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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CGGCGCCGAAGAAGCTATTGGCATCGGACTCCCGATTGAGGCCTGATAGATATGCCCTCGAGAAGGGTGACATGTCAAAATCAGGTTCAGAAAAGAGCAGgtaattgctcattttgtcctaaacctgcgttgttttaggtgtttaatttgaggcatgtggcaaccatccaattatcttgacatttcatttcgtggaaactttcag

Basic information

species Oryza sativa
transcript LOC_Os03g16690.1
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g16690.1 (Oryza sativa), 5'ss of exon 9
lower sequence: GRMZM2G174644_T01 (Zea mays), 5'ss of exon 9
CGGCGCCGAAGAAGCTATTGGCATCGGACTCCCGATTGAGGCCTGATAGATATGCCCTCGAGAAGGGTGACATGTCAAAATCAGGTTCAGAAAAGAGCAGgtaattgctc-attttgtcctaaacctgcgttgttttaggtgtttaatttgaggcatgtggcaaccatccaattatcttgacatttc--atttcgtggaaactttcag
|||| || |||||||| |||||||| || || ||  |||||||||||||||||||||||||||||||||||||||| || || ||  |||| ||||||||||| || | | ||| | | ||          | | || ||  |||    ||     | || |  || | || || |     ||   |  | ||  || ||||||||||
CGGCACCTAAGAAGCTGTTGGCATCTGATTCACGGCTGAGGCCTGATAGATATGCCCTCGAGAAGGGTGACATGTCTAAGTCCGGGGCAGAGAAGAGCAGgtactttccccattctctgcttttatgattatatatt-ggaatttcgaatggcctgtttgcctgcc-ttcagttttgacaccacccccgagtttctgcaaactttcag

upper sequence: LOC_Os03g16690.1 (Oryza sativa), 5'ss of exon 9
lower sequence: GRMZM2G114126_T01 (Zea mays), 5'ss of exon 9
CGGCGCCGAAGAAGCTATTGGCATCGGACTCCCGATTGAGGCCTGATAGATATGCCCTCGAGAAGGGTGACATGTCAAAATCAGGTTCAGAAAAGAGCAGgtaattgctcattttgtcctaaacctgcgttgttttaggtgtttaatttgaggcatgtggcaaccatccaattatcttgacatttcatttcgtggaaactttcag-----------------------------------------
|||| || |||||||| |||||||| || |||||  ||||||| ||||||||||||||||||||||| |||||||| || || || |||||||||||||||||  | |||       ||    ||| |  |  | |   | |   |||  |      |  | | ||||   || |         |   | | ||    | |||                                           
CGGCACCTAAGAAGCTGTTGGCATCTGATTCCCGGCTGAGGCCCGATAGATATGCCCTCGAGAAGGGCGACATGTCCAAGTCTGGCTCAGAAAAGAGCAGgtatctcctcccccgccccgcccccttctctcctctgcctttacgattgtattttaattccgaacatcttgttttgcctctgcctggctgcctgccttccttcctgacaccacccctggcccctgcgttcccgcaaaacttttcag

upper sequence: LOC_Os03g16690.1 (Oryza sativa), 5'ss of exon 9
lower sequence: GLYMA12G06690.1 (Glycine max), 5'ss of exon 9
CGGCGCCGAAGAAGCTATTGGCATCGGACTCCCGATTGAGGCCTGATAGATATGCCCTCGAGAAGGGTGACATGTCAAAATCAGGTTCAGAAAAGAGCAGgtaattgctcattttgtcctaaacctgcgttgttttaggtgtttaatttgaggcatgtggcaaccatccaattatcttgacatttcatttcgtggaaactttcag
| || || |  ||| | |||||||| || || ||| |  | || ||||||||||| ||||||| ||| ||  |||||||||| ||  ||||||||||||||| | |   | |||  |      |     |    ||  |     || || ||    |        |  || | |     |  |   |||  ||   ||| | |  
CTGCCCCTAGAAAGTTGTTGGCATCAGATTCTCGACTACGCCCAGATAGATATGCACTCGAGATGGGCGATCTGTCAAAATCTGGGACAGAAAAGAGCAGgttactcaccctttcttttgttcctcctatccccttgtgcccaaaaatttagcagagcattttagaagcactaacacgaatgtcaaattgagt---aacgtac--

upper sequence: LOC_Os03g16690.1 (Oryza sativa), 5'ss of exon 9
lower sequence: GLYMA11G14770.1 (Glycine max), 5'ss of exon 9
CGGCGCCGAAGAAGCTATTGGCATCGGACTCCCGATTGAGGCCTGATAGATATGCCCTCGAGAAGGGTGACATGTCAAAATCAGGTTCAGAAAAGAGCAGgtaattgctcattttgtcctaaacctgcgttgttttaggtgtttaatttgaggcatgtggcaaccatccaattatcttgacatttcatttcgtggaaactttcag
| || || || ||| | ||||| || || || ||  |  | || ||||||||||| ||||||| ||| ||  |||||||||| ||  ||||||||||||||| | ||  | |||  |      |    ||    ||  |     || || ||    |        |  || | ||  | |  |   |||  ||   |        
CTGCCCCTAAAAAGTTGTTGGCGTCAGATTCTCGTCTACGCCCAGATAGATATGCACTCGAGATGGGCGATCTGTCAAAATCTGGGGCAGAAAAGAGCAGgttactgaccctttcttttgtttctcctgtccccttgtgcccaaaaatttagcatagcattttagaagcactaatactaatgtaaaattgagtaacagac-----

upper sequence: LOC_Os03g16690.1 (Oryza sativa), 5'ss of exon 9
lower sequence: Vv08s0007g00480.t01 (Vitis vinifera), 5'ss of exon 9
CGGCGCCGAAGAAGCTATTGGCATCGGACTCCCGATTGAGGCCTGATAGATATGCCCTCGAGAAGGGTGACATGTCAAAATCAGGTTCAGAAAAGAGCAGgtaattgctcattttgtcctaaacctgcgttgttttaggtgtttaatttgaggcatgtg-gcaaccatccaattatcttgacatttcatttcgtggaaactttcag
| || || | |||| | |||||||| || || || ||| | |||||||||||||| || |||||||||||  | || |||||  |||| |||||||||||||   | |||  | | ||      ||   |   |  |       |     | |||      ||  ||  ||   |  |  || | |   |      | |  |    
CTGCTCCCAGGAAGTTGTTGGCATCAGATTCTCGTTTGCGTCCTGATAGATATGCACTTGAGAAGGGTGATCTATCCAAATCTAGTTCTGAAAAGAGCAGgtttcttctctctctctctc---tctctctctatacacacacacacacacacgcacacacacacacacacacacacatatacgtatacatatacatatatatg---

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|86433616|gb|CI093959.1|CI093959
EST:     TATGCCCTCGAGAAGGGTGACATGTCAAAATCAGGTTCAGAAAAGAGCAG                         GCTTGAAGAGCAACAAAGAGCTGAGAAAAGAACACGAGAGGCCAAGGGGGA
genomic: TATGCCCTCGAGAAGGGTGACATGTCAAAATCAGGTTCAGAAAAGAGCAGgtaattgctc ... aaactttcagGCTTGAAGAGCAACAAAGAGCTGAGAAAAGAACACGAGAGGCCAAGGGGGA
EST: gi|29618293|gb|CB623305.1|CB623305
EST:     TATGCCCTCGAGAAGGGTGACATGTCAAAATCAGGTTCAGAAAAGAGCAG                         GCTTGAAGAGCAACAAAGAGCTGAGAAAAGAACACGAGAGGCCAAGGGGGA
genomic: TATGCCCTCGAGAAGGGTGACATGTCAAAATCAGGTTCAGAAAAGAGCAGgtaattgctc ... aaactttcagGCTTGAAGAGCAACAAAGAGCTGAGAAAAGAACACGAGAGGCCAAGGGGGA
EST: gi|87019938|gb|CI299336.1|CI299336
EST:     TATGCCCTCGAGAAGGGTGACATGTCAAAATCAGGTTCAGAAAAGAGCAG                         GCTTGAAGAGCAACAAAGAGCTGAGAAAAGAACACGAGAGGCCAAGGGGGA
genomic: TATGCCCTCGAGAAGGGTGACATGTCAAAATCAGGTTCAGAAAAGAGCAGgtaattgctc ... aaactttcagGCTTGAAGAGCAACAAAGAGCTGAGAAAAGAACACGAGAGGCCAAGGGGGA
EST: gi|33686825|gb|CF315064.1|CF315064
EST:     TATGCCCTCGAGAAGGGTGACATGTCAAAATCAGGTTCAGAAAAGAGCAG                         GCTTGAAGAGCAACAAAGAGCTGAGAAAAGAACACGAGAGGCCAAGGGGGA
genomic: TATGCCCTCGAGAAGGGTGACATGTCAAAATCAGGTTCAGAAAAGAGCAGgtaattgctc ... aaactttcagGCTTGAAGAGCAACAAAGAGCTGAGAAAAGAACACGAGAGGCCAAGGGGGA
EST: gi|58671178|gb|CK059864.1|CK059864
EST:     TATGCCCTCGAGAAGGGTGACATGTCAAAATCAGGTTCAGAAAAGAGCAG                         GCTTGAAGAGCAACAAAGAGCTGAGAAAAGAACACGAGAGGCCAAGGGGGA
genomic: TATGCCCTCGAGAAGGGTGACATGTCAAAATCAGGTTCAGAAAAGAGCAGgtaattgctc ... aaactttcagGCTTGAAGAGCAACAAAGAGCTGAGAAAAGAACACGAGAGGCCAAGGGGGA
EST: gi|88214603|gb|CI214452.1|CI214452
EST:     ATCAGGTTCAGAAAAGAGCAG                         GCTTGAAGAGCAACAAAGAGCTGAGAAAAGAACACGAGAGGCCAAGGGGGA
genomic: ATCAGGTTCAGAAAAGAGCAGgtaattgctc ... aaactttcagGCTTGAAGAGCAACAAAGAGCTGAGAAAAGAACACGAGAGGCCAAGGGGGA
EST: gi|29682877|gb|CB679152.1|CB679152
EST:     TATGCCCTCGAGAAGGGTGACATGTCAAAATCAGGTTCAGAAAAGAGCAG                         GCTTGAAGAGCAACAAAGAGCTGAGAAAAGAACACGAGAGGCCAAGGGGGA
genomic: TATGCCCTCGAGAAGGGTGACATGTCAAAATCAGGTTCAGAAAAGAGCAGgtaattgctc ... aaactttcagGCTTGAAGAGCAACAAAGAGCTGAGAAAAGAACACGAGAGGCCAAGGGGGA
EST: gi|86884608|gb|CI312987.1|CI312987
EST:     TCAAAATCAGGTTCAGAAAAGAGCAG                         GCTTGAAGAGCAACAAAGAGCTTAGAAAAGAACACGAGAGGCCAAGGGGGA
genomic: TCAAAATCAGGTTCAGAAAAGAGCAGgtaattgctc ... aaactttcagGCTTGAAGAGCAACAAAGAGCTGAGAAAAGAACACGAGAGGCCAAGGGGGA
EST: gi|86593972|gb|CI260201.1|CI260201
EST:     TATGCCCTCGAGAAGGGTGACATGTCAAAATCAGGTTCAGAAAAGAGCAG                         GCTTGAAGAGCAACAAAGAGCTGAGAAAAGAACACGAGAGGCCAAGGGGGA
genomic: TATGCCCTCGAGAAGGGTGACATGTCAAAATCAGGTTCAGAAAAGAGCAGgtaattgctc ... aaactttcagGCTTGAAGAGCAACAAAGAGCTGAGAAAAGAACACGAGAGGCCAAGGGGGA
EST: gi|88834258|gb|CI000622.1|CI000622
EST:     TATGCCCTCGAGAAGGGTGACATGTCAAAATCAGGTTCAGAAAAGAGCAG                         GCTTGAAGAGCAACAAAGAGCTGAGAAAAGAACACGAGAGGCCAAGGGGGA
genomic: TATGCCCTCGAGAAGGGTGACATGTCAAAATCAGGTTCAGAAAAGAGCAGgtaattgctc ... aaactttcagGCTTGAAGAGCAACAAAGAGCTGAGAAAAGAACACGAGAGGCCAAGGGGGA
EST: gi|38471242|gb|CF955373.1|CF955373
EST:     TATGCCCTCGAGAAGGGTGACATGTCAAAATCAGGTGCAGAAAAGAGCAG                         GCTTGAAGAGCAACAAAGAGCTGAGAAAAGAACACGAGAGGCCAAGGGGGA
genomic: TATGCCCTCGAGAAGGGTGACATGTCAAAATCAGGTTCAGAAAAGAGCAGgtaattgctc ... aaactttcagGCTTGAAGAGCAACAAAGAGCTGAGAAAAGAACACGAGAGGCCAAGGGGGA
EST: gi|13420867|gb|AU174957.1|AU174957
EST:     GACATGTCAAAATCAGGTTCAGAAAAGAGCAG                         GCTTGAAGAGCAACAAAGAGCTGAGAAAAGAACACGAGAGGCCAAGGGGGA
genomic: GACATGTCAAAATCAGGTTCAGAAAAGAGCAGgtaattgctc ... aaactttcagGCTTGAAGAGCAACAAAGAGCTGAGAAAAGAACACGAGAGGCCAAGGGGGA
EST: gi|55409301|gb|CV721677.1|CV721677
EST:     TATGCCCTCGAGAAGGGTGACATGTCAAAATCAGGTTCAGAAAAGAGCAG                         GCTTGAAGAGCAACAAAGAGCTGAGAAAAGAACACGAGAGGCCAAGGGGGA
genomic: TATGCCCTCGAGAAGGGTGACATGTCAAAATCAGGTTCAGAAAAGAGCAGgtaattgctc ... aaactttcagGCTTGAAGAGCAACAAAGAGCTGAGAAAAGAACACGAGAGGCCAAGGGGGA
EST: gi|88990539|gb|CI107926.1|CI107926
EST:     CATGTCAAAATCAGGTTCAGAAAAGAGCAG                         GCTTGAAGAGCAACAAAGAGCTGAGAAAAGAACACGAGAGGCCAAGGGGGA
genomic: CATGTCAAAATCAGGTTCAGAAAAGAGCAGgtaattgctc ... aaactttcagGCTTGAAGAGCAACAAAGAGCTGAGAAAAGAACACGAGAGGCCAAGGGGGA
EST: gi|86433684|gb|CI094027.1|CI094027
EST:     TATGCCCTCGAGAAGGGTGACATGTCAAAATCAGGTTCAGAAAAGAGCAG                         GCTTGAAGAGCAACAAAGAGCTGAGAAAAGAACACGAGAGGCCAAGGGGGA
genomic: TATGCCCTCGAGAAGGGTGACATGTCAAAATCAGGTTCAGAAAAGAGCAGgtaattgctc ... aaactttcagGCTTGAAGAGCAACAAAGAGCTGAGAAAAGAACACGAGAGGCCAAGGGGGA
EST: gi|396941588|gb|HO188245.1|HO188245
EST:     AAGGGTGACATGTCAAAATCAGGTTCAGAAAAGAGCAG                         GCTTGAAGAGCAACAAAGAGCTGAGAAAAGAACACGAGAGGCCAAGGGGGA
genomic: AAGGGTGACATGTCAAAATCAGGTTCAGAAAAGAGCAGgtaattgctc ... aaactttcagGCTTGAAGAGCAACAAAGAGCTGAGAAAAGAACACGAGAGGCCAAGGGGGA

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), 73 (downstream exon)
Score: 106

CGGCGCCGAAGAAGCTATTGGCATCGGACTCCCGATTGAGGCCTGATAGATATGCCCTCGAGAAGGGTGACATGTCAAAATCAGGTTCAGAAAAGAGCAGgtaattgctc ... aaactttcagGCTTGAAGAGCAACAAAGAGCTGAGAAAAGAACACGAGAGGCCAAGGGGGAGCAATTTACTCCAAGATGGTTTAACAGGACCGATGAAATCGCCCCTACA




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CGGCGCCGAAGAAGCTATTGGCATCGGACTCCCGATTGAGGCCTGATAGATATGCCCTCGAGAAGGGTGACATGTCAAAATCAGGTTCAGAAAAGAGCAGgtaattgctcattttgtcctaaacctgcgttgttttaggtgtttaatttgaggcatgtggcaaccatccaattatcttgacatttcatttcgtggaaactttcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG