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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtcccatttccatttcctcctcctctctctctctctctcttttctttaataattttggcaaaaccctaatcatttattttgggattgatttggtccaaatcagATAGTGAAGGAAATTGAGCAAGACCTCTCCGGCTTCAAGTGTGGCCTAGCTCATCTCTTCT

Basic information

species Glycine max
transcript GLYMA07G34680.2
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA07G34680.2 (Glycine max), 3'ss of exon 1
lower sequence: Vv18s0122g00190.t01 (Vitis vinifera), 3'ss of exon 1
gtcccatttccatttcctcctcctctctctctctctctcttttctttaataattttggcaaaaccctaatcatttattttgggattgatttgg-----tccaaatcagATAGTGAAGGAAATTGAGCAAGACCTCTCCGGCTTCAAGTGTGGCCTAGCTCATCTCTTCT
          | |      ||          | ||  |     |   |||  | |     | |   ||    |||||  | |  || ||||       ||   || ||||| |||||||||||| ||||||||| || || ||||| |||||||| |||||||| ||| 
-------aatcgtcctgagctaagaaaataatttcaatgaag-caccaattgtatccagtagattttatctgtttatactcgtgttaatttaagattttcttcattagATATTGAAGGAAATTGGGCAAGACCTGTCAGGATTCAAATGTGGCCTTGCTCATCTATTCA
















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|209715443|gb|BW684715.1|BW684715
EST:     CCGTCAGCTTGCCCCCTCTCCGGCGCGGCTGTCATCTTGTCACTTCCAAG                         ATAGTGAAGGAAATTGAGCAAGACCTCTCCGGCTTCAAGTGTGGCCTAGCT
genomic: CCGTCAGCTTGCCCCCTCTCCGGCGCGGCTGTCATCTTGTCACTTCCAAGgtcccatttc ... tccaaatcagATAGTGAAGGAAATTGAGCAAGACCTCTCCGGCTTCAAGTGTGGCCTAGCT
EST: gi|18692788|gb|BM521636.1|BM521636
EST:     CCGTCAGCTTGCCCCCTCTCCGGCGCGGCTGTCATCTTGTCACTTCCAAG                         ATAGTGAAGGAAATTGAGCAAGACCTCTCCGGCTTCAAGTGTGGCCTAGCT
genomic: CCGTCAGCTTGCCCCCTCTCCGGCGCGGCTGTCATCTTGTCACTTCCAAGgtcccatttc ... tccaaatcagATAGTGAAGGAAATTGAGCAAGACCTCTCCGGCTTCAAGTGTGGCCTAGCT
EST: gi|23733010|gb|BU764686.1|BU764686
EST:     CCGTCAGCTTGCCCCCTCTCCGGCGCGGCTGTCATCTTGTCACTTCCAAG                         ATAGTGAAGGAAATTGAGCAAGACCTCTCCGGCTTCAAGTGTGGCCTAGCT
genomic: CCGTCAGCTTGCCCCCTCTCCGGCGCGGCTGTCATCTTGTCACTTCCAAGgtcccatttc ... tccaaatcagATAGTGAAGGAAATTGAGCAAGACCTCTCCGGCTTCAAGTGTGGCCTAGCT
EST: gi|7692412|gb|AW760519.1|AW760519
EST:     CCGTCAGCTTGCCCCCTCTCCGGCGCGGCTGTCATCTTGTCACTTCCAAG                         ATAGTGAAGGAAATTGAGCAAGACCTCTCCGGCTTCAAGTGTGGCCTAGCT
genomic: CCGTCAGCTTGCCCCCTCTCCGGCGCGGCTGTCATCTTGTCACTTCCAAGgtcccatttc ... tccaaatcagATAGTGAAGGAAATTGAGCAAGACCTCTCCGGCTTCAAGTGTGGCCTAGCT
EST: gi|31472535|gb|CD414563.1|CD414563
EST:     CGGCGCGGCTGTCATCTTGTCACTTCCAAG                         ATAGTGAAGGAAATTGAGCAAGACCTCTCCGGCTTCAAGTGTGGCCTAGCT
genomic: CGGCGCGGCTGTCATCTTGTCACTTCCAAGgtcccatttc ... tccaaatcagATAGTGAAGGAAATTGAGCAAGACCTCTCCGGCTTCAAGTGTGGCCTAGCT
EST: gi|298175025|gb|HO018020.1|HO018020
EST:     CCGTCAGCTTGCCCCCTCTCCGGCGCGGCTGTCATCTTGTCACTTCCAAT                         ATAGTGAAGGAAATTGAGCAAGACCTCTCCGGCTTCAAGTGTGGCCTAGCT
genomic: CCGTCAGCTTGCCCCCTCTCCGGCGCGGCTGTCATCTTGTCACTTCCAAGgtcccatttc ... tccaaatcagATAGTGAAGGAAATTGAGCAAGACCTCTCCGGCTTCAAGTGTGGCCTAGCT
EST: gi|23733507|gb|BU764952.1|BU764952
EST:     CCGTCAGCTTGCCCCCTCTCCGGCGCGGCTGTCATCTTGTCACTTCCAAG                         ATAGTGAAGGAAATTGAGCAAGACCTCTCCGGCTTCAAGTGTGGCCTAGCT
genomic: CCGTCAGCTTGCCCCCTCTCCGGCGCGGCTGTCATCTTGTCACTTCCAAGgtcccatttc ... tccaaatcagATAGTGAAGGAAATTGAGCAAGACCTCTCCGGCTTCAAGTGTGGCCTAGCT
EST: gi|120496558|gb|EH224725.1|EH224725
EST:     CCGTCAGCTTGCCCCCTCTCCGGCGCGGCTGTCATCTTGTCACTTCCAAG                         ATAGTGAAGGAAATTGAGCAAGACCTCTCCGGCTTCAAGTGTGGCCTAGCT
genomic: CCGTCAGCTTGCCCCCTCTCCGGCGCGGCTGTCATCTTGTCACTTCCAAGgtcccatttc ... tccaaatcagATAGTGAAGGAAATTGAGCAAGACCTCTCCGGCTTCAAGTGTGGCCTAGCT
EST: gi|298172343|gb|HO019383.1|HO019383
EST:     CGTCAGCTTGCCCCCCTCTCCGGCGCGGCTGTCATCTTGTCACTTCCAAG                         ATAGTGAAGGAAATTGAGCAAGACCTCTCCGGCTTCAAGTGTGGCCTAGCT
genomic: CGTCAGCTTG-CCCCCTCTCCGGCGCGGCTGTCATCTTGTCACTTCCAAGgtcccatttc ... tccaaatcagATAGTGAAGGAAATTGAGCAAGACCTCTCCGGCTTCAAGTGTGGCCTAGCT
EST: gi|120496987|gb|EH225154.1|EH225154
EST:     CCGTCAGCTTGCCCCCTCTCCGGCGCGGCTGTCATCTTGTCACTTCCAAG                         ATAGTGAAGGAAATTGAGCAAGACCTCTCCGGCTTCAAGTGTGGCCTAGCT
genomic: CCGTCAGCTTGCCCCCTCTCCGGCGCGGCTGTCATCTTGTCACTTCCAAGgtcccatttc ... tccaaatcagATAGTGAAGGAAATTGAGCAAGACCTCTCCGGCTTCAAGTGTGGCCTAGCT
EST: gi|27425952|gb|CA937472.1|CA937472
EST:     CCGTCAGCTTGCCCCCTCTCCGGCGCGGCTGTCATCTTGTCACTTCCAAG                         ATAGTGAAGGAAATTGAGCAAGACCTCTCCGGCTTCAAGTGTGGCCTAGCT
genomic: CCGTCAGCTTGCCCCCTCTCCGGCGCGGCTGTCATCTTGTCACTTCCAAGgtcccatttc ... tccaaatcagATAGTGAAGGAAATTGAGCAAGACCTCTCCGGCTTCAAGTGTGGCCTAGCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ataattttggcaaaaccctaatcatttattttgggattgatttggtccaaatcagATAGTGAAGGAAATTGAGCAAGACCTCTCCGGCTTCAAGTGTGGCCTAGCTCATCTCTTCT
                  taatcatttatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtcccatttccatttcctcctcctctctctctctctctcttttctttaataattttggcaaaaccctaatcatttattttgggattgatttggtccaaatcagATAGTGAAGGAAATTGAGCAAGACCTCTCCGGCTTCAAGTGTGGCCTAGCTCATCTCTTCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA