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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaattgccgacaccatcattgcgtttatttgtcccatggattgtgtgtgatgaaatattgaggttgcatatgtttgtttgcagCTCCTTCATGGATATATTTGATGTGGATCATTTCATTGATGTATTGAAGGATGATATTTCTATAGTTAAAGAGCTGCCTAAAGAGTTCAGCTGGAGCACA

Basic information

species Glycine max
transcript GLYMA09G33160.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA09G33160.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv00s0313g00030.t01 (Vitis vinifera), 3'ss of exon 5
gtaattgccgacaccatcattgcgtttatttgtcccatggatt------gtgtgtgatgaaatat----tgaggttgcatatgtttgtttgcagCTCCTTCATGGATATATTTGATGTGGATCATTTCATTGATGTATTGAAGGATGATATTTCTATAGTTAAAGAGCTGCCTAAAGAGTTCAGCTGGAGCACA
||| ||       | | |||     ||| || |  |||| |        || | |   || | ||    ||| || ||||   ||| | |||||||| |||||||||||||||||||| ||||| || ||| ||||  |||||||||||||||||||||||| |||| ||||| | || |||   |||||||||
gtagttttttgttcaagcatc-tacttactt-tttcatgaaccttattagtttttagggagacatattctgaagtggcattcttttttctgcagCTCATTCATGGATATATTTGATGTTGATCACTTTATTAATGTCCTGAAGGATGATATTTCTATAGTTAGAGAGTTGCCTTATGACTTCTCTTGGAGCACA
















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|151397506|gb|EV267379.1|EV267379
EST:     ACTCTGGTGATTCCATACCTTGAATTAAATCCTGTATGGCGAGATTCAAG                         CTCCTTCATGGATATATTTGATGTGGATCATTTCATTGATGTATTGAAGGA
genomic: ACTCTGGTGATTCCATACCTTGAATTAAATCCTGTATGGCGAGATTCAAGgtaattgccg ... ttgtttgcagCTCCTTCATGGATATATTTGATGTGGATCATTTCATTGATGTATTGAAGGA
EST: gi|9899441|gb|BE608409.1|BE608409
EST:     ACTCTGGTGATTCCATACCTTGA-TTAAATCCTGTATGGCGAGATTCAAG                         CTCCTTCATGGATATATTTGATGTGGATCATTTCATTGATGTATTGAAGGA
genomic: ACTCTGGTGATTCCATACCTTGAATTAAATCCTGTATGGCGAGATTCAAGgtaattgccg ... ttgtttgcagCTCCTTCATGGATATATTTGATGTGGATCATTTCATTGATGTATTGAAGGA
EST: gi|207697919|gb|GD680088.1|GD680088
EST:     ACTCTGGTGATTCCATACCTTGAATTAAATCCTGTATGGCGAGATTCAAG                         CTCCTTCATGGATATATTTGATGTGGATCATTTCATTGATGTATTGAAGGA
genomic: ACTCTGGTGATTCCATACCTTGAATTAAATCCTGTATGGCGAGATTCAAGgtaattgccg ... ttgtttgcagCTCCTTCATGGATATATTTGATGTGGATCATTTCATTGATGTATTGAAGGA
EST: gi|207747069|gb|GD720726.1|GD720726
EST:     ACTCTGGTGATTCCATACCTTGAATTAAATCCTGTATGGCGAGATTCAAG                         CTCCTTCATGGATATATTTGATGTGGATCATTTCATTGATGTATTGAAGGA
genomic: ACTCTGGTGATTCCATACCTTGAATTAAATCCTGTATGGCGAGATTCAAGgtaattgccg ... ttgtttgcagCTCCTTCATGGATATATTTGATGTGGATCATTTCATTGATGTATTGAAGGA
EST: gi|208169752|gb|GD967825.1|GD967825
EST:     ACTCTGGTGATTCCATACCTTGAATTAAATCCTGTATGGCGAGATTCAAG                         CTCCTTCATGGATATATTTGATGTGGATCATTTCATTGATGTATTGAAGGA
genomic: ACTCTGGTGATTCCATACCTTGAATTAAATCCTGTATGGCGAGATTCAAGgtaattgccg ... ttgtttgcagCTCCTTCATGGATATATTTGATGTGGATCATTTCATTGATGTATTGAAGGA
EST: gi|18734891|gb|BM528445.1|BM528445
EST:     ACTCTGGTGATTCCATACCTTGAATTAAATCCTGTATGGCGAGATTCAAG                         CTCCTTCATGGATATATTTGATGTGGATCATTTCATTGATGTATTGAAGGA
genomic: ACTCTGGTGATTCCATACCTTGAATTAAATCCTGTATGGCGAGATTCAAGgtaattgccg ... ttgtttgcagCTCCTTCATGGATATATTTGATGTGGATCATTTCATTGATGTATTGAAGGA
EST: gi|19053956|gb|BM732623.1|BM732623
EST:     ACTCTGGTGATTCCATACCTTGAATTAAATCCTGTATGGCGAGATTCAAG                         CTCCTTCATGGATATATTTGATGTGGATCATTTCATTGATGTATTGAAGGA
genomic: ACTCTGGTGATTCCATACCTTGAATTAAATCCTGTATGGCGAGATTCAAGgtaattgccg ... ttgtttgcagCTCCTTCATGGATATATTTGATGTGGATCATTTCATTGATGTATTGAAGGA
EST: gi|192308463|gb|FK000931.1|FK000931
EST:     ACTCTGGTGATTCCATACCTTGAATTAAATCCTGTATGGCGAGATTCAAG                         CTCCTTCATGGATATATTTGATGTGGATCATTTCATTGATGTATTGAAGGA
genomic: ACTCTGGTGATTCCATACCTTGAATTAAATCCTGTATGGCGAGATTCAAGgtaattgccg ... ttgtttgcagCTCCTTCATGGATATATTTGATGTGGATCATTTCATTGATGTATTGAAGGA
EST: gi|15813600|gb|BI785875.1|BI785875
EST:     ACTCTGGTGATTCCATACCTTGAATTAAATCCTGTATGGCGAGATTCAAG                         CTCCTTCATGGATATATTTGATGTGGATCATTTCATTGATGTATTGAAGGA
genomic: ACTCTGGTGATTCCATACCTTGAATTAAATCCTGTATGGCGAGATTCAAGgtaattgccg ... ttgtttgcagCTCCTTCATGGATATATTTGATGTGGATCATTTCATTGATGTATTGAAGGA
EST: gi|308098228|gb|HO759969.1|HO759969
EST:     ACTCTGGTGATTCCATACCTTGAATTAAATCCTGTATGGCGAGATTCAAG                         CTCCTTCATGGATATATTTGATGCGGATCATTTCATTGATGTATTGAAGGA
genomic: ACTCTGGTGATTCCATACCTTGAATTAAATCCTGTATGGCGAGATTCAAGgtaattgccg ... ttgtttgcagCTCCTTCATGGATATATTTGATGTGGATCATTTCATTGATGTATTGAAGGA
EST: gi|120534087|gb|EH262220.1|EH262220
EST:     ACTCTGGTGATTCCATACCTTGAATTAAATCCTGTATGGCGAGATTCAAG                         CTCCTTCATGGATATATTTGATGTGGATCATTTCATTGATGTATTGAAGGA
genomic: ACTCTGGTGATTCCATACCTTGAATTAAATCCTGTATGGCGAGATTCAAGgtaattgccg ... ttgtttgcagCTCCTTCATGGATATATTTGATGTGGATCATTTCATTGATGTATTGAAGGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgtcccatggattgtgtgtgatgaaatattgaggttgcatatgtttgtttgcagCTCCTTCATGGATATATTTGATGTGGATCATTTCATTGATGTATTGAAGGATGATATTTCTATAGTTAAAGAGCTGCCTAAAGAGTTCAGCTGGAGCACA
                                            tttgttt  CT-rich tract
                     atgaaatatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaattgccgacaccatcattgcgtttatttgtcccatggattgtgtgtgatgaaatattgaggttgcatatgtttgtttgcagCTCCTTCATGGATATATTTGATGTGGATCATTTCATTGATGTATTGAAGGATGATATTTCTATAGTTAAAGAGCTGCCTAAAGAGTTCAGCTGGAGCACA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA