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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagttgccagaatcagaagcttttttttttcaatcatatcatgttctttttcattgttccagtggtgcattttgggacaaattttgtttaaattttgaaaaatgatttttttttaccttaagctgaagctgatataagatattgctatgtcattatttaacagGGTCAGATCAAGACTGGAGCTCCCTGCCGATCTGAAAGGCTTGCCAAGTACAACCAG

Basic information

species Glycine max
transcript GLYMA09G28100.1
intron # 15
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA09G28100.1 (Glycine max), 3'ss of exon 15
lower sequence: LOC_Os10g08550.5 (Oryza sativa), 3'ss of exon 15
gtaagttgccagaatcagaagcttttttttttcaatcatatcatgttctttttcattgttccagtggtgcattttgggacaaattttgtttaaattttgaaaaatgatttttttttaccttaagctgaagctgatataagatattgctatgtcattatttaacagGGTCAGATCAAGACTGGAGCTCCCTGCCGATCTGAAAGGCTTGCCAAGTACAACCAG
                                      ||  ||  | |  |  |   |  | || ||| | |||  | ||  |  ||| | | || | |          | || |||   | |     |||||      ||||  || ||||||| |  ||||||||||||||||||||||||| ||||||||||| ||  | |||||||| |||||||||
-------------------------------------gtaagattctgtgctctacattcactgtagtgaactttacggca--tcctgtattagttgtta---------ctcttgtactgaatgtgagggctga------atatatctttgtcattctgaaacagGGTCAGATCAAGACTGGAGCACCCTGCCGATCAGAGCGCCTTGCCAAATACAACCAG

upper sequence: GLYMA09G28100.1 (Glycine max), 3'ss of exon 15
lower sequence: LOC_Os03g14450.2 (Oryza sativa), 3'ss of exon 12
gtaagttgccagaatcagaagcttttttttttcaatcatatcatgttctttttcattgttccagtggtgcattttgggacaaattttgtttaaattttgaaaaa--tgatttttttttaccttaa-gctgaagctgatataaga---tattgctatgtcattatttaacagGGTCAGATCAAGACTGGAGCTCCCTGCCGATCTGAAAGGCTTGCCAAGTACAACCAG
                                      ||| ||  | |   |   |  |  |||| ||| |      | | |    | |||  |||||||| |  |  |    |     ||||| | ||| | | |  |   |    ||   | | |  | ||  ||||||| |||||||||||||||||||| ||| |||||||  | ||||||||||||||||||
-------------------------------------gtat-atactttgcgtgccttctttagtg-tgcttcaacaaatataggccgcttatcttttgaaagagcttgtgagatccgctcttaatggtgatgataacttggaaatgcatcaatgttttgtcatgaaacagGGCCAGATCAAGACTGGAGCTCCTTGCAGATCTGAGCGCCTTGCCAAGTACAACCAG

upper sequence: GLYMA09G28100.1 (Glycine max), 3'ss of exon 15
lower sequence: GRMZM2G048371_T01 (Zea mays), 3'ss of exon 16
gtaagttgccagaatcagaagcttttttttttcaatcatatcatgttctttttcattgttccagtggtgcattt-tgggacaa-------attttgtttaaa--ttttgaaaaat----gatttttttttaccttaagctgaagc-tgatataagatattgctatgtcattatttaacagGGTCAGATCAAGACTGGAGCTCCCTGCCGATCTGAAAGGCTTGCCAAGTACAACCAG
           | || |    |||| | |    |   |    |      |||  ||  |||| ||  || |    || ||||        || ||  | |||  | ||   ||||      |||| ||| ||  ||||  | ||  | || |    | ||| | | |  |||| |||||||||||||| ||||||||||| |||||| |||| ||  | |||||||| |||||||||
-----------gtatgatttactttctgtgcatatctaggatagagaagtttcaatcattcctgttctgaaaacatgagacagtgccttcatatttctcaaaggtcttagcaaattcaaacttttatttgactgtaaggcgtagtatcatctgtctttttgttttctttttatataacagGGTCAGATTAAGACTGGAGCACCCTGCAGATCAGAGCGTCTTGCCAAATACAACCAG

upper sequence: GLYMA09G28100.1 (Glycine max), 3'ss of exon 15
lower sequence: Vv16s0022g01770.t01 (Vitis vinifera), 3'ss of exon 15
gtaagttgccagaatcagaagcttttttttttcaatcatatcatgttctttttcattgttccagtggtgcattttgggacaaattttgtttaaattttgaaaaatgatttttttttacctta-agctgaagctgatataagatattgctatgt-cattattt---aacagGGTCAGATCAAGACTGGAGCTCCCTGCCGATCTGAAAGGCTTGCCAAGTACAACCAG
                                                                   |  | ||   |    ||  | |||||     || |  |||   |||| |       | || ||| |||||| |  |  || | ||| | |||| |   ||||||| |||||||||||||||||||| ||| | |||||| | |||||||| || ||||||
-----------------------------------------------------------------aataaaattgtagtagtatcatatttaa-----gagatttgacagttttctggacagcatctcaagttgatatgacctgatgatgtgtgccttatatgcaaacagGGCCAGATCAAGACTGGAGCTCCTTGCAGGTCTGAACGCCTTGCCAAATATAACCAG

upper sequence: GLYMA09G28100.1 (Glycine max), 3'ss of exon 15
lower sequence: EFJ14601 (Selaginella moellendorffii), 3'ss of exon 12
gtaagttgccagaatcagaagcttttttttttcaatcatatcatgttctttttcattgttccagtggtgcattttgggacaaattttgtttaaattttgaaaaatgatttttttttaccttaagctgaagctgatataagatattgctatgtcattatttaacagGGTCAGATCAAGACTGGAGCTCCCTGCCGATCTGAAAGGCTTGCCAAGTACAACCAG
                                                                                                 | | ||  ||   |||  ||   | ||       |||| |  ||| ||    | |  || ||   ||||||||||||||||| |||||||| ||||||||||| |||||||| || ||||| |||
------------------------------------------------------------------------------------------------gtaagaacagaaaatttcata---tgag-------tgatctttgatgttttgtttttgttttt--gcagGGTCAGATCAAGACGGGAGCTCCATGCCGATCTGAGAGGCTTGCGAAATACAATCAG

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|22929060|gb|BU546199.1|BU546199
EST:     GTGAAACTGAGGATACCTTCATTGCTGACCTCTCAGTTGGATTAGCAACT                         GGTCAGATCAAGACTGGAGCTCCCTGCCGATCTGAAAGGCTTGCCAAGTAC
genomic: GTGAAACTGAGGATACCTTCATTGCTGACCTCTCAGTTGGATTAGCAACTgtaagttgcc ... tatttaacagGGTCAGATCAAGACTGGAGCTCCCTGCCGATCTGAAAGGCTTGCCAAGTAC
EST: gi|18719876|gb|BM523226.1|BM523226
EST:     ACTGAGGATACCTTCATTGCTGACCTCTCAGTTGGATTAGCAACT                         GGTCAGATCAAGACTGGAGCTCCCTGCCGATCTGAAAGGCTTGCCAAGTAC
genomic: ACTGAGGATACCTTCATTGCTGACCTCTCAGTTGGATTAGCAACTgtaagttgcc ... tatttaacagGGTCAGATCAAGACTGGAGCTCCCTGCCGATCTGAAAGGCTTGCCAAGTAC
EST: gi|254322344|gb|GR837758.1|GR837758
EST:     TGAAACTGAGGATACCTTCATTGCTGACCTCCTCAGTTGGATTAGCAACT                         GGTCAGATCA-GACTGGAGCTCC
genomic: TGAAACTGAGGATACCTTCATTGCTGACCTC-TCAGTTGGATTAGCAACTgtaagttgcc ... tatttaacagGGTCAGATCAAGACTGGAGCTCC
EST: gi|7234456|gb|AW569793.1|AW569793
EST:     GTGAAACTGAGGATACCTTCATTGCTGACCTCTCAGTTGGATTAGCAACT                         GGTCAGATCAAGACTGGAGCTCCCTGCCGATCTGAAAGGCTTGCCAAGTAC
genomic: GTGAAACTGAGGATACCTTCATTGCTGACCTCTCAGTTGGATTAGCAACTgtaagttgcc ... tatttaacagGGTCAGATCAAGACTGGAGCTCCCTGCCGATCTGAAAGGCTTGCCAAGTAC
EST: gi|16348781|gb|BI974376.1|BI974376
EST:     GTGAAACTGAGGATACCTTCATTGCTGACCTCTCAGTTGGATTAGCAACT                         GGTCAGATCAAGACTGGAGCTCCCTGCCGATCTGAAAGGCTTGCCAAGTAC
genomic: GTGAAACTGAGGATACCTTCATTGCTGACCTCTCAGTTGGATTAGCAACTgtaagttgcc ... tatttaacagGGTCAGATCAAGACTGGAGCTCCCTGCCGATCTGAAAGGCTTGCCAAGTAC
EST: gi|209704370|gb|BW678366.1|BW678366
EST:     GTGAAACTGAGGATACCTTCATCGCTGACCTCTCAGTTGGATTAGCAACT                         GGTCAGATCAAGACTGGAGCTCCCTGCCGATCTGAAAGGCTTGCCAAGTAC
genomic: GTGAAACTGAGGATACCTTCATTGCTGACCTCTCAGTTGGATTAGCAACTgtaagttgcc ... tatttaacagGGTCAGATCAAGACTGGAGCTCCCTGCCGATCTGAAAGGCTTGCCAAGTAC
EST: gi|209701949|gb|BW683178.1|BW683178
EST:     GTGAAACTGAGGATACCTTCATCGCTGACCTCTCAGTTGGATTAGCAACT                         GGTCAGATCAAGACTGGAGCTCCCTGCCGATCTGAAAGGCTTGCCAAGTAC
genomic: GTGAAACTGAGGATACCTTCATTGCTGACCTCTCAGTTGGATTAGCAACTgtaagttgcc ... tatttaacagGGTCAGATCAAGACTGGAGCTCCCTGCCGATCTGAAAGGCTTGCCAAGTAC
EST: gi|209709209|gb|BW657178.1|BW657178
EST:     GTGAAACTGAGGATACCTTCATCGCTGACCTCTCAGTTGGATTAGCAACT                         GGTCAGATCAAGACTGGAGCTCCCTGCCGATCTGAAAGGCTTGCCAAGTAC
genomic: GTGAAACTGAGGATACCTTCATTGCTGACCTCTCAGTTGGATTAGCAACTgtaagttgcc ... tatttaacagGGTCAGATCAAGACTGGAGCTCCCTGCCGATCTGAAAGGCTTGCCAAGTAC
EST: gi|254322345|gb|GR837759.1|GR837759
EST:     GTGAAACTGAGGATACCTTCATTGCTGACCTCTCAGTTGGATTAGCAACT                         GGTCAGATCAAGACTGGAGCTCCCTGCCGATCTGAAAGGCTTGCCAAGTAC
genomic: GTGAAACTGAGGATACCTTCATTGCTGACCTCTCAGTTGGATTAGCAACTgtaagttgcc ... tatttaacagGGTCAGATCAAGACTGGAGCTCCCTGCCGATCTGAAAGGCTTGCCAAGTAC
EST: gi|209703772|gb|BW670708.1|BW670708
EST:     GTGAAACTGAGGATACCTTCATCGCTGACCTCTCAGTTGGATTAGCAACT                         GGTCAGATCAAGACTGGAGCTCCCTGCCGATCTGAAAGGCTTGCCAAGTAC
genomic: GTGAAACTGAGGATACCTTCATTGCTGACCTCTCAGTTGGATTAGCAACTgtaagttgcc ... tatttaacagGGTCAGATCAAGACTGGAGCTCCCTGCCGATCTGAAAGGCTTGCCAAGTAC
EST: gi|254349416|gb|GR860413.1|GR860413
EST:     GTGAAACTGAGGATACCTTCATTGCTGACCTCTCAGTTGGATTAGCAACT                         GGTCAGATCAAGACTGGAGCTCCCTGCCGATCTGAAAGGCTTGCCAAGTAC
genomic: GTGAAACTGAGGATACCTTCATTGCTGACCTCTCAGTTGGATTAGCAACTgtaagttgcc ... tatttaacagGGTCAGATCAAGACTGGAGCTCCCTGCCGATCTGAAAGGCTTGCCAAGTAC
EST: gi|21479746|gb|BQ576429.1|BQ576429
EST:     GTGAAACTGAGGATACCTTCATCGCTGACCTCTCAGTTGGATTAGCAACT                         GGTCAGATCAAGACTGGAGCTCCCTGCCGATCTGAAAGGCTTGCCAAGTAC
genomic: GTGAAACTGAGGATACCTTCATTGCTGACCTCTCAGTTGGATTAGCAACTgtaagttgcc ... tatttaacagGGTCAGATCAAGACTGGAGCTCCCTGCCGATCTGAAAGGCTTGCCAAGTAC
EST: gi|254321288|gb|GR824605.1|GR824605
EST:     GTGAAACTGAGGATACCTTCATTGCTGACCTCTCAGTTGGATTAGCAACT                         GGTCAGATCAAGACTGGAGCTCCCTGCCGATCTGAAAGGCTTGCCAAGTAC
genomic: GTGAAACTGAGGATACCTTCATTGCTGACCTCTCAGTTGGATTAGCAACTgtaagttgcc ... tatttaacagGGTCAGATCAAGACTGGAGCTCCCTGCCGATCTGAAAGGCTTGCCAAGTAC
EST: gi|9204155|gb|BE330379.1|BE330379
EST:     GTGAAACTGAGGATACCTTCATTGCTGACCTCTCAGTTGGATTAGCAACT                         GGTCAGATCAAGACTGGAGCTCCCTGCCGATCTGAAAGGCTTGCCAAGTAC
genomic: GTGAAACTGAGGATACCTTCATTGCTGACCTCTCAGTTGGATTAGCAACTgtaagttgcc ... tatttaacagGGTCAGATCAAGACTGGAGCTCCCTGCCGATCTGAAAGGCTTGCCAAGTAC
EST: gi|254346398|gb|GR856120.1|GR856120
EST:     AGGATACCTTCATTGCTGACCTCTCAGTTGGATTAGCAACT                         GGTCAGATCAAGACTGGAGCTCCCTGCCGATCTGAAAGGCTTGCCAAGTAC
genomic: AGGATACCTTCATTGCTGACCTCTCAGTTGGATTAGCAACTgtaagttgcc ... tatttaacagGGTCAGATCAAGACTGGAGCTCCCTGCCGATCTGAAAGGCTTGCCAAGTAC
EST: gi|254320852|gb|GR827301.1|GR827301
EST:     GTGAAACTGAGGATACCTTCATTGCTGACCTCTCAGTTGGATTAGCAACT                         GGTCAGATCAAGACTGGAGCTCCCTGCCGATCTGAAAGGCTTGCCAAGTAC
genomic: GTGAAACTGAGGATACCTTCATTGCTGACCTCTCAGTTGGATTAGCAACTgtaagttgcc ... tatttaacagGGTCAGATCAAGACTGGAGCTCCCTGCCGATCTGAAAGGCTTGCCAAGTAC
EST: gi|207803882|gb|GD773611.1|GD773611
EST:     GACCTCTCAGTTGGATTAGCAACT                         GGTCAGATCAAGACTGGAGCTCCCTGCCGATCTGAAAGGCTTGCCAAGTAC
genomic: GACCTCTCAGTTGGATTAGCAACTgtaagttgcc ... tatttaacagGGTCAGATCAAGACTGGAGCTCCCTGCCGATCTGAAAGGCTTGCCAAGTAC
EST: gi|254326168|gb|GR840760.1|GR840760
EST:     GTGAAACTGAGGATACCTTCATTGCTGACCTCTCAGTTGGATTAGCAACT                         GGTCAGATCAAGACTGGAGCTCCCTGCCGATTTGAAAGGCTTGCCAAGTAC
genomic: GTGAAACTGAGGATACCTTCATTGCTGACCTCTCAGTTGGATTAGCAACTgtaagttgcc ... tatttaacagGGTCAGATCAAGACTGGAGCTCCCTGCCGATCTGAAAGGCTTGCCAAGTAC
EST: gi|254317750|gb|GR826734.1|GR826734
EST:     GTGAAACTGAGGATACCTTCATTGCTGACCTCTCAGTTGGATTAGCAACT                         GGTCAGATCAAGACTGGAGCTCCCTGCCGATCTGAAAGGCTTGCCAAGTAC
genomic: GTGAAACTGAGGATACCTTCATTGCTGACCTCTCAGTTGGATTAGCAACTgtaagttgcc ... tatttaacagGGTCAGATCAAGACTGGAGCTCCCTGCCGATCTGAAAGGCTTGCCAAGTAC
EST: gi|254319291|gb|GR828911.1|GR828911
EST:     GTGAAACTGAGGATACCTTCATTGCTGACCTCTCAGTTGGATTAGCAACT                         GGTCAGATCAAGACTGGAGCTCCCTGCCGATCTGAAAGGCTTGCCAAGTAC
genomic: GTGAAACTGAGGATACCTTCATTGCTGACCTCTCAGTTGGATTAGCAACTgtaagttgcc ... tatttaacagGGTCAGATCAAGACTGGAGCTCCCTGCCGATCTGAAAGGCTTGCCAAGTAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttttaccttaagctgaagctgatataagatattgctatgtcattatttaacagGGTCAGATCAAGACTGGAGCTCCCTGCCGATCTGAAAGGCTTGCCAAGTACAACCAG
                  agctgat  putative branch site (score: 4)
                                     tatgtcattatttaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagttgccagaatcagaagcttttttttttcaatcatatcatgttctttttcattgttccagtggtgcattttgggacaaattttgtttaaattttgaaaaatgatttttttttaccttaagctgaagctgatataagatattgctatgtcattatttaacagGGTCAGATCAAGACTGGAGCTCCCTGCCGATCTGAAAGGCTTGCCAAGTACAACCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT