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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...attgaaacttggtggtttcgttttcaccattcaagtaagttattaactagattttctacgaattcattaattgaatatggtggtggagcttcgtttgcagTGATTCTGGAAGAAAAGTGGAAGATCCGGAGTTGTTAGAGGCAATCCGTTTGACAATATTGAATAATATGATTCAGTATCACCCG

Basic information

species Glycine max
transcript GLYMA15G00560.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA15G00560.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv09s0018g01780.t01 (Vitis vinifera), 3'ss of exon 4
attgaaacttggtggtttcgttttcacca----ttcaagtaag-ttattaactagattttctacgaattcattaattgaatatggtggtggagcttcgtttgcagTGATTCTGGAAGAAAAGTGGAAGATCCGGAGTTGTTAGAGGCAATCCGTTTGACAATATTGAATAATATGATTCAGTATCACCCG
     |  ||||   ||   ||||||| |    || || | || || |    | ||| || |  |       |  |  ||| | ||| |||  | | |||||||||||| |||| |||||||| || ||||| |||||| | |||||||| |||||||| ||  | || |||||| ||||||||||||||
---atattttggacattgttttttcacaagcattttaaatgaggttgtgcgattgatgttttctgttgattctggtc-aatttagtgctggt-cgttgtttgcagTGATACTGGTAGAAAAGTTGAGGATCCTGAGTTGCTTGAGGCAATTCGTTTGACGATTATAAACAATATGCTTCAGTATCACCCG
















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|13180962|gb|BG352302.1|BG352302
EST:     GTCTTTCTAGATTCTTCTGGCAAGCACAACAAGTTTTCCATCACAAAAGC                         TGATTCTGGAAGAAAAGTGGAAGATCCGGAGTTGTTAGAGGCAATCCGTTT
genomic: GTCTTTCTAGATTCTTCTGGCAAGCACAACAAGTTTTCCATCACAAAAGCgtaagtacta ... tcgtttgcagTGATTCTGGAAGAAAAGTGGAAGATCCGGAGTTGTTAGAGGCAATCCGTTT
EST: gi|192321695|gb|FK014039.1|FK014039
EST:     GTCTTTCTAGATTCTTCTGGCAAGCACAACAAGTTTTCCATCACAAAAGC                         TGATTCTGGAAGAAAAGTGGAAGATCCGGAGTTGTTAGAGGCAATCCGTTT
genomic: GTCTTTCTAGATTCTTCTGGCAAGCACAACAAGTTTTCCATCACAAAAGCgtaagtacta ... tcgtttgcagTGATTCTGGAAGAAAAGTGGAAGATCCGGAGTTGTTAGAGGCAATCCGTTT
EST: gi|120529813|gb|EH257947.1|EH257947
EST:     GTCTTTCTAGATTCTTCTGGCAAGCACAACAAGTTTTCCATCACAAAAGC                         TGATTCTGGAAGAAAAGTGGAAGATCCGGAGTTGTTAGAGGCAATCCGTTT
genomic: GTCTTTCTAGATTCTTCTGGCAAGCACAACAAGTTTTCCATCACAAAAGCgtaagtacta ... tcgtttgcagTGATTCTGGAAGAAAAGTGGAAGATCCGGAGTTGTTAGAGGCAATCCGTTT
EST: gi|22522966|gb|BU081777.1|BU081777
EST:     GTCTTTCTAGATTCTTCTGGCAAGCACAACAAGTTTTCCATCACAAAAGC                         TGATTCTGGAAGAAAAGTGGAAGATCCGGAGTTGTTAGAGGCAATCCGTTT
genomic: GTCTTTCTAGATTCTTCTGGCAAGCACAACAAGTTTTCCATCACAAAAGCgtaagtacta ... tcgtttgcagTGATTCTGGAAGAAAAGTGGAAGATCCGGAGTTGTTAGAGGCAATCCGTTT
EST: gi|21993858|gb|BQ785386.1|BQ785386
EST:     GTCTTTCTAGATTCTTCTGGCAAGCACAACAAGTTTTCCATCACAAAAGC                         TGATTCTGGAAGAAAAGTGGAAGATCCGGAGTTGT
genomic: GTCTTTCTAGATTCTTCTGGCAAGCACAACAAGTTTTCCATCACAAAAGCgtaagtacta ... tcgtttgcagTGATTCTGGAAGAAAAGTGGAAGATCCGGAGTTGT
EST: gi|31561420|gb|CD487258.1|CD487258
EST:     TCTTTCTAGATTCTTCTGGGAGAGCACAACAAGTTTTCCATCACAAAAGC                         TGATTCTGGAAGAAAAGTGGAAGATCCGGAGTTGTTAGAGGCAATCCGTTT
genomic: TCTTTCTAGATTCTTCTGGCA-AGCACAACAAGTTTTCCATCACAAAAGCgtaagtacta ... tcgtttgcagTGATTCTGGAAGAAAAGTGGAAGATCCGGAGTTGTTAGAGGCAATCCGTTT
EST: gi|213604289|gb|DB970577.1|DB970577
EST:     GTCTTTCTAGATTCTTCTGGCAAGCACAACAAGTTTTCCATCACAAAAGC                         TGATTCTGGAAGAAAAGTGGAAGATCCGGAGTTGTTAGAGGCAATCCGTTT
genomic: GTCTTTCTAGATTCTTCTGGCAAGCACAACAAGTTTTCCATCACAAAAGCgtaagtacta ... tcgtttgcagTGATTCTGGAAGAAAAGTGGAAGATCCGGAGTTGTTAGAGGCAATCCGTTT
EST: gi|120491081|gb|EH219248.1|EH219248
EST:     GTCTTTCTAGATTCTTCTGGCAAGCACAACAAGTTTTCCATCACAAAAGC                         TGATTCTGGAAGAAAAGTGGAAGATCCGGAGTTGTTAGAGGCAATCCGTTT
genomic: GTCTTTCTAGATTCTTCTGGCAAGCACAACAAGTTTTCCATCACAAAAGCgtaagtacta ... tcgtttgcagTGATTCTGGAAGAAAAGTGGAAGATCCGGAGTTGTTAGAGGCAATCCGTTT
EST: gi|7685965|gb|AW756613.1|AW756613
EST:     GTTTTCCATCACAAAAGC                         TGATTCTGGAAGAAAAGTGGAAGATCCGGAGTTGTTAGAGGCAATCCGTTT
genomic: GTTTTCCATCACAAAAGCgtaagtacta ... tcgtttgcagTGATTCTGGAAGAAAAGTGGAAGATCCGGAGTTGTTAGAGGCAATCCGTTT
EST: gi|120494269|gb|EH222436.1|EH222436
EST:     GTCTTTCTAGATTCTTCTGGCAAGCACAACAAGTTTTCCATCACAAAAGC                         TGATTCTGGAAGAAAAGTGGAAGATCCGGAGTTGTTAGAGGCAATCCGTTT
genomic: GTCTTTCTAGATTCTTCTGGCAAGCACAACAAGTTTTCCATCACAAAAGCgtaagtacta ... tcgtttgcagTGATTCTGGAAGAAAAGTGGAAGATCCGGAGTTGTTAGAGGCAATCCGTTT
EST: gi|22525030|gb|BU083841.1|BU083841
EST:     GTCTTTCTAGATTCTTCTGGCAAGCACAACAAGTTTTCCATCACAAAAGC                         TGATTCTGGAAGAAAAGTGGAAGATCCGGAGTTGTTAGAGGCAATCCGTTT
genomic: GTCTTTCTAGATTCTTCTGGCAAGCACAACAAGTTTTCCATCACAAAAGCgtaagtacta ... tcgtttgcagTGATTCTGGAAGAAAAGTGGAAGATCCGGAGTTGTTAGAGGCAATCCGTTT
EST: gi|213605246|gb|DB966862.1|DB966862
EST:     GTCTTTCTAGATTCTTCTGGCAAGCACAACAAGTTTTCCATCACAAAAGC                         TGATTCTGGAAGAAAAGTGGAAGATCCGGAGTTGTTAGAGGCAATCCGTTT
genomic: GTCTTTCTAGATTCTTCTGGCAAGCACAACAAGTTTTCCATCACAAAAGCgtaagtacta ... tcgtttgcagTGATTCTGGAAGAAAAGTGGAAGATCCGGAGTTGTTAGAGGCAATCCGTTT
EST: gi|18734777|gb|BM528381.1|BM528381
EST:     GTCTTTCTAGATTCTTCTGGCAAGCACAACAAGTTTTCCATCACAAAAGC                         TGATTCTGGAAGAAAAGTGGAAGATCCGGAGTTGTTAGAGGCAATCCGTTT
genomic: GTCTTTCTAGATTCTTCTGGCAAGCACAACAAGTTTTCCATCACAAAAGCgtaagtacta ... tcgtttgcagTGATTCTGGAAGAAAAGTGGAAGATCCGGAGTTGTTAGAGGCAATCCGTTT
EST: gi|120534006|gb|EH262139.1|EH262139
EST:     GTCTTTCTAGATTCTTCTGGCAAGCACAACAAGTTTTCCATCACAAAAGC                         TGATTCTGGAAGAAAAGTGGAAGATCCGGAGTTGTTAGAGGCAATCCGTTT
genomic: GTCTTTCTAGATTCTTCTGGCAAGCACAACAAGTTTTCCATCACAAAAGCgtaagtacta ... tcgtttgcagTGATTCTGGAAGAAAAGTGGAAGATCCGGAGTTGTTAGAGGCAATCCGTTT
EST: gi|8670493|gb|BE191600.1|BE191600
EST:     GTCTTTCTAGATTCTTCTGGCAAGCACAACAAGTTTTCCATCACAAAAGC                         TGATTCTGGAAGAAAAGTGGAAGATCCGGAGTTGTTAGAGGCAATCCGTTT
genomic: GTCTTTCTAGATTCTTCTGGCAAGCACAACAAGTTTTCCATCACAAAAGCgtaagtacta ... tcgtttgcagTGATTCTGGAAGAAAAGTGGAAGATCCGGAGTTGTTAGAGGCAATCCGTTT
EST: gi|120531918|gb|EH260051.1|EH260051
EST:     GTCTTTCTAGATTCTTCTGGCAAGCACAACAAGTTTTCCATCACAAAAGC                         TGATTCTGGAAGAAAAGTGGAAGATCCGGAGTTGTTAGAGGCAATCCGTTT
genomic: GTCTTTCTAGATTCTTCTGGCAAGCACAACAAGTTTTCCATCACAAAAGCgtaagtacta ... tcgtttgcagTGATTCTGGAAGAAAAGTGGAAGATCCGGAGTTGTTAGAGGCAATCCGTTT
EST: gi|14999665|gb|BI320487.1|BI320487
EST:     GTCTTTCTAGATTCTTCTGGCAAGCACAACAAGTTTTCCATCACAAAAGC                         TGATTCTGGAAGAAAAGTGGAAGATCCGGAGTTGTTA
genomic: GTCTTTCTAGATTCTTCTGGCAAGCACAACAAGTTTTCCATCACAAAAGCgtaagtacta ... tcgtttgcagTGATTCTGGAAGAAAAGTGGAAGATCCGGAGTTGTTA
EST: gi|17519613|gb|BM188655.1|BM188655
EST:     GTCTTTCTAGATTCTTCTGGCAAGCACAACAAGTTTTCCATCACAAAAGC                         TGATTCTGGAAGAAAAGTGGAAGATCCGGAGTTGTTAGAGGCAATCCGTTT
genomic: GTCTTTCTAGATTCTTCTGGCAAGCACAACAAGTTTTCCATCACAAAAGCgtaagtacta ... tcgtttgcagTGATTCTGGAAGAAAAGTGGAAGATCCGGAGTTGTTAGAGGCAATCCGTTT
EST: gi|120530189|gb|EH258323.1|EH258323
EST:     GTCTTTCTAGATTCTTCTGGCAAGCACAACAAGTTTTCCATCACAAAAGC                         TGATTCTGGAAGAAAAGTGGAAGATCCGGAGTTGTTAGAGGCAATCCGTTT
genomic: GTCTTTCTAGATTCTTCTGGCAAGCACAACAAGTTTTCCATCACAAAAGCgtaagtacta ... tcgtttgcagTGATTCTGGAAGAAAAGTGGAAGATCCGGAGTTGTTAGAGGCAATCCGTTT
EST: gi|120531854|gb|EH259987.1|EH259987
EST:     GTCTTTCTAGATTCTTCTGGCAAGCACAACAAGTTTTCCATCACAAAAGC                         TGATTCTGGAAGAAAAGTGGAAGATCCGGAGTTGTTAGAGGCAATCCGTTT
genomic: GTCTTTCTAGATTCTTCTGGCAAGCACAACAAGTTTTCCATCACAAAAGCgtaagtacta ... tcgtttgcagTGATTCTGGAAGAAAAGTGGAAGATCCGGAGTTGTTAGAGGCAATCCGTTT
EST: gi|10233251|gb|BE802139.1|BE802139
EST:     GTCTTTCTAGATTCTTCTGGCAAGCACAACAAGTTTTCCATCACAAAAGC                         TGATTCTGGAAGAAAAGTGGAAGATCCGGAGTTGTTAGAGGCAATCCGTTT
genomic: GTCTTTCTAGATTCTTCTGGCAAGCACAACAAGTTTTCCATCACAAAAGCgtaagtacta ... tcgtttgcagTGATTCTGGAAGAAAAGTGGAAGATCCGGAGTTGTTAGAGGCAATCCGTTT
EST: gi|22525094|gb|BU083905.1|BU083905
EST:     GTCTTTCTAGATTCTTCTGGCAAGCACAACAAGTTTTCCATCACAAAAGC                         TGATTCTGGAAGAAAAGTGGAAGATCCGGAGTTGTTAGAGGCAATCCGTTT
genomic: GTCTTTCTAGATTCTTCTGGCAAGCACAACAAGTTTTCCATCACAAAAGCgtaagtacta ... tcgtttgcagTGATTCTGGAAGAAAAGTGGAAGATCCGGAGTTGTTAGAGGCAATCCGTTT
EST: gi|13125321|gb|BG315891.1|BG315891
EST:     GTCTTTCTAGATTCTTCTGGCAAGCACAACAAGTTTTCCATCACAAAAGC                         TGATTCTGGAAGAAAAGTGGAAGATCCGGAGTTGTTAGAGGCAATCCGTTT
genomic: GTCTTTCTAGATTCTTCTGGCAAGCACAACAAGTTTTCCATCACAAAAGCgtaagtacta ... tcgtttgcagTGATTCTGGAAGAAAAGTGGAAGATCCGGAGTTGTTAGAGGCAATCCGTTT
EST: gi|120497144|gb|EH225311.1|EH225311
EST:     GTCTTTCTAGATTCTTCTGGCAAGCACAACAAGTTTTCCATCACAAAAGC                         TGATTCTGGAAGAAAAGTGGAAGATCCGGAGTTGTTAGAGGCAATCCGTTT
genomic: GTCTTTCTAGATTCTTCTGGCAAGCACAACAAGTTTTCCATCACAAAAGCgtaagtacta ... tcgtttgcagTGATTCTGGAAGAAAAGTGGAAGATCCGGAGTTGTTAGAGGCAATCCGTTT
EST: gi|20813196|gb|BQ297674.1|BQ297674
EST:     GTCTTTCTAGATTCTTCTGGCAAGCACAACAAGTTTTCCATCACAAAAGC                         TGATTCTGGAAGAAAAGTGGAAGATCCGGAGTTGTTAGAGGCAATCCGTTT
genomic: GTCTTTCTAGATTCTTCTGGCAAGCACAACAAGTTTTCCATCACAAAAGCgtaagtacta ... tcgtttgcagTGATTCTGGAAGAAAAGTGGAAGATCCGGAGTTGTTAGAGGCAATCCGTTT
EST: gi|22522210|gb|BU081021.1|BU081021
EST:     GTCTTTCTAGATTCTTCTGGCAAGCACAACAAGTTTTCCATCACAAAAGC                         TGATTCTGGAAGAAAAGTGGAAGATCCGGAGTTGTTAGAGGCAATCCGTTT
genomic: GTCTTTCTAGATTCTTCTGGCAAGCACAACAAGTTTTCCATCACAAAAGCgtaagtacta ... tcgtttgcagTGATTCTGGAAGAAAAGTGGAAGATCCGGAGTTGTTAGAGGCAATCCGTTT
EST: gi|7925937|gb|AW831963.1|AW831963
EST:     GTCTTTCTAGATTCTTCTGGCAAGCACAACAAGTTTTCCATCACAAAAGC                         TGATTCTGGAAGAAAAGTGGAAGATCCGGAGTTGTTAGAGGCAATCCGTTT
genomic: GTCTTTCTAGATTCTTCTGGCAAGCACAACAAGTTTTCCATCACAAAAGCgtaagtacta ... tcgtttgcagTGATTCTGGAAGAAAAGTGGAAGATCCGGAGTTGTTAGAGGCAATCCGTTT
EST: gi|6134645|gb|AW133038.1|AW133038
EST:     GTCTTTCTAGATTCTTCTGGCAAGCACAACAAGTTTTCCATCACAAAAGC                         TGATTCTGGAA
genomic: GTCTTTCTAGATTCTTCTGGCAAGCACAACAAGTTTTCCATCACAAAAGCgtaagtacta ... tcgtttgcagTGATTCTGGAA
EST: gi|12690942|gb|BG157278.1|BG157278
EST:     GTCTTTCTAGATTCTTCTGGCAAGCACAACAAGTTTTCCATCACAAAAGC                         TGATTCTGGAAGAAAAGTGGAAGATCCGGAGTTGTTAGAGGCAATCCGTTT
genomic: GTCTTTCTAGATTCTTCTGGCAAGCACAACAAGTTTTCCATCACAAAAGCgtaagtacta ... tcgtttgcagTGATTCTGGAAGAAAAGTGGAAGATCCGGAGTTGTTAGAGGCAATCCGTTT
EST: gi|120491074|gb|EH219241.1|EH219241
EST:     GGCAAGCACAACAAGTTTTCCATCACAAAAGC                         TGATTCTGGAAGAAAAGTGGAAGATCCGGAGTTGTTAGAGGCAATCCGTTT
genomic: GGCAAGCACAACAAGTTTTCCATCACAAAAGCgtaagtacta ... tcgtttgcagTGATTCTGGAAGAAAAGTGGAAGATCCGGAGTTGTTAGAGGCAATCCGTTT
EST: gi|120531768|gb|EH259901.1|EH259901
EST:     GTCTTTCTAGATTCTTCTGGCAAGCACAACAAGTTTTCCATCACAAAAGC                         TGATTCTGGAAGAAAAGTGGAAGATCCGGAGTTGTTAGAGGCAATCCGTTT
genomic: GTCTTTCTAGATTCTTCTGGCAAGCACAACAAGTTTTCCATCACAAAAGCgtaagtacta ... tcgtttgcagTGATTCTGGAAGAAAAGTGGAAGATCCGGAGTTGTTAGAGGCAATCCGTTT
EST: gi|209697454|gb|BW669954.1|BW669954
EST:     GTCTTTCTAGATTCTTCTGGCAAGCACAACAAGTTTTCCATCACAAAAGC                         TGATTCTGGAAGAAAAGTGGAAGATCCGGAGTTGTTAGAGGCAATCCGTTT
genomic: GTCTTTCTAGATTCTTCTGGCAAGCACAACAAGTTTTCCATCACAAAAGCgtaagtacta ... tcgtttgcagTGATTCTGGAAGAAAAGTGGAAGATCCGGAGTTGTTAGAGGCAATCCGTTT
EST: gi|192320913|gb|FK013107.1|FK013107
EST:     GTCTTTCTAGATTCTTCTGGCAAGCACAACAAGTTTTCCATCACAAAAGC                         TGATTCTGGAAGAAAAGTGGAAGATCCCGGAGTTGTTAGAGGCAATCCGTT
genomic: GTCTTTCTAGATTCTTCTGGCAAGCACAACAAGTTTTCCATCACAAAAGCgtaagtacta ... tcgtttgcagTGATTCTGGAAGAAAAGTGGAAGATCC-GGAGTTGTTAGAGGCAATCCGTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

actagattttctacgaattcattaattgaatatggtggtggagcttcgtttgcagTGATTCTGGAAGAAAAGTGGAAGATCCGGAGTTGTTAGAGGCAATCCGTTTGACAATATTGAATAATATGATTCAGTATCACCCG
                                           cttcgttt  CT-rich tract
               aattcattaattgaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
attgaaacttggtggtttcgttttcaccattcaagtaagttattaactagattttctacgaattcattaattgaatatggtggtggagcttcgtttgcagTGATTCTGGAAGAAAAGTGGAAGATCCGGAGTTGTTAGAGGCAATCCGTTTGACAATATTGAATAATATGATTCAGTATCACCCG

- - - - -tggtggt
- - - - - - - - - - - -tcaccat