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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atataataaggaccattctaactgcaaccattctaactgcaactcgtatatagcacaggcttgtagtataacatgaattttcttcatatatgtcaaccagGATGTTTGTTGAATCATGCAAGCGTTTACGCATCATGAAAGGAAAGGAGGCTATTGGTCTTGGTCTTG

Basic information

species Glycine max
transcript GLYMA19G34380.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA19G34380.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os12g40890.1 (Oryza sativa), 3'ss of exon 3
--------------------------------------------atataataaggaccattctaactgca--accattctaa----ctgcaactcgtatatagcacaggcttgtagtataa--catga--attttcttcatatatgtcaa--ccagGATGTTTGTTGAATCATGCAAGCGTTTACGCATCATGAAAGGAAAGGAGGCTATTGGTCTTGGTCTTG
                                             | ||||    |  |    || |     || | ||| |    |||  |   ||  ||          |||  | | |    |||  ||||| ||   | |||  ||   |||||||||||||||||||||||||||  |  | || |||||||||   || |||||||| ||||      
gtcagtaatctctacttaaattttctattatctaatatctaagtgtttaattttaataacctgaattaaggtactagtctgaatctctgatatgagtccatgctctgcatctgtgttctgaattctgaccattttgtttggaaatggaaatttcagGATGTTTGTTGAATCATGCAAGCGCCTTAGGATAATGAAAGGATCAGAAGCTATTGGCCTTG------

upper sequence: GLYMA19G34380.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv07s0141g00290.t01 (Vitis vinifera), 3'ss of exon 3
---atataataaggaccattctaactgcaaccattctaactgcaactcgtatatagcacaggcttgtagt--ataacatgaattttcttcatatatgtcaaccagGATGTTTGTTGAATCATGCAAGCGTTTACGCATCATGAAAGGAAAGGAGGCTATTGGTCTTGGTCTTG
   ||   | |  || | ||  |  |      |||     |  | | |  | |||  |     |   | |  |||||||  |   | ||  |      ||  |||||||||||| || |||||||| || || ||||| ||||||||||| ||||| || || || |      
taaattctaaatagatcctttaagttatc-ttatttggtttaaaccactaagatattaataaataacaattgataacatctacccttttggttc----cattcagGATGTTTGTGGATTCATGCAAACGCTTGCGCATAATGAAAGGAAAAGAGGCGATAGGGCTCG------
















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|9440021|gb|BE440532.1|BE440532
EST:     TATGAGGACAAGGATGGTGACTGGATGCTTGTCGGTGATGTCCCATGGGA                         GATGTTTGTTGAATCATGCAAGCGTTTACGC
genomic: TATGAGGACAAGGATGGTGACTGGATGCTTGTCGGTGATGTCCCATGGGAgtaagtcttt ... tgtcaaccagGATGTTTGTTGAATCATGCAAGCGTTTACGC
EST: gi|151405703|gb|EV275517.1|EV275517
EST:     TATGAGGACAAGGATGGTGACTGGATGCTTGTCGGTGATGTCCCATGGGA                         GATGTTTGTTGAATCATGCAAGCGTTTACGCATCATGAAAAGAAAGGAGGC
genomic: TATGAGGACAAGGATGGTGACTGGATGCTTGTCGGTGATGTCCCATGGGAgtaagtcttt ... tgtcaaccagGATGTTTGTTGAATCATGCAAGCGTTTACGCATCATGAAAGGAAAGGAGGC
EST: gi|8825818|gb|BE209548.1|BE209548
EST:     TATGAGGACAAGGATGGTGACTGGATGCTTGTCGGTGATGTCCCATGGGA                         GATGTTTGTTGAATCATGCAAGCGTTTACGCATCATGAAAGGAAAGGAGGC
genomic: TATGAGGACAAGGATGGTGACTGGATGCTTGTCGGTGATGTCCCATGGGAgtaagtcttt ... tgtcaaccagGATGTTTGTTGAATCATGCAAGCGTTTACGCATCATGAAAGGAAAGGAGGC
EST: gi|9204440|gb|BE330664.1|BE330664
EST:     TATGAGGACAAGGATGGTGACTGGATGCTTGTCGGTGATGTCCCATGGGA                         GATGTTTGTTGAATCATGCAAGCGTTTACGCATCATGAAAGGAAAGGAGGC
genomic: TATGAGGACAAGGATGGTGACTGGATGCTTGTCGGTGATGTCCCATGGGAgtaagtcttt ... tgtcaaccagGATGTTTGTTGAATCATGCAAGCGTTTACGCATCATGAAAGGAAAGGAGGC
EST: gi|192303187|gb|FG997763.1|FG997763
EST:     TATGAGGACAAGGATGGTGACTGGATGCTTGTCGGTGATGTCCCATGGGA                         GATGTTTGTTGAATCATGCAAGCGTTTACGCATCATGAAAGGAAAGGAGGC
genomic: TATGAGGACAAGGATGGTGACTGGATGCTTGTCGGTGATGTCCCATGGGAgtaagtcttt ... tgtcaaccagGATGTTTGTTGAATCATGCAAGCGTTTACGCATCATGAAAGGAAAGGAGGC
EST: gi|209700152|gb|BW656269.1|BW656269
EST:     TATGAGGACAAGGATGGTGACTGGATGCTTGTCGGTGATGTCCCATGGGA                         GATGTTTGTTGAATCATG
genomic: TATGAGGACAAGGATGGTGACTGGATGCTTGTCGGTGATGTCCCATGGGAgtaagtcttt ... tgtcaaccagGATGTTTGTTGAATCATG
EST: gi|57574134|gb|CX547109.1|CX547109
EST:     TATGAGGACAAGGATGGTGACTGGATGCTTGTCGGTGATGTCCCATGGGA                         GATGTTTGTTGAATCATGCAAGCGTTTACGCATCATGAAAGGAAAGGAGGC
genomic: TATGAGGACAAGGATGGTGACTGGATGCTTGTCGGTGATGTCCCATGGGAgtaagtcttt ... tgtcaaccagGATGTTTGTTGAATCATGCAAGCGTTTACGCATCATGAAAGGAAAGGAGGC
EST: gi|9259241|gb|BE347449.1|BE347449
EST:     TATGAGGACAAGGATGGTGACTGGATGCTTGTCGGTGATGTCCCATGGGA                         GATGTTTGTTGAATCATGCAAGCGTTTACGCATCATGAAAGGAAAGGAGGC
genomic: TATGAGGACAAGGATGGTGACTGGATGCTTGTCGGTGATGTCCCATGGGAgtaagtcttt ... tgtcaaccagGATGTTTGTTGAATCATGCAAGCGTTTACGCATCATGAAAGGAAAGGAGGC
EST: gi|151409764|gb|EV279572.1|EV279572
EST:     TATGAGGACAAGGATGGTGACTGGATGCTTGTCGGTGATGTCCCATGGGA                         GATGTTTGTTGAATCATGCAAGCGTTTACGCATCATGAAAGGAAAGGAGGC
genomic: TATGAGGACAAGGATGGTGACTGGATGCTTGTCGGTGATGTCCCATGGGAgtaagtcttt ... tgtcaaccagGATGTTTGTTGAATCATGCAAGCGTTTACGCATCATGAAAGGAAAGGAGGC
EST: gi|12772578|gb|BG237569.1|BG237569
EST:     TATGAGGACAAGGATGGTGACTGGATGCTTGTCGGTGATGTCCCATGGGA                         GATGTTTGTTGAATTATGCAAGCGGTTACGCTTCATGAAAGGAAAGGAGGC
genomic: TATGAGGACAAGGATGGTGACTGGATGCTTGTCGGTGATGTCCCATGGGAgtaagtcttt ... tgtcaaccagGATGTTTGTTGAATCATGCAAGCGTTTACGCATCATGAAAGGAAAGGAGGC
EST: gi|209707049|gb|BW661555.1|BW661555
EST:     TATGAGGACAAGGATGGTGACTGGATGCTTGTCGGTGATGTCCCATGGGA                         GATGTTTGTTGAATCATGCAAGCGTTTACGCATCATGAAAGGAAAGGAGGC
genomic: TATGAGGACAAGGATGGTGACTGGATGCTTGTCGGTGATGTCCCATGGGAgtaagtcttt ... tgtcaaccagGATGTTTGTTGAATCATGCAAGCGTTTACGCATCATGAAAGGAAAGGAGGC
EST: gi|214007491|gb|DB987334.1|DB987334
EST:     TATGAGGACAAGGATGGTGACTGGATGCTTGTCGGTGATGTCCCATGGGA                         GATGTTTGTTGAATCATGCAAGCGTTTACGCATCATGAAAGGAAAGGAGGC
genomic: TATGAGGACAAGGATGGTGACTGGATGCTTGTCGGTGATGTCCCATGGGAgtaagtcttt ... tgtcaaccagGATGTTTGTTGAATCATGCAAGCGTTTACGCATCATGAAAGGAAAGGAGGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtatatagcacaggcttgtagtataacatgaattttcttcatatatgtcaaccagGATGTTTGTTGAATCATGCAAGCGTTTACGCATCATGAAAGGAAAGGAGGCTATTGGTCTTGGTCTTG
                    gtataac  putative branch site (score: 3)
                              aattttcttcatatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atataataaggaccattctaactgcaaccattctaactgcaactcgtatatagcacaggcttgtagtataacatgaattttcttcatatatgtcaaccagGATGTTTGTTGAATCATGCAAGCGTTTACGCATCATGAAAGGAAAGGAGGCTATTGGTCTTGGTCTTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG
- - - - - - ccattct
- - - - - - - - - - -ctgcaac
- - - - - - - - - - - tgcaacc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - gcttgta
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - acatgaa