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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AAAGCTCCATATGAAGCCAAGGCTGCAAAAAGGAAAGCTGAGTATGAAAAACTTATCAAAGCTTATGAGAAAAAGCAGgtcagaaacctgtgccagttgttctgttgtgtgtggcacctttgattgtcttgtgtttatatactttattttctatgatgttgccag

Basic information

species Glycine max
transcript GLYMA01G28820.4
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA01G28820.4 (Glycine max), 5'ss of exon 6
lower sequence: AT3G51880.1 (Arabidopsis thaliana), 5'ss of exon 6
---AAAGCTCCATATGAAGCCAAGGCTGCAAAAAGGAAAGCTGAGTATGAAAAACTTATCAAAGCTTATGAGAAAAAGCAGgtcagaaacctgtgccagttgttctgttgtgtgtggcacctttgattgtcttgtgtttatatactttattttctatgatgttgccag
   ||||||||||||||||  || |||||||||||||||||||| ||||| || |  ||  | || ||  | |||||   |||   |  |||  |||  ||  |||  | | |     ||   |   |  ||     | ||     ||  || | |||  |    |||
GAAAAAGCTCCATATGAAGAGAAAGCTGCAAAAAGGAAAGCTGAATATGAGAAGCAAATGGATGCATACAACAAAAACTTGgt--aagccctaagcc--ttactctcatatatacaa-actcgtacatagctaactctgat-----ttccttgcaatgggg--aacag

upper sequence: GLYMA01G28820.4 (Glycine max), 5'ss of exon 6
lower sequence: Vv08s0007g02200.t01 (Vitis vinifera), 5'ss of exon 6
---AAAGCTCCATATGAAGCCAAGGCTGCAAAAAGGAAAGCTGAGTATGAAAAACTTATCAAAGCTTATGAGAAAAAGCAGgtcagaaacctgtgccagttgttctgttgtgtgtggcacctttgattgtcttgtgt-ttatatactttattttctatgatgttgccag--
   |||||||||||||| ||||| |||||||||| ||| |||||||| |||||| |||| || |||||  | || |||||||| | | || ||    ||   || | |  |    |  |   ||  |  |      | | |  | | | | ||||| |  ||||       
GAAAAAGCTCCATATGAGGCCAAAGCTGCAAAAAAGAAGGCTGAGTACGAAAAAATTATGAATGCTTACAACAAGAAGCAGgtga-acacatgcataagcctttttctcatcaaagaaatgattcttcattgccgatatcacttgcctgactttcttttgtgttattgcag
















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|6566111|gb|AW233871.1|AW233871
EST:     AAAGGAAAGCTGAGTATGAAAAACTTATCAAAGCTTATGAGAAAAAGCAG                         GCAAGCTCTGCAGATGATGATGAATCAGACAAGTCCAAATCTGAAGTGAAT
genomic: AAAGGAAAGCTGAGTATGAAAAACTTATCAAAGCTTATGAGAAAAAGCAGgtcagaaacc ... atgttgccagGCAAGCTCTGCAGATGATGATGAATCAGACAAGTCCAAATCTGAAGTGAAT
EST: gi|17023119|gb|BM094153.1|BM094153
EST:     AAAGGAAAGCTGAGTATGAAAAACTTATCAAAGCTTATGAGAAAAAGCAG                         GCAAGCTCTGCAGATGATGATGAATCAGACAAGTCCAAATCTGAAGTGAAT
genomic: AAAGGAAAGCTGAGTATGAAAAACTTATCAAAGCTTATGAGAAAAAGCAGgtcagaaacc ... atgttgccagGCAAGCTCTGCAGATGATGATGAATCAGACAAGTCCAAATCTGAAGTGAAT
EST: gi|10235981|gb|BE804869.1|BE804869
EST:     AAAGGAAAGCTGAGTATGAAAAACTTATCAAAGCTTATGAGAAAAAGCAG                         GCAAGCTCTGCAGATGATGATGAATCATACAAGTCCAAATCTGAAGTGAAT
genomic: AAAGGAAAGCTGAGTATGAAAAACTTATCAAAGCTTATGAGAAAAAGCAGgtcagaaacc ... atgttgccagGCAAGCTCTGCAGATGATGATGAATCAGACAAGTCCAAATCTGAAGTGAAT
EST: gi|21602103|gb|BQ612434.1|BQ612434
EST:     AAAGGAAAGCTGAGTATGAAAAACTTATCAAAGCTTATGAGAAAAAGCAG                         GCAAGCTCTGCAGATGATGATGAATCAGACAAGTCCAAATCTGAAG
genomic: AAAGGAAAGCTGAGTATGAAAAACTTATCAAAGCTTATGAGAAAAAGCAGgtcagaaacc ... atgttgccagGCAAGCTCTGCAGATGATGATGAATCAGACAAGTCCAAATCTGAAG
EST: gi|4290052|gb|AI441563.1|AI441563
EST:     AAAGGAAAGCTGAGTATGAAAAACTTATCAAAGCTTATGAGAAAAAGCAG                         GCAAGCTCTGCAGATGATGATGAA
genomic: AAAGGAAAGCTGAGTATGAAAAACTTATCAAAGCTTATGAGAAAAAGCAGgtcagaaacc ... atgttgccagGCAAGCTCTGCAGATGATGATGAA
EST: gi|6566794|gb|AW234426.1|AW234426
EST:     AAAGGAAAGCTGAGTATGAAAAACTTATCAAAGCTTATGAGAAAAAGCAG                         GCAAGCTCTGCAGATGATGATGAATCAGACAAGTCCAAATCTGAAGTGAAT
genomic: AAAGGAAAGCTGAGTATGAAAAACTTATCAAAGCTTATGAGAAAAAGCAGgtcagaaacc ... atgttgccagGCAAGCTCTGCAGATGATGATGAATCAGACAAGTCCAAATCTGAAGTGAAT
EST: gi|11273697|gb|BF324073.1|BF324073
EST:     AAAGGAAAGCTGAGTATGAAAAACTTATCAAAGCTTATGAGAAAAAGCAG                         GCAAGCTCTGCAGATGATGATGAATCAGACAAGTCCAAATCTGATGTGAAT
genomic: AAAGGAAAGCTGAGTATGAAAAACTTATCAAAGCTTATGAGAAAAAGCAGgtcagaaacc ... atgttgccagGCAAGCTCTGCAGATGATGATGAATCAGACAAGTCCAAATCTGAAGTGAAT
EST: gi|15000368|gb|BI321182.1|BI321182
EST:     AAAGGAAAGCTGAGTATGAAAAACTTATCAAAGCTTATGAGAAAAAGCAG                         GCAAGCTCTGCAGATGATGATGAATCAGACAAGTCCAAATCTGAAGTGAAT
genomic: AAAGGAAAGCTGAGTATGAAAAACTTATCAAAGCTTATGAGAAAAAGCAGgtcagaaacc ... atgttgccagGCAAGCTCTGCAGATGATGATGAATCAGACAAGTCCAAATCTGAAGTGAAT
EST: gi|15812656|gb|BI784931.1|BI784931
EST:     AAAGGAAAGCTGAGTATGAAAAACTTATCAAAGCTTATGAGAAAAAGCAG                         GCAAGCTCTGCAGATGATGATGAATCAGACAAGTCCAAATCTGAAGTGAAT
genomic: AAAGGAAAGCTGAGTATGAAAAACTTATCAAAGCTTATGAGAAAAAGCAGgtcagaaacc ... atgttgccagGCAAGCTCTGCAGATGATGATGAATCAGACAAGTCCAAATCTGAAGTGAAT
EST: gi|16347142|gb|BI972737.1|BI972737
EST:     AAAGGAAAGCTGAGTATGAAAAACTTATCAAAGCTTATGAGAAAAAGCAG                         GCAAGCTCTGCAGATGATGATGAATCAGACAAGTCCAAATCTGAAGTGAAT
genomic: AAAGGAAAGCTGAGTATGAAAAACTTATCAAAGCTTATGAGAAAAAGCAGgtcagaaacc ... atgttgccagGCAAGCTCTGCAGATGATGATGAATCAGACAAGTCCAAATCTGAAGTGAAT
EST: gi|298179538|gb|HO028009.1|HO028009
EST:     AAAGGAAAGCTGAGTATGAAAAACTTATCAAAGCTTATGAGAAAAAGCAG                         GCAAGCTCTGCAGATGATGATGAATCAGACAAGTCCAAATCTGAAGTGAAT
genomic: AAAGGAAAGCTGAGTATGAAAAACTTATCAAAGCTTATGAGAAAAAGCAGgtcagaaacc ... atgttgccagGCAAGCTCTGCAGATGATGATGAATCAGACAAGTCCAAATCTGAAGTGAAT
EST: gi|298166580|gb|HO010019.1|HO010019
EST:     AAAGGAAAGCTGAGTATGAAAAACTTATCAAAGCTTATGAGAAAAAGCAG                         GCAAGCTCTGCAGATGATGATGAATCAGACAAGTCCAAATCTGGAGTGAAT
genomic: AAAGGAAAGCTGAGTATGAAAAACTTATCAAAGCTTATGAGAAAAAGCAGgtcagaaacc ... atgttgccagGCAAGCTCTGCAGATGATGATGAATCAGACAAGTCCAAATCTGAAGTGAAT
EST: gi|7029350|gb|AW459133.1|AW459133
EST:     AAAGGAAAGCTGAGTATGAAAAACTTATCAAAGCTTATGAGAAAAAGCAG                         GCAAGCTCTGCAGATGATGATGAATCAGACAAGTCCAAATCTGAAGTGAAT
genomic: AAAGGAAAGCTGAGTATGAAAAACTTATCAAAGCTTATGAGAAAAAGCAGgtcagaaacc ... atgttgccagGCAAGCTCTGCAGATGATGATGAATCAGACAAGTCCAAATCTGAAGTGAAT
EST: gi|15000806|gb|BI321620.1|BI321620
EST:     AAAGGAAAGCTGAGTATGAAAAACTTATCAAAGCTTATGAGAAAAAGCAG                         GCAAGCTCTGCAGATGATGATGAATCAGACAAGTCCAAATCTGAAGTGAAT
genomic: AAAGGAAAGCTGAGTATGAAAAACTTATCAAAGCTTATGAGAAAAAGCAGgtcagaaacc ... atgttgccagGCAAGCTCTGCAGATGATGATGAATCAGACAAGTCCAAATCTGAAGTGAAT
EST: gi|15200575|gb|BI424419.1|BI424419
EST:     AAAGGAAAGCTGAGTATGAAAAACTTATCAAAGCTTATGAGAAAAAGCAG                         GCAAGCTCTGCAGATGATGATGAATCAGACAAGTCCAAATCTGAAGTGAAT
genomic: AAAGGAAAGCTGAGTATGAAAAACTTATCAAAGCTTATGAGAAAAAGCAGgtcagaaacc ... atgttgccagGCAAGCTCTGCAGATGATGATGAATCAGACAAGTCCAAATCTGAAGTGAAT
EST: gi|18732491|gb|BM527074.1|BM527074
EST:     AAAGGAAAGCTGAGTATGAAAAACTTATCAAAGCTTATGAGAAAAAGCAG                         GCAAGCTCTGCAGATGATGATGAATCAGACAAGTCCAAATCTGAAGTGAAT
genomic: AAAGGAAAGCTGAGTATGAAAAACTTATCAAAGCTTATGAGAAAAAGCAGgtcagaaacc ... atgttgccagGCAAGCTCTGCAGATGATGATGAATCAGACAAGTCCAAATCTGAAGTGAAT
EST: gi|15287921|gb|BI471812.1|BI471812
EST:     AAAGGAAAGCTGAGTATGAAAAACTTATCAAAGCTTATGAGAAAAAGCAG                         GCAAGCTCTGCAGATGATGATGAATCAGACAAGTCCAAATCTGAAGTGAAT
genomic: AAAGGAAAGCTGAGTATGAAAAACTTATCAAAGCTTATGAGAAAAAGCAGgtcagaaacc ... atgttgccagGCAAGCTCTGCAGATGATGATGAATCAGACAAGTCCAAATCTGAAGTGAAT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AAAGCTCCATATGAAGCCAAGGCTGCAAAAAGGAAAGCTGAGTATGAAAAACTTATCAAAGCTTATGAGAAAAAGCAGgtcagaaacctgtgccagttgttctgttgtgtgtggcacctttgattgtcttgtgtttatatactttattttctatgatgttgccag

- - - - - - - - - - - - - -  AAGGAA
- - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - -  AGCTGA