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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aggagttaaaataatctctctttttttcttttgaacgaaaaagagttttattttatttatatttatctttcttcccccaccccctttttgtctcttgcagGATTGATAATTGGAAACGTGAGCATATACTGCAGTTCCTCCGAGAGAAGGTGAAGCCTCTGGCTTCTGATTGAGAGAATCTTTGACCCATTCTCTAGCAA

Basic information

species Glycine max
transcript GLYMA07G32960.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA07G32960.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv05s0094g00490.t01 (Vitis vinifera), 3'ss of exon 3
aggagttaaaataatctctcttttt-----ttcttttgaacgaaaaagagttttattttatttatatttatctttcttcccccaccccctttttgtctcttgcagGATTGATAATTGGAAACGTGAGCATATACTGCAGTTCCTCCGAGAGAAGGTGAAGCCTCTGGCTTCTGA---TTGAGAGAATCTTTGACCCATTCTCTAGCAA
     ||  |   | || | |         |   |||||| |  |||  |||||   | ||| ||| | |   |      |  |    ||   | | | || ||||||||| |||||||||||||| ||||||||||| |||||  |||||||||| ||||||    | || |     | |        || | | | |  | |    
---ttttttaggtacctttatgggaaaagatatatttgaatgggaaaaggttttgcatcatt-atactcactatggcattcttattttctgcctttatttt-cagGATTGACAATTGGAAACGTGAACATATACTGCAATTCCTGAGAGAGAAGGTCAAGCCTGCTTCATCAGCAATCTAACCAGGCAGTTCAGCAAATAACCAA---
















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|298186107|gb|HO036740.1|HO036740
EST:     CCAAAGCTAATTATGCTGGATGATGCGGGTCAGCAAAAAGAAACAATCAG                         GATTGATAATTGGAAACGTGAGCATATACTGCAGTTCCTCCGAGAGAAGGT
genomic: CCAAAGCTAATTATGCTGGATGATGCGGGTCAGCAAAAAGAAACAATCAGgtgacactta ... tctcttgcagGATTGATAATTGGAAACGTGAGCATATACTGCAGTTCCTCCGAGAGAAGGT
EST: gi|298172471|gb|HO019511.1|HO019511
EST:     CCAAAGCTAATTATGCTGGATGATGCGGGTCAGCAAAAGGAAACAATCAG                         GATTGATAATTGGAAACGTGAGCATATACTGCAGTTCCTCCGAG
genomic: CCAAAGCTAATTATGCTGGATGATGCGGGTCAGCAAAAAGAAACAATCAGgtgacactta ... tctcttgcagGATTGATAATTGGAAACGTGAGCATATACTGCAGTTCCTCCGAG
EST: gi|192294091|gb|FG986180.1|FG986180
EST:     CCAAAGCTAATTATGCTGGATGATGCGGGTCAGCAAAAAGAAACAATCAG                         GATTGATAATTGGAAACGTGAGCATATACTGCAGTTCCTCCGAGAGAAGGT
genomic: CCAAAGCTAATTATGCTGGATGATGCGGGTCAGCAAAAAGAAACAATCAGgtgacactta ... tctcttgcagGATTGATAATTGGAAACGTGAGCATATACTGCAGTTCCTCCGAGAGAAGGT
EST: gi|298181841|gb|HO026016.1|HO026016
EST:     CCAAAGCTAATTATGCTGGATGATGCGGGTCAGCAAAAAGAAACAATCAG                         GAGTGATAATTGGAAACGTGAGCATATACTGCAGTTCCTCCGAGAGAAGGT
genomic: CCAAAGCTAATTATGCTGGATGATGCGGGTCAGCAAAAAGAAACAATCAGgtgacactta ... tctcttgcagGATTGATAATTGGAAACGTGAGCATATACTGCAGTTCCTCCGAGAGAAGGT
EST: gi|10709622|gb|BF009346.1|BF009346
EST:     CCAAAGCTAATTATGCTGGATGATGCGGGTCAGCAAAAAGAAACAATCAG                         GATTGATAATTGGAAACGTGAGCATATACTGCAGTTCCTGCGAGAGAAGGT
genomic: CCAAAGCTAATTATGCTGGATGATGCGGGTCAGCAAAAAGAAACAATCAGgtgacactta ... tctcttgcagGATTGATAATTGGAAACGTGAGCATATACTGCAGTTCCTCCGAGAGAAGGT
EST: gi|298198605|gb|HO040144.1|HO040144
EST:     CCAAAGCTAATTATGCTGGATGATGCGGGTCAGCAAAAAGAAACAATCAG                         GATTGATAATTGGAAACGTGAGCATATACTGCAGTTCCTCCGAGAGAAGGT
genomic: CCAAAGCTAATTATGCTGGATGATGCGGGTCAGCAAAAAGAAACAATCAGgtgacactta ... tctcttgcagGATTGATAATTGGAAACGTGAGCATATACTGCAGTTCCTCCGAGAGAAGGT
EST: gi|9439728|gb|BE440242.1|BE440242
EST:     CCAAAGCTAATTATGCTGGATGATGCGGGTCAGCAAAAAGAAACAATCAG                         GATTGATAATTGGAAACGTGAGCATATACTGCAGTTCCTNCGAGAGAA
genomic: CCAAAGCTAATTATGCTGGATGATGCGGGTCAGCAAAAAGAAACAATCAGgtgacactta ... tctcttgcagGATTGATAATTGGAAACGTGAGCATATACTGCAGTTCCTCCGAGAGAA
EST: gi|192300920|gb|FG992980.1|FG992980
EST:     CCAAAGCTAATTATGCTGGATGATGCGGGTCAGCAAAAAGAAACAATCAG                         GATTGATAATTGGAAACGTGAGCATATACTGCAGTTCCTCCGAGAGAAAGT
genomic: CCAAAGCTAATTATGCTGGATGATGCGGGTCAGCAAAAAGAAACAATCAGgtgacactta ... tctcttgcagGATTGATAATTGGAAACGTGAGCATATACTGCAGTTCCTCCGAGAGAAGGT
EST: gi|7029651|gb|AW459368.1|AW459368
EST:     CCAAAGCTAATTATGCTGGATGATGCGGGTCAGCAAAAAGAAACAATCAT                         GATTGATAATTGGAAACGTGAGCATATACTGCAGTTCCTCCGAGAGAA
genomic: CCAAAGCTAATTATGCTGGATGATGCGGGTCAGCAAAAAGAAACAATCAGgtgacactta ... tctcttgcagGATTGATAATTGGAAACGTGAGCATATACTGCAGTTCCTCCGAGAGAA
EST: gi|298172644|gb|HO019684.1|HO019684
EST:     CCAAAGCTAATTATGCTGGATGATGCGGGTCAGCAAAAAGAAACAATCTG                         GATTGATAATTGGAAACGTGAGCATATACTGCAGTTCCTCCGA
genomic: CCAAAGCTAATTATGCTGGATGATGCGGGTCAGCAAAAAGAAACAATCAGgtgacactta ... tctcttgcagGATTGATAATTGGAAACGTGAGCATATACTGCAGTTCCTCCGA
EST: gi|19270075|gb|BM886331.1|BM886331
EST:     CCAAAGCTAATTATGCTGGATGATGC-GGTCAGCAAAAAGAAACAATCAG                         GATTGATAATTGGAAACGTGAGCATATACTGCAGTTCCTCCGAGAGAAGGT
genomic: CCAAAGCTAATTATGCTGGATGATGCGGGTCAGCAAAAAGAAACAATCAGgtgacactta ... tctcttgcagGATTGATAATTGGAAACGTGAGCATATACTGCAGTTCCTCCGAGAGAAGGT
EST: gi|298178377|gb|HO024112.1|HO024112
EST:     CTAAAGCTAATTATGTTGGATGATGCGGGTCAGCAAAAAGAAACAATCAG                         GATTGATAATTGGAAACGTGTGCATATACTGCAGTTCCTCCGAGAGAAGGT
genomic: CCAAAGCTAATTATGCTGGATGATGCGGGTCAGCAAAAAGAAACAATCAGgtgacactta ... tctcttgcagGATTGATAATTGGAAACGTGAGCATATACTGCAGTTCCTCCGAGAGAAGGT
EST: gi|298174849|gb|HO017958.1|HO017958
EST:     CCAAAGCTAATTATGCTGGATGATGCGGGTCAGCAAAAAGAAACAATCAG                         GATTGATAATTGGAAACGTGAGCATATACTGCAGTTCCTCCGAGAGAAGGT
genomic: CCAAAGCTAATTATGCTGGATGATGCGGGTCAGCAAAAAGAAACAATCAGgtgacactta ... tctcttgcagGATTGATAATTGGAAACGTGAGCATATACTGCAGTTCCTCCGAGAGAAGGT
EST: gi|192300921|gb|FG992981.1|FG992981
EST:     CCAAAGCTAATTATGCTGGATGATGCGGGTCAGCAAAAAGAAACAATCAG                         GATTGATAATTGGAAACGTGAGCATATACTGCAGTTCCTCCGAGAGAAGGT
genomic: CCAAAGCTAATTATGCTGGATGATGCGGGTCAGCAAAAAGAAACAATCAGgtgacactta ... tctcttgcagGATTGATAATTGGAAACGTGAGCATATACTGCAGTTCCTCCGAGAGAAGGT
EST: gi|23054540|gb|BU577628.1|BU577628
EST:     CCAAAGCTAATTATGCTGGATGATGCGGGTCAGCAAAAAGAAACAATCAG                         GATTGATAATTGGAAACGTGAGCATATACTGCAGTTCCTCCGAGAGAAGGT
genomic: CCAAAGCTAATTATGCTGGATGATGCGGGTCAGCAAAAAGAAACAATCAGgtgacactta ... tctcttgcagGATTGATAATTGGAAACGTGAGCATATACTGCAGTTCCTCCGAGAGAAGGT
EST: gi|15201665|gb|BI424992.1|BI424992
EST:     CCAAAGCTAATTATGCTGGATGATGCGGGTCAGCAAAAAGAAACAATCAG                         GATTGATAATTGGAAACGTGAGCATATACTGCAGTTCCTCCGAGAGAAGGT
genomic: CCAAAGCTAATTATGCTGGATGATGCGGGTCAGCAAAAAGAAACAATCAGgtgacactta ... tctcttgcagGATTGATAATTGGAAACGTGAGCATATACTGCAGTTCCTCCGAGAGAAGGT
EST: gi|298196432|gb|HO041175.1|HO041175
EST:     CCAAAGCTAATTATGCTGGATGATGCGGGTCAGCAAAAAGAAACAATCAG                         GATTGATAATTGGAAACGTGAGCATATACTGCAGTTCCTCCGAGAGAAGGT
genomic: CCAAAGCTAATTATGCTGGATGATGCGGGTCAGCAAAAAGAAACAATCAGgtgacactta ... tctcttgcagGATTGATAATTGGAAACGTGAGCATATACTGCAGTTCCTCCGAGAGAAGGT
EST: gi|193598549|gb|FK553735.1|FK553735
EST:     GCAAAAAGAAACAATCAG                         GATTGATAATTGGAAACGTGAGCATATACTGCAGTTCCCCCGAGAGAAGGT
genomic: GCAAAAAGAAACAATCAGgtgacactta ... tctcttgcagGATTGATAATTGGAAACGTGAGCATATACTGCAGTTCCTCCGAGAGAAGGT
EST: gi|298177783|gb|HO027336.1|HO027336
EST:     CCAAAGCTAATTATGCTGGATGATGCGGGTCAGCAAAAAGAAACAATCAG                         GATTGATAATTGGAAACGTGAGCATATACTGCAGTTCCTCCGAG
genomic: CCAAAGCTAATTATGCTGGATGATGCGGGTCAGCAAAAAGAAACAATCAGgtgacactta ... tctcttgcagGATTGATAATTGGAAACGTGAGCATATACTGCAGTTCCTCCGAG
EST: gi|193637669|gb|FK583530.1|FK583530
EST:     CCAAAGCTAATTATGCTGGATGATGCGGGTCAGCAAAAAGAAACAATCAG                         GATTGATAATTGGAAACGTGAGCATATACTGCAGTTCCTCCGAGAGAAGGT
genomic: CCAAAGCTAATTATGCTGGATGATGCGGGTCAGCAAAAAGAAACAATCAGgtgacactta ... tctcttgcagGATTGATAATTGGAAACGTGAGCATATACTGCAGTTCCTCCGAGAGAAGGT
EST: gi|298170253|gb|HO018877.1|HO018877
EST:     CCAAAGCTAATTATGCTGGATGATGCGGGTCAGCAAAAAGAAACAATCAG                         GATTGATAATTGGAAACGTGAGCATATACTGCAGTTCCTCCGAGAGAAGGT
genomic: CCAAAGCTAATTATGCTGGATGATGCGGGTCAGCAAAAAGAAACAATCAGgtgacactta ... tctcttgcagGATTGATAATTGGAAACGTGAGCATATACTGCAGTTCCTCCGAGAGAAGGT
EST: gi|298176443|gb|HO026678.1|HO026678
EST:     CCAAAGCTAATTATGCCGGATGATGCGGGTCAGCAAAAAGAAACAATCAG                         GATTGATAATTGGAAACGTGAGCATATACTGCAGTTCCTCCGAGAGAAGGT
genomic: CCAAAGCTAATTATGCTGGATGATGCGGGTCAGCAAAAAGAAACAATCAGgtgacactta ... tctcttgcagGATTGATAATTGGAAACGTGAGCATATACTGCAGTTCCTCCGAGAGAAGGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttattttatttatatttatctttcttcccccaccccctttttgtctcttgcagGATTGATAATTGGAAACGTGAGCATATACTGCAGTTCCTCCGAGAGAAGGTGAAGCCTCTGGCTTCTGATTGAGAGAATCTTTGACCCATTCTCTAGCAA
          tttatatttatctttc  CT-rich tract
     ttttatttatatttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aggagttaaaataatctctctttttttcttttgaacgaaaaagagttttattttatttatatttatctttcttcccccaccccctttttgtctcttgcagGATTGATAATTGGAAACGTGAGCATATACTGCAGTTCCTCCGAGAGAAGGTGAAGCCTCTGGCTTCTGATTGAGAGAATCTTTGACCCATTCTCTAGCAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - -aaaataa
- - - - - - - - - - - - - - - - - - -aaaaaga