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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAACCTTATGGGAGAAGATCTTGGTCCTTTAAGCAGCAAAGAGCTCGAGTCTCTTGAAAGGCAGCTAGATTCGTCCTTGAAGCAAATAAGATCAACCAGGgtactcaagtttccaacttttcttttccaatttccatatgaaattgtagatctaggaacatattaagagcccaatcttgaaatatccctatgtctatatg...

Basic information

species Glycine max
transcript GLYMA05G28140.2
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA05G28140.1 (Glycine max), 5'ss of exon 4
lower sequence: GRMZM2G159397_T01 (Zea mays), 5'ss of exon 4
GAACCTTATGGGAGAAGATCTTGGTCCTTTAAGCAGCAAAGAGCTCGAGTCTCTTGAAAGGCAGCTAGATTCGTCCTTGAAGCAAATAAGATCAACCAGGgtactcaagtttccaacttttcttttccaatt----tccatatgaaattgtagatctaggaacatattaagagcccaatcttgaaatatccctatgtctatatg
|||| |  | || ||||||||||   | ||| |||  |||||||| |||   || || | |||||| ||||||||||||||||| |||||||| || |||||||| ||   | | |      |   | ||||    |  || |    || || ||  || |  | ||  |      ||  |     | |   ||   || |   
GAACTTGCTTGGTGAAGATCTTGAGTCATTAGGCATAAAAGAGCTGGAGCACCTGGAGAAGCAGCTCGATTCGTCCTTGAAGCACATAAGATCTACAAGGgtactgaaaagtgctaacaccataaacgaattatattgtatttcctgttttatatgaagaagtacatggaatatttaagttctccct-tttgtaaaactgt---

upper sequence: GLYMA05G28140.1 (Glycine max), 5'ss of exon 4
lower sequence: AT1G24260.2 (Arabidopsis thaliana), 5'ss of exon 4
GAACCTTATGGGAGAAGATCTTGGTCCTTTAAGCAGCAAAGAGCTCGAGTCTCTTGAAAGGCAGCTAGATTCGTCCTTGAAGCAAATAAGATCAACCAGGgtactcaagtttccaacttttcttttccaatttccatatgaaattgtagatctaggaacatattaagagcccaatcttgaaatatccctatgtctatatg
||| ||  |||||||||||||||| ||| |||| |  || ||||| ||||| ||||| || ||||| ||||| ||||||||||| || ||| |   |||||||||    | | || |  |   |||   ||   |  ||  | ||  | |  || ||  | |||  | |   |||  || |                   
GAATCTGTTGGGAGAAGATCTTGGACCTCTAAGTACAAAGGAGCTTGAGTCACTTGAGAGACAGCTTGATTCTTCCTTGAAGCAGATCAGAGCTCTCAGGgtactactttgttcatcaatatcttt---atacactgatctatttccatag-taagattaaatttggtgtttaattctgcag------------------
















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|207697641|gb|GD680482.1|GD680482
EST:     CTCTTGAAAGGCAGCTAGATTCGTCCTTGAAGCAAATAAGATCAACCAGG                         ACCCAGTTCATGTTGGATCAGCTCTCTGATCTTCAACGTAAG
genomic: CTCTTGAAAGGCAGCTAGATTCGTCCTTGAAGCAAATAAGATCAACCAGGgtactcaagt ... taatttacagACCCAGTTCATGTTGGATCAGCTCTCTGATCTTCAACGTAAG
EST: gi|193711279|gb|FK646100.1|FK646100
EST:     CTCTTGAAAGGCAGCTAGATTCGTCCTTGAAGCAAATAAGATCAACCAGG                         ACCCAGTTCATGTTGGATCAGCTCTCTGATCTTCAACGTAAG
genomic: CTCTTGAAAGGCAGCTAGATTCGTCCTTGAAGCAAATAAGATCAACCAGGgtactcaagt ... taatttacagACCCAGTTCATGTTGGATCAGCTCTCTGATCTTCAACGTAAG
EST: gi|207840968|gb|GD810209.1|GD810209
EST:     CTCTTGAAAGGCAGCTAGATTCGTCCTTGAAGCAAATAAGATCAACCAGG                         ACCCAGTTCATGTTGGATCAGCTCTCTGATCTTCAACGTAAG
genomic: CTCTTGAAAGGCAGCTAGATTCGTCCTTGAAGCAAATAAGATCAACCAGGgtactcaagt ... taatttacagACCCAGTTCATGTTGGATCAGCTCTCTGATCTTCAACGTAAG
EST: gi|193314124|gb|FK282529.1|FK282529
EST:     CTCTTGAAAGGCAGCTAGATTCGTCCTTGAAGCAAATAAGATCAACCAGG                         ACCCAGTTCATGTTGGATCAGCTCTCTGATCTTCAACGTAAGG
genomic: CTCTTGAAAGGCAGCTAGATTCGTCCTTGAAGCAAATAAGATCAACCAGGgtactcaagt ... taatttacagACCCAGTTCATGTTGGATCAGCTCTCTGATCTTCAACGTAAGG
EST: gi|193556591|gb|FK515244.1|FK515244
EST:     CTCTTGAAAGGCAGCTAGATTCGTCCTTGAAGCAAATAAGATCAACCAGG                         ACCCAGTTCAATAGTTGGATCAGC
genomic: CTCTTGAAAGGCAGCTAGATTCGTCCTTGAAGCAAATAAGATCAACCAGGgtactcaagt ... taatttacagACCCAGTTCA-T-GTTGGATCAGC
EST: gi|6455734|gb|AW186417.1|AW186417
EST:     CTCTTGAAAGGCAGCTAGATTCGTCCTTGAAGCAAATAAGATCAACCAGG                         ACCCAGTTCATGTTGGATCAGCTCTCTGATCTTCAACGTAAG
genomic: CTCTTGAAAGGCAGCTAGATTCGTCCTTGAAGCAAATAAGATCAACCAGGgtactcaagt ... taatttacagACCCAGTTCATGTTGGATCAGCTCTCTGATCTTCAACGTAAG
EST: gi|208096065|gb|GD895035.1|GD895035
EST:     CTCTTGAAAGGCAGCTAGATTCGTCCTTGAAGCAAATAAGATCAACCAGG                         ACCCAGTTCATGTTGGATCAGCTCTCTGATCTTCAA
genomic: CTCTTGAAAGGCAGCTAGATTCGTCCTTGAAGCAAATAAGATCAACCAGGgtactcaagt ... taatttacagACCCAGTTCATGTTGGATCAGCTCTCTGATCTTCAA
EST: gi|207777183|gb|GD748278.1|GD748278
EST:     CTCTTGAAAGGCAGCTAGATTCGTCCTTGAAGCAAATAAGATCAACCAGG                         ACCCAGTTCATGTTGGATCAGCTCTCTGATCTTCAACGTAAG
genomic: CTCTTGAAAGGCAGCTAGATTCGTCCTTGAAGCAAATAAGATCAACCAGGgtactcaagt ... taatttacagACCCAGTTCATGTTGGATCAGCTCTCTGATCTTCAACGTAAG
EST: gi|207731537|gb|GD707066.1|GD707066
EST:     CTCTTGAAAGGCAGCTAGATTCGTCCTTGAAGCAAATAAGATCAACCAGG                         ACCCAGTTCATGTTGGATCAGCTCTCTGATCTTCAACGTAAG
genomic: CTCTTGAAAGGCAGCTAGATTCGTCCTTGAAGCAAATAAGATCAACCAGGgtactcaagt ... taatttacagACCCAGTTCATGTTGGATCAGCTCTCTGATCTTCAACGTAAG
EST: gi|208188384|gb|GD983152.1|GD983152
EST:     CTCTTGAAAGGCAGCTAGATTCGTCCTTGAAGCAAATAAGATCAACCAGG                         ACCCAGTTCATGTTGGATCAGCTCTCTGATCTTCAACGTAAG
genomic: CTCTTGAAAGGCAGCTAGATTCGTCCTTGAAGCAAATAAGATCAACCAGGgtactcaagt ... taatttacagACCCAGTTCATGTTGGATCAGCTCTCTGATCTTCAACGTAAG
EST: gi|193412704|gb|FK376927.1|FK376927
EST:     CTCTTGAAAGGCAGCTAGATTCGTCCTTGAAGCAAATAAGATCAACCAGG                         ACCCAGTTCATGTTGGATCAGCTCTCTGATCTTCAACGTAAGG
genomic: CTCTTGAAAGGCAGCTAGATTCGTCCTTGAAGCAAATAAGATCAACCAGGgtactcaagt ... taatttacagACCCAGTTCATGTTGGATCAGCTCTCTGATCTTCAACGTAAGG
EST: gi|208310598|gb|GE105986.1|GE105986
EST:     TTGAAGCAAATAAGATCAACCAGG                         ACCCAGTTCATGTTGGATCAGCTCTCTGATCTTCAACGTAAG
genomic: TTGAAGCAAATAAGATCAACCAGGgtactcaagt ... taatttacagACCCAGTTCATGTTGGATCAGCTCTCTGATCTTCAACGTAAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAACCTTATGGGAGAAGATCTTGGTCCTTTAAGCAGCAAAGAGCTCGAGTCTCTTGAAAGGCAGCTAGATTCGTCCTTGAAGCAAATAAGATCAACCAGGgtactcaagtttccaacttttcttttccaatttccatatgaaattgtagatctaggaacatattaagagcccaatcttgaaatatccctatgtctatatg

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA