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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaatatctaaaatattttaaaaatactttttaaaatttatccgattagttttgctgcatatttagattataaatatgataaattttccacttgatactgcagGCTGCGGTGCTGATATACATGTCATCGTAAAAATTGAAAGTGCAGACTCTATACCAAATTTGCATTCAATTATCACTGCATCTGATGGG

Basic information

species Glycine max
transcript GLYMA16G28980.2
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA16G28980.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os01g47080.1 (Oryza sativa), 3'ss of exon 5
gtaaatatctaaaatattttaaaaatactttttaaaatttatccgattagttttgctgcatatttagattataaatatgataaattttccacttgatactgcagGCTGCGGTGCTGATATACATGTCATCGTAAAAATTGAAAGTGCAGACTCTATACCAAATTTGCATTCAATTATCACTGCATCTGATGGG
            |||| ||      ||| || | ||| ||||||              | |||| | | | |    ||  |   ||||    ||||| || |||||| |  ||| ||||||||||| || ||||| |||||||||||||| || || |||||  | || ||||| ||||| ||||| ||||||
----------gtaataattatcccctacattatgaaaattatccagc----------acttattca-actgtcttaatagtgtgttttgt-tttgattct-cagGCTCCAATGCCGATATACATGTAATTGTAAAGATTGAAAGTGCAGATTCCATTCCAAACCTACACTCAATCATCACAGCATCGGATGGG

upper sequence: GLYMA16G28980.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G152686_T01 (Zea mays), 3'ss of exon 5
gtaaatatctaaaatattttaaaaatactttttaaa--atttatccgattagttttgctgcatatttagattataaatatgataaatt--ttccacttgatactgcagGCTGCGGTGCTGATATACATGTCATCGTAAAAATTGAAAGTGCAGACTCTATACCAAATTTGCATTCAATTATCACTGCATCTGATGGG
                         || | || ||   |  | |   |  | |  |       |  |   ||   ||| |  | |  |  ||| | |  || || |||| |||  |||||| |||||||| ||||||||||| |||||||||||||| || || || || |||||||| ||||| ||||||||||||
------------------------gtaatcttcaacccaactttgtaaaaaatcatatcatgcacctttttttacaatttactgagctcattctattctattct-cagGTTGCAATGCTGACATACATGTTATCGTAAAAATAGAAAGTGCAGACTCCATCCCCAACTTACATTCAATCATCACAGCATCTGATGGG

upper sequence: GLYMA16G28980.1 (Glycine max), 3'ss of exon 5
lower sequence: AT5G52920.1 (Arabidopsis thaliana), 3'ss of exon 5
gtaaatatctaaaatattttaaaaatactttttaaaatttatccgattagttttgctgcatatttagattataaatatgataaattttccacttgatactgcagGCTGCGGTGCTGATATACATGTCATCGTAAAAATTGAAAGTGCAGACTCTATACCAAATTTGCATTCAATTATCACTGCATCTGATGGG
|||||||  |  ||  | ||      |   |     | | ||  |  || |  |  | | | ||| |  ||    |  |||   |||   ||       |||||   | |||||||||||||| || || || |||||||| ||||||||||| ||||| || ||||| || |||||||| ||||| ||||||
gtaaatacttggaacctatt----ccatcctaagtgaatgatttgccta-tgatatttcctttttggtctaaccttgagattg-tttgttacaaatatttgcagATAGTGGTGCTGATATACACGTGATAGTGAAAATTGAGAGTGCAGACTCCATACCTAACTTGCACTCCATTATCACAGCATCAGATGGG

upper sequence: GLYMA16G28980.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv16s0050g02180.t01 (Vitis vinifera), 3'ss of exon 5
gtaaatatctaaaatatt---ttaaaaatactttttaaaatttatccgattagttttgctgcatatttagattataaatatgataaattttccacttgatactgcagGCTGCGGTGCTGATATACATGTCATCGTAAAAATTGAAAGTGCAGACTCTATACCAAATTTGCATTCAATTATCACTGCATCTGATGGG
|||||||  ||  |||||   ||  |||||  |   | || ||    |||  ||  |  |||   || | ||| ||    | ||||  ||| | |||| | | ||||||||   ||| ||||| |||||||| || |||||||||||||| ||||| || || ||| | ||||||||||| || ||||||||||||
gtaaatacttaggatattcatttggaaataactaa-ataacttgcttgatctgtaat-ttgc---ttcaaattttaccacttataatctttac-cttgtttcggcagGCTGTAATGCAGATATCCATGTCATTGTTAAAATTGAAAGTGCCGACTCCATTCCCAATCTACATTCAATTATTACCGCATCTGATGGG

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|23734545|gb|BU765511.1|BU765511
EST:     TGTTAAGGATGCTGAAGTTGTTCATGAACTGAAGAATTATTTGAAGA                         GCTGCGGTGCTGATATACATGTCATCGTAAAAATTGAAAGTGCAGACTCTA
genomic: TGTTAAGGATGCTGAAGTTGTTCATGAACTGAAGAATTATTTGAAGAgtaaatatct ... gatactgcagGCTGCGGTGCTGATATACATGTCATCGTAAAAATTGAAAGTGCAGACTCTA
EST: gi|193466016|gb|FK430205.1|FK430205
EST:     CTTTGTTAAGGATGCTGAAGTTGTTCATGAACTGAAGAATTATTTGAAGA                         GCTGCGGTGCTGATATACATGTCATCGTAAAAATTGAAAGTGCAGACTCCA
genomic: CTTTGTTAAGGATGCTGAAGTTGTTCATGAACTGAAGAATTATTTGAAGAgtaaatatct ... gatactgcagGCTGCGGTGCTGATATACATGTCATCGTAAAAATTGAAAGTGCAGACTCTA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttttgctgcatatttagattataaatatgataaattttccacttgatactgcagGCTGCGGTGCTGATATACATGTCATCGTAAAAATTGAAAGTGCAGACTCTATACCAAATTTGCATTCAATTATCACTGCATCTGATGGG
                                         acttgat  putative branch site (score: 5)
          atatttagattataaa  TA-rich tract