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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tcatttctattattttccctcccccgtttctaacatgaatcaattaatttattatgcaatcttgatgtcgtgatcatgatgatatgtacatttgtcacagTTTTTTGACGGATATGGATATCATGGGACATCATTTGAGCAGATATATCGATGCTACCCAGCTTCCTTTATTGAAAAG

Basic information

species Glycine max
transcript GLYMA08G05030.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA08G05030.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv03s0038g00750.t01 (Vitis vinifera), 3'ss of exon 2
tcatttctattattttccctcccccgtttctaacatgaatcaattaatttattatgcaatcttgatgtcgtgatcatgatgatatgtacatt----tgtcacagTTTTTTGACGGATATGGATATCATGGGACATCATTTGAGCAGATATATCGATGCTACCCAGCTTCCTTTATTGAAAAG
  |    | |||| |    |  |  || |  || |       |||| | |||||     | ||| | |  | || ||     | |||   ||      |  |||| |||||  ||||||||||||||||| |  ||||| ||||||| ||||||||| ||||| || || ||||| || |||
ataacattgttatatgttttgaca-gtattgaataattgcttatta-tatattaatagtttttgttattattattatt-cactctgttggttgtgacattgcaGTATTTTGGTGGATATGGATATCATGGAATGTCATTCGAGCAGAAATATCGATGTTACCCTGCATCTTTTATAGATAAG
















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|19269563|gb|BM885819.1|BM885819
EST:     TAGCAATCAGCACAATAGAAAATG                         TTTTTTGACGGATATGGATATCATGGGACATCATTTGAGCAGATATATCGA
genomic: TAGCAATCAGCACAATAGAAAATGgtatgcttct ... tttgtcacagTTTTTTGACGGATATGGATATCATGGGACATCATTTGAGCAGATATATCGA
EST: gi|13312371|gb|BG406022.1|BG406022
EST:     CTTTGAGGGTTGATTCTCTGGTGTGGTAGCAATCAGCACAATAGAAAATG                         TTTTTTGACGGATATGGATATCATGGGACATCATTTGAGCAGATATATCGA
genomic: CTTTGAGGGTTGATTCTCTGGTGTGGTAGCAATCAGCACAATAGAAAATGgtatgcttct ... tttgtcacagTTTTTTGACGGATATGGATATCATGGGACATCATTTGAGCAGATATATCGA
EST: gi|192296041|gb|FG993404.1|FG993404
EST:     CTTTGAGGGTTGATTCTCTGGTGTGGTAGCAATCAGCACAATAGAAAATG                         TTTTTTGACGGATATGGATATCATGGGACATCATTTGAGCAGATATATCGA
genomic: CTTTGAGGGTTGATTCTCTGGTGTGGTAGCAATCAGCACAATAGAAAATGgtatgcttct ... tttgtcacagTTTTTTGACGGATATGGATATCATGGGACATCATTTGAGCAGATATATCGA
EST: gi|37994740|gb|CF806346.1|CF806346
EST:     GGTTGATTCTCTGGTGTAGTAGCAATCAGCACAATAGAAAATG                         TTTTTTGACGGATATGGATATCATGGGACATCATTTGAGCAGATATATCGA
genomic: GGTTGATTCTCTGGTGTGGTAGCAATCAGCACAATAGAAAATGgtatgcttct ... tttgtcacagTTTTTTGACGGATATGGATATCATGGGACATCATTTGAGCAGATATATCGA
EST: gi|192325065|gb|FK016176.1|FK016176
EST:     CTTTGAGGGTTGATTCTCTGGTGTGGTAGCAATCAGCACAATAGAAAATG                         TTTTTTGACGGATATGGATATCATGGGACATCATTTGAGCAGATATATCGA
genomic: CTTTGAGGGTTGATTCTCTGGTGTGGTAGCAATCAGCACAATAGAAAATGgtatgcttct ... tttgtcacagTTTTTTGACGGATATGGATATCATGGGACATCATTTGAGCAGATATATCGA
EST: gi|15816027|gb|BI788302.1|BI788302
EST:     CTTTGAGGGTTGATTCTCTGGTGTAGTAGCAATCAGCACAATAGAAAATG                         TTTTTTGACGGATATGGATATCATGGGACATCATTTGAGCAGATATATCGA
genomic: CTTTGAGGGTTGATTCTCTGGTGTGGTAGCAATCAGCACAATAGAAAATGgtatgcttct ... tttgtcacagTTTTTTGACGGATATGGATATCATGGGACATCATTTGAGCAGATATATCGA
EST: gi|254326846|gb|GR836455.1|GR836455
EST:     CTTTGAGGGTTGATTCTCTGGTGTGGTAGCAATCAGCACAATAGAAAATG                         TTTTTTGACGGATATGGATATCATGGGACATCATTTGAGCAGATATATCGA
genomic: CTTTGAGGGTTGATTCTCTGGTGTGGTAGCAATCAGCACAATAGAAAATGgtatgcttct ... tttgtcacagTTTTTTGACGGATATGGATATCATGGGACATCATTTGAGCAGATATATCGA
EST: gi|209716428|gb|BW653869.1|BW653869
EST:     CTTTGAGGGTTGATTCTCTGGTGTGGTAGCAATCAGCACAATAGAAAATG                         TTTTTTGACGGATATGGATATCATGGGACATCATTTGAGCAGATATATCGA
genomic: CTTTGAGGGTTGATTCTCTGGTGTGGTAGCAATCAGCACAATAGAAAATGgtatgcttct ... tttgtcacagTTTTTTGACGGATATGGATATCATGGGACATCATTTGAGCAGATATATCGA
EST: gi|16996631|gb|BM086003.1|BM086003
EST:     CTCTGGTGTAGTAGCAATCAGCACAATAGAAAATG                         TTTTTTGACGGATATGGATATCATGGGACATCATTTGAGCAGATATATCGA
genomic: CTCTGGTGTGGTAGCAATCAGCACAATAGAAAATGgtatgcttct ... tttgtcacagTTTTTTGACGGATATGGATATCATGGGACATCATTTGAGCAGATATATCGA
EST: gi|209712046|gb|BW674191.1|BW674191
EST:     CTTTGAGGGTTGATTCTCTGGTGTGGTAGCAATCAGCACAATAGAAAATG                         TTTTTTGACGGATATGGATATCATGGGACATCATTTGAGCAGATATATCGA
genomic: CTTTGAGGGTTGATTCTCTGGTGTGGTAGCAATCAGCACAATAGAAAATGgtatgcttct ... tttgtcacagTTTTTTGACGGATATGGATATCATGGGACATCATTTGAGCAGATATATCGA
EST: gi|14125023|gb|BG789461.1|BG789461
EST:     CTTTGAGGGTTGATTCTCTGGTGTGGTAGCAATCAGCACAATAGAAAATG                         TTTTTTGACGGATATGGATATCATGGGACATCATTTGAGCAGATATATCGA
genomic: CTTTGAGGGTTGATTCTCTGGTGTGGTAGCAATCAGCACAATAGAAAATGgtatgcttct ... tttgtcacagTTTTTTGACGGATATGGATATCATGGGACATCATTTGAGCAGATATATCGA
EST: gi|192309316|gb|FK000524.1|FK000524
EST:     CTTTGAGGGTTGATTCTCTGGTGTAGTAGCAATCAGCACAATAGAAAATG                         TTTTTTGACGGATATGGATATCATGGGACATCATTTGAGCAGATATATCGA
genomic: CTTTGAGGGTTGATTCTCTGGTGTGGTAGCAATCAGCACAATAGAAAATGgtatgcttct ... tttgtcacagTTTTTTGACGGATATGGATATCATGGGACATCATTTGAGCAGATATATCGA
EST: gi|254313714|gb|GR831343.1|GR831343
EST:     CTTTGAGGGTTGATTCTCTGGTGTGGTAGCAATCAGCACAATAGAAAATG                         TTTTTTGACGGATATGGATATCATGGGACATCATTTGAGCAGATATATCGA
genomic: CTTTGAGGGTTGATTCTCTGGTGTGGTAGCAATCAGCACAATAGAAAATGgtatgcttct ... tttgtcacagTTTTTTGACGGATATGGATATCATGGGACATCATTTGAGCAGATATATCGA
EST: gi|298172847|gb|HO019831.1|HO019831
EST:     CTTTGAGGGTTGATTCTCTGGTGTGGTAGCAATCAGCACAATAGAAAATG                         TTTTTTGACGGATATGGATATCATGGGACATCATTTGAGCAGATATATCGA
genomic: CTTTGAGGGTTGATTCTCTGGTGTGGTAGCAATCAGCACAATAGAAAATGgtatgcttct ... tttgtcacagTTTTTTGACGGATATGGATATCATGGGACATCATTTGAGCAGATATATCGA
EST: gi|17153552|gb|BM143485.1|BM143485
EST:     CTTTGAGGGTTGATTCTCTGGTGTAGTAGCAATCAGCACAATAGAAAATG                         TTTTTTGACGGATATGGATATCATGGGACATCATTTGAGCAGATATATCGA
genomic: CTTTGAGGGTTGATTCTCTGGTGTGGTAGCAATCAGCACAATAGAAAATGgtatgcttct ... tttgtcacagTTTTTTGACGGATATGGATATCATGGGACATCATTTGAGCAGATATATCGA
EST: gi|4304277|gb|AI443596.1|AI443596
EST:     CTTTGAGGGTTGATTCTCTGGTGTAGTAGCAATCAGCACAATAGAAAATG                         TTTTTTGACGGATATGGATATCATGGGACATCATTTGAGCAGATATATCGA
genomic: CTTTGAGGGTTGATTCTCTGGTGTGGTAGCAATCAGCACAATAGAAAATGgtatgcttct ... tttgtcacagTTTTTTGACGGATATGGATATCATGGGACATCATTTGAGCAGATATATCGA
EST: gi|213604953|gb|DB956328.1|DB956328
EST:     CTTTGAGGGTTGATTCTCTGGTGTGGTAGCAATCAGCACAATAGAAAATG                         TTTTTTGACGGATATGGATATCATGGGACATCATTTGAGCAGATATATCGA
genomic: CTTTGAGGGTTGATTCTCTGGTGTGGTAGCAATCAGCACAATAGAAAATGgtatgcttct ... tttgtcacagTTTTTTGACGGATATGGATATCATGGGACATCATTTGAGCAGATATATCGA
EST: gi|192330755|gb|FK022018.1|FK022018
EST:     CTTTGAGGGTTGATTCTCTGGTGTGGTAGCAATCAGCACAATAGAAAATG                         TTTTTTGACGGATATGGATATCATGGGACATCATTTGAGCAGATATATCGA
genomic: CTTTGAGGGTTGATTCTCTGGTGTGGTAGCAATCAGCACAATAGAAAATGgtatgcttct ... tttgtcacagTTTTTTGACGGATATGGATATCATGGGACATCATTTGAGCAGATATATCGA
EST: gi|24205916|gb|BU965169.1|BU965169
EST:     CTTTGAGGGTTGATTCTCTGGTGTAGTAGCAATCAGCACAATAGAAAATG                         TTTTTTGACGGATATGGATATCATGGGACATCATTTGAGCAGATATATCGA
genomic: CTTTGAGGGTTGATTCTCTGGTGTGGTAGCAATCAGCACAATAGAAAATGgtatgcttct ... tttgtcacagTTTTTTGACGGATATGGATATCATGGGACATCATTTGAGCAGATATATCGA
EST: gi|213599556|gb|DB968353.1|DB968353
EST:     CTTTGAGGGTTGATTCTCTGGTGTGGTAGCAATCAGCACAATAGAAAATG                         TTTTTTGACGGATATGGATATCATGGGACATCATTTGAGCAGATATATCGA
genomic: CTTTGAGGGTTGATTCTCTGGTGTGGTAGCAATCAGCACAATAGAAAATGgtatgcttct ... tttgtcacagTTTTTTGACGGATATGGATATCATGGGACATCATTTGAGCAGATATATCGA
EST: gi|23727320|gb|BU761687.1|BU761687
EST:     CTTTGAGGGTTGATTCTCTGGTGTAGTAGCAATCAGCACAATAGAAAATG                         TTTTTTGACGGATATGGATATCATGGGACATCATTTGAGCAGATATATCGA
genomic: CTTTGAGGGTTGATTCTCTGGTGTGGTAGCAATCAGCACAATAGAAAATGgtatgcttct ... tttgtcacagTTTTTTGACGGATATGGATATCATGGGACATCATTTGAGCAGATATATCGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aatttattatgcaatcttgatgtcgtgatcatgatgatatgtacatttgtcacagTTTTTTGACGGATATGGATATCATGGGACATCATTTGAGCAGATATATCGATGCTACCCAGCTTCCTTTATTGAAAAG
                                 atgatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tcatttctattattttccctcccccgtttctaacatgaatcaattaatttattatgcaatcttgatgtcgtgatcatgatgatatgtacatttgtcacagTTTTTTGACGGATATGGATATCATGGGACATCATTTGAGCAGATATATCGATGCTACCCAGCTTCCTTTATTGAAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT