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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagattccatattttgcgcagtctaactttttgattcctgtttgttcgttctctttgagggaattctcccttttcaactgatcaactaatttcagttaaaatatgtgcttttcactgtagGAGCCAGAGTCCCGTGCATGCTTGCTAGAATTAACATGGAATGGACAAAACACAGTGTCAGTGAATGAGTTAAATCGGAAATTTCTTGAAGATGGAGACG

Basic information

species Glycine max
transcript GLYMA09G01270.1
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA09G01270.1 (Glycine max), 3'ss of exon 12
lower sequence: Vv00s0187g00300.t01 (Vitis vinifera), 3'ss of exon 9
----------------------gtaagattccatattttgcgcagtctaactttttgattcctgtttgttcgttctctttgagggaattctcccttttcaactgatcaact-aatttcagttaaaatatgtgcttttcactgtagGAGCCAGAGTCCCGTGCATGCTTGCTAGAATTAACATGGAATGGACAAAACACAGTGTCAGTGAATGAGTTAAATCGGAAATTTCTTGAAGATGGAGACG
                      | |||||  | || |   |    |||| |||  |  ||       |  | |    |     |   |      || |    |  |   || || ||||  |   | ||    ||  |||   |||| || || ||    | |||||||||||||||||||||||||||||||||  |||| ||  || |||    ||  ||   |||||||||||||||||| |
gtatgatttaaatttgtttataggaagatgtcgtagtgctcttgttctaccttcattttttaatgcagcacatagcttaaatagttgtaaatgtttcttggatatttttctgaagttcacctgccacattaatttcacac---agGAACCGGAATCTTTGGGATGCTTGCTAGAATTAACATGGAATGGACAAAAGCCAGTATCTTTGGATGGAACAACCCGTGGATTTCTTGAAGATGGAGATG

upper sequence: GLYMA09G01270.1 (Glycine max), 3'ss of exon 12
lower sequence: Vv00s0187g00340.t01 (Vitis vinifera), 3'ss of exon 12
----------------------gtaagattccatattttgcgcagtctaactttttgattcctgtttgttcgttctctttgagggaattctcccttttcaactgatcaact-aatttcagttaaaatatgtgcttttcactgtagGAGCCAGAGTCCCGTGCATGCTTGCTAGAATTAACATGGAATGGACAAAACACAGTGTCAGTGAATGAGTTAAATCGGAAATTTCTTGAAGATGGAGACG
                      | |||||  | || |   |    |||| ||| ||  ||       |  | |    |     |   |      || |    |  |   || || ||||  |   | ||    ||  |||   |||| || || ||    | |||||||||||||||||||||||||||||||||  |||| ||  || |||    ||  ||   |||||||||||||||||| |
gtatgatttaaatttgtttataggaagatgtcgtagtgctcttgttctaccttctttttttaatgcagcacatagcttaaatagttgtaaatgtttcttggatatttttctgaagttcacctgccacattaatttcacac---agGAACCGGAATCTTTGGGATGCTTGCTAGAATTAACATGGAATGGACAAAAGCCAGTATCTTTGGATGGAACAACCCGTGGATTTCTTGAAGATGGAGATG
















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|193560435|gb|FK517194.1|FK517194
EST:     GGCCGGGCGATCTCCTTGGAACTGGGACAGTTAGTGGTCCT                         GAGCCAGAGTCCCGTGCATGCTTGCTAGAATTAACATGGAATGGACAAAAC
genomic: GGCCAGGCGATCTCCTTGGAACTGGGACAGTTAGTGGTCCTgtaagattcc ... ttcactgtagGAGCCAGAGTCCCGTGCATGCTTGCTAGAATTAACATGGAATGGACAAAAC
EST: gi|298195581|gb|HO043972.1|HO043972
EST:     GCAACCTTAGGCCAGGCGATCTCCTTGGAACTGGGACAGTTAGTGGTCCT                         GAGCCAGAGTCCCGTGCATGCTTGCTAGAATTAACATGGAATGGACAAAAC
genomic: GCAACCTTAGGCCAGGCGATCTCCTTGGAACTGGGACAGTTAGTGGTCCTgtaagattcc ... ttcactgtagGAGCCAGAGTCCCGTGCATGCTTGCTAGAATTAACATGGAATGGACAAAAC
EST: gi|193628042|gb|FK572708.1|FK572708
EST:     GGCCGGGCGATCTCCTTGGAACTGGGACAGTTAGTGGTCCT                         GAGCCAGAGTCCCGTGCATGCTTGCTAGAATTAACATGGAATGGACAAAAC
genomic: GGCCAGGCGATCTCCTTGGAACTGGGACAGTTAGTGGTCCTgtaagattcc ... ttcactgtagGAGCCAGAGTCCCGTGCATGCTTGCTAGAATTAACATGGAATGGACAAAAC
EST: gi|208170378|gb|GD968857.1|GD968857
EST:     GCAACCTTAGGCCAGGCGATCTCCTTGGAACTGGGACAGTTAGTGGTCCT                         GAGCCAGAGTCCCGTGCATGCTTGCTAGAATTAACATGGAATGGACAAAAC
genomic: GCAACCTTAGGCCAGGCGATCTCCTTGGAACTGGGACAGTTAGTGGTCCTgtaagattcc ... ttcactgtagGAGCCAGAGTCCCGTGCATGCTTGCTAGAATTAACATGGAATGGACAAAAC
EST: gi|15202674|gb|BI425525.1|BI425525
EST:     GCAACCTTAGGCCAGGCGATCTCCTTGGAACTGGGACAGTTAGTGGTCCT                         GAGCCAGAGTCCCGTGCATGCTTGCTAGAATTAACATGGAATGGACAAAAC
genomic: GCAACCTTAGGCCAGGCGATCTCCTTGGAACTGGGACAGTTAGTGGTCCTgtaagattcc ... ttcactgtagGAGCCAGAGTCCCGTGCATGCTTGCTAGAATTAACATGGAATGGACAAAAC
EST: gi|208157945|gb|GD957810.1|GD957810
EST:     GGCCGGGCGATCTTCCTTTGGTAACTGGGACAGTTAGTGGTCCT                         GAGCCAGAGT-CCGTGCATGCTTGCTAGAATTAACATGGAATGGACAAAAC
genomic: GGCCAGGCGATC-TCC-TTGG-AACTGGGACAGTTAGTGGTCCTgtaagattcc ... ttcactgtagGAGCCAGAGTCCCGTGCATGCTTGCTAGAATTAACATGGAATGGACAAAAC
EST: gi|193421161|gb|FK391378.1|FK391378
EST:     GGCCGGGCGATCTCCTTGGAACTGGGACAGTTAGTGGTCCT                         GAGCCAGAGTCCCGTGCATGCCTGCTAGAATTAACATGGAATGGACAAAAC
genomic: GGCCAGGCGATCTCCTTGGAACTGGGACAGTTAGTGGTCCTgtaagattcc ... ttcactgtagGAGCCAGAGTCCCGTGCATGCTTGCTAGAATTAACATGGAATGGACAAAAC
EST: gi|14011019|gb|BG725941.1|BG725941
EST:     GCAACCTTAGGCCAGGCGATCTCCTTGGAACTGGGACAGTTAGTGGTCCT                         GAGCCAGAGTCCCGTGCATGCTTGCTAGAATTAACATGGAATGGACAAAAC
genomic: GCAACCTTAGGCCAGGCGATCTCCTTGGAACTGGGACAGTTAGTGGTCCTgtaagattcc ... ttcactgtagGAGCCAGAGTCCCGTGCATGCTTGCTAGAATTAACATGGAATGGACAAAAC
EST: gi|207839569|gb|GD811750.1|GD811750
EST:     CGATCTCCTTGGAACTGGGACAGTTAGTGGTCCT                         GAGCCAGAGTCCCGTGCATGCTTGCTAGAATTAACATGGAATGGACAAAAC
genomic: CGATCTCCTTGGAACTGGGACAGTTAGTGGTCCTgtaagattcc ... ttcactgtagGAGCCAGAGTCCCGTGCATGCTTGCTAGAATTAACATGGAATGGACAAAAC
EST: gi|193676085|gb|FK620071.1|FK620071
EST:     GGACAGTTAGTGGTCCT                         GAGCCAGAGTCCCGTGCATGCTTGCTAGAATTAACATGGAATGGACAAAAC
genomic: GGACAGTTAGTGGTCCTgtaagattcc ... ttcactgtagGAGCCAGAGTCCCGTGCATGCTTGCTAGAATTAACATGGAATGGACAAAAC
EST: gi|207848848|gb|GD818879.1|GD818879
EST:     GGCCGGGCGATCTCCTTGGAACTGGGACAGTTAGTGGTCCT                         GAGCCAGAGTCCCGTGCATGCTTGCTAGAATTAACATGGAATGGACAAAAC
genomic: GGCCAGGCGATCTCCTTGGAACTGGGACAGTTAGTGGTCCTgtaagattcc ... ttcactgtagGAGCCAGAGTCCCGTGCATGCTTGCTAGAATTAACATGGAATGGACAAAAC
EST: gi|7693176|gb|AW761273.1|AW761273
EST:     AGGCCAGGCGATCTCCTTGGAACTGGGACAGTTAGTGGTCCT                         GAGCCAGAGTCCCGTGCATGCTTGCTAGAATTAACATGGAATGGACAAAAC
genomic: AGGCCAGGCGATCTCCTTGGAACTGGGACAGTTAGTGGTCCTgtaagattcc ... ttcactgtagGAGCCAGAGTCCCGTGCATGCTTGCTAGAATTAACATGGAATGGACAAAAC
EST: gi|208300214|gb|GE098901.1|GE098901
EST:     GGCCGGGCGATCTTCCTTGGAACTGGGACAGTTAGTGGTCCT                         GAGCCAGAGTCCCGTGCATGCTTGCTAGAATTAACATGGAATGGACAAAAC
genomic: GGCCAGGCGATC-TCCTTGGAACTGGGACAGTTAGTGGTCCTgtaagattcc ... ttcactgtagGAGCCAGAGTCCCGTGCATGCTTGCTAGAATTAACATGGAATGGACAAAAC
EST: gi|7232656|gb|AW568010.1|AW568010
EST:     GCAACCTTAGGCCAGGCGATCTCCTTGGAACTGGGACAGTTAGTGGTCCT                         GAGCCAGAGTCCCGTGCATGCTTGCTAGAATTAACATGGAATGGACAAAAC
genomic: GCAACCTTAGGCCAGGCGATCTCCTTGGAACTGGGACAGTTAGTGGTCCTgtaagattcc ... ttcactgtagGAGCCAGAGTCCCGTGCATGCTTGCTAGAATTAACATGGAATGGACAAAAC
EST: gi|208028953|gb|GD829189.1|GD829189
EST:     CGATCTCCTTGGAACTGGGACAGTTAGTGGTCCT                         GAGCCAGAGTCCCGTGCATGCTTGCTAGAATTAACATGGAATGGACAAAAC
genomic: CGATCTCCTTGGAACTGGGACAGTTAGTGGTCCTgtaagattcc ... ttcactgtagGAGCCAGAGTCCCGTGCATGCTTGCTAGAATTAACATGGAATGGACAAAAC
EST: gi|7232634|gb|AW567988.1|AW567988
EST:     GCAACCTTAGGCCAGGCGATCTCCTTGGAACTGGGACAGTTAGTGGTCCT                         GAGCCAGAGTCCCGTGCATGCTTGCTAGAATTAACATGGAATGGACAAAAC
genomic: GCAACCTTAGGCCAGGCGATCTCCTTGGAACTGGGACAGTTAGTGGTCCTgtaagattcc ... ttcactgtagGAGCCAGAGTCCCGTGCATGCTTGCTAGAATTAACATGGAATGGACAAAAC
EST: gi|193414084|gb|FK376118.1|FK376118
EST:     GGCCGGGCGATCTCCTTGGAACTGGGACTAGTTAGTGGTCCT                         GAGCCAGAGTCCCGTGCATGCTTGCTAGAATTAACATGGAATGGACAAAAC
genomic: GGCCAGGCGATCTCCTTGGAACTGGGAC-AGTTAGTGGTCCTgtaagattcc ... ttcactgtagGAGCCAGAGTCCCGTGCATGCTTGCTAGAATTAACATGGAATGGACAAAAC
EST: gi|193576429|gb|FK530796.1|FK530796
EST:     CGATCTCCTTGGAACTGGGACAGTTAGTGGTCCT                         GAGCCAGAGTCCCGTGCATGCTTGCTAGAATTAACATGGAATGGACAAAAC
genomic: CGATCTCCTTGGAACTGGGACAGTTAGTGGTCCTgtaagattcc ... ttcactgtagGAGCCAGAGTCCCGTGCATGCTTGCTAGAATTAACATGGAATGGACAAAAC
EST: gi|298184616|gb|HO029829.1|HO029829
EST:     GCAACCTTAGGCCAGGCGATCTCCTTGGAACTGGGACAGTTAGTGGTCCT                         GAGCCAGAGTCCCGTGCATGCTTGCTAGAATTAACATGGAATGGACAAAAC
genomic: GCAACCTTAGGCCAGGCGATCTCCTTGGAACTGGGACAGTTAGTGGTCCTgtaagattcc ... ttcactgtagGAGCCAGAGTCCCGTGCATGCTTGCTAGAATTAACATGGAATGGACAAAAC
EST: gi|10847964|gb|BF071656.1|BF071656
EST:     GCAACCTTAGGCCAGGCGATCTCCTTGGAACTGGGACAGTTAGTGGTCCT                         GAGCCAGAGTCCCGTGCATGCTTGCTAGAATTAACATGGAATGGACAAAAC
genomic: GCAACCTTAGGCCAGGCGATCTCCTTGGAACTGGGACAGTTAGTGGTCCTgtaagattcc ... ttcactgtagGAGCCAGAGTCCCGTGCATGCTTGCTAGAATTAACATGGAATGGACAAAAC
EST: gi|208178383|gb|GD978336.1|GD978336
EST:     CGATCTCCTTGGAACTGGGACAGTTAGTGGTCCT                         GAGCCAGAGTCCCGTGCATGCTTGCTAGAATTAACATGGAATGGACAAAAC
genomic: CGATCTCCTTGGAACTGGGACAGTTAGTGGTCCTgtaagattcc ... ttcactgtagGAGCCAGAGTCCCGTGCATGCTTGCTAGAATTAACATGGAATGGACAAAAC
EST: gi|31464504|gb|CD406532.1|CD406532
EST:     CGATCTCCTTGGAACTGGGACAGTTAGTGGTCCT                         GAGCCAGAGTCCCGTGCATGCTTGCTAGAATTAACATGGAATGGACAAAAC
genomic: CGATCTCCTTGGAACTGGGACAGTTAGTGGTCCTgtaagattcc ... ttcactgtagGAGCCAGAGTCCCGTGCATGCTTGCTAGAATTAACATGGAATGGACAAAAC
EST: gi|208158655|gb|GD956056.1|GD956056
EST:     GGCCGGGCGATCTTCCTTTGGAACTGGGACAGTTAGTGGTCCT                         GAGCCAGAGTCCCGTGCATGCTTGCTAGAATTAACATGGAATGGACAAAAC
genomic: GGCCAGGCGATC-TCC-TTGGAACTGGGACAGTTAGTGGTCCTgtaagattcc ... ttcactgtagGAGCCAGAGTCCCGTGCATGCTTGCTAGAATTAACATGGAATGGACAAAAC
EST: gi|193381620|gb|FK347057.1|FK347057
EST:     GGCCGGGCGATCTCCTTGGAACTGGGACAGTTAGTGGTCCT                         GAGCCAGAGTCCCGTGCATGCTTGCTAGAATTAACATGGAATGGACAAAAC
genomic: GGCCAGGCGATCTCCTTGGAACTGGGACAGTTAGTGGTCCTgtaagattcc ... ttcactgtagGAGCCAGAGTCCCGTGCATGCTTGCTAGAATTAACATGGAATGGACAAAAC
EST: gi|208301747|gb|GE098977.1|GE098977
EST:     GGCCGGGCGATCTCCTTGGAACTGGGACAGTTAGTGGTCCT                         GAGCCAGAGTCCCGTGCATGCTTGCTAGAATTAACATGGAATGGACAAAAC
genomic: GGCCAGGCGATCTCCTTGGAACTGGGACAGTTAGTGGTCCTgtaagattcc ... ttcactgtagGAGCCAGAGTCCCGTGCATGCTTGCTAGAATTAACATGGAATGGACAAAAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctcccttttcaactgatcaactaatttcagttaaaatatgtgcttttcactgtagGAGCCAGAGTCCCGTGCATGCTTGCTAGAATTAACATGGAATGGACAAAACACAGTGTCAGTGAATGAGTTAAATCGGAAATTTCTTGAAGATGGAGACG
                  aactaat  putative branch site (score: 2)
                                          cttttcact  putative PPT
                  aactaatttcagttaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagattccatattttgcgcagtctaactttttgattcctgtttgttcgttctctttgagggaattctcccttttcaactgatcaactaatttcagttaaaatatgtgcttttcactgtagGAGCCAGAGTCCCGTGCATGCTTGCTAGAATTAACATGGAATGGACAAAACACAGTGTCAGTGAATGAGTTAAATCGGAAATTTCTTGAAGATGGAGACG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA