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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCACCTTTTTGACTGGGAGTGAACACAATGATGAGTTCTATATAGATGAACATGGAAACACAAGAACAAGAACAAATCGCTCTGGTGGGATACAGgtatttgtgctgttctataattactaattagttttttctagatatgcactgacagtcacatttctatatttgttttacttatattatctgtattgacaatcag

Basic information

species Glycine max
transcript GLYMA20G31980.1
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA20G31980.1 (Glycine max), 5'ss of exon 10
lower sequence: AT1G48850.2 (Arabidopsis thaliana), 5'ss of exon 10
GCACCTTTTTGACTGGGAGTGAACACAATGATGAGTTCTATATAGATGAACATGGAAACACAAGAACAAGAACAAATCGCTCTGGTGGGATACAGgtatttgtgctgttctataattacta-attagtttttt-ctagatatgcactgacagtcacatttctatatttgttttacttatattatctgtattgacaatcag
| ||||||||||||||   |||||||||||||||||||||||  |||||| ||||||  | | | || ||||| || || |||||||| || |||||  | ||   ||  | || ||| ||  | | |  |   ||| || |   |||| ||    ||| |||   ||| |  | || |||                   
GTACCTTTTTGACTGGTCTTGAACACAATGATGAGTTCTATACCGATGAAAATGGAAGAATACGTACCAGAACCAACCGATCTGGTGGAATTCAGgt--tagttaagtcttgtatttaatatgtcaataataaactacatttctcctgagaga---attcctaatattggtcaatttgtatag-----------------

upper sequence: GLYMA20G31980.1 (Glycine max), 5'ss of exon 10
lower sequence: Vv13s0019g04190.t01 (Vitis vinifera), 5'ss of exon 10
GCACCTTTTTGACTGGGAGTGAACACAATGATGAGTTCTATATAGATGAACATGGAAACACAAGAACAAGAACAAATCGCTCTGGTGGGATACAGgtatttgtgctgttctataattactaattagtttttt---ctagatatgcactgacagtcacatttctatatttgttttactt-atattatctgtattgacaatcag
| || ||| |||||||||||||||| |||||||||||||  |  |||| |||||||   |  || |||||||| |||||||||||||||||||||||| ||||  ||| || |||  | |  |  || |||     ||||| ||   || ||      |||    || |    | ||| | ||  | | |  |||||| |||
GTACATTTATGACTGGGAGTGAACATAATGATGAGTTCTTCACGGATGCACATGGACGAATCAGGACAAGAACTAATCGCTCTGGTGGGATACAGgtacttgttatgtactttaagcatttgtatgtgtttgggattagatttgttatg-caccattttttaagcatcttcagtccttgagatcgtttctgctgacaaacag

upper sequence: GLYMA20G31980.1 (Glycine max), 5'ss of exon 10
lower sequence: EFJ25489 (Selaginella moellendorffii), 5'ss of exon 10
GCACCTTTTTGACTGGGAGTGAACACAATGATGAGTTCTATATAGATGAACATGGAAACACAAGAACAAGAACAAATCGCTCTGGTGGGATACAGgtatttgtg-ctgttctataattactaattagttttttctagatatgcactgacagtcacatttctatatttgttttacttatattatctgtattgacaatcag
| ||     |||| || || |||||||||||||||||||| || || |||  ||| |||  ||||||| | |||||||| |||||||| || ||||||  ||   || |  | || | |||   |    || | |   | |  |||  |   || |||| |  |                                   
GAACTAAAATGACAGGCAGCGAACACAATGATGAGTTCTACATTGACGAAATTGGTAACGTAAGAACACGTACAAATCGATCTGGTGGCATCCAGgtacgtggaactataatctactgacttcctctgcttctttttttctaaacttgcgaaca-atttatgcag----------------------------------

upper sequence: GLYMA20G31980.1 (Glycine max), 5'ss of exon 10
lower sequence: EFJ22409 (Selaginella moellendorffii), 5'ss of exon 9
GCACCTTTTTGACTGGGAGTGAACACAATGATGAGTTCTATATAGATGAACATGGAAACACAAGAACAAGAACAAATCGCTCTGGTGGGATACAGgtatttgtg-ctgttctataattactaattagttttttctagatatgcactgacagtcacatttctatatttgttttacttatattatctgtattgacaatcag
| ||     |||| || || |||||||||||||||||||| || || |||  ||| |||  ||||||| | |||||||| |||||||| || ||||||  ||   || |  | || | |||   |    |||| |   | |  |||  |   || |||| |  |                                   
GAACTAAAATGACAGGCAGCGAACACAATGATGAGTTCTACATTGACGAAATTGGTAACGTAAGAACACGTACAAATCGATCTGGTGGCATCCAGgtacgtggaactataatctactgacttcctctcctttttttt-tctaaacttgcgaaca-atttatgcag----------------------------------

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|58017502|gb|CX704244.1|CX704244
EST:     ATGAACATGGAAACACAAGAACAAGAACAAATCGCTCTGGTGGGATACAG                         GGTGGAATTTCCAATGGGGAAATCATTAATATGAGAATAGCTTTCAAGCCA
genomic: ATGAACATGGAAACACAAGAACAAGAACAAATCGCTCTGGTGGGATACAGgtatttgtgc ... tgacaatcagGGTGGAATTTCCAATGGGGAAATCATTAATATGAGAATAGCTTTCAAGCCA
EST: gi|19052637|gb|BM731304.1|BM731304
EST:     GAACAAATCGCTCTGGTGGGATACAG                         GGTGGAATTTCCAATGGGGAAATCATTAATATGAGAATAGCTTTCAAGCCA
genomic: GAACAAATCGCTCTGGTGGGATACAGgtatttgtgc ... tgacaatcagGGTGGAATTTCCAATGGGGAAATCATTAATATGAGAATAGCTTTCAAGCCA
EST: gi|120533980|gb|EH262113.1|EH262113
EST:     ATGAACATGGAAACACAAGAACAAGAACAAATCGCTCTGGTGGGATACAG                         GGTGGAATTTCCAATGGGGAAATCATTAATATGAGAATAGCTTTCAAGCCA
genomic: ATGAACATGGAAACACAAGAACAAGAACAAATCGCTCTGGTGGGATACAGgtatttgtgc ... tgacaatcagGGTGGAATTTCCAATGGGGAAATCATTAATATGAGAATAGCTTTCAAGCCA
EST: gi|6668053|gb|AW279504.1|AW279504
EST:     ATGAACATGGAAACACAAGAACAAGAACAAATCGCTCTGGTGGGATACAG                         GGTGGAATTTCCAATGGGGAAATCATTAATATGAGAATAGCTTTCAAGCCA
genomic: ATGAACATGGAAACACAAGAACAAGAACAAATCGCTCTGGTGGGATACAGgtatttgtgc ... tgacaatcagGGTGGAATTTCCAATGGGGAAATCATTAATATGAGAATAGCTTTCAAGCCA
EST: gi|254340229|gb|GR858354.1|GR858354
EST:     ATGAACATGGAAACACAAGAACAAGAACAAATCGCTCTGGTGGGATACAG                         GGTGGAATTTCCAATGGGGAAATCATTAATATGAGAATAGCTTTCAAGCCA
genomic: ATGAACATGGAAACACAAGAACAAGAACAAATCGCTCTGGTGGGATACAGgtatttgtgc ... tgacaatcagGGTGGAATTTCCAATGGGGAAATCATTAATATGAGAATAGCTTTCAAGCCA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCACCTTTTTGACTGGGAGTGAACACAATGATGAGTTCTATATAGATGAACATGGAAACACAAGAACAAGAACAAATCGCTCTGGTGGGATACAGgtatttgtgctgttctataattactaattagttttttctagatatgcactgacagtcacatttctatatttgttttacttatattatctgtattgacaatcag

- - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG