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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gaattgtttgatgtttatcttgtttattgtgtattcccttgtgagggtcaactgtattttcgttttttcctttttcactaagaattaattatttaaatagGGTGTTGTGAAGAACATCATACCAGCTATAGCTTCAACGAATGCAATTATATCGGCTGCATGTGCACTAGAAACATTAAAGATTGCAACAGAGTGCAGCA

Basic information

species Glycine max
transcript GLYMA17G01940.2
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA17G01940.2 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os01g16540.1 (Oryza sativa), 3'ss of exon 6
gaattgtttgatgtttatcttgtttattgtgtattcccttgtgagggtcaactgtattttcgtt----ttttcctttttcactaagaattaattatttaaat---agGGTGTTGTGAAGAACATCATACCAGCTATAGCTTCAACGAATGCAATTATATCGGCTGCATGTGCACTAGAAACATTAAAGATTGCAACAGAGTGCAGCA
        | |   |||  |  | |   ||||| |   | |  ||       |||   || | |    | |  | | |  || |     || ||   | |||   |||||||||| ||||| ||||| ||||| || |||||||| ||||||||| | || |||||||||||  | ||| |  | ||| ||    | | ||||||||
-------cttaccattagttgatatgccgtgtaattattggaaagtcatggttgttaatttgatgggatgtgacatatgtaccactgtgtattttcatgaattacagGGTGTTGTCAAGAATATCATCCCAGCCATTGCTTCAACAAATGCAATTGTTTCTGCTGCATGTGCGTTGGAAGCTCTTAAGCTTATCTCTGGGTGCAGCA

upper sequence: GLYMA17G01940.2 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G007915_T02 (Zea mays), 3'ss of exon 6
-gaattgtttgatgtttatcttgtttattgtgtattcccttgtgagggtcaactgtattttcgttttttcctttttcactaagaattaattatttaaat-agGGTGTTGTGAAGAACATCATACCAGCTATAGCTTCAACGAATGCAATTATATCGGCTGCATGTGCACTAGAAACATTAAAGATTGCAACAGAGTGCAGCA
  |  | ||   |  | || |  |  || |  | |   ||||  | |   |    ||     ||    |   |  || || |  | |  || |  |  | |||||||||| || || || || ||||| || || |||||||||||||||||||||||||| |||||| | ||| | |||||| ||    | | ||||||||
tcagcttttatgttctaatgtgatgcatagctt-tctacttgaaaagtctattcataggacagtgacatatgtagtc-ctgactactttttgtgaatttcagGGTGTTGTCAAAAATATAATCCCAGCCATTGCATCAACGAATGCAATTATATCGGCTGCTTGTGCATTGGAAGCCTTAAAGCTTATTTCTGGGTGCAGCA

upper sequence: GLYMA17G01940.2 (Glycine max), 3'ss of exon 6
lower sequence: Vv05s0020g02820.t01 (Vitis vinifera), 3'ss of exon 6
gaattgtttgatgtttatcttgtttattgtgtattcccttgtgagggt-caactgtattttcgttttttccttttt-cactaagaattaattatttaa-----atagGGTGTTGTGAAGAACATCATACCAGCTATAGCTTCAACGAATGCAATTATATCGGCTGCATGTGCACTAGAAACATTAAAGATTGCAACAGAGTGCAGCA
          |    ||| |   | | ||   ||    || | |   | ||  | ||  |||    ||   |  |  ||| |  |  || || |||       | ||||||| ||||| || || ||||| || || || || || ||||||||||| || |||||||||||||| ||||| || ||||||| | |||  |||||||
-------gcaacacatatatgtatgagtggcaatatttttctaattatacagatttaaattcacagttctgtgataacacaagcaggtatttctttgttgtttacagGGTGTGGTGAAAAATATTATACCGGCCATTGCATCCACAAATGCAATTATTTCAGCTGCATGTGCACTGGAAACCTTGAAGATTGTATCAGGATGCAGCA

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|254338438|gb|GR849856.1|GR849856
EST:     AGAGGGCTGAGCTTTTTGGCATTCCTGGAGTTACTTATTCTCTTACCCAG                         GGTGTTGTGAAGAACATCATACCAGCTATAGCTTCAACGAATGCAATTATA
genomic: AGAGGGCTGAGCTTTTTGGCATTCCTGGAGTTACTTATTCTCTTACCCAGgtagatgatt ... atttaaatagGGTGTTGTGAAGAACATCATACCAGCTATAGCTTCAACGAATGCAATTATA






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggtcaactgtattttcgttttttcctttttcactaagaattaattatttaaatagGGTGTTGTGAAGAACATCATACCAGCTATAGCTTCAACGAATGCAATTATATCGGCTGCATGTGCACTAGAAACATTAAAGATTGCAACAGAGTGCAGCA
                                     aattaat  putative branch site (score: 3)
                 ttttttcctttttcac  TA-rich tract