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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgcatcatttcattgtgttaaactgattttgattatagtgctccatgtagattgagttgctacttagtatttgctgcaaatgttcataattgcagCTATTGAAAGTGAAGCCAGAAGAAGTATTAATTGAATCCACTGGTGTAATTGGTCAAAGAATAAAAAAG

Basic information

species Glycine max
transcript GLYMA13G19450.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA13G19450.1 (Glycine max), 3'ss of exon 6
lower sequence: AT2G37500.1 (Arabidopsis thaliana), 3'ss of exon 6
gtatgcatcatttcattgtgttaaactgattttgattatagtgctccatgtagattgagttgctacttagtatttgctgcaaatgttcataattgcagCTATTGAAAGTGAAGCCAGAAGAAGTATTAATTGAATCCACTGGTGTAATTGGTCAAAGAATAAAAAAG
    | ||  |||   ||| ||  | |    |   |         |   |||  ||      ||  |||   |||| |     | || |   ||| ||||| | |||||||||||||| ||||| |||||||| || |||||||| || ||||| ||||||||||||
----gtatgcttttggtgtctttcattcccatgtctcccgcgaaacttcgtatctttcaacactg-ttaccgtttgtt-----tctttaccgttgtagCTACTTAAAGTGAAGCCAGAGGAAGTGTTAATTGAGTCAACTGGTGTTATCGGTCAGAGAATAAAAAAG
















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|209727148|gb|BW655213.1|BW655213
EST:     GCAAAGAAGGTTACCAGGACATGATAGAATGTGTGGAAAGCCTTGCTAAG                         CTATTGAAAGTGAAGCCAGAAGAAGTATTAATTGAATCCACTGGTGTAATT
genomic: GCAAAGAAGGTTACCAGGACATGATAGAATGTGTGGAAAGCCTTGCTAAGgtatgcatca ... ataattgcagCTATTGAAAGTGAAGCCAGAAGAAGTATTAATTGAATCCACTGGTGTAATT
EST: gi|120530228|gb|EH258362.1|EH258362
EST:     GCAAAGAAGGTTACCAGGACATGATAGAATGTGTGGAAAGCCTTGCTAAG                         CTATTGAAAGTGAAGCCAGAAGAAGTATTAATTGAATCCACTGGTGTAATT
genomic: GCAAAGAAGGTTACCAGGACATGATAGAATGTGTGGAAAGCCTTGCTAAGgtatgcatca ... ataattgcagCTATTGAAAGTGAAGCCAGAAGAAGTATTAATTGAATCCACTGGTGTAATT
EST: gi|192294186|gb|FG986275.1|FG986275
EST:     GCAAAGAAGGTTACCAGGACATGATAGAATGTGTGGAAAGCCTTGCTAAG                         CTATTGAAAGTGAAGCCAGAAGAAGTATTAATTGAATCCACTGGTGTAATT
genomic: GCAAAGAAGGTTACCAGGACATGATAGAATGTGTGGAAAGCCTTGCTAAGgtatgcatca ... ataattgcagCTATTGAAAGTGAAGCCAGAAGAAGTATTAATTGAATCCACTGGTGTAATT
EST: gi|213601471|gb|DB956735.1|DB956735
EST:     GCAAAGAAGGTTACCAGGACATGATAGAATGTGTGGAAAGCCTTGCTAAG                         CTATTGAAAGTGAAGCCA
genomic: GCAAAGAAGGTTACCAGGACATGATAGAATGTGTGGAAAGCCTTGCTAAGgtatgcatca ... ataattgcagCTATTGAAAGTGAAGCCA
EST: gi|209725373|gb|BW658260.1|BW658260
EST:     GCAAAGAAGGTTACCAGGACATGATAGAATGTGTGGAAAGCCTTGCTAAG                         CTATTGAAAGTGAAGCCAGAAGAAGTATTAATTGAATCCACTGGTGTAATT
genomic: GCAAAGAAGGTTACCAGGACATGATAGAATGTGTGGAAAGCCTTGCTAAGgtatgcatca ... ataattgcagCTATTGAAAGTGAAGCCAGAAGAAGTATTAATTGAATCCACTGGTGTAATT
EST: gi|209727793|gb|BW658717.1|BW658717
EST:     GCAAAGAAGGTTACCAGGACATGATAGAATGTGTGGAAAGCCTTGCTAAG                         CTATTGAAAGTGA
genomic: GCAAAGAAGGTTACCAGGACATGATAGAATGTGTGGAAAGCCTTGCTAAGgtatgcatca ... ataattgcagCTATTGAAAGTGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctccatgtagattgagttgctacttagtatttgctgcaaatgttcataattgcagCTATTGAAAGTGAAGCCAGAAGAAGTATTAATTGAATCCACTGGTGTAATTGGTCAAAGAATAAAAAAG
                                     aaatgttcataatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgcatcatttcattgtgttaaactgattttgattatagtgctccatgtagattgagttgctacttagtatttgctgcaaatgttcataattgcagCTATTGAAAGTGAAGCCAGAAGAAGTATTAATTGAATCCACTGGTGTAATTGGTCAAAGAATAAAAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA