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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agtgatctcccttgcttgtttgaaactacagaacatgcaattagtttatatttttttttcccatgacacttttgttccactaattggtttcatgctgcagGACAAAGGGTAATTGGAGAGCCCGTTGCCTCTGGGTTAGCCCTTGATGAATCTTGGCTTTGGCATCCTGACTTTGAGACTGCTGCAAA

Basic information

species Glycine max
transcript GLYMA15G06100.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA15G06100.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv06s0009g02790.t01 (Vitis vinifera), 3'ss of exon 6
--agtgatctccc--ttgcttgtttgaaactacagaacatgcaattagtttatatttttttttcccatgacacttttgttccactaattggtttcatgctgcagGACAAAGGGTAATTGGAGAGCCCGTTGCCTCTGGGTTAGCCCTTGATGAATCTTGGCTTTGGCATCCTGACTTTGAGACTGCTGCAAA
   ||||| ||     ||    | |||  | ||  |  ||   ||    | || ||   | ||     |         ||| |||  ||  |||    |||||||||| ||||| ||||||||||| || |  |||||||||| ||||||||| ||| |||| ||| ||||||||||    |  || |||||
taggtgatatctgaactgaacttctgatgcaact-attatctgatctaatgattttgagtcttaatcaggagtaaccattc-act--tttcttttgaactgcagGACAGAGGGTTATTGGAGAGCCAGTAGTTTCTGGGTTAGTCCTTGATGATTCTGGGCTCTGGGATCCTGACTTCATCAACGCAGCAAA
















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|193321319|gb|FK283635.1|FK283635
EST:     TGTAATGAGCATTGATGCAATGGAAGAAATTGCTAAGGCCCGGAAATCAG                         GACAAAGGGTAATTGGAGAGCCCGTTGCCTCTGGGTTAGCCCTTGATGAAT
genomic: TGTAATGAGCATTGATGCAATGGAAGAAATTGCTAAGGCCCGGAAATCAGgttaatttta ... catgctgcagGACAAAGGGTAATTGGAGAGCCCGTTGCCTCTGGGTTAGCCCTTGATGAAT
EST: gi|11274766|gb|BF325101.1|BF325101
EST:     TGTAATGAGCATTGATGCAATGGAAGAAATTGCTAAGGCCCGGAAATCAG                         GACAAAGGGTAATTGGAGAGCCCGTTGCCTCTGGGTTAGCCCTTGATGAAT
genomic: TGTAATGAGCATTGATGCAATGGAAGAAATTGCTAAGGCCCGGAAATCAGgttaatttta ... catgctgcagGACAAAGGGTAATTGGAGAGCCCGTTGCCTCTGGGTTAGCCCTTGATGAAT
EST: gi|37995958|gb|CF807547.1|CF807547
EST:     TGTAATGAGCATTGATGCAATGGAAGAAATTGCTAAGGCCCGGAAATCAG                         GACAAAGGGTAATTGGAGAGCCCGTTGCCTCTGGGTTAGCCCTTGATGAAT
genomic: TGTAATGAGCATTGATGCAATGGAAGAAATTGCTAAGGCCCGGAAATCAGgttaatttta ... catgctgcagGACAAAGGGTAATTGGAGAGCCCGTTGCCTCTGGGTTAGCCCTTGATGAAT
EST: gi|207777154|gb|GD748249.1|GD748249
EST:     GTAATGAGCATTGATGCAATGGAAGAAATTGTCTAAGGCCCGGAAATCAG                         GACAAAGGGTAATTGGAGAGCCCGTTGCCTCTGGGTTAGCCCTTGATGAAT
genomic: GTAATGAGCATTGATGCAATGGAAGAAATTG-CTAAGGCCCGGAAATCAGgttaatttta ... catgctgcagGACAAAGGGTAATTGGAGAGCCCGTTGCCTCTGGGTTAGCCCTTGATGAAT
EST: gi|27445929|gb|CA953052.1|CA953052
EST:     TGTAATGAGCATTGATGCAATGGAAGAAATTGCTAAGGCCCGGAAATCAG                         GACAAAGGGTAATTGGAGAGCCCGTTGCCTCTGGGTTAGCCCTTGATGAAT
genomic: TGTAATGAGCATTGATGCAATGGAAGAAATTGCTAAGGCCCGGAAATCAGgttaatttta ... catgctgcagGACAAAGGGTAATTGGAGAGCCCGTTGCCTCTGGGTTAGCCCTTGATGAAT
EST: gi|17400710|gb|BM177492.1|BM177492
EST:     TGTAATGAGCATTGATGCAATGGAAGAAATTGCTAAGGCCCGGAAATCAG                         GACAAAGGGTAATTGGAGAGCCCGTTGCCTCTGGGTTAGCCCTTGATGAAT
genomic: TGTAATGAGCATTGATGCAATGGAAGAAATTGCTAAGGCCCGGAAATCAGgttaatttta ... catgctgcagGACAAAGGGTAATTGGAGAGCCCGTTGCCTCTGGGTTAGCCCTTGATGAAT
EST: gi|193561837|gb|FK516856.1|FK516856
EST:     TGTAATGAGCATTGATGCAATGGAAGAAATTGCTAAGGCCCGGAAATCAG                         GACAAAGGGTAATTGGAGAGCCCGTTGCCTCTGGGTT-GCCCTTGATGAAT
genomic: TGTAATGAGCATTGATGCAATGGAAGAAATTGCTAAGGCCCGGAAATCAGgttaatttta ... catgctgcagGACAAAGGGTAATTGGAGAGCCCGTTGCCTCTGGGTTAGCCCTTGATGAAT
EST: gi|207829995|gb|GD801911.1|GD801911
EST:     TGTAATGAGCATTGATGCAATGGAAGAAATTGCTAAGGCCCGGAAATCAG                         GACAAAGGGTAATTGGAGAGCCCGTTGCCTCTGGGTTAGCCCTTGATGAAT
genomic: TGTAATGAGCATTGATGCAATGGAAGAAATTGCTAAGGCCCGGAAATCAGgttaatttta ... catgctgcagGACAAAGGGTAATTGGAGAGCCCGTTGCCTCTGGGTTAGCCCTTGATGAAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttatatttttttttcccatgacacttttgttccactaattggtttcatgctgcagGACAAAGGGTAATTGGAGAGCCCGTTGCCTCTGGGTTAGCCCTTGATGAATCTTGGCTTTGGCATCCTGACTTTGAGACTGCTGCAAA
                                cactaat  putative branch site (score: 2)
     ttttttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
agtgatctcccttgcttgtttgaaactacagaacatgcaattagtttatatttttttttcccatgacacttttgttccactaattggtttcatgctgcagGACAAAGGGTAATTGGAGAGCCCGTTGCCTCTGGGTTAGCCCTTGATGAATCTTGGCTTTGGCATCCTGACTTTGAGACTGCTGCAAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC
- - - ctccctt
- - - - - - -gcttgtt
- - - - - - - - - - - - - - - - acatgca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgacact
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ccactaa