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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCCAAGGACCACAACCCCACCGTCTGGTTCGCCGACAACGGCGAACGCCTCGGCACCTACCGCGGCCACAACGGCGCCGTTTGGTGCTGCGACGTCTCAAgcaagctcttcatcactgttttcaattcatctttttaataatattgatactgatagtaattaatttggattctgatgctgcttcag

Basic information

species Glycine max
transcript GLYMA01G03610.2
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA01G03610.2 (Glycine max), 5'ss of exon 1
lower sequence: AT2G46280.3 (Arabidopsis thaliana), 5'ss of exon 1
GCCAAGGACCACAACCCCACCGTCTGGTTCGCCGACAACGGCGAACGCCTCGGCACCTACCGCGGCCACAACGGCGCCGTTTGGTGCTGCGACGTCTCAAgcaagctcttcatcactgttttcaatt-catctttttaataatattgat--actgatagtaattaatttggattctgatgctgcttcag------------------------------------------------------------
|||||||||||||  |||||| ||||||| ||||| |||||||| ||||| || || ||||| || |||||||| || ||||||||||| || |||||  | ||| |  |||       ||  |||   |||   |  || || | |||  | || |     |||  |   |   || |   | || |                                                             
GCCAAGGACCACACACCCACCCTCTGGTTTGCCGATAACGGCGAGCGCCTTGGAACTTACCGTGGTCACAACGGTGCTGTTTGGTGCTGTGATGTCTCCCgtaagtttctcaatttctcttcaaatagtatcgagtcgatgat-tagattcattgtttccccttagctacaagcttgtttagggtttatagtatcgagtgaattctgtcgtcttagtctttcaaagctgaatgtttagtgatttcttag

upper sequence: GLYMA01G03610.2 (Glycine max), 5'ss of exon 1
lower sequence: AT2G46290.1 (Arabidopsis thaliana), 5'ss of exon 2
GCCAAGGACCACAACCCCACCGTCTGGTTCGCCGACAACGGCGAACGCCTCGGCACCTACCGCGGCCACAACGGCGCCGTTTGGTGCTGCGACGTCTCAAgcaag----ctcttcatcactgttttcaatt-catctttttaataatattgatactgatagtaattaatttggattctgatgctgcttcag--------------------------------------------
||||| |||||||  ||||| |||||||| ||||| |||||||| || || ||||| ||||| |||||||  || || ||||||||||| ||  |||| || |||    |||  | || |   ||  |||   || |  |  ||   || ||| | | |    ||| |  | | |     || || || ||                                            
GCCAAAGACCACACTCCCACAGTCTGGTTTGCCGATAACGGCGAGCGTCTTGGCACTTACCGTGGCCACAGTGGTGCTGTTTGGTGCTGTGATATCTCCAgtaagtggtctcagcctctcaaattcaaatagtatatagtggatggaatggattcagtttaggatttaagtcgttgtctttgttgttttagtctttcatagcttaacgattagtgttttgtttgtgatttcttag

upper sequence: GLYMA01G03610.2 (Glycine max), 5'ss of exon 1
lower sequence: Vv01s0011g06630.t01 (Vitis vinifera), 5'ss of exon 1
GCCAAGGACCACAACCCCACCGTCTGGTTCGCCGACAACGGCGAACGCCTCGGCACCTACCGCGGCCACAACGGCGCCGTTTGGTGCTGCGACGTCTCAAgcaagctcttcatc-actgttttcaattcatctttttaataatattgatactgatagtaattaatttggattctgatgctgcttcag--------------------------------------------------
|||||||| ||||  |||||||||||||||||||||||||| || |||||||||||||| || || |||||||| |||||||||  |||||| ||||| || | |   | | ||   |||| |   | ||| |||||  ||   |||  | | ||       |    || ||  | |  |   ||||                                                  
GCCAAGGATCACACTCCCACCGTCTGGTTCGCCGACAACGGGGAGCGCCTCGGCACCTATCGTGGACACAACGGTGCCGTTTGGACCTGCGATGTCTCCAgtatgtcttccttctgatgttattcgtccattttttt--tagccttggaagttatttcggcgaccaggggttagggttttctatcaggagaggtatcatggttaattgattgattaattggttggtcgattgttcag

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|209726207|gb|BW659572.1|BW659572
EST:     CGGCACCTACCGCGGCCACAACGGCGCCGTTTGGTGCTGCGACGTCTCAA                         GAGATTCGGGTCGGCTCATAACGGGAAGTGCGGATCAGACCGCCAAGCTAT
genomic: CGGCACCTACCGCGGCCACAACGGCGCCGTTTGGTGCTGCGACGTCTCAAgcaagctctt ... gctgcttcagGAGATTCGGGTCGGCTCATAACGGGAAGTGCGGATCAGACCGCCAAGCTAT
EST: gi|213593280|gb|DB966105.1|DB966105
EST:     CGGCACCTACCGCGGCCACAACGGCGCCGTTTGGTGCTGCGACGTCTCAA                         GAGATTCGGGTCGGCTCATAACGGGAAGTGCGGATCAGACCGCCAAGCTAT
genomic: CGGCACCTACCGCGGCCACAACGGCGCCGTTTGGTGCTGCGACGTCTCAAgcaagctctt ... gctgcttcagGAGATTCGGGTCGGCTCATAACGGGAAGTGCGGATCAGACCGCCAAGCTAT
EST: gi|14126517|gb|BG790955.1|BG790955
EST:     CGGCACCTACCGCGGCCACAACGGCGCCGTTTGGTGCTGCGACGTCTCAA                         GAGATTCGGGTCGGCTCATAACGGGAAGTGCGGATCAGACCGCCAAGCTAT
genomic: CGGCACCTACCGCGGCCACAACGGCGCCGTTTGGTGCTGCGACGTCTCAAgcaagctctt ... gctgcttcagGAGATTCGGGTCGGCTCATAACGGGAAGTGCGGATCAGACCGCCAAGCTAT
EST: gi|18717773|gb|BM522996.1|BM522996
EST:     CGGCACCTACCGCGGCCACAACGGCGCCGTTTGGTGCTGCGACGTCTCAA                         GAGATTCGGGTCGGCTCATAACGGGAAGTGCGGATCAGACCGCCAAGCTAT
genomic: CGGCACCTACCGCGGCCACAACGGCGCCGTTTGGTGCTGCGACGTCTCAAgcaagctctt ... gctgcttcagGAGATTCGGGTCGGCTCATAACGGGAAGTGCGGATCAGACCGCCAAGCTAT
EST: gi|20814918|gb|BQ299396.1|BQ299396
EST:     CGGCACCTACCGCGGCCACAACGGCGCCGTTTGGTGCTGCGACGTCTCAA                         GAGATTCGGGTCGGCTCATAACGGGAAGTGCGGATCAGACCGCCAAGCTAT
genomic: CGGCACCTACCGCGGCCACAACGGCGCCGTTTGGTGCTGCGACGTCTCAAgcaagctctt ... gctgcttcagGAGATTCGGGTCGGCTCATAACGGGAAGTGCGGATCAGACCGCCAAGCTAT
EST: gi|213587349|gb|DB955515.1|DB955515
EST:     CGGCACCTACCGCGGCCACAACGGCGCCGTTTGGTGCTGCGACGTCTCAA                         GAGATTCGGGTCGGCTCATAAACGGGAAGTGCGGATCAGACCGCCAAGCTA
genomic: CGGCACCTACCGCGGCCACAACGGCGCCGTTTGGTGCTGCGACGTCTCAAgcaagctctt ... gctgcttcagGAGATTCGGGTCGGCTCATAA-CGGGAAGTGCGGATCAGACCGCCAAGCTA
EST: gi|9899499|gb|BE608467.1|BE608467
EST:     CGGCACCTACCGCGGCCACAACGGCGCCGTTTGGTGCTGCGACGTCTCAA                         GAGATTCGGGTCGGCTCATAACGGGAAGTGCGGATCAGACCGCCAAGCTAT
genomic: CGGCACCTACCGCGGCCACAACGGCGCCGTTTGGTGCTGCGACGTCTCAAgcaagctctt ... gctgcttcagGAGATTCGGGTCGGCTCATAACGGGAAGTGCGGATCAGACCGCCAAGCTAT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCCAAGGACCACAACCCCACCGTCTGGTTCGCCGACAACGGCGAACGCCTCGGCACCTACCGCGGCCACAACGGCGCCGTTTGGTGCTGCGACGTCTCAAgcaagctcttcatcactgttttcaattcatctttttaataatattgatactgatagtaattaatttggattctgatgctgcttcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC