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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtctactttttttttcttagtgtaaaagattgcaactgtgagtacaatttcaggactgacttttgcaatgttcacttttctcagAACAAATGTAATGTGGGGTATGCTTTTATCAATATGACTGATCCGCAGCACATAATCCCATTCTATAAG

Basic information

species Oryza sativa
transcript LOC_Os05g01240.1
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g01240.2 (Oryza sativa), 3'ss of exon 12
lower sequence: GRMZM2G156956_T02 (Zea mays), 3'ss of exon 13
gtctactttttttttcttagtgtaaaagattgcaactgtgagtacaatt--tcaggactgacttttgcaatgttcacttttctcagAACAAATGTAATGTGGGGTATGCTTTTATCAATATGACTGATCCGCAGCACATAATCCCATTCTATAAG
      | | |  || |  |||| || | ||| ||||   |||   |||  |  || |||||| |||   ||||  |||| ||||||| |||||||| ||||| ||||| || ||||||||||| ||||| ||||| ||| | ||||| || |||
-----gtatgtcattatgtgtgtgaagg-ttggaacttgtagtgagattaatagggtctgactcttgtggtgtttgctttcctcagAATAAATGTAACGTGGGATATGCATTCATCAATATGACGGATCCACAGCAGATAGTTCCATTTTACAAG

upper sequence: LOC_Os05g01240.2 (Oryza sativa), 3'ss of exon 12
lower sequence: GLYMA06G17250.1 (Glycine max), 3'ss of exon 10
------------------------------------------gtctactttttttttcttagtgtaaaagattgcaactgtgagtacaatttcaggactgacttttgcaatgttcacttttctcagAACAAATGTAATGTGGGGTATGCTTTTATCAATATGACTGATCCGCAGCACATAATCCCATTCTATAAG
                                          |     |  ||  |||||    |||| ||  |||| | | | |    ||  | | |  | || | |||       |  |  ||||||||||||||||| || ||||| || |||||||||| ||||||    || || || |||||| |  ||
gtatttgccaattgatttcaaggcaagtatttatttggacttgctagttgcttgattctttacttaaatgaa-gcaattataaatgtgtttctaagGC--AATTCTACAAA------TGGTTGCAGAACAAATGTAATGTTGGCTATGCATTCATCAATATGATTGATCCTGGACAAATTATTCCATTCCACCAG

upper sequence: LOC_Os05g01240.2 (Oryza sativa), 3'ss of exon 12
lower sequence: AT5G61960.2 (Arabidopsis thaliana), 3'ss of exon 11
-----------gtctacttttttttt----------cttagt--gtaaaagattgcaactgtgagtacaatttcaggactgacttttgcaatgttcacttttc---tcagAACAAATGTAATGTGGGGTATGCTTTTATCAATATGACTGATCCGCAGCACATAATCCCATTCTATAAG
             |||| |||||| |          |||| |  | | |    |  |  | |  |||   |   |  ||   ||  |  ||| ||  | | ||   |||||||||||| |||||||| |||||||| |||||| | | ||| ||  |  | ||  ||||||| | ||||
gcaagcaggcgtcctaccttttttatataagaaagtcttattaagcagacacgtagaggttttggtattttgcaataacgatctaatctaatcttaccctgtcatttcagAACAAATGCAATGTGGGATATGCTTTCATCAATCTTATTGAACCTGAAAAGATTGTCCCATTTTTTAAG

upper sequence: LOC_Os05g01240.2 (Oryza sativa), 3'ss of exon 12
lower sequence: Vv17s0000g00240.t01 (Vitis vinifera), 3'ss of exon 12
-------------gtctactttttttttcttagtgtaa-aagattgcaactgtga-gtaca-atttcaggactgacttttgcaatgttcacttttctcagAACAAATGTAATGTGGGGTATGCTTTTATCAATATGACTGATCCGCAGCACATAATCCCATTCTATAAG
             |  |   ||   |||||| | | || || ||  ||  ||  |  | || || || |    | |||||   |  |||   |||  ||||||||||| |||||||| ||||||||| |||| |||| |||||| |  || ||  | |||||| || ||
gtaagtaaatcttgcatggattgaatttctttggggaagaaaatcacatatgacatatgcacatatctgattcgcctttttgcaaattc-tgttttgcagAACAAATGCAATGTGGGCTATGCTTTTGTCAACATGATTGATCCTCTTCATATTGTTCCATTCCATCAG

upper sequence: LOC_Os05g01240.2 (Oryza sativa), 3'ss of exon 12
lower sequence: Vv01s0150g00090.t01 (Vitis vinifera), 3'ss of exon 13
---------------------------------------------------------------------------------------gtctactttttttttctta-gtgtaaaagattgcaactg-tgagtacaatttcaggactgacttttgcaatgttcacttttctcagAACAAATGTAATGTGGGGTATGCTTTTATCAATATGACTGATCCGCAGCACATAATCCCATTCTATAAG
                                                                                        |  |||||   || |||  |||| | | | | ||  || |   |||   ||      | | | ||  | |  |   ||||  ||||||||||| ||||| |||||||| |||||||| ||||| |||||    || || || ||||||||| ||
gcaagtgcattttttaccagaaagaaatgcttttatcatgtagagtggggatgatgattgagggaggaatcactattaccatttaaatttcactttggcttccttgtgtgttatacaattcatttggtctatacccctttttatttaattatttaatttatttatttttgcagAACAAATGCAATGTAGGGTATGCCTTTATCAACATGACCGATCCTTGCCAGATTATTCCATTCTATCAG

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|58602954|gb|CK013482.1|CK013482
EST:     AGAACCACCGTGGAACCTACGATTTCATCTATCTCCCAATTGATTTTAAG                         AACCAATGTAATGTGGGGTATGCT
genomic: AGAACCACCGTGGAACCTACGATTTCATCTATCTCCCAATTGATTTTAAGgtctactttt ... cttttctcagAACAAATGTAATGTGGGGTATGCT
EST: gi|33381398|gb|CF196741.1|CF196741
EST:     AGAACCACCGTGGAACCTACGATTTCATCTATCTCCCAATTGATTTTAAG                         AACAAATGTAATGTGGGGTATGCTTTTATCAATATGACTGATCCGCAGCAC
genomic: AGAACCACCGTGGAACCTACGATTTCATCTATCTCCCAATTGATTTTAAGgtctactttt ... cttttctcagAACAAATGTAATGTGGGGTATGCTTTTATCAATATGACTGATCCGCAGCAC
EST: gi|29674666|gb|CB670941.1|CB670941
EST:     AGAACCACCGTGGAACCTACGATTTCATCTATCTCCCAATTGATTTTAAG                         AACAAATGTAATGTGGGCGTATGCTTTTATCAATATGACTGATCCGCAGCA
genomic: AGAACCACCGTGGAACCTACGATTTCATCTATCTCCCAATTGATTTTAAGgtctactttt ... cttttctcagAACAAATGTAATGTGGG-GTATGCTTTTATCAATATGACTGATCCGCAGCA
EST: gi|29674667|gb|CB670942.1|CB670942
EST:     TTGATTTTAAG                         AACAAATGTAATGTGGGGTATGCTTTTATCAATATGACTGATCCGCAGCAC
genomic: TTGATTTTAAGgtctactttt ... cttttctcagAACAAATGTAATGTGGGGTATGCTTTTATCAATATGACTGATCCGCAGCAC
EST: gi|218489237|gb|FG949713.1|FG949713
EST:     AGAACCACCGTGGAACCTACGATTTCATCTATCTCCCAATTGATTTTAAG                         AACAAATGTAATGTGGGGTATGCTTTTATCAATATGACTGATCCGCAGCAC
genomic: AGAACCACCGTGGAACCTACGATTTCATCTATCTCCCAATTGATTTTAAGgtctactttt ... cttttctcagAACAAATGTAATGTGGGGTATGCTTTTATCAATATGACTGATCCGCAGCAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgcaactgtgagtacaatttcaggactgacttttgcaatgttcacttttctcagAACAAATGTAATGTGGGGTATGCTTTTATCAATATGACTGATCCGCAGCACATAATCCCATTCTATAAG
                        gactgac  putative branch site (score: 2)
                                       tgttcacttttctc  putative PPT
             tacaattt  TA-rich tract