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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAAGCCCAAGGCAGAGAGCCCTATAAACGAGAACGAGATACGCGTTACTTCTCAAGGAAGGACGAGGAATTACATCACCTACGCCACCACTCTCCTTCAGgttaccgtgcatttttttcacataataataactcttcatgtttttgtctaacccaaaactcgccgtttattttattgcctccatgtcgatacttttttct...

Basic information

species Glycine max
transcript GLYMA04G39480.2
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA04G39480.1 (Glycine max), 5'ss of exon 2
lower sequence: Vv07s0031g02040.t01 (Vitis vinifera), 5'ss of exon 3
GAAGCCCAAGGCAGAGAGCCCTATAAACGAGAACGAGATACGCGTTACTTCTCAAGGAAGGACGAGGAATTACATCACCTACGCCACCACTCTCCTTCAGgttaccgtgcatttttttcacataataataactcttcatgtttttgtcta-acccaaaactcgccgtttattttattgcctccatgtcgatacttttttct-
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GAAGCCAAGGACAGAAACACCTATAAACGAGAATGAGATTCGGATTACTACTCAAGGCAGAATGAGAAATTACATTACCTATGCCACCACTTTGCTCCAGgttattctccgcgttat--gttttatagtctttgttttagttttcattttcacacatggagatctacagagtgctagacaaccagaggtataattttgaaat
















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|7588095|gb|AW703898.1|AW703898
EST:     CTCAAGGAAGGACGAGGAATTACATCACCTACGCCACCACTCTCCTTCAG                         GAGAAAGGATCTAGTGAAATTGTTCTCAAAGCAATGGGACGTGCAATAAAT
genomic: CTCAAGGAAGGACGAGGAATTACATCACCTACGCCACCACTCTCCTTCAGgttaccgtgc ... tgctctacagGAGAAAGGATCTAGTGAAATTGTTCTCAAAGCAATGGGACGTGCAATAAAT
EST: gi|16280150|gb|BI943809.1|BI943809
EST:     CTCAAGGAAGGACGAGGAATTACATCACCTACGCCACCACTCTCCTTCAG                         GAGAAAGGATCTAGTGAAATTGTTCTCAAAGCAATGGGACGTGCAATAAAT
genomic: CTCAAGGAAGGACGAGGAATTACATCACCTACGCCACCACTCTCCTTCAGgttaccgtgc ... tgctctacagGAGAAAGGATCTAGTGAAATTGTTCTCAAAGCAATGGGACGTGCAATAAAT
EST: gi|19936967|gb|BQ081088.1|BQ081088
EST:     CTCAAGGAAGGACGAGGAATTACATCACCTACGCCACCACTCTCCTTCAG                         GAGAAAGGATCTAGTGAAATTGTTCTCAAAGCAATGGGACGTGCAATAAAT
genomic: CTCAAGGAAGGACGAGGAATTACATCACCTACGCCACCACTCTCCTTCAGgttaccgtgc ... tgctctacagGAGAAAGGATCTAGTGAAATTGTTCTCAAAGCAATGGGACGTGCAATAAAT
EST: gi|10235369|gb|BE804257.1|BE804257
EST:     CTCAAGGAAGGACGAGGAATTACATCACCTACGCCACCACTCTCCTTCAG                         GAGAAAGGATCTAGTGAAATTGTTCTCAAAGCAATGGGACGTGCAATAAAT
genomic: CTCAAGGAAGGACGAGGAATTACATCACCTACGCCACCACTCTCCTTCAGgttaccgtgc ... tgctctacagGAGAAAGGATCTAGTGAAATTGTTCTCAAAGCAATGGGACGTGCAATAAAT
EST: gi|254331474|gb|GR843431.1|GR843431
EST:     CTCAAGGAAGGACGAGGAATTACATCACCTACGCCACCACTCTCCTTCAG                         GAGAAAGGATCTAGTGAAATTGTTCTCAAAGCAATGGGACGTGCAATAAAT
genomic: CTCAAGGAAGGACGAGGAATTACATCACCTACGCCACCACTCTCCTTCAGgttaccgtgc ... tgctctacagGAGAAAGGATCTAGTGAAATTGTTCTCAAAGCAATGGGACGTGCAATAAAT
EST: gi|8827115|gb|BE210845.1|BE210845
EST:     TCAAGGAAGGACGAGGAATTACATCACCTTACGCC-CC-CTCTC-TT-AG                         GAGAAAGGATCTAGTGAAATTGTTCTCAAAGCAATGGGACGTGCAATAAAT
genomic: TCAAGGAAGGACGAGGAATTACATCACCT-ACGCCACCACTCTCCTTCAGgttaccgtgc ... tgctctacagGAGAAAGGATCTAGTGAAATTGTTCTCAAAGCAATGGGACGTGCAATAAAT
EST: gi|15336844|gb|BI497500.1|BI497500
EST:     CT-ATTGAAGGACGAGGAATTACATCACCTACGCCACCACTCTCCTTCAG                         GAGAAAGGATCTAGTGAAATTGTTCTCAAAGCAATGGGACGTGCAATAAAT
genomic: CTCAAGGAAGGACGAGGAATTACATCACCTACGCCACCACTCTCCTTCAGgttaccgtgc ... tgctctacagGAGAAAGGATCTAGTGAAATTGTTCTCAAAGCAATGGGACGTGCAATAAAT
EST: gi|17962956|gb|BM269711.1|BM269711
EST:     CTCAAGGAAGGACGAGGAATTACATCACCTACGCCACCACTCTCCTTCAG                         GAGAAAGGATCTAGTGAAATTGTTCTCAAAGCAATGGGACGTGCAATAAAT
genomic: CTCAAGGAAGGACGAGGAATTACATCACCTACGCCACCACTCTCCTTCAGgttaccgtgc ... tgctctacagGAGAAAGGATCTAGTGAAATTGTTCTCAAAGCAATGGGACGTGCAATAAAT
EST: gi|7684754|gb|AW755402.1|AW755402
EST:     CTCAAGGAAGGACGAGGAATTACATCACCTACGCCACCACTCTCCTTCAG                         GAGAAAGGATCTAGTGAAATTGTTCTCAAAGCAATGGGACGTGCAATAAAT
genomic: CTCAAGGAAGGACGAGGAATTACATCACCTACGCCACCACTCTCCTTCAGgttaccgtgc ... tgctctacagGAGAAAGGATCTAGTGAAATTGTTCTCAAAGCAATGGGACGTGCAATAAAT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAAGCCCAAGGCAGAGAGCCCTATAAACGAGAACGAGATACGCGTTACTTCTCAAGGAAGGACGAGGAATTACATCACCTACGCCACCACTCTCCTTCAGgttaccgtgcatttttttcacataataataactcttcatgtttttgtctaacccaaaactcgccgtttattttattgcctccatgtcgatacttttttct

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