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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ccactatgcatgttatctgtaaccaattaggatgattggtgactgcatatgttctgctatttactgcagtcccaaatttatgtgtgttgaatctgtgcagGAAGAACTGGACAACATGGCCAAAACCTACCCTGATCGCTTTAAGATCTACTATGTCTTGAATCAG

Basic information

species Oryza sativa
transcript LOC_Os01g59930.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g59930.2 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G133213_T01 (Zea mays), 3'ss of exon 6
ccactatgcatgttatctgtaaccaattaggatgattggtgactgca-----tatgttctgctatt-tactgcagtcccaaatttatgtgtgttgaatctgtgcagGAAGAACTGGACAACATGGCCAAAACCTACCCTGATCGCTTTAAGATCTACTATGTCTTGAATCAG
       |  | |||||| | | |  | ||  ||||| |    |||      |||| |  |||    ||||| | |    ||||| | |    |  |    | ||||| || |||||| |||||||||||||||| ||||  |||||||||||||||||||| |||||||||
------ggattcttatcttttatctgtcagactgatttgcacatgctctctttatgatgggctgccatactgaatttgataatttctattcaatccaatcatacagGATGAGCTGGACGACATGGCCAAAACCTATCCTGGCCGCTTTAAGATCTACTATGTGTTGAATCAG
















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|117244284|gb|CT843075.1|CT843075
EST:     AAGTTCATTTAGTCTATGCAAATGTCACGCATGACGACATTCTTCTGAAG                         GAAGAACTGGACAACATGGCCAAAACCTACCCTGATCGCTTTAAGATCTAC
genomic: AAGTTCATTTAGTCTATGCAAATGTCACGCATGACGACATTCTTCTGAAGgtggaatcac ... atctgtgcagGAAGAACTGGACAACATGGCCAAAACCTACCCTGATCGCTTTAAGATCTAC
EST: gi|88201419|gb|CI201774.1|CI201774
EST:     AAGTTCATTTAGTCTATGCAAATGTCACGCATGACGACATTCTTCTGAAG                         GAAGAACTGGACAACATGGCCCAAACCTACCCTGATCGCTTTAAGATCTAC
genomic: AAGTTCATTTAGTCTATGCAAATGTCACGCATGACGACATTCTTCTGAAGgtggaatcac ... atctgtgcagGAAGAACTGGACAACATGGCCAAAACCTACCCTGATCGCTTTAAGATCTAC
EST: gi|3767653|gb|AU031680.1|AU031680
EST:     CAAATGTCACGCATGACGACATTCTTTCTGAAG                         GAAGAACTGGACAACATGGCCAAAACCTACCCTGATCGCTTTAAGATCTA
genomic: CAAATGTCACGCATGACGACATTC-TTCTGAAGgtggaatcac ... atctgtgcagGAAGAACTGGACAACATGGCCAAAACCTACCCTGATCGCTTTAAGATCTA
EST: gi|88987863|gb|CI017952.1|CI017952
EST:     AAGTTCATTTAGTCTATGCAAATGTCACGCATGACGACATTCTTCTGAAG                         GAAGAACTGGACAACATGGCCAAAACCTACCCTGATCGCTTTAAGATCTAC
genomic: AAGTTCATTTAGTCTATGCAAATGTCACGCATGACGACATTCTTCTGAAGgtggaatcac ... atctgtgcagGAAGAACTGGACAACATGGCCAAAACCTACCCTGATCGCTTTAAGATCTAC
EST: gi|88214448|gb|CI214297.1|CI214297
EST:     GCATGACGACATTCTTCTGAAG                         GAAGAACTGGACAACATGGCCAAAACCTACCCTGATCGCTTTAAGATCTAC
genomic: GCATGACGACATTCTTCTGAAGgtggaatcac ... atctgtgcagGAAGAACTGGACAACATGGCCAAAACCTACCCTGATCGCTTTAAGATCTAC
EST: gi|58689499|gb|CK078186.1|CK078186
EST:     AAGTTCATTTAGTCTATGCAAATGTCACGCATGACGACATTCTTCTGAAG                         GAAGAACTGGACAACATGGCCAAAACCTACCCTGATCGCTTTAAGATCTAC
genomic: AAGTTCATTTAGTCTATGCAAATGTCACGCATGACGACATTCTTCTGAAGgtggaatcac ... atctgtgcagGAAGAACTGGACAACATGGCCAAAACCTACCCTGATCGCTTTAAGATCTAC
EST: gi|88832171|gb|CI017405.1|CI017405
EST:     TCTATGCAAATGTCACGCATGACGACATTCTTCTGAAG                         GAAGAACTGGACAACATGGCCAAAACCTACCCTGATCGCTTTAAGATCTAC
genomic: TCTATGCAAATGTCACGCATGACGACATTCTTCTGAAGgtggaatcac ... atctgtgcagGAAGAACTGGACAACATGGCCAAAACCTACCCTGATCGCTTTAAGATCTAC
EST: gi|88214584|gb|CI214433.1|CI214433
EST:     AAGTTCATTTAGTCTATGCAAATGTCACGCAGGACGACATTCTTCTGAAG                         GAAGAACTGGACAACATGGCCTAAACCTACCCTGATCGCTTTAAGATCTAC
genomic: AAGTTCATTTAGTCTATGCAAATGTCACGCATGACGACATTCTTCTGAAGgtggaatcac ... atctgtgcagGAAGAACTGGACAACATGGCCAAAACCTACCCTGATCGCTTTAAGATCTAC
EST: gi|58678583|gb|CK067270.1|CK067270
EST:     AAGTTCATTTAGTCTATGCAAATGTCACGCATGACGACATTCTTCTGAAG                         GAAGAACTGGACAACATGGCCAAAACCTACCCTGATCGCTTTAAGATCTAC
genomic: AAGTTCATTTAGTCTATGCAAATGTCACGCATGACGACATTCTTCTGAAGgtggaatcac ... atctgtgcagGAAGAACTGGACAACATGGCCAAAACCTACCCTGATCGCTTTAAGATCTAC
EST: gi|88848493|gb|CI087015.1|CI087015
EST:     AAGGTCATTTAGTCTATGCAAATGTCACGCATGACGACATTCTTCTGAAG                         GAAGAACTGGACAACATGGCCAAAACCTACCCTGATCGCTTTAAGATCTAC
genomic: AAGTTCATTTAGTCTATGCAAATGTCACGCATGACGACATTCTTCTGAAGgtggaatcac ... atctgtgcagGAAGAACTGGACAACATGGCCAAAACCTACCCTGATCGCTTTAAGATCTAC
EST: gi|86418467|gb|CI032676.1|CI032676
EST:     GTCACGCATGACGACATTCTTCTGAAG                         GAAGAACTGGACAACATGGCCAAAACCTACCCTGATCGCTTTAAGATCTAC
genomic: GTCACGCATGACGACATTCTTCTGAAGgtggaatcac ... atctgtgcagGAAGAACTGGACAACATGGCCAAAACCTACCCTGATCGCTTTAAGATCTAC
EST: gi|58608501|gb|CK036534.1|CK036534
EST:     AAGTTCATTTAGTCTATGCAAATGTCACGCATGACGACATTCTTCTGAAG                         GAAGAACTGGACAACATGGCCAAAACCTACCCTGATCGCTTTAAGATCTAC
genomic: AAGTTCATTTAGTCTATGCAAATGTCACGCATGACGACATTCTTCTGAAGgtggaatcac ... atctgtgcagGAAGAACTGGACAACATGGCCAAAACCTACCCTGATCGCTTTAAGATCTAC
EST: gi|88988656|gb|CI039075.1|CI039075
EST:     AAGTTCATTTAGTCTATGCAAATGTCACGCATGACGACATTCTTCTGAAG                         GAAGAACTGGACAACATGGCCNAAACCTACCCTGATCGCTTTAAGATCTAC
genomic: AAGTTCATTTAGTCTATGCAAATGTCACGCATGACGACATTCTTCTGAAGgtggaatcac ... atctgtgcagGAAGAACTGGACAACATGGCCAAAACCTACCCTGATCGCTTTAAGATCTAC

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: 66 (upstream exon), 75 (downstream exon)
Score: 47

GTTGCAAGGGCAATTCTTGAGAACCCTAATGATATCACAAAAGTTCATTTAGTCTATGCAAATGTCACGCATGACGACATTCTTCTGAAGgtggaatcac ... atctgtgcagGAAGAACTGGACAACATGGCCAAAACCTACCCTGATCGCTTTAAGATCTACTATGTCTTGAATCAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

catatgttctgctatttactgcagtcccaaatttatgtgtgttgaatctgtgcagGAAGAACTGGACAACATGGCCAAAACCTACCCTGATCGCTTTAAGATCTACTATGTCTTGAATCAG
                            aaatttatgt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ccactatgcatgttatctgtaaccaattaggatgattggtgactgcatatgttctgctatttactgcagtcccaaatttatgtgtgttgaatctgtgcagGAAGAACTGGACAACATGGCCAAAACCTACCCTGATCGCTTTAAGATCTACTATGTCTTGAATCAG

- - - tgcatgt
- - - - - - - - - -taaccaa
- - - - - - - - - - - - - - - gatgatt
- - - - - - - - - - - - - - - - - - - - gactgca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tactgca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgtgttg