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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATGGGAAAGGAATGAAAATCACACACTTTGCCTCAACTCTGCTAAAGCAATTGGATGTACAGTAGTCAACATTGGCACCCAGGACTTCATTGAAGGAAGGgtatgcttgtaggcattcaagtttccacccataaaagcagaattattgtgggcgtgtacactgcagaacaacaaaatttaagattaaatttaatttataa...

Basic information

species Glycine max
transcript GLYMA03G22450.1
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA03G22450.1 (Glycine max), 5'ss of exon 5
lower sequence: AT5G48460.1 (Arabidopsis thaliana), 5'ss of exon 4
ATGGGAAAGGAATGAAAATCACACACTTTGCCTCAACTCTGCTAAAGCAATTGGATGTACAGTAGTCAACATTGGCACCCAGGACTTCATTGAAGGAAGGgtatgcttgtaggcattcaagtttccacccataaaagcagaattattgtgggcgtgtacactgcagaacaacaaaatttaagattaaatttaatttataa
|||||| || ||||||||||| || ||||| || |||||||| || || ||||| ||||| || || || || || || || ||  |||||||||||||||||||  || |   | | |  ||  || |  |||      |||| | |||   ||    |||         |    | |   |||  |            
ATGGGAGAGAAATGAAAATCATACGCTTTGTCTTAACTCTGCCAAGGCTATTGGGTGTACTGTGGTTAATATAGGAACACAAGATATCATTGAAGGAAGGgtatg--tgaatcaagtgactttgtcatcagtaatcttgaaattttggtgatggttatgactaagatttctctgtttctctaattgcag-----------

upper sequence: GLYMA03G22450.1 (Glycine max), 5'ss of exon 5
lower sequence: Vv00s1365g00010.t01 (Vitis vinifera), 5'ss of exon 2
ATGGGAAAGGAATGAAAATCACACACTTTGCCTCAACTCTGCTAAAGCAATTGGATGTACAGTAGTCAACATTGGCACCCAGGACTTCATTGAAGGAAGGgtatgcttgtaggcattcaagtttccacccataaaagcagaattattgtgggcgtgtacactgcagaacaacaaaatttaagattaaatttaatttataa-------
 ||||| ||||||||||||||||| || |||||||||||||| ||||| ||||||||||| || ||||| || || || |||||||||||||||||||||||||  ||| | || ||      ||||   || || ||    || | |  |  |  |       |     |   |  ||  |||    ||||     |||       
TTGGGAGAGGAATGAAAATCACACCCTCTGCCTCAACTCTGCCAAAGCTATTGGATGTACTGTGGTCAATATCGGGACACAGGACTTCATTGAAGGAAGGgtatatttgcatgcctt------tccatatatgaatgctttgtt-tgggagttgaatttttgatatcttgaatgatgttttgatgggttttatcgggtaatatgtct

upper sequence: GLYMA03G22450.1 (Glycine max), 5'ss of exon 5
lower sequence: PP1S271_37V6.1 (Physcomitrella patens), 5'ss of exon 1
ATGGGAAAGGAATGAAAATCACACACTTTGCCTCAACTCTGCTAAAGCAATTGGATGTACAGTAGTCAACATTGGCACCCAGGACTTCATTGAAGGAAGGgtatgcttgtaggcattcaagtttccacccataaaagcagaattattgtg-ggcgtgtacactgcagaacaacaaaatttaagattaaatttaatt-tataa-----------------------------------------------------
 |||||  | |  || |||||||| ||||| ||||| ||||||||||| ||||| ||  | || |||||||||||||| || |||||    || |||||||||   |     |    | | |||        | |     ||  | |||  |  |  |    ||  |      |     |       | ||||||  | | |                                                     
GTGGGAGCGAATAGAGAATCACACCCTTTGTCTCAATTCTGCTAAAGCTATTGGTTGCTCTGTTGTCAACATTGGCACTCAAGACTTGGGCGACGGAAGGgtaa--tgactagtgcacgatttttactaaggatagatgtaacgaatgtacgaagcttgtgttgttggttgttagctgatgttggacattttaatggtgtgaccatccatagttggtgcttgatctcattagtcatgatgtgtgggttggtgcag

upper sequence: GLYMA03G22450.1 (Glycine max), 5'ss of exon 5
lower sequence: PP1S314_45V6.1 (Physcomitrella patens), 5'ss of exon 4
ATGGGAAAGGAATGAAAATCACACACTTTGCCTCAACTCTGCTAAAGCAATTGGATGTACAGTAGTCAACATTGGCACCCAGGACTTCATTGAAGGAAGGgtat--gcttgtaggcattcaagtttccacccataaaagcagaattattgtgggcgtgtacactgcag--aacaacaaaatttaagattaaatttaatttataa------------------------------------------------------------------
||||||| | |  || |||||||||||||||||||| || |||||||| ||||||||  | ||||||||||||||||| ||||||||    || |||||||||    |  ||   | |    ||||      |    | | ||||   ||      ||||   ||  |   |||| || |  |    ||    | ||||| ||                                                                   
ATGGGAACGAATAGAGAATCACACACTTTGCCTCAATTCCGCTAAAGCCATTGGATGCTCTGTAGTCAACATTGGCACTCAGGACTTAGGCGACGGAAGGgtaatgacaagtgcacgtctttgtttaggatgaacgtaac-gaatatatgaaactttgtatgttgatgtggacaataagacgtgttcttttcgtgaatttgtattagaatgagatggtaaaacacacttcttgcttaattttgtgagtcattttgtgtgggtgaatgcag

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|193546295|gb|FK501772.1|FK501772
EST:     TTCATTGAAGGAAGG                         CGTCATCTGGTGCTTGGGGTGATTTCTCAGATTATTAAG
genomic: TTCATTGAAGGAAGGgtatgcttgt ... ctcatttcagCGTCATCTGGTGCTTGGGGTGATTTCTCAGATTATTAAG
EST: gi|193486184|gb|FK451698.1|FK451698
EST:     TTGGATGTACAGTAGTCAACATTGGCACCCAAGACTTCATTGAAGGAAGG                         CGTCATCTGGTGCTTGGGGTGATTTCTCAGATTATTAAG
genomic: TTGGATGTACAGTAGTCAACATTGGCACCCAGGACTTCATTGAAGGAAGGgtatgcttgt ... ctcatttcagCGTCATCTGGTGCTTGGGGTGATTTCTCAGATTATTAAG
EST: gi|208245262|gb|GE041628.1|GE041628
EST:     TTGGATGTACAGTAGTCAACATTGGCACCCAGGACTTCATTGAAGGAAGG                         CGTCATCTGGTGCTTGGGGTGATTTCTCAGATTATTAAG
genomic: TTGGATGTACAGTAGTCAACATTGGCACCCAGGACTTCATTGAAGGAAGGgtatgcttgt ... ctcatttcagCGTCATCTGGTGCTTGGGGTGATTTCTCAGATTATTAAG
EST: gi|193536063|gb|FK491347.1|FK491347
EST:     ATTGAAGGAAGG                         CGTCATCTGGTGCTT-GGGTGAATTTACTCAGATTATTAAG
genomic: ATTGAAGGAAGGgtatgcttgt ... ctcatttcagCGTCATCTGGTGCTTGGGGTG-ATTT-CTCAGATTATTAAG
EST: gi|208075796|gb|GD874753.1|GD874753
EST:     TTGGATGTACAGTAGTCAACATTGGCACCCAGGACTTCATTGAAGGAAGG                         CGTCATCTGGTGCTTGGGGTGATTTCTCAGATTATTAAG
genomic: TTGGATGTACAGTAGTCAACATTGGCACCCAGGACTTCATTGAAGGAAGGgtatgcttgt ... ctcatttcagCGTCATCTGGTGCTTGGGGTGATTTCTCAGATTATTAAG
EST: gi|208188002|gb|GD986816.1|GD986816
EST:     TTGGATGTACAGTAGTCAACATTGGCACCCAGGACTTCATTGAAGGAAGG                         CGTCATCTGGTGCTTGGGGTGATTTCTCAGATTATTAAG
genomic: TTGGATGTACAGTAGTCAACATTGGCACCCAGGACTTCATTGAAGGAAGGgtatgcttgt ... ctcatttcagCGTCATCTGGTGCTTGGGGTGATTTCTCAGATTATTAAG
EST: gi|193480645|gb|FK446407.1|FK446407
EST:     TTGGATGTACAGTAGTCAACATTGGCACCCAAGACTTCATTGAAGGAAGG                         CGTCATCTGGTGCTTGGGGTGATTTCTCAGATTATTAAG
genomic: TTGGATGTACAGTAGTCAACATTGGCACCCAGGACTTCATTGAAGGAAGGgtatgcttgt ... ctcatttcagCGTCATCTGGTGCTTGGGGTGATTTCTCAGATTATTAAG
EST: gi|208276418|gb|GE076952.1|GE076952
EST:     TTGGATGTACAGTAGTCAACATTGGCACCCAGGACTTCATTGAAGGAAGG                         CGTCATCTGGTGCTTGGGGTGATTTCTCAGATTATTAAG
genomic: TTGGATGTACAGTAGTCAACATTGGCACCCAGGACTTCATTGAAGGAAGGgtatgcttgt ... ctcatttcagCGTCATCTGGTGCTTGGGGTGATTTCTCAGATTATTAAG
EST: gi|192305988|gb|FG993620.1|FG993620
EST:     TTGGATGTACAGTAGTCAACATTGGCACCCAGGACTTCATTGAAGGAAGG                         CGTCATCTGGTGCTTGGGGTGATTTCTCAGATTATTAAG
genomic: TTGGATGTACAGTAGTCAACATTGGCACCCAGGACTTCATTGAAGGAAGGgtatgcttgt ... ctcatttcagCGTCATCTGGTGCTTGGGGTGATTTCTCAGATTATTAAG
EST: gi|208261266|gb|GE058174.1|GE058174
EST:     TGTACAGTAGTCAACATTGGCACCCAGGACTTCATTGAAGGAAGG                         CGTCATCTGGTGCTTGGGGTGATTTCTCAGATTATTAAG
genomic: TGTACAGTAGTCAACATTGGCACCCAGGACTTCATTGAAGGAAGGgtatgcttgt ... ctcatttcagCGTCATCTGGTGCTTGGGGTGATTTCTCAGATTATTAAG
EST: gi|208151760|gb|GD945575.1|GD945575
EST:     TTGGATGTACAGTAGTCAACATTGGCACCCAGGACTTCATTGAAGGAAGG                         CGTCATC-GGATGCTTGGGGTGATTTCTCAGATTATTAAG
genomic: TTGGATGTACAGTAGTCAACATTGGCACCCAGGACTTCATTGAAGGAAGGgtatgcttgt ... ctcatttcagCGTCATCTGG-TGCTTGGGGTGATTTCTCAGATTATTAAG
EST: gi|193656419|gb|FK602891.1|FK602891
EST:     TTCATTGAAGGAAGG                         CGTCATCTGGTGCTTGGGGTGATTTCTCAGATTATTAAG
genomic: TTCATTGAAGGAAGGgtatgcttgt ... ctcatttcagCGTCATCTGGTGCTTGGGGTGATTTCTCAGATTATTAAG
EST: gi|193419101|gb|FK382275.1|FK382275
EST:     TTGGATGTACAGTAGTCAACATTGGCACCCAGGACTTCATTGAAGGAAGG                         CGTCATCTGGTGCTTGGGGTGATTTCTCAGATTATTAAG
genomic: TTGGATGTACAGTAGTCAACATTGGCACCCAGGACTTCATTGAAGGAAGGgtatgcttgt ... ctcatttcagCGTCATCTGGTGCTTGGGGTGATTTCTCAGATTATTAAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATGGGAAAGGAATGAAAATCACACACTTTGCCTCAACTCTGCTAAAGCAATTGGATGTACAGTAGTCAACATTGGCACCCAGGACTTCATTGAAGGAAGGgtatgcttgtaggcattcaagtttccacccataaaagcagaattattgtgggcgtgtacactgcagaacaacaaaatttaagattaaatttaatttataa

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ccaccca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gtgggcg