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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagttgagtcattgactcattgtgccatggcacgaccaagataatttttattgtacttcccatgatagcatgctaattgtgatgatgaaagagtattatcttaatagtagccctgtttgattccctattcttttaaaggcttgagttacctcttgcggtgattgtatttgacttattagctatggttatctaaacagCATAACAGTAACCAGAGCACGTATTGAAACATCTATTCCTCGGAAGCATGGCCCTGCGATTGCTGGTTATGAGTCG

Basic information

species Oryza sativa
transcript LOC_Os04g56480.2
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g56480.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G044011_T01 (Zea mays), 3'ss of exon 7
gtaagttgagtcattgactcattgtgccatggcacgaccaagataatttttattgtacttcccatgatagcatgctaattgtgatgatgaaagagtattatcttaatagtagccctgtttgattccctattcttttaaaggcttgagttacctcttgcggtgattgtatttgacttattagc-tatggttatctaaacagCATAACAGTAACCAGAGCACGTATTGAAACATCTATTCCTCGGAAGCATGGCCCTGCGATTGCTGGTTATGAGTCG
                                                                                            |  ||  | ||  ||| |       ||| |||   |||  ||||||     |||   ||   |   | |   | ||  || | |  |    |||  || ||||||||||||||||| |||| | ||||||||||||||||| |||||| |||||||||||||||| |||||||| || ||| ||
-------------------------------------------------------------------------------------------tggttagcagctacatattttaagactttaatt---tatatttttaa----ctgaagaacacatattgcta--tatagatggcatcctgatgtatcattttctaaacagCATAACAGCAACCCGGGCACGTATTGAAACATCAATTCCTAGGAAGCATGGCCCTGCAATTGCTGGCTACGAGACG

upper sequence: LOC_Os04g56480.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA10G31310.1 (Glycine max), 3'ss of exon 7
gtaagttgagtcattgactcattgtgccatggcacgaccaagataatttttattgtacttcccatgatagcatgctaattgtgatgatgaaagagtattatcttaatagtagccctgtttgattccctattcttttaaaggcttgagttacctctt-gcggtgattgtatttgacttat--tagctatggttatctaaacagCATAACAGTAACCAGAGCACGTATTGAAACATCTATTCCTCGGAAGCATGGCCCTGCGATTGCTGGTTATGAGTCG
                                                                                                      |   |  |  |  ||  | |   |  |  ||   ||     |   | | ||  | |  |  |||  | || | || |  ||  | ||  ||   ||| || || || || ||  |  | || || |||||||| |||||||| || ||||| ||||| |||||||||||||||   
------------------------------------------------------------------------------------------------------tggttgatttctgtgggtaaccacaaacactggaaattaaatacatgatcttctagttgatatttgaattaatttgtcttatttttgtctaataaaatagTATGACTGTTACTCGTTCGCGGATAGAAACATCAATTCCTCGCAAACATGGGCCTGCAATTGCTGGTTATGAGAAA

upper sequence: LOC_Os04g56480.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA20G36200.1 (Glycine max), 3'ss of exon 7
gtaagttgagtcattgactcattgtgccatggcacgaccaagataatttttattgtacttcccatgatagcatgctaattgtgatgatgaaagagtattatcttaatagtagccctgtttgattccctattcttttaaaggcttg-agttacctc-ttgcggtgattgtatttgacttattagctatggttatctaaacagCATAACAGTAACCAGAGCACGTATTGAAACATCTATTCCTCGGAAGCATGGCCCTGCGATTGCTGGTTATGAGTCG
                                                                                                ||||  |  ||  |   | |||| |||   ||| |    |   ||| || | ||   || ||||  ||| |  ||||| ||||||    |||  ||   |||||| || || || ||  |  | || || |||||||| |||||||| || ||||| ||||| |||||||||||||||   
------------------------------------------------------------------------------------------------attaaatacatgttcttcttgtt-gatagtctagttaacttttggcatgtaattgtgtcattgcaatgaattgatttgtcttatt----atgtctaataaaacagTATGACTGTTACTCGTTCGCGGATAGAAACATCAATTCCTCGCAAACATGGGCCTGCAATTGCTGGTTATGAGAAA

upper sequence: LOC_Os04g56480.1 (Oryza sativa), 3'ss of exon 6
lower sequence: AT4G27650.1 (Arabidopsis thaliana), 3'ss of exon 8
gtaagttgagtcattgactcattgtgccatggcacgaccaagataatttttattgtacttcccatgatagcatgctaattgtgatgatgaaagagtattatcttaatagtagccctgtttgattccctattcttttaaaggcttgagttacctcttgcggtgattgtatttgacttattagctatggttatctaaacagCATAACAGTAACCAGAGCACGTATTGAAACATCTATTCCTCGGAAGCATGGCCCTGCGATTGCTGGTTATGAGTCG
                ||| |||  ||  || || |  |     | | | | |   | ||   ||       |  |  || |||  |        | |  | ||     | |     ||||  |    |    |  || || |  |   |  || | |  |   |||  |||  |  ||   | |  || | |   |||  | |||   | | | ||||| || |||||||| |||||| |||||||||| ||||| ||||||||||| ||||| 
--------------gtactgatt--gcagtgacaaggtc----cattgtctgtgaaatttgttatttcctagtttttgttttgacaacatgtagttctcttatttcacctgggtggttttggctgaacaagtatgaaacgggtcaaagaaattcatccaatt-ctgttcttgtttactttattgtc-ttgtttgg-cagTGTGACAAGTAGCCGTGCACGAATAGAAACATCCATTCCTAGGAAGCATGGACCTGCAATTGCTGGTTACGAGTCT

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|29659831|gb|CB656106.1|CB656106
EST:     GTTATTCTCATGCAAGAAGGACTTGCACATTTGTTCCTCATTGGTAGAAG                         CATAACAGTAACCAGAGCACGTATTGAAACATCTATTCCTCGGAAGCATGG
genomic: GTTATTCTCATGCAAGAAGGACTTGCACATTTGTTCCTCATTGGTAGAAGgtaagttgag ... atctaaacagCATAACAGTAACCAGAGCACGTATTGAAACATCTATTCCTCGGAAGCATGG
EST: gi|87006648|gb|CI295031.1|CI295031
EST:     CATGCAAGAAGGACTTGCACATTTGTTCCTCATTGGTAGAAG                         CATAACAGTAACCAGAGCACGTATTGAAACATCTATTCCTCGGAAGCATGG
genomic: CATGCAAGAAGGACTTGCACATTTGTTCCTCATTGGTAGAAGgtaagttgag ... atctaaacagCATAACAGTAACCAGAGCACGTATTGAAACATCTATTCCTCGGAAGCATGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gagttacctcttgcggtgattgtatttgacttattagctatggttatctaaacagCATAACAGTAACCAGAGCACGTATTGAAACATCTATTCCTCGGAAGCATGGCCCTGCGATTGCTGGTTATGAGTCG
                       atttgac  putative branch site (score: 4)
                      tatttgacttatta  TA-rich tract