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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtcttattctcttgttgattaatgccaaggatagctttaaatattctgaatgccagttgtgatttgcctttgatttgtggatgacttgttggatacagGAAGACTTTGGAGGAGGACACCCAGACCCCAATTTGACATATGCAAAAGAGTTGGTTGCTCGTATGGGATTGGGCAAATCCGAACCACAAGATGATCCCC

Basic information

species Glycine max
transcript GLYMA05G34790.1
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA05G34790.1 (Glycine max), 3'ss of exon 9
lower sequence: AT1G23190.1 (Arabidopsis thaliana), 3'ss of exon 9
gtcttattctcttgttgattaatgccaaggatagctttaaatattctgaatgccagttgtgatttgcctttgatttgtggatgacttgttggatacagGAAGACTTTGGAGGAGGACACCCAGACCCCAATTTGACATATGCAAAAGAGTTGGTTGCTCGTATGGGATTGGGCAAATCCGAACCACAAGATGATCCCC
|||||||| |  |  | |  ||        ||  | | ||  |||   ||| |   |   |  |     || |       |  ||   |||    ||||| |||||||||||||| || || || ||||||||||| ||||| || ||| | || || || |||||||| || ||||||||  |   || ||| || |
gtcttatttttgt-ctaaccaagaaacgctattccataaatgattacaaatacacctccaggctcaatatttaccacaatacaacgatttg----cagGAGGACTTTGGAGGAGGGCATCCGGATCCCAATTTGACCTATGCTAAGGAGCTTGTGGCACGAATGGGATTAGGTAAATCCGACACTGGAGGTGAACCTC

upper sequence: GLYMA05G34790.1 (Glycine max), 3'ss of exon 9
lower sequence: Vv01s0011g05370.t01 (Vitis vinifera), 3'ss of exon 10
----------------gtcttattctcttgttgattaatgccaaggatagctttaaatattctgaatgccagttgtgatttgcc--tttgatttgtggatgacttgttggatacagGAAGACTTTGGAGGAGGACACCCAGACCCCAATTTGACATATGCAAAAGAGTTGGTTGCTCGTATGGGATTGGGCAAATCCGAACCACAAGATGATCCCC
                |   |||| ||||||   ||  |   |     |   | ||  |||   ||  | |    |  ||||    ||   ||| ||| ||| ||  || | ||||||||||||||||||||| || ||||| || ||| | || |||||||| |||||||||||  ||||||||||||| ||||| ||  |  || |||| || |
gtttgactgacttgatggactatt-tcttgtctgttg-taaaattatcaaactgaataatttcaaaacctaagaatcttttgttatttctttttttggctgatttcatgcaaacagGAAGACTTTGGAGGAGGGCATCCAGATCCTAATCTAACCTATGCAAAGGAGTTGGTTGCATGTATGGGATTGGGTAAATCAGATGCTAAAAATGAGCCAC
















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|254347113|gb|GR856783.1|GR856783
EST:     TGGATGAGCTTGGGGCACAAGAAAGCTCTTTACTGAACTGTACACCAAAG                         GAAGACTTTGGAGGAGGACACCCAGACCCCAATTTGACATATGCAAAAGAG
genomic: TGGATGAGCTTGGGGCACAAGAAAGCTCTTTACTGAACTGTACACCAAAGgtcttattct ... ttggatacagGAAGACTTTGGAGGAGGACACCCAGACCCCAATTTGACATATGCAAAAGAG
EST: gi|16349332|gb|BI974927.1|BI974927
EST:     TGGATGAGCTTGGGGCACAAGAAAGCTCTTTACTGAACTGTACACCAAAG                         GAAGACTTTGGAGGAGGACACCCAGACCCCAATTTGACATATGCAAAAGAG
genomic: TGGATGAGCTTGGGGCACAAGAAAGCTCTTTACTGAACTGTACACCAAAGgtcttattct ... ttggatacagGAAGACTTTGGAGGAGGACACCCAGACCCCAATTTGACATATGCAAAAGAG
EST: gi|6567342|gb|AW234953.1|AW234953
EST:     TGGATGAGCTTGGGGCACAAGAAAGCTCTTTACTGAACTGTACACCAAAG                         GAAGACTTTGGAGGAGGACACCCAGACCCCAATTTGACATATGC
genomic: TGGATGAGCTTGGGGCACAAGAAAGCTCTTTACTGAACTGTACACCAAAGgtcttattct ... ttggatacagGAAGACTTTGGAGGAGGACACCCAGACCCCAATTTGACATATGC
EST: gi|208318113|gb|GE110636.1|GE110636
EST:     TGGATGAGCTTGGGGCACAAGAAAGCTCTTTACTGAACTGTACACCAAAG                         GAAGACTTTGGAGGAGGACACCCAGACCCCAATTTGACATATGCAAAAGAG
genomic: TGGATGAGCTTGGGGCACAAGAAAGCTCTTTACTGAACTGTACACCAAAGgtcttattct ... ttggatacagGAAGACTTTGGAGGAGGACACCCAGACCCCAATTTGACATATGCAAAAGAG
EST: gi|10845957|gb|BF068962.1|BF068962
EST:     TGGATGAGCTTGGGGCACAAGAAAGCTCTTTACTGAACTGTACACCAAAG                         GAAGACTTTGGAGGAGGACACCCAGACCCCAATTTGACATATGC
genomic: TGGATGAGCTTGGGGCACAAGAAAGCTCTTTACTGAACTGTACACCAAAGgtcttattct ... ttggatacagGAAGACTTTGGAGGAGGACACCCAGACCCCAATTTGACATATGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttctgaatgccagttgtgatttgcctttgatttgtggatgacttgttggatacagGAAGACTTTGGAGGAGGACACCCAGACCCCAATTTGACATATGCAAAAGAGTTGGTTGCTCGTATGGGATTGGGCAAATCCGAACCACAAGATGATCCCC
                        ctttgat  putative branch site (score: 5)
                         tttgattt  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtcttattctcttgttgattaatgccaaggatagctttaaatattctgaatgccagttgtgatttgcctttgatttgtggatgacttgttggatacagGAAGACTTTGGAGGAGGACACCCAGACCCCAATTTGACATATGCAAAAGAGTTGGTTGCTCGTATGGGATTGGGCAAATCCGAACCACAAGATGATCCCC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG