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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagtgtttttcttttgctgattttcattttagatcttccatagcattgtttctggtagggcactactccacagatagtttctgtctcctcccttattcacttcaggcctcattctgcaatattttgagctttacttgcctctaagatgtatggtttaaccaacccttactacctgttctgacaaaaaatgcagACTCCTGTGCACACAATTGCTTCAAATGCAGGAGTTGAGGGTGCTGTTGTTGTTGGCAAACTATTGGAACAGAATGATCCTGATCTTGGATATGATGCAG

Basic information

species Glycine max
transcript GLYMA20G33910.1
intron # 15
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA20G33910.1 (Glycine max), 3'ss of exon 15
lower sequence: LOC_Os03g04970.1 (Oryza sativa), 3'ss of exon 15
gttagtgtttttcttttgctgattttcattttagatcttccatagcattgtttctggtagggcactactccacagatagtttctgtctcctcccttattcacttcaggcctcattctgcaatattttgagctttacttgcctctaagatgtatggtttaaccaacccttactacctgttctgacaaaaaatgcagACTCCTGTGCACACAATTGCTTCAAATGCAGGAGTTGAGGGTGCTGTTGTTGTTGGCAAACTATTGGAACAGAATGATCCTGATCTTGGATATGATGCAG
                                                                                                                         | |    | |     |||  |  ||    |    | |  |   | |   |||   |  |||   ||   ||||||| || ||||||||||||||||| ||||| || || || ||  ||||  || ||||||| || ||||||||| || || ||||||| || |||||||| |
------------------------------------------------------------------------------------------------------------------------gtttacaaatcccattttgttttcaattgttcctctcttgcttgctccatctaatgg--ctggataatgctgcagACCCCAGTGCACACAATTGCTTCGAATGCGGGTGTAGAAGGATCTGTCATTATTGGCAAGCTTTTGGAACAGGATAATACTGATCTAGGTTATGATGCTG

upper sequence: GLYMA20G33910.1 (Glycine max), 3'ss of exon 15
lower sequence: AT3G23990.1 (Arabidopsis thaliana), 3'ss of exon 13
gttagtgtttttcttttgctgattttcattttagatcttccatagcattgtttctggtagggcactactccacagatagtttctgtctcctcccttattcacttcaggcctcattctgcaatattttgagctttacttgcctc-taagatgtatggtt-taaccaacccttactacctgttctgacaaaaaatgcagACTCCTGTGCACACAATTGCTTCAAATGCAGGAGTTGAGGGTGCTGTTGTTGTTGGCAAACTATTGGAACAGAATGATCCTGATCTTGGATATGATGCAG
                                                                                                                 || |  | | ||| || ||  | |   ||  |  |||   || |   ||  ||   ||   ||  ||| ||    |     |||||||||||  ||||||| ||||||||||| |||||||| ||||||||| |||||||||| || ||||| ||  || | || || || || |||||||| |
----------------------------------------------------------------------------------------------------------------gttttctattctttagaactaaaatcctctgatctgataattgatgacaagaaattgttttaacgagttttggtttac----cagACTCCTGTTTACACAATCGCTTCAAATGCTGGAGTTGAAGGTGCTGTTATTGTTGGCAAGCTCTTGGAGCAAGATAACCCAGACCTCGGTTATGATGCTG

upper sequence: GLYMA20G33910.1 (Glycine max), 3'ss of exon 15
lower sequence: EFJ20894 (Selaginella moellendorffii), 3'ss of exon 13
gttagtgtttttcttttgctgattttcattttagatcttccatagcattgtttctggtagggcactactccacagatagtttctgtctcctcccttattcacttcaggcctcattctgcaatattttgagctttacttgcctctaagatgtatggtttaaccaacccttactacctgttctgacaaaaaatgcagACTCCTGTGCACACAATTGCTTCAAATGCAGGAGTTGAGGGTGCTGTTGTTGTTGGCAAACTATTGGAACAGAATGATCCTGATCTTGGATATGATGCAG
                                                                                                                           | | | ||  |       | | || ||  |   ||      ||  ||| |  ||||||       |    |||  ||   | | ||||||||| | ||||| ||||| ||||| || || ||||| ||||| |||| ||||||||||||     |  | || || || || |
--------------------------------------------------------------------------------------------------------------------------gtatggcgcggtgacactattttagttgctt---ttgcgtggccactacaa--tgttctctttgtga---tagATGCCCACGTATACAATTGCTGCCAATGCCGGAGTGGAGGGAGCGGTCGTTGTAGGCAAGCTATGGGAACAGAATGACTACAACTTGGGTTACGACGCGG

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|15814111|gb|BI786386.1|BI786386
EST:     CCAACTTTGATCAAAAGATAGGTGTCCAGATCATCCAAAATGCTTTGAAG                         ACTCCTGTGCACACAATTGCTTCAAATGCAGGAGTTGAGGGTGCTGTTGTT
genomic: CCAACTTTGATCAAAAGATAGGTGTCCAGATCATCCAAAATGCTTTGAAGgttagtgttt ... aaaaatgcagACTCCTGTGCACACAATTGCTTCAAATGCAGGAGTTGAGGGTGCTGTTGTT
EST: gi|209725420|gb|BW658282.1|BW658282
EST:     CCAACTTTGATCAAAAGATAGGTGTCCAGATCATCCAAAATGCTTTGAAG                         ACTCCTGTGCACACAATTGCTTCAAATGCAGGAGTTGAGGGTGCTGTTGTT
genomic: CCAACTTTGATCAAAAGATAGGTGTCCAGATCATCCAAAATGCTTTGAAGgttagtgttt ... aaaaatgcagACTCCTGTGCACACAATTGCTTCAAATGCAGGAGTTGAGGGTGCTGTTGTT
EST: gi|16344877|gb|BI970472.1|BI970472
EST:     CCAACTTTGATCAAAAGATAGGTGTCCAGATCATCCAAAATGCTTTGAAG                         ACTCCTGTGCACACAATTGCTTCAAATGCAGGAGTTGAGGGTGCTGTTGTT
genomic: CCAACTTTGATCAAAAGATAGGTGTCCAGATCATCCAAAATGCTTTGAAGgttagtgttt ... aaaaatgcagACTCCTGTGCACACAATTGCTTCAAATGCAGGAGTTGAGGGTGCTGTTGTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctctaagatgtatggtttaaccaacccttactacctgttctgacaaaaaatgcagACTCCTGTGCACACAATTGCTTCAAATGCAGGAGTTGAGGGTGCTGTTGTTGTTGGCAAACTATTGGAACAGAATGATCCTGATCTTGGATATGATGCAG
                                     ttctgac  putative branch site (score: 2)
                                          acaaaaaat  TA-rich tract