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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgaatgctagattgtagtttcatggctgatcattatttcattttttacaaagtatcatgtaaccattggtttacatgttcttttttagGGCTCCAGTATTGGGTTGTATTTTATTAACAGACCTGAGTGGCTCATTGTTGATCATGCTTGCTCTGCATACTCATTTGTATCAGTGCCTCTGTATGATA

Basic information

species Glycine max
transcript GLYMA20G28200.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA20G28200.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os12g04990.1 (Oryza sativa), 3'ss of exon 5
-------------------------------------------------------------------gtgaatgctagattgtagtttcatggctgatcattatttcat-tttttacaaagtatcatgtaaccattggtttacatgttcttttttagGGCTCCAGTATTGGGTTGTATTTTATTAACAGACCTGAGTGGCTCATTGTTGATCATGCTTGCTCTGCATACTCATTTGTATCAGTGCCTCTGTATGATA
                                                                      | ||| | | ||   |  |||   || | |   || ||  ||  |       | | || |   | |  ||| |     ||     ||||  |  | ||||| ||||||||||| |||||||||||||||  ||| ||||||||||| ||  | ||||| |||| |||||| ||||| || |||||||
gtgagtcattatgatctcaacaagcaccgtccttctgattttaactactaacaggcagatcttgtcacacattgccataatgatatagcatttgtggttacacttacagattcctttttttaaacttgcattaaataattttctaaaactgaaccagGGTGCGCGCATTGGTTTGTATTTTATAAACAGACCTGAGTGGACCATAGTTGATCATGCCTGTGCGGCATATTCATATGTATCCGTGCCACTTTATGATA

upper sequence: GLYMA20G28200.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os11g04980.1 (Oryza sativa), 3'ss of exon 5
-----------------------------------------------gtgaatgctagattgtagt-ttcatggctgatcat----tattt-cattt---tttacaaagtatcatgtaaccattggtttacatgttcttttt----------tagGGCTCCAGTATTGGGTTGTATTTTATTAACAGACCTGAGTGGCTCATTGTTGATCATGCTTGCTCTGCATACTCATTTGTATCAGTGCCTCTGTATGATA
                                               ||    |  ||||  |      |||||   || ||     ||||  ||||    ||| | |||  | | |     |   ||    | || |||||           ||||  |  | ||||| ||||||||||| ||||||||||||||| |||| ||||||||||| ||  | ||||| ||||| || || ||||| || ||||| |
gtgagtcataatggtcgcaacaagtaccgtccttctttttttaactagtagcaggcagatcttgtcacacatggacaatgatataacatttgtatttacacttagagagtcccttttttttttaacttgctttattttttttaactctgaaccagGGTGCATGCATTGGTTTGTATTTTATAAACAGACCTGAGTGGATCATAGTTGATCATGCCTGTGCAGCATATTCATTCGTGTCTGTGCCACTTTATGACA

upper sequence: GLYMA20G28200.1 (Glycine max), 3'ss of exon 5
lower sequence: AT3G05970.1 (Arabidopsis thaliana), 3'ss of exon 5
gtgaat-gctagattgt-agtttcatggctgatcattatttcattttttacaaagtatcatgtaaccattggtttacatgttcttttttagGGCTCCAGTATTGGGTTGTATTTTATTAACAGACCTGAGTGGCTCATTGTTGATCATGCTTGCTCTGCATACTCATTTGTATCAGTGCCTCTGTATGATA
|| |||   | |||| | | | || |  |||||   | ||| | |||  |   ||  ||| ||  |  ||        | |  | |   |||| ||   | ||||  | || || || ||  | || |||||||||||||||||||||||||| ||| | || || | ||| || || ||| |||||||||
gtaaattattggattcttactctccttcctgattgatttttaagtttgcagctagactcaagtctctgtt--------tttcttctaccagGGATCTTCTGTTGGAATTTACTTCATCAATCGCCCAGAGTGGCTCATTGTTGATCATGCTTGTTCTTCTTATTCTTATGTGTCTGTTCCTTTGTATGATA

upper sequence: GLYMA20G28200.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv05s0020g03080.t01 (Vitis vinifera), 3'ss of exon 5
----------------------------------------------------------------------------------------------------gtgaatgctagattgt-agtttcatggctgatcattatttcattttttacaaagtatcatgtaaccattggtttacatgttctttttt--------agGGCTCCAGTATTGGGTTGTATTTTATTAACAGACCTGAGTGGCTCATTGTTGATCATGCTTGCTCTGCATACTCATTTGTATCAGTGCCTCTGTATGATA
                                                                                                     |  |  | ||||| | |  | |||   |  | |  ||||  || |  |   | | || | |     ||  |||| || ||||||  |        |||| ||  || ||||  | |||||||| |||||||||||||||||||||||||||||||| ||||||||||  |||| ||||||||| ||| | ||||| |
gtgagttgtccaaattctaaattaagtttgaacattgtcatgcactcttaattttgttcttggattggacttatgtttttctaaaatgttttgtgaaaacatctactcaagattttcaaatccattctttcttaacatttggttatccattgattttccttt--ttttttttttaaattttctttaatgctgtaacagGGATCTTGTGTTGGCCTATATTTTATCAACAGACCTGAGTGGCTCATTGTTGATCATGCCTGCTCTGCATTTTCATATGTATCAGTTCCTTTATATGACA

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|213598584|gb|DB964234.1|DB964234
EST:     CGGCCCGGTCAGCAATAGGTTCTGGTTTGATTTATTATGGAATCCAAAAG                         GGCTCCAGTATTGGGTTGTATTTTATTAACAGACCTGAGTGGCTCATTGTT
genomic: CGGCCCGGTCAGCAATAGGTTCTGGTTTGATTTATTATGGAATCCAAAAGgtgaatgcta ... tcttttttagGGCTCCAGTATTGGGTTGTATTTTATTAACAGACCTGAGTGGCTCATTGTT






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatttcattttttacaaagtatcatgtaaccattggtttacatgttcttttttagGGCTCCAGTATTGGGTTGTATTTTATTAACAGACCTGAGTGGCTCATTGTTGATCATGCTTGCTCTGCATACTCATTTGTATCAGTGCCTCTGTATGATA
                       atgtaac  putative branch site (score: 3)
                                          tgttctttttt  putative PPT
      attttttacaaagtat  TA-rich tract