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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ggaaaattttcgaaacagcctcccatatatttagagtatcaccccattactatgtaattagttatattaacatgaaattttttttctttatgtcaaccagGATGTTTGTTGAATCATGCAAGCGTTTACGTATCATGAAAGGAAAGGAAGCTATTGGACTGG

Basic information

species Glycine max
transcript GLYMA10G03720.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA10G03720.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os12g40890.1 (Oryza sativa), 3'ss of exon 3
-----------------------------------------------------ggaaaattttcgaaacagc-ctcccatatatttagagtatcaccccattactatgtaatta-gttatattaacatgaaattttttttctttatgtcaa--ccagGATGTTTGTTGAATCATGCAAGCGTTTACGTATCATGAAAGGAAAGGAAGCTATTGGACTGG
                                                       | ||  |     |  |  ||    |  || |    ||| |  ||||  || || |  |  ||| |     |     ||||| |||    |||  ||   |||||||||||||||||||||||||||  |  | || |||||||||   ||||||||||| || |
gtcagtaatctctacttaaattttctattatctaatatctaagtgtttaattttaataacctgaattaaggtactagtctgaatctctgatatgagtccat-gctctgcatctgtgttctgaattctgaccattttgtttggaaatggaaatttcagGATGTTTGTTGAATCATGCAAGCGCCTTAGGATAATGAAAGGATCAGAAGCTATTGGCCTTG
















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|8283204|gb|BE020765.1|BE020765
EST:     TATGAAGACAGGGATGGCGACTGGATGCTTGTCGGTGATGTGCCATGGGA                         GATGTTTGTTGAATCATGCAAGCGTTTACGTATCATGAAAGGAAAGGAAGC
genomic: TATGAAGACAGGGATGGCGACTGGATGCTTGTCGGTGATGTGCCATGGGAgtaatttttt ... tgtcaaccagGATGTTTGTTGAATCATGCAAGCGTTTACGTATCATGAAAGGAAAGGAAGC
EST: gi|12772249|gb|BG237176.1|BG237176
EST:     TATGAAGACAGGGATGGCGACTGGATGCTTGTCGGTGATGTGCCATGGGA                         GATGTTTGTTGAATCATGCAAGCGTTTACGTATCATGAAAGGAAAGGAAGC
genomic: TATGAAGACAGGGATGGCGACTGGATGCTTGTCGGTGATGTGCCATGGGAgtaatttttt ... tgtcaaccagGATGTTTGTTGAATCATGCAAGCGTTTACGTATCATGAAAGGAAAGGAAGC
EST: gi|16345396|gb|BI970991.1|BI970991
EST:     TATGAAGACAGGGATGGCGACTGGATGCTTGTCGGTGATGTGCCATGGGA                         GATGTTTGTTGAATCATGCAAGCGTTTACGTATCATGAAAGGAAAGGAAGC
genomic: TATGAAGACAGGGATGGCGACTGGATGCTTGTCGGTGATGTGCCATGGGAgtaatttttt ... tgtcaaccagGATGTTTGTTGAATCATGCAAGCGTTTACGTATCATGAAAGGAAAGGAAGC
EST: gi|214005956|gb|DB986559.1|DB986559
EST:     TATGAAGACAGGGATGGCGATTGGATGCTTGTCGGTGATGTGCCATGGGA                         GATGTTTGTTGAATCATGCAAGCGTTTACGTATCATGAAAGGAAAGGAAGC
genomic: TATGAAGACAGGGATGGCGACTGGATGCTTGTCGGTGATGTGCCATGGGAgtaatttttt ... tgtcaaccagGATGTTTGTTGAATCATGCAAGCGTTTACGTATCATGAAAGGAAAGGAAGC
EST: gi|192319340|gb|FK009882.1|FK009882
EST:     GCTTGTCGGTGATGTGCCATGGGA                         GATGTTTGTTGAATCATGCAAGCGTTTACGTATCATGAAAGGAAAGGAAGC
genomic: GCTTGTCGGTGATGTGCCATGGGAgtaatttttt ... tgtcaaccagGATGTTTGTTGAATCATGCAAGCGTTTACGTATCATGAAAGGAAAGGAAGC
EST: gi|192319341|gb|FK009883.1|FK009883
EST:     GTGATGTGCCATGGGA                         GATGTTTGTTGAATCATGCAAGCGTTTACGTATCATGAAAGGAAAGGAAGT
genomic: GTGATGTGCCATGGGAgtaatttttt ... tgtcaaccagGATGTTTGTTGAATCATGCAAGCGTTTACGTATCATGAAAGGAAAGGAAGC
EST: gi|16345395|gb|BI970990.1|BI970990
EST:     TATGAAGACAGGGATGGCGACTGGATGCTTGTCGGTGATGTGCCATGGGA                         GATGTTTGTTGAATCATGCAAGCGTTTACGTATCATGAAAGGAAAGGAAGC
genomic: TATGAAGACAGGGATGGCGACTGGATGCTTGTCGGTGATGTGCCATGGGAgtaatttttt ... tgtcaaccagGATGTTTGTTGAATCATGCAAGCGTTTACGTATCATGAAAGGAAAGGAAGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attactatgtaattagttatattaacatgaaattttttttctttatgtcaaccagGATGTTTGTTGAATCATGCAAGCGTTTACGTATCATGAAAGGAAAGGAAGCTATTGGACTGG
                   tattaac  putative branch site (score: 1)
                                ttttttttctttatgt  putative PPT
     tatgtaattagttata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ggaaaattttcgaaacagcctcccatatatttagagtatcaccccattactatgtaattagttatattaacatgaaattttttttctttatgtcaaccagGATGTTTGTTGAATCATGCAAGCGTTTACGTATCATGAAAGGAAAGGAAGCTATTGGACTGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA
- - - - - - - - - cctccca
- - - - - - - - - - - - - - - - - - - - -ccccatt
- - - - - - - - - - - - - - - - - - - - - - - - -ctatgta
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - catgaaa