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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaggttaatctcgtttgtttgatatcaaggtgctttaaagtgataaatattttctgtttcttaattaaagcaagtggttcacacactaaaggtgcatcattggtcacttttgcagAGTGCTATTGGTGAGGGAATGACTAGAAAGGATCATTCTGATGTGTCCAACCAG

Basic information

species Glycine max
transcript GLYMA10G42940.2
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA10G42940.2 (Glycine max), 3'ss of exon 12
lower sequence: LOC_Os06g37180.1 (Oryza sativa), 3'ss of exon 12
gtaaggttaatctcgtttgtttgatatcaaggtgctttaaagtgataaatattttctgtttcttaattaaagcaagtggttcacacactaaaggtgcatcattggtcacttttgcagAGTGCTATTGGTGAGGGAATGACTAGAAAGGATCATTCTGATGTGTCCAACCAG
|| || |||  ||| |   | | |  |  |  |    |    | ||||   ||   || | |  ||| |   | |    ||  |   ||||       |   |  | | | ||||||||||||||||||||||| |||||  |    || ||||| |||||||| ||||||
gtgagatta--ctcatcaatataaatttcacataaactggtttcataacagttacatgctac--aataatttcca----tttgcgttctaagaac---tgtctaataattcttgcagAGTGCTATTGGTGAGGGTATGACCCGTCGAGACCATTCAGATGTGTCTAACCAG

upper sequence: GLYMA10G42940.2 (Glycine max), 3'ss of exon 12
lower sequence: PP1S100_117V6.1 (Physcomitrella patens), 3'ss of exon 12
gtaaggttaatctcgtttgtttgatatcaaggtgct--ttaaagtgataaatattttctgtttcttaattaaagcaagtggttcacacactaaaggtgcatcattggtcacttttgcagAGTGCTATTGGTGAGGGAATGACTAGAAAGGATCATTCTGATGTGTCCAACCAG
              ||||| ||  ||   |  | |   |||| ||  ||  | |  |    || |  || |   | | | | |     |||||  | |   | |    ||||  ||||||||||||||||  ||||||||||| |||||||||||||||| || || ||||||
-------------tgtttgctttttaagtatttcccacttaacgtt-taggtgtgattgagttatgtatcatttcgatttggttggg-actaactgagttcctt----cactcctgcagAGTGCTATTGGACAGGGAATGACTCGAAAGGATCATTCTGAAGTCTCTAACCAG
















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|19452473|gb|BM953883.1|BM953883
EST:     ATATACCCACCAATCAATGTCCTCCCGTCACTATCTCGGTTGATGAAG                         AGTGCTATTGGTGAGGGAATGACTAGAAAGGATCATTCTGATGTGTCCAAC
genomic: ATATACCCACCAATCAATGTCCTCCCGTCACTATCTCGGTTGATGAAGgtaaggttaa ... acttttgcagAGTGCTATTGGTGAGGGAATGACTAGAAAGGATCATTCTGATGTGTCCAAC
EST: gi|15813509|gb|BI785784.1|BI785784
EST:     ATATACCCACCAATCAATGTCCTCCCGTCACTATCTCGGTTGATGAAG                         AGTGCTATTGGTGAGGGAATGACTAGAAAGGATCATTCTGATGTGTCCAAC
genomic: ATATACCCACCAATCAATGTCCTCCCGTCACTATCTCGGTTGATGAAGgtaaggttaa ... acttttgcagAGTGCTATTGGTGAGGGAATGACTAGAAAGGATCATTCTGATGTGTCCAAC
EST: gi|16283344|gb|BI945501.1|BI945501
EST:     ATATACCCACCAATCAATGTCCTCCCGTCACTATCTCGGTTGATGAAG                         AGTGCTATTGGTGAGGGAATGACTAGAAAGGGATCATTCTGATGTGTCCAA
genomic: ATATACCCACCAATCAATGTCCTCCCGTCACTATCTCGGTTGATGAAGgtaaggttaa ... acttttgcagAGTGCTATTGGTGAGGGAATGACTAGAAA-GGATCATTCTGATGTGTCCAA
EST: gi|16283207|gb|BI945427.1|BI945427
EST:     ATATACCCACCAATCAATGTCCTCCCGTCACTATCTCGGTTGATGAAG                         AGTGCTATTGGTGAGGGAATGACTAGAAAGGATCATTCTGATGTGTCCAAC
genomic: ATATACCCACCAATCAATGTCCTCCCGTCACTATCTCGGTTGATGAAGgtaaggttaa ... acttttgcagAGTGCTATTGGTGAGGGAATGACTAGAAAGGATCATTCTGATGTGTCCAAC
EST: gi|16279679|gb|BI943560.1|BI943560
EST:     ATATACCCACCAATCAATGTCCTCCCGTCACTATCTCGGTTGATGAAG                         AGTGCTATTGGTGAAGGAATGACTAGAAAGGATCATTCTGATGTGTCCAAC
genomic: ATATACCCACCAATCAATGTCCTCCCGTCACTATCTCGGTTGATGAAGgtaaggttaa ... acttttgcagAGTGCTATTGGTGAGGGAATGACTAGAAAGGATCATTCTGATGTGTCCAAC
EST: gi|16278507|gb|BI942940.1|BI942940
EST:     ATATACCCACCAATCAATGTTCTGCCGTCACTATCTCGGTGGATGAAG                         AGTGCTATTGGTGA
genomic: ATATACCCACCAATCAATGTCCTCCCGTCACTATCTCGGTTGATGAAGgtaaggttaa ... acttttgcagAGTGCTATTGGTGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttaattaaagcaagtggttcacacactaaaggtgcatcattggtcacttttgcagAGTGCTATTGGTGAGGGAATGACTAGAAAGGATCATTCTGATGTGTCCAACCAG
                       cactaaa  putative branch site (score: 2)
                                           tcactttt  putative PPT