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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aacttgtctttttataacaggaaatatgtttccatgttgcattattttgttgttttattcacggacttgtgccatcatgaagtgatatgtaaattggcagAACCACAACTATGCTGTTGACCCTGCCACACTGCCGGAAGGAGTGGAGGTTACTCATATCAATCTAAATGATGGAAGTTGTGCTGGTCTTGCTTTCCCTG

Basic information

species Glycine max
transcript GLYMA06G15510.1
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA06G15510.4 (Glycine max), 3'ss of exon 8
lower sequence: Vv04s0044g00550.t01 (Vitis vinifera), 3'ss of exon 8
-------aacttgtc--tttttataacaggaaatatgtttccatgttgcattattttgttgttttattcacggacttgtgccatcatgaagtgatatgtaaattggcagAACCACAACTATGCTGTTGACCCTGCCACACTGCCGGAAGGAGTGGAGGTTACTCATATCAATCTAAATGATGGAAGTTGTGCTGGTCTTGCTTTCCCTG
          | ||   |||   |||   |||  |||| |     ||   || | || || || | |||| |      |  ||   | || | || |||    |||||||| || |||||||| || ||||||||  ||||||| || || ||||| || || ||| |||| || ||||||||||||||||| || ||||| |  ||||
tgataccgtttggttgatttcagtaatttgaatcatgtctatgcattcacttttcttttttttcttttcatg-----ttttcacttttaattcat-tgtg---tggcagAATCATAACTATGCAGTAGACCCTGCATCACTGCCTGAGGGTGTGGAAGTGACGCATGTCAACCTTAATGATGGAAGTTGTGCAGGCCTTGCCTATCCTG
















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|209727966|gb|BW666686.1|BW666686
EST:     ATCATCCTGTTCGCAACCTTCGAAGTGGCCATGTTGAAATTAGTGCTCAG                         AACCACAACTATGCTGTTGACCCTGCCACACTGCCGGAAGGAGTGGAGGTT
genomic: ATCATCCTGTTCGCAACCTTCGAAGTGGCCATGTTGAAATTAGTGCTCAGgtatgcgaac ... aaattggcagAACCACAACTATGCTGTTGACCCTGCCACACTGCCGGAAGGAGTGGAGGTT
EST: gi|17963310|gb|BM270060.1|BM270060
EST:     ATCATCCTGTTCGCAACCTTCGAAGTGGCCATGTTGAAATTAGTGCTCAG                         AACCACAACTATGCTGTTGACCCTGCCACACTGCCGGAAGGAGTGGAGGTT
genomic: ATCATCCTGTTCGCAACCTTCGAAGTGGCCATGTTGAAATTAGTGCTCAGgtatgcgaac ... aaattggcagAACCACAACTATGCTGTTGACCCTGCCACACTGCCGGAAGGAGTGGAGGTT
EST: gi|151397657|gb|EV267530.1|EV267530
EST:     ATCATCCTGTTCGCAACCTTCGAAGTGGCCATGTTGAAATTAGTGCTCAG                         AACCACAACTATGCTGTTGACCCTGCCACACTGCCGGAAGGAGTGGAGGTT
genomic: ATCATCCTGTTCGCAACCTTCGAAGTGGCCATGTTGAAATTAGTGCTCAGgtatgcgaac ... aaattggcagAACCACAACTATGCTGTTGACCCTGCCACACTGCCGGAAGGAGTGGAGGTT
EST: gi|10848315|gb|BF070826.1|BF070826
EST:     ATCATCCTGTTCGCAACCTTCGAAGTGGCCATGTTGAAATTAGTGCTCAG                         AACCACAACTATGCTGTTGACCCTGCCACACTGCCGGAAGGAGTGGAGGTT
genomic: ATCATCCTGTTCGCAACCTTCGAAGTGGCCATGTTGAAATTAGTGCTCAGgtatgcgaac ... aaattggcagAACCACAACTATGCTGTTGACCCTGCCACACTGCCGGAAGGAGTGGAGGTT
EST: gi|20497897|gb|BQ272827.1|BQ272827
EST:     ATCATCCTGTTCGCAACCTTCGAAGTGGCCATGTTGAAATTAGTGCTCAG                         AACCACAACTATGCTGTTGACCCTGCCACACTGCCGGAAGGAGTGGAGGTT
genomic: ATCATCCTGTTCGCAACCTTCGAAGTGGCCATGTTGAAATTAGTGCTCAGgtatgcgaac ... aaattggcagAACCACAACTATGCTGTTGACCCTGCCACACTGCCGGAAGGAGTGGAGGTT
EST: gi|151401872|gb|EV271685.1|EV271685
EST:     ATCATCCTGTTCGCAACCTTCGAAGTGGCCATGTTGAAATTAGTGCTCAG                         AACCACAACTATGCTGTTGACCCTGCCACACTGCCGGAAGGAGTGGAGGTT
genomic: ATCATCCTGTTCGCAACCTTCGAAGTGGCCATGTTGAAATTAGTGCTCAGgtatgcgaac ... aaattggcagAACCACAACTATGCTGTTGACCCTGCCACACTGCCGGAAGGAGTGGAGGTT
EST: gi|16342798|gb|BI968393.1|BI968393
EST:     ATCATCCTGTTCGCAACCTTCGAAGTGGCCATGTTGAAATTAGTGCTCAG                         AACCACAACTATGCTGTTGACCCTGCCACACTGCCGGAAGGAGTGGAGGTT
genomic: ATCATCCTGTTCGCAACCTTCGAAGTGGCCATGTTGAAATTAGTGCTCAGgtatgcgaac ... aaattggcagAACCACAACTATGCTGTTGACCCTGCCACACTGCCGGAAGGAGTGGAGGTT
EST: gi|151402745|gb|EV272558.1|EV272558
EST:     ATCATCCTGTTCGCAACCTTCGAAGTGGCCATGTTGAAATTAGTGCTCAG                         AACCACAACTATGCTGTTGACCCTGCCACACTGCCGGAAGGAGTGGAGGTT
genomic: ATCATCCTGTTCGCAACCTTCGAAGTGGCCATGTTGAAATTAGTGCTCAGgtatgcgaac ... aaattggcagAACCACAACTATGCTGTTGACCCTGCCACACTGCCGGAAGGAGTGGAGGTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttgttgttttattcacggacttgtgccatcatgaagtgatatgtaaattggcagAACCACAACTATGCTGTTGACCCTGCCACACTGCCGGAAGGAGTGGAGGTTACTCATATCAATCTAAATGATGGAAGTTGTGCTGGTCTTGCTTTCCCTG
                                       atatgtaaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aacttgtctttttataacaggaaatatgtttccatgttgcattattttgttgttttattcacggacttgtgccatcatgaagtgatatgtaaattggcagAACCACAACTATGCTGTTGACCCTGCCACACTGCCGGAAGGAGTGGAGGTTACTCATATCAATCTAAATGATGGAAGTTGTGCTGGTCTTGCTTTCCCTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG
- - - - - - - - - - - - - tgtttcc
- - - - - - - - - - - - - - - - - - -tgcatta
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgccatc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgaagtg