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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aatcatgcttgcatgtacaatgggatgtgattttgactcatttgaaattgctgaagaactgttatggtatgaacctgatttggtgttgttcatgtcctagCTATCTCCTCTGCACAGTAGGATCTGTGTACATTAAATCAAAAGAGGCTCCTGCGAAAGACGTTCTTAAAGACCTTGTTGAAATGTGTCGAGGCATCCAA

Basic information

species Oryza sativa
transcript LOC_Os03g58700.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g58700.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM5G844195_T02 (Zea mays), 3'ss of exon 3
aatcatgcttgcatgtacaatgggatgtgattttgactcattt---gaaattgctgaagaactgttatggtatgaacctgatttggtgttgttcatgtcctagCTATCTCCTCTGCACAGTAGGATCTGTGTACATTAAATCAAAAGAGGCTCCTGCGAAAGACGTTCTTAAAGACCTTGTTGAAATGTGTCGAGGCATCCAA
  || ||      | |  ||   |    ||  |   ||  ||    || | | |  | ||  | | |    ||  | || ||||||||||    |  | | ||||||||||| ||||| || || ||||||||||| ||||| |||||||||||||| ||||| ||||||||||| || ||||||||||| |||||||| |||
gctcttgaacatctatgaaacttgtgaagaactgatcttcttctaggagaatacctatgatttatgaaaacatacatcttatttggtgtt---tacatgccagCTATCTCCTGTGCACGGTGGGGTCTGTGTACATCAAATCGAAAGAGGCTCCTGCTAAAGATGTTCTTAAAGATCTCGTTGAAATGTGCCGAGGCATTCAA

upper sequence: LOC_Os03g58700.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM5G825524_T02 (Zea mays), 3'ss of exon 3
-----aatcatgcttgcatgtacaatgggatgtgattttgactcatttgaaattgctgaagaactgttatggtatgaacctgatttggtgttgttcatgtcctagCTATCTCCTCTGCACAGTAGGATCTGTGTACATTAAATCAAAAGAGGCTCCTGCGAAAGACGTTCTTAAAGACCTTGTTGAAATGTGTCGAGGCATCCAA
      | |||   || |  |  |    ||  | || ||   |||   || | | |  | ||  | | |    ||  | |||||||||||||    |  | | ||||||||||| ||||| || |||||||||||||| ||||| |||||||||||||| ||||| ||||||||||| || ||||||||||| |||||||| || 
ctcttgaacatctatg-aaatttatgaagagctaatcttttttcaag-gataatacctatgatttatgaaaacatacatctgatttggtgtt---tacatgccagCTATCTCCTGTGCACGGTGGGATCTGTGTACATCAAATCGAAAGAGGCTCCTGCTAAAGATGTTCTTAAAGATCTCGTTGAAATGTGCCGAGGCATTCAG

upper sequence: LOC_Os03g58700.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA01G36870.1 (Glycine max), 3'ss of exon 3
----aatcatgctt-gcatgtacaatgggatgtgattttgactcatttgaaattgctgaagaactgttatggtatgaacctgatttggtgttgttcatgtcctagCTATCTCCTCTGCACAGTAGGATCTGTGTACATTAAATCAAAAGAGGCTCCTGCGAAAGACGTTCTTAAAGACCTTGTTGAAATGTGTCGAGGCATCCAA
      | |||||| | |  |     | | |    | |  | || || ||  ||  | | |     |  | ||  |    | ||||  || |    ||     || ||||||||||| ||||||||||| || ||||| ||||| || || |||||||| || || |||||||| || || || || |||||||||||||| || 
ggggtttaatgctttgaagatttgcagtggttaagtgtacattctttcgagtttaat-atgcttcttacttgtgagctgttaattttatgattgcgat----cagGTATCTCCTCTGTACAGTAGGATCAGTATACATCAAATCCAAGGAAGCTCCTGCAAAGGATGTTCTTAAGGATCTCGTGGAGATGTGTCGAGGCATTCAG

upper sequence: LOC_Os03g58700.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA11G08390.1 (Glycine max), 3'ss of exon 3
---aatcatgcttgcatgtacaatgggatgtgattttgactcatttgaaattgctgaagaactgttatggtatgaacctgatttggtgttgttcatgtcct-agCTATCTCCTCTGCACAGTAGGATCTGTGTACATTAAATCAAAAGAGGCTCCTGCGAAAGACGTTCTTAAAGACCTTGTTGAAATGTGTCGAGGCATCCAA
    |  | | ||  |||| |  ||   | |     ||  | | ||   |||  |  |    |  |||| |    | |||  ||  | || |   ||   | || || |||||||| ||||||||||| || ||||| ||||| || || |||||||| || || |||||||| || ||||| || ||||| || ||||| || 
agtgagaagggtttaatgttc--tgaagttttgccgtgcttaagttttcattctttcatgtttaatatgcttgtgagctg--ttaatattatgattgcaatcagGTACCTCCTCTGTACAGTAGGATCAGTATACATCAAATCCAAGGAAGCTCCTGCAAAGGATGTTCTTAAGGATCTTGTGGAGATGTGCCGTGGCATTCAG

upper sequence: LOC_Os03g58700.1 (Oryza sativa), 3'ss of exon 3
lower sequence: Vv18s0001g14680.t01 (Vitis vinifera), 3'ss of exon 3
-aatcatgcttgcatgtacaatgggatgtgattttgactcatttgaaattgctgaagaactgttatggtatgaacctgatttggtgttgttcatgtcctagCTATCTCCTCTGCACAGTAGGATCTGTGTACATTAAATCAAAAGAGGCTCCTGCGAAAGACGTTCTTAAAGACCTTGTTGAAATGTGTCGAGGCATCCAA
   | | | ||| || |      | |||| |   |     ||||  || |     |   |   |     | | |  ||| |  |||||||| || |   || |||||| | || || ||||||||||| || || |||||||| ||||||||| | || || || |||||||| ||||| |||||||| || || || |||
gcttgaagtttgtattttagtctgtatgttagcatatgcaatttttaaatatgccatctccaattctaga-gcatatgaatatgtgttgttgatttatcagGTATCTCTTATGTACGGTAGGATCTGTATATATCAAATCAAAGGAGGCTCCTCCTAAGGATGTCCTTAAAGATCTTGTGGAAATGTGCCGTGGTATTCAA

upper sequence: LOC_Os03g58700.1 (Oryza sativa), 3'ss of exon 3
lower sequence: Vv04s0023g03870.t01 (Vitis vinifera), 3'ss of exon 3
-aatcatgc-ttgcatgtacaatgggatgtgattttgactcatttgaaattgctgaagaactgttatggtatgaacctga-tttggtgttgttcatgtcctagCTATCTCCTCTGCACAGTAGGATCTGTGTACATTAAATCAAAAGAGGCTCCTGCGAAAGACGTTCTTAAAGACCTTGTTGAAATGTGTCGAGGCATCCAA
  ||  | | ||  |   |||   |  |||    |  | |  | |    ||  || |    |   |||   | |   ||| ||  ||||| |  ||  || || ||||| ||||| ||||| |||||||||||||| ||||| || ||||||||||| || || |||||||| || ||||| |||||||| || |||||||||
ggattgtacattatagagacatcagtttgta---taaatttttatttttttcatgtaatgtttccatgtcttaattttgaattctgtgttctctattgcccagGTATCTTCTCTGTACAGTTGGATCTGTGTACATCAAATCTAAGGAGGCTCCTGCTAAGGATGTTCTTAAGGATCTTGTGGAAATGTGCCGTGGCATCCAA

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|29628687|gb|CB633698.1|CB633698
EST:     GTTGATTTGTATGAGCTTGTGCAGCATGCTGGCAACGTACTGCCCAGACT                         CTATCTCCTCTGCACAGTAGGATCTGTGTACATTAAATCAAAAGAGGCTCC
genomic: GTTGATTTGTATGAGCTTGTGCAGCATGCTGGCAACGTACTGCCCAGACTgtaagactaa ... catgtcctagCTATCTCCTCTGCACAGTAGGATCTGTGTACATTAAATCAAAAGAGGCTCC
EST: gi|88585635|gb|CI703290.1|CI703290
EST:     GTTGATTTGTATGAGCTTGTGCAGCATGCTGGCAACGTACTGCCCAGACT                         CTATCTCCTCTGCACAGTAGGATCTGTGTACATTAAATCAAAAGAGGCTCC
genomic: GTTGATTTGTATGAGCTTGTGCAGCATGCTGGCAACGTACTGCCCAGACTgtaagactaa ... catgtcctagCTATCTCCTCTGCACAGTAGGATCTGTGTACATTAAATCAAAAGAGGCTCC
EST: gi|58660347|gb|CK049027.1|CK049027
EST:     GTTGATTTGTATGAGCTTGTGCAGCATGCTGGCAACGTACTGCCCAGACT                         CTATCTCCTCTGCACAGTAGGATCTGTGTACATTAAATCAAAAGAGGCTCC
genomic: GTTGATTTGTATGAGCTTGTGCAGCATGCTGGCAACGTACTGCCCAGACTgtaagactaa ... catgtcctagCTATCTCCTCTGCACAGTAGGATCTGTGTACATTAAATCAAAAGAGGCTCC
EST: gi|88425407|gb|CI567127.1|CI567127
EST:     GTTGATTTGTATGAGCTTGTGCAGCATGCTGGCAACGTACTGGCCAGACT                         CTATCTCCTCTGCACAGTAGGATCTGTG
genomic: GTTGATTTGTATGAGCTTGTGCAGCATGCTGGCAACGTACTGCCCAGACTgtaagactaa ... catgtcctagCTATCTCCTCTGCACAGTAGGATCTGTG
EST: gi|29634546|gb|CB639555.1|CB639555
EST:     GTTGATTTGTATGAGCTTGTGCAGCATGCTGGCAACGTACTGCCCAGACT                         CTATCTCCTCTGCACAGTAGGATCTGTGTACATTAAATCAAAAGAGGCTCC
genomic: GTTGATTTGTATGAGCTTGTGCAGCATGCTGGCAACGTACTGCCCAGACTgtaagactaa ... catgtcctagCTATCTCCTCTGCACAGTAGGATCTGTGTACATTAAATCAAAAGAGGCTCC
EST: gi|88339082|gb|CI677904.1|CI677904
EST:     GTTGATTTGTATGAGCTTGTGCAGCATGCTGGCAACGTACTGCCCAGACT                         CTATCTCCTCTGCACAGTAGGATCTGTGTACATTAAATCAAAAGAGGCTCC
genomic: GTTGATTTGTATGAGCTTGTGCAGCATGCTGGCAACGTACTGCCCAGACTgtaagactaa ... catgtcctagCTATCTCCTCTGCACAGTAGGATCTGTGTACATTAAATCAAAAGAGGCTCC
EST: gi|29627956|gb|CB632967.1|CB632967
EST:     GTTGATTTGTATGAGCTTGTGCAGCATGCTGGCAACGTACTGCCCAGACT                         CTATCTCCTCTGCACAGTAGGATCTGTGTACATTAAATCAAAAGAGGCTCC
genomic: GTTGATTTGTATGAGCTTGTGCAGCATGCTGGCAACGTACTGCCCAGACTgtaagactaa ... catgtcctagCTATCTCCTCTGCACAGTAGGATCTGTGTACATTAAATCAAAAGAGGCTCC
EST: gi|33675182|gb|CF303421.1|CF303421
EST:     GTTGATTTGTATGAGCTTGTGCAGCATGCTGGCAACGTACTGCCCAGACT                         CTATCTCCTCTGCACAGTAGGATCTGTGTACATTAAATCAAAAGAGGCTCC
genomic: GTTGATTTGTATGAGCTTGTGCAGCATGCTGGCAACGTACTGCCCAGACTgtaagactaa ... catgtcctagCTATCTCCTCTGCACAGTAGGATCTGTGTACATTAAATCAAAAGAGGCTCC
EST: gi|58662129|gb|CK050809.1|CK050809
EST:     GTTGATTTGTATGAGCTTGTGCAGCATGCTGGCAACGTACTGCCCAGACT                         CTATCTCCTCTGCACAGTAGGATCTGTGTACATTAAATCAAAAGAGGCTCC
genomic: GTTGATTTGTATGAGCTTGTGCAGCATGCTGGCAACGTACTGCCCAGACTgtaagactaa ... catgtcctagCTATCTCCTCTGCACAGTAGGATCTGTGTACATTAAATCAAAAGAGGCTCC
EST: gi|88369738|gb|CI680407.1|CI680407
EST:     GTTGATTTGTATGAGCTTGTGCAGCATGCTGGCAACGTACTGCCCAGACT                         CTATCTCCTCTGCACAGTAGGATCTGTGTACATTAAATCAAAAGAGGCTCC
genomic: GTTGATTTGTATGAGCTTGTGCAGCATGCTGGCAACGTACTGCCCAGACTgtaagactaa ... catgtcctagCTATCTCCTCTGCACAGTAGGATCTGTGTACATTAAATCAAAAGAGGCTCC
EST: gi|29634961|gb|CB639970.1|CB639970
EST:     GTTGATTTGTATGAGCTTGTGCAGCATGCTGGCAACGTACTGCCCAGACT                         CTATCTCCTCTGCACAGTAGGATCTGTGTACATTAAATCAAAAGAGGCTCC
genomic: GTTGATTTGTATGAGCTTGTGCAGCATGCTGGCAACGTACTGCCCAGACTgtaagactaa ... catgtcctagCTATCTCCTCTGCACAGTAGGATCTGTGTACATTAAATCAAAAGAGGCTCC
EST: gi|87008988|gb|CI304931.1|CI304931
EST:     GTTGATTTGTATGAGCTTGTGCAGCATGCTGGCAACGTACTGCCCAGACT                         CTATCTCCTCT
genomic: GTTGATTTGTATGAGCTTGTGCAGCATGCTGGCAACGTACTGCCCAGACTgtaagactaa ... catgtcctagCTATCTCCTCT
EST: gi|88719457|gb|CI742967.1|CI742967
EST:     GTTGATTTGTATGAGCTTGTGCAGCATGCTGGCAACGTACTGCCCAGACT                         CTATCTCCTCTGCACAGTAGGATCTGTGTACATTA
genomic: GTTGATTTGTATGAGCTTGTGCAGCATGCTGGCAACGTACTGCCCAGACTgtaagactaa ... catgtcctagCTATCTCCTCTGCACAGTAGGATCTGTGTACATTA
EST: gi|88314794|gb|CI608253.1|CI608253
EST:     GTTGATTTGTATGAGCTTGTGCAGCATGCTGGCAACGTACTGCCCAGACT                         CTATCTCCTCTGCACAGTAGGATCTGTGTACATTAAATCAAAAGAG
genomic: GTTGATTTGTATGAGCTTGTGCAGCATGCTGGCAACGTACTGCCCAGACTgtaagactaa ... catgtcctagCTATCTCCTCTGCACAGTAGGATCTGTGTACATTAAATCAAAAGAG
EST: gi|88388322|gb|CI627861.1|CI627861
EST:     GTTGATTTGTATGAGCTTGTGCAGCATGCTGGCAACGTACTGCCCAGACT                         CTATCTCCTCTGCACAGTAGGATCT
genomic: GTTGATTTGTATGAGCTTGTGCAGCATGCTGGCAACGTACTGCCCAGACTgtaagactaa ... catgtcctagCTATCTCCTCTGCACAGTAGGATCT

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), 74 (downstream exon)
Score: 35

AGCTGGAGATGTTCTTCAGGGAGGAGACCCGTCGTGGCAGCTGCTCCGTTGTTGATTTGTATGAGCTTGTGCAGCATGCTGGCAACGTACTGCCCAGACTgtaagactaa ... catgtcctagCTATCTCCTCTGCACAGTAGGATCTGTGTACATTAAATCAAAAGAGGCTCCTGCGAAAGACGTTCTTAAAGACCTTGTTGAAATGTGTCGAGGCATCCAA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aattgctgaagaactgttatggtatgaacctgatttggtgttgttcatgtcctagCTATCTCCTCTGCACAGTAGGATCTGTGTACATTAAATCAAAAGAGGCTCCTGCGAAAGACGTTCTTAAAGACCTTGTTGAAATGTGTCGAGGCATCCAA
                           acctgat  putative branch site (score: 35)
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aatcatgcttgcatgtacaatgggatgtgattttgactcatttgaaattgctgaagaactgttatggtatgaacctgatttggtgttgttcatgtcctagCTATCTCCTCTGCACAGTAGGATCTGTGTACATTAAATCAAAAGAGGCTCCTGCGAAAGACGTTCTTAAAGACCTTGTTGAAATGTGTCGAGGCATCCAA

-atcatgc
- - - - -tgcatgt
- - - - - - - - - - - ggatgtg
- - - - - - - - - - - - - - - - - - -tcatttg
- - - - - - - - - - - - - - - - - - - - - - - - tgctgaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgttatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gaacctg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ggtgttg