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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATTGGAGGAGCCAGTGAGGCTGAAGTTGGTGAGAAGAAGGATAGAGTGACAGATGCCTTAAATGCAACCAAGGCAGCTGTAGAGGAGGGCATAGTACCTGgtagattattagcacttgcagttgtatgctgagttctaattctacgtcgttcaatcaaatttgatgtgttgtgctttgcgcag

Basic information

species Glycine max
transcript GLYMA20G33910.1
intron # 14
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA20G33910.1 (Glycine max), 5'ss of exon 14
lower sequence: LOC_Os10g32550.1 (Oryza sativa), 5'ss of exon 14
ATTGGAGGAGCCAGTGAGGCTGAAGTTGGTGAGAAGAAGGATAGAGTGACAGATGCCTTAAATGCAACCAAGGCAGCTGTAGAGGAGGGCATAGTACCTGgtagattatta--gcactt--gcagttgtatgctga---gttctaattctacgtcgttcaatcaaatttgatg--tgttgtgctttgcgcag-----------------------------------
|| |||||||||||||| |||||||||||||||||||||||||||||||||||||| || ||||| || || || ||||| || ||||| || ||||| ||||     ||    |||||  | || | | |    |   ||| |  || ||      |   |||  ||  ||   ||   |  | ||| ||                                    
ATCGGAGGAGCCAGTGAAGCTGAAGTTGGTGAGAAGAAGGATAGAGTGACAGATGCATTGAATGCCACTAAAGCTGCTGTGGAAGAGGGTATTGTACCAGgtatgcagttgctccacttcagtagatttctttcaatatgttttccttgtaatgtacttgttcagtttgcatctttgcattattatgcccaagtatgctgacatgacatctttgcattacaatacag

upper sequence: GLYMA20G33910.1 (Glycine max), 5'ss of exon 14
lower sequence: LOC_Os03g04970.1 (Oryza sativa), 5'ss of exon 14
ATTGGAGGAGCCAGTGAGGCTGAAGTTGGTGAGAAGAAGGATAGAGTGACAGATGCCTTAAATGCAACCAAGGCAGCTGTAGAGGAGGGCATAGTACCTGgta--gattattagcacttgcagtt-gtatgctgagttctaattcta---------cgtcgttcaatcaaatttgatgtg-ttgtgctttgcgcag
||||| ||||| ||||| || || |||||||||||||||||||||||||| |||||  ||||||| ||||| || |||||||||||||| || ||||| ||||  |  | | | | ||   | ||  | | |||   | || |  ||         |  | ||  |    ||   || || || |  ||| || ||
ATTGGTGGAGCTAGTGAAGCGGAGGTTGGTGAGAAGAAGGATAGAGTGACTGATGCACTAAATGCTACCAAAGCTGCTGTAGAGGAGGGTATTGTACCAGgtactgtatgtcatcgctgctattttattttctgcagtttactattagcagcatatcaccattgcagagcatcatatctgattctaatttacgtag

upper sequence: GLYMA20G33910.1 (Glycine max), 5'ss of exon 14
lower sequence: GRMZM2G416120_T01 (Zea mays), 5'ss of exon 13
ATTGGAGGAGCCAGTGAGGCTGAAGTTGGTGAGAAGAAGGATAGAGTGACAGATGCCTTAAATGCAACCAAGGCAGCTGTAGAGGAGGGCATAGTACCTGgtagattattagc----actt---------gcagt-tgtatgctgagttctaattctacgtcgttcaatcaaatt-tgatgtgttgtgctttgcgcag--------------------------------------------------------------
|||||||||||||| || || |||||||||||||||||||||||||||||||||||  | ||||| || || || ||||| || |||||||| ||||| ||||   ||| |      | ||         |  || | |||||||| |||   |  ||  |  | | |   | |  || ||  |     |||| |                                                                 
ATTGGAGGAGCCAGCGAAGCAGAAGTTGGTGAGAAGAAGGATAGAGTGACAGATGCACTGAATGCTACTAAAGCTGCTGTTGAAGAGGGCATTGTACCAGgtaatgtatcaattaaaatttcatggggggggggtgtttatgctgatttcctgtgttatttgctcctactgattcctgttgcatcagtatttgtgttagttattcctgatttcctgttgcgtcagtatgcccgggagtcaatctttaattgtgtatgcag

upper sequence: GLYMA20G33910.1 (Glycine max), 5'ss of exon 14
lower sequence: GRMZM2G111477_T02 (Zea mays), 5'ss of exon 2
ATTGGAGGAGCCAGTGAGGCTGAAGTTGGTGAGAAGAAGGATAGAGTGACAGATGCCTTAAATGCAACCAAGGCAGCTGTAGAGGAGGGCATAGTACCTGgtagattattagc--acttgcagttgtatgctgagttctaattctacgtcgttcaatcaaatttgatgtgttgtgct-ttgcg-cag-------------
||||| ||||| || || || |||||||||||||||||||||||||||||||||||  | ||||| || || || ||||| || ||||| || ||||| ||||   ||| |    | |    | |||   | |  |  | || ||   |   |   |   |||     || | | || ||||  |||             
ATTGGGGGAGCTAGCGAAGCAGAAGTTGGTGAGAAGAAGGATAGAGTGACAGATGCACTGAATGCTACTAAAGCTGCTGTTGAAGAGGGTATTGTACCAGgtaatgtatcatttgaatatttgatgttcacgggatgttcatgctgatttcctttgtgttattcctactgatctcctgttgcatcagtatgcctgatagt

upper sequence: GLYMA20G33910.1 (Glycine max), 5'ss of exon 14
lower sequence: GRMZM2G111477_T01 (Zea mays), 5'ss of exon 2
ATTGGAGGAGCCAGTGAGGCTGAAGTTGGTGAGAAGAAGGATAGAGTGACAGATGCCTTAAATGCAACCAAGGCAGCTGTAGAGGAGGGCATAGTACCTGgtagattattagc--acttgcagttgtatgctgagttctaattctacgtcgttcaatcaaatttgatgtgttgtgct-ttgcg-cag----------------------------------
||||| ||||| || || || |||||||||||||||||||||||||||||||||||  | ||||| || || || ||||| || ||||| || ||||| ||||   ||| |    | |    | |||   | |  |  | || ||   |   |   |   |||     || | | || ||||  |||                                  
ATTGGGGGAGCTAGCGAAGCAGAAGTTGGTGAGAAGAAGGATAGAGTGACAGATGCACTGAATGCTACTAAAGCTGCTGTTGAAGAGGGTATTGTACCAGgtaatgtatcatttgaatatttgatgttcacgggatgttcatgctgatttcctttgtgttattcctactgatctcctgttgcatcagtatgcctgatagtcatctttaattgtatatgcag

upper sequence: GLYMA20G33910.1 (Glycine max), 5'ss of exon 14
lower sequence: AT3G23990.1 (Arabidopsis thaliana), 5'ss of exon 12
ATTGGAGGAGCCAGTGAGGCTGAAGTTGGTGAGAAGAAGGATAGAGTGACAGATGCCTTAAATGCAACCAAGGCAGCTGTAGAGGAGGGCATAGTACCTGgtagattattagcacttgcagttgtatgctgagttctaattctacgtcgttcaat-----caaatttgatgtgttgtgctttgcgcag
||||||||||| ||||| |||||||||||||||||||| || |||||||||||||| || ||||| || || ||||| || || ||||| ||  |||| ||||  |   |  || |   ||    |  ||  | | || | |||    |||   |     | ||    |    |          ||||
ATTGGAGGAGCAAGTGAAGCTGAAGTTGGTGAGAAGAAAGACAGAGTGACAGATGCTTTGAATGCCACTAAAGCAGCAGTTGAAGAGGGTATTTTACCAGgtatgtctcttccagtg--aggaagactctttgatatagtgctaaaaagtttgctatgtgctaaagaaacaaatcaaaacacttgcag

upper sequence: GLYMA20G33910.1 (Glycine max), 5'ss of exon 14
lower sequence: AT2G33210.1 (Arabidopsis thaliana), 5'ss of exon 13
ATTGGAGGAGCCAGTGAGGCTGAAGTTGGTGAGAAGAAGGATAGAGTGACAGATGCCTTAAATGCAACCAAGGCAGCTGTAGAGGAGGGCATAGTACCTGgtagattat-tagcacttgcagttgtatgctgagttctaattct--acgtcgttcaatcaaatttgatgtgttgtgctttgcgcag-------
||||||||||| |||||| | |||||| |||| ||||| |||||||| || |||||  ||||||| || || ||||| ||||||||||| || || || |||| | | | |  ||  |  |     |   |  |||  |   ||  |     ||   | | |   ||  | |  | ||||| |          
ATTGGAGGAGCAAGTGAGACAGAAGTTAGTGAAAAGAAAGATAGAGTAACGGATGCTCTAAATGCCACTAAAGCAGCCGTAGAGGAGGGTATTGTTCCAGgtataatctatcccaaatctaaaacaaaatttggttgaatcccttaagaaaattgcgtgagaagagaattatattactttgtgtgtattacag

upper sequence: GLYMA20G33910.1 (Glycine max), 5'ss of exon 14
lower sequence: PP1S378_9V6.2 (Physcomitrella patens), 5'ss of exon 13
ATTGGAGGAGCCAGTGAGGCTGAAGTTGGTGAGAAGAAGGATAGAGTGACAGATGCCTTAAATGCAACCAAGGCAGCTGTAGAGGAGGGCATAGTACCTGgtagatt-attagcacttgcagttgtatgctgagttctaattctacgtcgttcaat-caaatttgatgtgttgtgctttgcgcag----------------
||||||||||| ||||| | ||| ||| |||||||||| ||  | || || ||||| || ||||| ||||| || ||||| ||||||||||| || |||||||  ||    |  |||  |  || | || |||    ||| |       | ||| |  | ||      |||| |   ||||                    
ATTGGAGGAGCTAGTGAAGTTGAGGTTAGTGAGAAGAAAGACCGTGTTACTGATGCATTGAATGCCACCAAAGCCGCTGTTGAGGAGGGCATTGTTCCTGgtatgttcgagattactaactcttttttg-tgatccgtaacttagtccggctcattgtatatagcgaatgttttctcttgctttaggttccgttgattatt

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|15814111|gb|BI786386.1|BI786386
EST:     AGATGCCTTAAATGCAACCAAGGCAGCTGTAGAGGAGGGCATAGTACCTG                         GTGGTGGTGTTGCTCTTCTTTATGCATCGAGTGAGTTGGATAAGCTTCAAA
genomic: AGATGCCTTAAATGCAACCAAGGCAGCTGTAGAGGAGGGCATAGTACCTGgtagattatt ... ctttgcgcagGTGGTGGTGTTGCTCTTCTTTATGCATCGAGTGAGTTGGATAAGCTTCAAA
EST: gi|209725420|gb|BW658282.1|BW658282
EST:     AGATGCCTTAAATGCAACCAAGGCAGCTGTAGAGGAGGGCATAGTACCTG                         GTGGTGGTGTTGCTCTTCTTTATGCATCGAGTGAGTTGGATAAGCTTCAAA
genomic: AGATGCCTTAAATGCAACCAAGGCAGCTGTAGAGGAGGGCATAGTACCTGgtagattatt ... ctttgcgcagGTGGTGGTGTTGCTCTTCTTTATGCATCGAGTGAGTTGGATAAGCTTCAAA
EST: gi|16344877|gb|BI970472.1|BI970472
EST:     AGATGCCTTAAATGCAACCAAGGCAGCTGTAGAGGAGGGCATAGTACCTG                         GTGGTGGTGTTGCTCTTCTTTATGCATCGAGTGAGTTGGATAAGCTTCAAA
genomic: AGATGCCTTAAATGCAACCAAGGCAGCTGTAGAGGAGGGCATAGTACCTGgtagattatt ... ctttgcgcagGTGGTGGTGTTGCTCTTCTTTATGCATCGAGTGAGTTGGATAAGCTTCAAA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATTGGAGGAGCCAGTGAGGCTGAAGTTGGTGAGAAGAAGGATAGAGTGACAGATGCCTTAAATGCAACCAAGGCAGCTGTAGAGGAGGGCATAGTACCTGgtagattattagcacttgcagttgtatgctgagttctaattctacgtcgttcaatcaaatttgatgtgttgtgctttgcgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG