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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgaatgctagattgtagtttcatggttgattattattttattttttacaaagtatcatgtaaccattggtttacatgctcatttttagGGCTCCAGTATTGGGTTGTATTTTATTAACAGACCTGAGTGGCTCATTGTTGATCATGCTTGCTCTTCATACTCATTTGTATCAGTGCCTCTGTATGATA

Basic information

species Glycine max
transcript GLYMA10G39540.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA10G39540.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os11g04980.1 (Oryza sativa), 3'ss of exon 5
-----------------------------------------------gtgaatgctagattgtagt-ttcatggttgat----tattattt-tattt---tttacaaagtatcatgtaaccattggtttacatgctcattttta-----------gGGCTCCAGTATTGGGTTGTATTTTATTAACAGACCTGAGTGGCTCATTGTTGATCATGCTTGCTCTTCATACTCATTTGTATCAGTGCCTCTGTATGATA
                                               ||    |  ||||  |      |||||   ||    ||  |||| |||||    ||| | |||  | | |     ||   || | |  |  ||||||           |||  |  | ||||| ||||||||||| ||||||||||||||| |||| ||||||||||| ||  |  |||| ||||| || || ||||| || ||||| |
gtgagtcataatggtcgcaacaagtaccgtccttctttttttaactagtagcaggcagatcttgtcacacatggacaatgatataacatttgtatttacacttagagagtccctttttttt-ttaacttgctttattttttttaactctgaaccagGGTGCATGCATTGGTTTGTATTTTATAAACAGACCTGAGTGGATCATAGTTGATCATGCCTGTGCAGCATATTCATTCGTGTCTGTGCCACTTTATGACA

upper sequence: GLYMA10G39540.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os12g04990.1 (Oryza sativa), 3'ss of exon 5
----------------------------------------------------------------------gtgaatgctagattgtagt-ttcatggttg-attattattttattttttacaaagtatcatgtaaccattggtttacatgctcatttttagGGCTCCAGTATTGGGTTGTATTTTATTAACAGACCTGAGTGGCTCATTGTTGATCATGCTTGCTCTTCATACTCATTTGTATCAGTGCCTCTGTATGATA
                                                                       |       |   | |||  ||  |||||  | |   |  ||  |||||  ||| |  |||  ||  |||  ||   |  || |     ||||  |  | ||||| ||||||||||| |||||||||||||||  ||| ||||||||||| ||  |  |||| |||| |||||| ||||| || |||||||
gtgagtcattatgatctcaacaagcaccgtccttctgattttaactactaacaggcagatcttgtcacacattgccataatgatatagcatttgtggttacacttacagattcctttttttaaacttgcattaaataatt--ttctaaaactgaacc--agGGTGCGCGCATTGGTTTGTATTTTATAAACAGACCTGAGTGGACCATAGTTGATCATGCCTGTGCGGCATATTCATATGTATCCGTGCCACTTTATGATA

upper sequence: GLYMA10G39540.1 (Glycine max), 3'ss of exon 5
lower sequence: AT3G05970.1 (Arabidopsis thaliana), 3'ss of exon 5
gtgaat-gctagattgt-agtttcatggttgattattattttattttttacaaagtatcatgtaaccattggtttacatgctcatttttagGGCTCCAGTATTGGGTTGTATTTTATTAACAGACCTGAGTGGCTCATTGTTGATCATGCTTGCTCTTCATACTCATTTGTATCAGTGCCTCTGTATGATA
|| |||   | |||| | | | || |   |||||  | ||| | |||  |   ||  ||| ||  |  ||  | | |        |   |||| ||   | ||||  | || || || ||  | || |||||||||||||||||||||||||| ||||| || || | ||| || || ||| |||||||||
gtaaattattggattcttactctccttcctgattgatttttaagtttgcagctagactcaagtctctgtttttcttc--------taccagGGATCTTCTGTTGGAATTTACTTCATCAATCGCCCAGAGTGGCTCATTGTTGATCATGCTTGTTCTTCTTATTCTTATGTGTCTGTTCCTTTGTATGATA

upper sequence: GLYMA10G39540.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv05s0020g03080.t01 (Vitis vinifera), 3'ss of exon 5
----------------------------------------------------------------------------------------------------gtgaatgctagattgt-agtttcatggttgattattattttattttttacaaagtatcatgtaaccattggtttacatgctcattttt--------agGGCTCCAGTATTGGGTTGTATTTTATTAACAGACCTGAGTGGCTCATTGTTGATCATGCTTGCTCTTCATACTCATTTGTATCAGTGCCTCTGTATGATA
                                                                                                     |  |  | ||||| | |  | |||  ||  |||  ||||  || |  |   | | || | |     ||  |||| ||  || ||  |        |||| ||  || ||||  | |||||||| |||||||||||||||||||||||||||||||| |||||| |||  |||| ||||||||| ||| | ||||| |
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|213605762|gb|DB968594.1|DB968594
EST:     CGGCCCGGTCAGCAATAGGTTCTGGTTTGATTTATCATGGAATCGAAAAG                         GGCTCCAGTATTGCGTTGTATTTTATTAACAGACCTGAGTGGCTCATTGT
genomic: CGGCCCGGTCAGCAATAGGTTCTGGTTTGATTTATCATGGAATCGAAAAGgtgaatgcta ... tcatttttagGGCTCCAGTATTGGGTTGTATTTTATTAACAGACCTGAGTGGCTCATTGT






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tattttattttttacaaagtatcatgtaaccattggtttacatgctcatttttagGGCTCCAGTATTGGGTTGTATTTTATTAACAGACCTGAGTGGCTCATTGTTGATCATGCTTGCTCTTCATACTCATTTGTATCAGTGCCTCTGTATGATA
                       atgtaac  putative branch site (score: 3)
                                            ctcattttt  putative PPT
     tattttttacaaagta  TA-rich tract