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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGACTGGAGGATTGATGATATTAAAGGGCTTCTTGGGCGTTGTAATTTTAAAGCTGATATGCTTGACCGAAAAGTTTCACTATTGAGTGGTGGTGAGAAGgtaaattcaagatttgtgtcttctttttcagttgacatttatttagcatttgtgagcaacataacattcaaattccaacttaattctatgactgaatggt...

Basic information

species Glycine max
transcript GLYMA04G39670.1
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA04G39670.1 (Glycine max), 5'ss of exon 5
lower sequence: AT5G09930.1 (Arabidopsis thaliana), 5'ss of exon 5
GGACTGGAGGATTGATGATATTAAAGGGCTTCTTGGGCGTTGTAATTTTAAAGCTGATATGCTTGACCGAAAAGTTTCACTATTGAGTGGTGGTGAGAAGgtaaattcaagatttgtgtcttctttttcagt-tgacatttatttagcatttgtgagcaacataacattcaaattccaacttaattctatgactgaatggt
 || ||||| ||||||||||| ||||  |||||||| || || || || |||||||| ||| | ||  |||| || || || ||||||||||||||||||||||   ||  || | | || |  |  ||| | | | | | ||      ||  | | |  | |     |     ||  |                      
AGATTGGAGAATTGATGATATAAAAGCTCTTCTTGGTCGGTGCAACTTCAAAGCTGACATGTTGGATAGAAAGGTCTCTCTTTTGAGTGGTGGTGAGAAGgtaa---cataatgtctatcattatcctcaatataatactcatc--atgttcttcatcgccttttttcttgcggtcttag---------------------

upper sequence: GLYMA04G39670.1 (Glycine max), 5'ss of exon 5
lower sequence: Vv07s0031g01640.t01 (Vitis vinifera), 5'ss of exon 5
GGACTGGAGGATTGATGATATTAAAGGGCTTCTTGGGCGTTGTAATTTTAAAGCTGATATGCTTGACCGAAAAGTTTCACTATTGAGTGGTGGTGAGAAGgtaaattcaagatttgtgtcttctttttcagttgacatttatttagcatttgtgagcaacataacattcaaattccaacttaattctatgactgaatggt--
| | ||||  ||||| ||||| || || || ||||||||||||||||| ||||| |||||||||||  |||| ||||| || |||||||||||||||||||| | || ||    | |  ||| ||| | | ||   || | |   |  ||  ||| ||  |    |   |   |     | | |    ||||          
GAATTGGAAAATTGACGATATAAAGGGACTACTTGGGCGTTGTAATTTCAAAGCCGATATGCTTGATAGAAAGGTTTCCCTTTTGAGTGGTGGTGAGAAGgtgagttaaaccagtata-cttgtttgttattttgtatctctcgtgt-ttattgaacattaatttagctattcttgttttcactgtgctgacaagggaactc
















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|209707109|gb|BW653221.1|BW653221
EST:     AAGCTGATATGCTTGACCGAAAAGTTTCACTATTGAGTGGTGGTGAGAAG                         GCACGGCTGGCCTTTTGCAAATTCATGGTAAAGCCATCAACTATGCTTGTG
genomic: AAGCTGATATGCTTGACCGAAAAGTTTCACTATTGAGTGGTGGTGAGAAGgtaaattcaa ... gttttactagGCACGGCTGGCCTTTTGCAAATTCATGGTAAAGCCATCAACTATGCTTGTG
EST: gi|192312580|gb|FK003274.1|FK003274
EST:     AAGCTGATATGCTTGACCGAAAAGTTTCACTATTGAGTGGTGGTGAGAAG                         GCACGGCTGGCCTTTTGCAAATTCATGGTAAAGCCATCAACTATGCTTGTG
genomic: AAGCTGATATGCTTGACCGAAAAGTTTCACTATTGAGTGGTGGTGAGAAGgtaaattcaa ... gttttactagGCACGGCTGGCCTTTTGCAAATTCATGGTAAAGCCATCAACTATGCTTGTG
EST: gi|151403285|gb|EV273095.1|EV273095
EST:     AAGCTGATATGCTTGACCGAAGAGTTTCACTATTGAGTGGTGGTGAGAAG                         GCACGGCTGGCCTTTTGCAAATTCATGGTAAAGCCATCAACTATGCTTGTG
genomic: AAGCTGATATGCTTGACCGAAAAGTTTCACTATTGAGTGGTGGTGAGAAGgtaaattcaa ... gttttactagGCACGGCTGGCCTTTTGCAAATTCATGGTAAAGCCATCAACTATGCTTGTG
EST: gi|16342504|gb|BI968099.1|BI968099
EST:     AAGCTGATATGCTTGACCGAAAAGTTTCACTATTGAGTGGTGGTGAGAAG                         GCACGGCTGGCCTTTTGCAAATTCATGGTAAAGCCATCAACTATGCTTGTG
genomic: AAGCTGATATGCTTGACCGAAAAGTTTCACTATTGAGTGGTGGTGAGAAGgtaaattcaa ... gttttactagGCACGGCTGGCCTTTTGCAAATTCATGGTAAAGCCATCAACTATGCTTGTG
EST: gi|213591107|gb|DB979354.1|DB979354
EST:     TATGCTTGACCGAAAAGTTTCACTATTGAGTGGTGGTGAGAAG                         GCACGGCTGGCCCTTTGCAAATTCATGGTAAAGCCATCAACTATGCTTGTG
genomic: TATGCTTGACCGAAAAGTTTCACTATTGAGTGGTGGTGAGAAGgtaaattcaa ... gttttactagGCACGGCTGGCCTTTTGCAAATTCATGGTAAAGCCATCAACTATGCTTGTG
EST: gi|254327297|gb|GR836906.1|GR836906
EST:     AAGCTGATATGCTTGACCGAAAAGTTTCACTATTGAGTGGTGGTGAGAAG                         GCACGGCTGGCCTTTTGCAAATTCATGGTAAAGCCATCAACTATGCTTGTG
genomic: AAGCTGATATGCTTGACCGAAAAGTTTCACTATTGAGTGGTGGTGAGAAGgtaaattcaa ... gttttactagGCACGGCTGGCCTTTTGCAAATTCATGGTAAAGCCATCAACTATGCTTGTG
EST: gi|151402499|gb|EV272312.1|EV272312
EST:     AAGCTGATATGCTTGACCGAAAAGTTTCACTATTGAGTGGTGGTGAGAAG                         GCACGGCTGGCCTTTTGCAAATTCATGGTAAAGCCATCA-CTATGCTTGTG
genomic: AAGCTGATATGCTTGACCGAAAAGTTTCACTATTGAGTGGTGGTGAGAAGgtaaattcaa ... gttttactagGCACGGCTGGCCTTTTGCAAATTCATGGTAAAGCCATCAACTATGCTTGTG
EST: gi|193556422|gb|FK511071.1|FK511071
EST:     AAGCTGATATGCTTGACCGAAAAGTTTCACTATTGAGTGGTGGTGAGAAG                         GCACGGCTGGCCTTTTGCAAATTCATGGTAAAGCCATCAACTATGCTTGTG
genomic: AAGCTGATATGCTTGACCGAAAAGTTTCACTATTGAGTGGTGGTGAGAAGgtaaattcaa ... gttttactagGCACGGCTGGCCTTTTGCAAATTCATGGTAAAGCCATCAACTATGCTTGTG
EST: gi|209699162|gb|BW656175.1|BW656175
EST:     AAGCTGATATGCTTGACCGAAAAGTTTCACTATTGAGTGGTGGTGAGAAG                         GCACGGCTGGCCTTTTGCAAATTCATGGTAAAGCCATCAACTATGCTTGTG
genomic: AAGCTGATATGCTTGACCGAAAAGTTTCACTATTGAGTGGTGGTGAGAAGgtaaattcaa ... gttttactagGCACGGCTGGCCTTTTGCAAATTCATGGTAAAGCCATCAACTATGCTTGTG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGACTGGAGGATTGATGATATTAAAGGGCTTCTTGGGCGTTGTAATTTTAAAGCTGATATGCTTGACCGAAAAGTTTCACTATTGAGTGGTGGTGAGAAGgtaaattcaagatttgtgtcttctttttcagttgacatttatttagcatttgtgagcaacataacattcaaattccaacttaattctatgactgaatggt

- - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG