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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaacgattttgattgattgagaagatttatcatgtctatttttatctagtttgcagtaatagaaatttacattataaccttttgcatctatcttactgatttcttgtgtgactggggcagGTAGTGTATGCAATAATGCACAGGCAGGAAGTCTTTCAGCCATTCAAGAATCATCCACGTTTCAATGAACTGATTGATAACATTTATACT

Basic information

species Glycine max
transcript GLYMA20G28880.1
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA20G28880.1 (Glycine max), 3'ss of exon 12
lower sequence: GRMZM2G078576_T04 (Zea mays), 3'ss of exon 13
gtaaacgattttgattgattgagaagatttatcatgtctatttttatctagtttgcagtaata-gaaatttacattataaccttttgcatctatcttactgatttcttgtgtgactggggcagGTAGTGTATGCAATAATGCACAGGCAGGAAGTCTTTCAGCCATTCAAGAATCATCCACGTTTCAATGAACTGATTGATAACATTTATACT
                                                  || || | |     | |||| |  |||      ||  ||    |   ||||  ||||    |   ||   ||||| || |||||  || ||||  | || || || ||| ||||||| || |||||||||||||| ||||||||| |||| ||||| || |||
--------------------------------------------------gtatgtattggcctgcaattcagtttac-----ttgacaggactagcactg-cttctaacatttttgta-cagGTTGTATATGCTGTATTGCATCGACAAGAGGTTTTTGAGCCATTTAAAAATCATCCACGTTTTAATGAACTGCTTGAGAACATATACACT

upper sequence: GLYMA20G28880.1 (Glycine max), 3'ss of exon 12
lower sequence: Vv05s0020g04100.t01 (Vitis vinifera), 3'ss of exon 13
gtaaacgattttgattgattgagaagatttatcatgtctatttttatctagtttg---cagtaataga-aatttacattataaccttttgcatctatcttactgatttcttgtgtgactggggcagGTAGTGTATGCAATAATGCACAGGCAGGAAGTCTTTCAGCCATTCAAGAATCATCCACGTTTCAATGAACTGATTGATAACATTTATACT
|||      |||| |||  ||  ||    ||   | |  | || |||||  | ||   ||  |||| | || |   ||||  ||||||| |||   |  ||    |      |||   | |||||||| || ||||||||||||||||| ||||| ||||||||||| ||||||||||||||||| |||||||| ||| |||| || || || |||
gtatcatcatttgtttgtgtggcaactaatacattatagacttgtatctgttatgtctcacaaatatacaaatcttattagcacctttt-catgctttataaaattactcactgtattttgggcagGTTGTATATGCAATAATGCACAGACAGGAGGTCTTTCAGCCTTTCAAGAATCATCCACGATTCAATGAGCTGCTTGAAAATATCTACACT
















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|192321413|gb|FK012833.1|FK012833
EST:     TAGAAATAA-AAATGCAATCCTGACTTATGCACTACCTCG-AATCCTGAA                         GTAGTGTATGCA
genomic: TAGAAATAATAAATGCAATCCTGACTTATGCACTACCTCGGAATCCTGAGgtaaacgatt ... actggggcagGTAGTGTATGCA
EST: gi|193668384|gb|FK612664.1|FK612664
EST:     TAGAAATAATAAATGCAATCCTGACTTATGCACTACCTCGGAATCCTGAG                         GTAGTGTATGCAATAATGCACAGGCAGGAAGTCTTTCAGCCATTCAAGAAT
genomic: TAGAAATAATAAATGCAATCCTGACTTATGCACTACCTCGGAATCCTGAGgtaaacgatt ... actggggcagGTAGTGTATGCAATAATGCACAGGCAGGAAGTCTTTCAGCCATTCAAGAAT
EST: gi|9901403|gb|BE610371.1|BE610371
EST:     TAGAAATAATAAATGCAATCCTGACTTATGCACTACCTCGGAATCCTGAG                         GTAGTGTATGCAATAATGCACAGGCAGGAAGTCTTTCAGCCATTCAAGAAT
genomic: TAGAAATAATAAATGCAATCCTGACTTATGCACTACCTCGGAATCCTGAGgtaaacgatt ... actggggcagGTAGTGTATGCAATAATGCACAGGCAGGAAGTCTTTCAGCCATTCAAGAAT
EST: gi|193658848|gb|FK602043.1|FK602043
EST:     TAGAAATAATAAATGCAATCCTGACTTATGCACTACCTCGGAATCCTGAG                         GTAGTGTATGCAATAATGCACAGGCAGGAAGTCTTTCAGCCATTCAAGAAT
genomic: TAGAAATAATAAATGCAATCCTGACTTATGCACTACCTCGGAATCCTGAGgtaaacgatt ... actggggcagGTAGTGTATGCAATAATGCACAGGCAGGAAGTCTTTCAGCCATTCAAGAAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttacattataaccttttgcatctatcttactgatttcttgtgtgactggggcagGTAGTGTATGCAATAATGCACAGGCAGGAAGTCTTTCAGCCATTCAAGAATCATCCACGTTTCAATGAACTGATTGATAACATTTATACT
                            tactgat  putative branch site (score: 2)
     attataa  TA-rich tract