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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gcaggatttctttgttcttctcaaaccagccaatcatgctgtgtaacctggatataccagagctaacttcggttatttcttattgaccagACAGAGCAAATGAGCAGAATTGTTAATGAGCTGGATTCCATTCATTTCTCCATTAAAAAGGCATCACAAATGGTGAAAGAAATTGGTAGGCAG

Basic information

species Oryza sativa
transcript LOC_Os06g50120.1
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g50120.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G065105_T05 (Zea mays), 3'ss of exon 1
gcaggatttctttgttcttctcaaa---------ccagccaatcatgctgtgtaacctggatataccagagctaacttcggttatttcttattgaccagACAGAGCAAATGAGCAGAATTGTTAATGAGCTGGATTCCATTCATTTCTCCATTAAAAAGGCATCACAAATGGTGAAAGAAATTGGTAGGCAG-------
| | | ||  ||| || ||  || |                || ||| |||  || | ||| |    |  || |  || || |||| ||| || | |||||||| |||||||||||| ||||||||||| |||||||||| ||||||||||| ||||||||||| ||| ||||||||||||| ||| | |||       
gtacgtttcttttcttatttccagaaggaatccattgctttattatgttgtccaatcaggaaagctaaaggcaattttgggctattccttcttcatcagACAGAACAAATGAGCAGAGTTGTTAATGAGTTGGATTCCATCCATTTCTCCATCAAAAAGGCATCTCAATTGGTGAAAGAAATCGGTCGACAGGTAAATT

upper sequence: LOC_Os06g50120.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G065105_T02 (Zea mays), 3'ss of exon 7
gcaggatttctttgttcttctcaaa---------ccagccaatcatgctgtgtaacctggatataccagagctaacttcggttatttcttattgaccagACAGAGCAAATGAGCAGAATTGTTAATGAGCTGGATTCCATTCATTTCTCCATTAAAAAGGCATCACAAATGGTGAAAGAAATTGGTAGGCAG
| | | ||  ||| || ||  || |                || ||| |||  || | ||| |    |  || |  || || |||| ||| || | |||||||| |||||||||||| ||||||||||| |||||||||| ||||||||||| ||||||||||| ||| ||||||||||||| ||| | |||
gtacgtttcttttcttatttccagaaggaatccattgctttattatgttgtccaatcaggaaagctaaaggcaattttgggctattccttcttcatcagACAGAACAAATGAGCAGAGTTGTTAATGAGTTGGATTCCATCCATTTCTCCATCAAAAAGGCATCTCAATTGGTGAAAGAAATCGGTCGACAG

upper sequence: LOC_Os06g50120.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GLYMA17G15990.1 (Glycine max), 3'ss of exon 7
gcaggatttctttgttct-tctcaaacc----agccaatcatgctgtgtaacctggatataccagagctaacttcggttatttcttat-tgaccagACAGAGCAAATGAGCAGAATTGTTAATGAGCTGGATTCCATTCATTTCTCCATTAAAAAGGCATCACAAATGGTGAAAGAAATTGGTAGGCAG
| | || |  |  |     || || |||    |   |||   |      | | ||  | | |||  |  |     ||||   |||| | || | |||| || |||||||||||| |||| |||||||||||||| || |||||||| || || || || ||  || |||| || ||||| |||||||||
gtatgaatcttaagcctagtcccacaccccagaattaattgagaaaaaaagcttgagtttgccatgggaactaagggttcactcttctatgtctagACGGAACAAATGAGCAGAGTTGTCAATGAGCTGGATTCAATCCATTTCTCTATAAAGAAAGCCTCTAAATTGGTCAAGGAAATCGGTAGGCAG

upper sequence: LOC_Os06g50120.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GLYMA05G05720.2 (Glycine max), 3'ss of exon 4
gcaggatttctttgttct-tctcaaacc----agccaatcatgctgtgtaacctggatataccagagctaacttcggttat-ttcttat-tgaccagACAGAGCAAATGAGCAGAATTGTTAATGAGCTGGATTCCATTCATTTCTCCATTAAAAAGGCATCACAAATGGTGAAAGAAATTGGTAGGCAG
| | || |  | ||     || || |||    |  |||    |      | | || || | |||  |  ||||  || ||   |||| | || | ||||||| |||||||| ||| |||| |||||||||||||| || |||||||| || || || || ||  || |||| || |||||||        
gtatgaatcttatgcctagtcccacacctcagaatcaactgagaaaaaaagcttgaatttgccat-gtgaactaagggtacactcttctatgtctagACAGAACAAATGAGTAGAGTTGTCAATGAGCTGGATTCAATCCATTTCTCTATGAAGAAAGCCTCTAAATTGGTCAAGGAAATTG--------

upper sequence: LOC_Os06g50120.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GLYMA05G05720.1 (Glycine max), 3'ss of exon 4
gcaggatttctttgttct-tctcaaacc----agccaatcatgctgtgtaacctggatataccagagctaacttcggttat-ttcttat-tgaccagACAGAGCAAATGAGCAGAATTGTTAATGAGCTGGATTCCATTCATTTCTCCATTAAAAAGGCATCACAAATGGTGAAAGAAATTGGTAGGCAG
| | || |  | ||     || || |||    |  |||    |      | | || || | |||  |  ||||  || ||   |||| | || | ||||||| |||||||| ||| |||| |||||||||||||| || |||||||| || || || || ||  || |||| || |||||||||||||||
gtatgaatcttatgcctagtcccacacctcagaatcaactgagaaaaaaagcttgaatttgccat-gtgaactaagggtacactcttctatgtctagACAGAACAAATGAGTAGAGTTGTCAATGAGCTGGATTCAATCCATTTCTCTATGAAGAAAGCCTCTAAATTGGTCAAGGAAATTGGTAGGCAG

upper sequence: LOC_Os06g50120.1 (Oryza sativa), 3'ss of exon 7
lower sequence: AT2G35190.1 (Arabidopsis thaliana), 3'ss of exon 6
------------------------------------------------gcaggatttctttgttcttctcaaaccagccaatcatgctgtgtaacctggatataccagagctaacttcggttatttcttattgaccagACAGAGCAAATGAGCAGAATTGTTAATGAGCTGGATTCCATTCATTTCTCCATTAAAAAGGCATCACAAATGGTGAAAGAAATTGGTAGGCAG
                                                 | | || || || || |||  | |      | |  || |||| |  |||   ||     || ||  ||   || || ||| ||   ||||| ||||||||||| ||| |||| |||||||| ||||| |||||||||||  | || || || ||  |  |||| || |||||||||||||||
gtgtgtagttagcccacacttgtttctttccaaacagtcctgcttctacctgaatctcatt-tttttccaagattgtgtatttgtg-tgtgaattctgagaattattaagatagtttacatt-ttccttgtt---cagACCGAGCAAATGAGTAGAGTTGTCAATGAGCTCGATTCTATTCATTTCTCACTCAAGAAAGCCTCCAAGCTGGTCAAGGAAATTGGTAGGCAG

upper sequence: LOC_Os06g50120.1 (Oryza sativa), 3'ss of exon 7
lower sequence: Vv02s0012g00140.t01 (Vitis vinifera), 3'ss of exon 7
-------------------------------------------------------------------gcaggatttctttgttcttctcaaaccagccaatcatgctgtgtaacctggatataccagagctaacttcggttatttcttattgaccagACAGAGCAAATGAGCAGAATTGTTAATGAGCTGGATTCCATTCATTTCTCCATTAAAAAGGCATCACAAATGGTGAAAGAAATTGGTAGGCAG
                                                                    ||| | || | | ||    |       |    |  | ||  |  || |||       || | |    |    | |   ||  ||  ||||| || ||||||||||| |||||||| ||||| ||||| || |||||||| || || || || |||||  |||| || |||||||||||||||
gtctgtacctcatcaatattaaatttttttctgattctgacacattgctacaatttagattcaatttacagcacttgtattttacctttctttttgaaggttttcctaag--acatggtagcttaagtgtttcaatttactttacgtttatgttcagACTGAACAAATGAGCAGGATTGTTAACGAGCTAGATTCTATCCATTTCTCAATCAAGAAAGCTTCACAGCTGGTCAAGGAAATTGGTAGGCAG

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|88964764|gb|CI084762.1|CI084762
EST:     TGCTCTCAAATCACAG                         ACAGAGCAAATGAGCAGAATTGTTAATGAGCTGGATTCCATTCATTTCTCC
genomic: TGCTCTCAAATCACAGgcaggatttc ... tattgaccagACAGAGCAAATGAGCAGAATTGTTAATGAGCTGGATTCCATTCATTTCTCC
EST: gi|88964517|gb|CI055213.1|CI055213
EST:     AGAGACCATCAATGTAGGTACAGAAACTGCAGCTGCTCTCAAATCACAG                         ACAGAGCAAATGAGCAGAATTGTTAATGAGCTGGATTCCATTCATTTCTCC
genomic: AGAGACCATCAATGTAGGTACAGAAACTGCAGCTGCTCTCAAATCACAGgcaggatttc ... tattgaccagACAGAGCAAATGAGCAGAATTGTTAATGAGCTGGATTCCATTCATTTCTCC
EST: gi|86497255|gb|CI139888.1|CI139888
EST:     AAGAGACCATCAATGTAGGTACAGAAACTGCAGCTGCTCTCAAATCACAG                         ACAGAGCAAATGAGCAGAATTGTTAATGAGCTGGATTCCATTCATTTCTCC
genomic: AAGAGACCATCAATGTAGGTACAGAAACTGCAGCTGCTCTCAAATCACAGgcaggatttc ... tattgaccagACAGAGCAAATGAGCAGAATTGTTAATGAGCTGGATTCCATTCATTTCTCC
EST: gi|58675298|gb|CK063985.1|CK063985
EST:     AAGAGACCATTAATGTAGGTACAGAAACTGCAGCTGCTCTCAAATCACAG                         ACAGAGCAAATGAGCAGAATTGTTAATGAACTGGATTCCATTCATTTCTCC
genomic: AAGAGACCATCAATGTAGGTACAGAAACTGCAGCTGCTCTCAAATCACAGgcaggatttc ... tattgaccagACAGAGCAAATGAGCAGAATTGTTAATGAGCTGGATTCCATTCATTTCTCC
EST: gi|86251814|gb|CI019006.1|CI019006
EST:     AAGAGACCATCAATGTAGGTACAGAAACTGCAGCTGCTCTCAAATCACAG                         ACAGAGCAAATGAGCAGAATTGTTAATGAGCTGGATTCCATTCATTTCTCC
genomic: AAGAGACCATCAATGTAGGTACAGAAACTGCAGCTGCTCTCAAATCACAGgcaggatttc ... tattgaccagACAGAGCAAATGAGCAGAATTGTTAATGAGCTGGATTCCATTCATTTCTCC
EST: gi|44679310|gb|CR292744.1|CR292744
EST:     AAGAGACCATCAATGTAGGTACAGAAACTGCAGCTGCTCTCAAATCACAG                         ACAGAGCAAATGA
genomic: AAGAGACCATCAATGTAGGTACAGAAACTGCAGCTGCTCTCAAATCACAGgcaggatttc ... tattgaccagACAGAGCAAATGA
EST: gi|86427669|gb|CI072766.1|CI072766
EST:     GCTGCTCTCAAATCACAG                         ACAGAGCAAATGAGCAGAATTG-TANATGAGCTGGATTCCATTCATTTCTC
genomic: GCTGCTCTCAAATCACAGgcaggatttc ... tattgaccagACAGAGCAAATGAGCAGAATTGTTA-ATGAGCTGGATTCCATTCATTTCTC
EST: gi|89185473|gb|CI051801.1|CI051801
EST:     AGGTACAGAAACTGCAGCTGCTCTCAAATCACAG                         ACAGAGCAAATGAGCAGAATTGTTAATGAGCTGGATTCCATTCATTTCTCC
genomic: AGGTACAGAAACTGCAGCTGCTCTCAAATCACAGgcaggatttc ... tattgaccagACAGAGCAAATGAGCAGAATTGTTAATGAGCTGGATTCCATTCATTTCTCC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atgctgtgtaacctggatataccagagctaacttcggttatttcttattgaccagACAGAGCAAATGAGCAGAATTGTTAATGAGCTGGATTCCATTCATTTCTCCATTAAAAAGGCATCACAAATGGTGAAAGAAATTGGTAGGCAG
                         agctaac  putative branch site (score: 2)
                                     ttatttctt  putative PPT
                                     ttatttcttattga  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gcaggatttctttgttcttctcaaaccagccaatcatgctgtgtaacctggatataccagagctaacttcggttatttcttattgaccagACAGAGCAAATGAGCAGAATTGTTAATGAGCTGGATTCCATTCATTTCTCCATTAAAAAGGCATCACAAATGGTGAAAGAAATTGGTAGGCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA