGAGCAAGAATCAGCAGGACGCACAGCTTCAACTCCAGGTTCAACCAgtaagtatat ... tttttcccagTCAAGCGAGAGCATCGACGCAGCTATCGGTGATGTTTTATCGAAACCGTGG
EST: gi|89198749|gb|CI003486.1|CI003486
EST:     TGGCGAGCAAGAATCAGCAGGACGCACAGCTTCAACTCCAGGTTCAACCA                         TCAAGCGAGAGCATCGACGCAGCTATCGGTGATGTTTTATCGAAACCGTGG
genomic: TGGCGAGCAAGAATCAGCAGGACGCACAGCTTCAACTCCAGGTTCAACCAgtaagtatat ... tttttcccagTCAAGCGAGAGCATCGACGCAGCTATCGGTGATGTTTTATCGAAACCGTGG
EST: gi|88967370|gb|CI002522.1|CI002522
EST:     TGGCGAGCAAGAATCAGCAGGACGCACAGCTTCAACTCCAGGTTCAACCA                         TCAAGCGAGAGCATCGACGCAGCTATCGGTGATGTTTTATCGAAACCGTGG
genomic: TGGCGAGCAAGAATCAGCAGGACGCACAGCTTCAACTCCAGGTTCAACCAgtaagtatat ... tttttcccagTCAAGCGAGAGCATCGACGCAGCTATCGGTGATGTTTTATCGAAACCGTGG
EST: gi|22306077|gb|BQ907299.1|BQ907299
EST:     TGACGAGCAAGAATCAGCAGGACGCACAGCTTCAACTCCAGGTTCAACCA                         TCAAGCGAGAGCATCGACGCAGCTATCGGTGATGTTTTATCGAAACCGTGG
genomic: TGGCGAGCAAGAATCAGCAGGACGCACAGCTTCAACTCCAGGTTCAACCAgtaagtatat ... tttttcccagTCAAGCGAGAGCATCGACGCAGCTATCGGTGATGTTTTATCGAAACCGTGG
EST: gi|86888922|gb|CI314538.1|CI314538
EST:     GGCGAGCAAGAATCAGGCAGGACGCACAGCTTCAACTCCAGGTTCAACCA                         TCAAGCGAGAGCATCGACGCAGCTATCGGTGATGTTTTATCGAAACCGTGG
genomic: GGCGAGCAAGAATCA-GCAGGACGCACAGCTTCAACTCCAGGTTCAACCAgtaagtatat ... tttttcccagTCAAGCGAGAGCATCGACGCAGCTATCGGTGATGTTTTATCGAAACCGTGG
EST: gi|58587108|gb|CF985416.1|CF985416
EST:     TGGCGAGCAAGAATCAGCAGGACGCACAGCTTCAACTCCAGGTTCAACCA                         TCAAGCGAGAGCATCGACGCAGCTATCGGTGATGTTTTATCGAAACCGTGG
genomic: TGGCGAGCAAGAATCAGCAGGACGCACAGCTTCAACTCCAGGTTCAACCAgtaagtatat ... tttttcccagTCAAGCGAGAGCATCGACGCAGCTATCGGTGATGTTTTATCGAAACCGTGG

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: 67 (upstream exon), 70 (downstream exon)
Score: 20

GCCAGGAGTTGTCCCGTGTCCAATGTATAGGCCATTGACTCCACCAGCACTGGCGAGCAAGAATCAGCAGGACGCACAGCTTCAACTCCAGGTTCAACCAgtaagtatat ... tttttcccagTCAAGCGAGAGCATCGACGCAGCTATCGGTGATGTTTTATCGAAACCGTGGTTGCCTTTGCCTCTTGGACTGAAGCCACCTTCAGTGGACAGTGTGATGG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agtttcttcatgaattaaattgcttcattttcattgttttaattttttttcccagTCAAGCGAGAGCATCGACGCAGCTATCGGTGATGTTTTATCGAAACCGTGGTTGCCTTTGCCTCTTGGACTGAAGCCACCTTCAGTGGACAGTGTGATGG
                                    ttttaat  putative branch site (score: 20)
                                    ttttaattttttttcc  CT-rich tract
            aattaaattgcttcat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtatatatcaaacatttgtaactataacttcatcagaaggaacataaatattgaagatccatactggcaatgtttagctgaaactatcatatctctaaccatataacttcatcacaaggaagattcagaagtttcttcatgaattaaattgcttcattttcattgttttaattttttttcccagTCAAGCGAGAGCATCGACGCAGCTATCGGTGATGTTTTATCGAAACCGTGGTTGCCTTTGCCTCTTGGACTGAAGCCACCTTCAGTGGACAGTGTGATGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGTGGA