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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgttaatttatctcctatttcttgtgcagtgctacttatcctttcttaatgatggtatttaggaagtatgtttgttattctgtagGTGTTACGCCGGCTTGCTCAAAATCGTGAGGCTGCAAGAAAAAGTCGGCTGAGAAAAAAG

Basic information

species Oryza sativa
transcript LOC_Os03g20310.2
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g20310.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G174284_T01 (Zea mays), 3'ss of exon 4
gtgttaatttatctcctatttcttgtgca-------gtgctacttatcctttcttaatgatggtatttaggaagtatgtttgttattctgtagGTGTTACGCCGGCTTGCTCAAAATCGTGAGGCTGCAAGAAAAAGTCGGCTGAGAAAAAAG
  |||  |||||||| ||| |||| || |       ||| |  ||| | ||||  |||||||| || |||  | |   |||| |||||| ||||| ||||| |||||||| |||||||||||||| ||||| |||||||||||||| ||||||
--gtttttttatctcatatgtcttctgtactctttagtgtttgttaccatttcacaatgatggaatctagataatgcatttgatattctttagGTTTTACGACGGCTTGCCCAAAATCGTGAGGCAGCAAGGAAAAGTCGGCTGAGGAAAAAG

upper sequence: LOC_Os03g20310.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G056099_T02 (Zea mays), 3'ss of exon 3
gtgttaattt-atctcctatttct-tgtgc-----agtgctacttatcctttcttaatgatggtatttaggaagtatgtttgttattctgtagGTGTTACGCCGGCTTGCTCAAAATCGTGAGGCTGCAAGAAAAAGTCGGCTGAGAAAAAAG
|| |||||||  |||||||| ||| ||| |     |||| |  ||| | ||||  ||||||||||| |||    |   |||| |||||| ||||| ||||| |||||||| |||||||||||||| ||||||||||| |||||||| ||||||
gtattaattttgtctcctatctctctgtactctttagtgtttgttaccatttcacaatgatggtatctagatgatgcatttggtattctttagGTTTTACGACGGCTTGCCCAAAATCGTGAGGCAGCAAGAAAAAGCCGGCTGAGGAAAAAG

upper sequence: LOC_Os03g20310.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA19G31050.3 (Glycine max), 3'ss of exon 6
gtgttaatttatctcctatttcttgtgcag-tgctacttatcctttcttaatg-atggtatttaggaagtatgtttgttattctgtagGTGTTACGCCGGCTTGCTCAAAATCGTGAGGCTGCAAGAAAAAGTCGGCTGAGAAAAAAG
       | |||    || || | |||||  |   |     | ||| ||| ||  || || ||      |   ||| | ||||   ||   ||| | |||||||||||||||||||||||||| || ||||| || ||||| ||||||
-----gttgtatgcagtaattgt-gtgcaaatagcataagccttttgttactgtgtgctaattt-----ttcatttttcattc---agACATTAAGACGGCTTGCTCAAAATCGTGAGGCTGCCAGGAAAAGCCGACTGAGGAAAAAG

upper sequence: LOC_Os03g20310.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA20G39050.2 (Glycine max), 3'ss of exon 4
-------gtgttaatt-tatctcctatttc-ttgtgcagt-gctacttatcctttcttaatgatggtatttagg-aagtat--gtttgttattc--tgtagGTGTTACGCCGGCTTGCTCAAAATCGTGAGGCTGCAAGAAAAAGTCGGCTGAGAAAAAAG
        |||| | | ||| |   ||||  || ||| ||   ||  ||   ||| | |||| |  |  ||| |  | |||   ||| ||| |   || ||    | ||  |||||||||| ||||||||||| ||||||||||||||| ||||||| || 
aaaacaaatgtttactctattttaaatttggttatgcggttaatatctaaaattt-taaatggtatttgttacgtgattattgattttttaattattgcagACTCTCCGAAGGCTTGCTCAGAATCGTGAGGCAGCAAGAAAAAGTCGGTTGAGAAAGAAA

upper sequence: LOC_Os03g20310.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA03G28400.1 (Glycine max), 3'ss of exon 1
-------------gtgttaatttatctcctatttcttgtgcagtgctacttatcctttcttaatgatggtatttaggaagtatgtttgttattc-tgtagGTGTTACGCCGGCTTGCTCAAAATCGTGAGGCTGCAAGAAAAAGTCGGCTGAGAAAAAAG
               ||||| |    |  |  |  |      |    |   | |||||  | |  |||   |        | | ||| || ||| |  ||   ||| | |||||||||||||||||||||||||| || ||||| || ||||| |||| |
ttgaccaatcaaaaggttaaatgcagtaattgtgttcaaatggcataagcaagccttttgttactatgcattaatttttctttttttatttttcattcagACATTAAGACGGCTTGCTCAAAATCGTGAGGCTGCCAGGAAAAGCCGACTGAGGAAAATG

upper sequence: LOC_Os03g20310.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA03G28320.2 (Glycine max), 3'ss of exon 6
gtgttaatttatctcctatttcttgtgcagtgctacttatcctttcttaatgatggtatttaggaagtatgtttgttattc-tgtagGTGTTACGCCGGCTTGCTCAAAATCGTGAGGCTGCAAGAAAAAGTCGGCTGAGAAAAAAG
       | |||    || || |  |  | ||  | | | |||||  | |  |||   |        | | ||| || ||| |  ||   ||| | |||||||||||||||||||||||||| || ||||| || ||||| ||||||
-----gttgtatgcagtaattgtgttcaaatggca-taagccttttgttactatgcattaatttttctttttttatttttcattcagACATTAAGACGGCTTGCTCAAAATCGTGAGGCTGCCAGGAAAAGCCGACTGAGGAAAAAG

upper sequence: LOC_Os03g20310.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA10G44270.1 (Glycine max), 3'ss of exon 4
-------gtgttaatt-tatctcctatttc-ttgtgcagtgctacttatcctttcttaatgatggtattta---ggaagtatgtttgttattc--tgtagGTGTTACGCCGGCTTGCTCAAAATCGTGAGGCTGCAAGAAAAAGTCGGCTGAGAAAAAAG
        |||| | | ||| |   ||||  || ||| ||  |  |      || | |||| |  |  |||   |    |   ||| ||| |   || ||    | ||  |||||||||| ||||| ||||||||||||||||||||| ||||||| || 
aaaacaaatgtttactctattttaaattttgttatgcggttatcatctaaaattttaaatggtatttgttacatgatcattgattttttaattattgcagAGTCTCCGGAGGCTTGCTCAGAATCGCGAGGCTGCAAGAAAAAGTCGGTTGAGAAAGAAA

upper sequence: LOC_Os03g20310.2 (Oryza sativa), 3'ss of exon 4
lower sequence: AT3G12250.5 (Arabidopsis thaliana), 3'ss of exon 4
gtgttaatttatctcctatttcttgtgcagtg-ctacttatcctttcttaatg-atggtat-ttaggaagtatgtttgttat--tctgtagGTGTTACGCCGGCTTGCTCAAAATCGTGAGGCTGCAAGAAAAAGTCGGCTGAGAAAAAAG
||| ||  ||     || |   |     ||   ||   |||  |      ||| ||  | | ||  |     | || ||| |  ||  |||    | ||  |||||||||||||||||||||| |||||||||||  |  |||| || |||
gtgatagattcatctctgtggatcaactagcatctgtgtatattacgcatatgcataatctgttttgtttccttttcgttttgatccatagACCCTTCGTAGGCTTGCTCAAAATCGTGAGGCAGCAAGAAAAAGCAGATTGAGGAAGAAG

upper sequence: LOC_Os03g20310.2 (Oryza sativa), 3'ss of exon 4
lower sequence: Vv08s0007g05170.t01 (Vitis vinifera), 3'ss of exon 5
gtgttaatttatctcctattt-cttgtgcagtgctacttatcctttcttaatgatggtatttaggaagtatgtttgttattctgtagGTGTTACGCCGGCTTGCTCAAAATCGTGAGGCTGCAAGAAAAAGTCGGCTGAGAAAAAAG
||   ||||||  |    | |  ||      | |  |||| | |    ||||| |  || || |    | || |   | ||||  ||   |||||||||||||||||||||||||| ||||| |||||||| ||  | || ||||||
gttaaaatttaaattagttatatttagatgatacagcttagcataa--taatgttcttaatttgttcctttgatcaatcttcttcagACATTACGCCGGCTTGCTCAAAATCGTGAAGCTGCCAGAAAAAGCCGATTAAGGAAAAAG

upper sequence: LOC_Os03g20310.2 (Oryza sativa), 3'ss of exon 4
lower sequence: Vv13s0084g00660.t01 (Vitis vinifera), 3'ss of exon 6
gtgttaatttatctcctatttcttgtgcagtgctacttatcctttcttaatg--atggtatttaggaag--tatgtttgtt---attctgtagGTGTTACGCCGGCTTGCTCAAAATCGTGAGGCTGCAAGAAAAAGTCGGCTGAGAAAAAAG
    | || ||  ||  | |  ||| |   ||    | |||    || ||||   |   ||||    |   | ||||||||   |||    ||    | ||  ||||||||||||||||||| |||||| ||||||| ||  ||||||| || 
---gtcatatagatcaaactaattgcg---tgtatatcatctcaactgaatgcagtaacatttgatgatcttttgtttgtttgtatttcacagACTCTTCGTAGGCTTGCTCAAAATCGTGAAGCTGCACGAAAAAGCCGATTGAGAAAGAAA

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|29622238|gb|CB627249.1|CB627249
EST:     CTAATTCATCTGATCGGTCTGACAGATCTGACAAGCCCATGGACCAAAAG                         GTGTTACGCCGGCTTGCTCAAAATCGTGAGGCTGCAAGAAAAAGTCGGCTG
genomic: CTAATTCATCTGATCGGTCTGACAGATCTGACAAGCCCATGGACCAAAAGgtgttaattt ... tattctgtagGTGTTACGCCGGCTTGCTCAAAATCGTGAGGCTGCAAGAAAAAGTCGGCTG
EST: gi|58592490|gb|CF990798.1|CF990798
EST:     CTAATTCATCTGATCGGTCTGACAGATCTGACAAGCCCATGGACCAAAAG                         GTGTTACGCCGGCTTGCTCAGAATCGTGAGGCTGCAAGAAAAAGTCGGCTG
genomic: CTAATTCATCTGATCGGTCTGACAGATCTGACAAGCCCATGGACCAAAAGgtgttaattt ... tattctgtagGTGTTACGCCGGCTTGCTCAAAATCGTGAGGCTGCAAGAAAAAGTCGGCTG
EST: gi|5803454|gb|AI978424.1|AI978424
EST:     CTAATTCATCTGATCGGTCTGACAGATCTGACAAGCCCATGGACCAAAAG                         GTGTTACGCCGGCTTGCTCAAAATCGTGAGGCTGCAAGAAAAAGTCGGCTG
genomic: CTAATTCATCTGATCGGTCTGACAGATCTGACAAGCCCATGGACCAAAAGgtgttaattt ... tattctgtagGTGTTACGCCGGCTTGCTCAAAATCGTGAGGCTGCAAGAAAAAGTCGGCTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gctacttatcctttcttaatgatggtatttaggaagtatgtttgttattctgtagGTGTTACGCCGGCTTGCTCAAAATCGTGAGGCTGCAAGAAAAAGTCGGCTGAGAAAAAAG
             tcttaat  putative branch site (score: 3)
                                            ttattct  putative PPT
           tttcttaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgttaatttatctcctatttcttgtgcagtgctacttatcctttcttaatgatggtatttaggaagtatgtttgttattctgtagGTGTTACGCCGGCTTGCTCAAAATCGTGAGGCTGCAAGAAAAAGTCGGCTGAGAAAAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA