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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGCAAAAGAAGAAGCTTTAAGCCGAAAAGATATATTGGACAAGGTTGAGAAATGGATGTCAGCATGTGAAGAAGAAAGTTGGCTTGAAGATTATAATCGGgtacttaaaatctcgcttctgctttattttttttctgagtttgaatgattggttgtgcacagtcgtggatagagaggtgaagtagtattatgatcagaac...

Basic information

species Glycine max
transcript GLYMA02G46450.1
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA02G46450.3 (Glycine max), 5'ss of exon 7
lower sequence: LOC_Os06g20370.1 (Oryza sativa), 5'ss of exon 7
AGCAAAAGAAGAAGCTTTAAGCCGAAAAGATATATTGGACAAGGTTGAGAAATGGATGTCAGCATGTGAAGAAGAAAGTTGGCTTGAAGATTATAATCGGgtact-taaaatctcgct--------tctgctttatt-ttttttctgagtttgaatgattggttgtgcacagtcgtgg-atagagaggtgaagtag--tattatgatcagaac------------
|||||| |||||||| || ||  ||||||| ||||| ||||| ||||| | ||||||||| || |||||||||||||| ||||||||||||||||| ||||||   | | || | | |        ||     ||||   | || |    ||  ||||||        |    |     ||   |   | || |||  ||| ||||   |||             
AGCAAAGGAAGAAGCATTGAGTAGAAAAGAAATATTAGACAAAGTTGAAAGATGGATGTCTGCTTGTGAAGAAGAAAGCTGGCTTGAAGATTATAACCGGgtaagatgatattttgttgtagcaaatcaaaagtattacatcttttattctttcatgatttaagtgatattaccaaattattctgtttttaaatagcctatcatgaattgaaaatccttctgcag

upper sequence: GLYMA02G46450.3 (Glycine max), 5'ss of exon 7
lower sequence: LOC_Os06g40840.1 (Oryza sativa), 5'ss of exon 7
AGCAAAAGAAGAAGCTTTAAGCCGAAAAGATATATTGGACAAGGTTGAGAAATGGATGTCAGCATGTGAAGAAGAAAGTTGGCTTGAAGATTATAATCGGgtacttaaaatctcgcttctgctttattttttttctgagtttgaatgattggttgtgcacagtcgtggatagagaggtgaagtagtattatgatcagaac
|||||||||||| ||  ||||| |||| || ||  |||| |||||||| |  |||||||||||||| |||||||| || ||||||||||| ||||  | |||| | ||||     |   |   | | || ||   ||  |||||        |  |  |||||| |  ||    |  |  | || | | || ||   |  
AGCAAAAGAAGAGGCACTAAGCAGAAAGGACATTCTGGAGAAGGTTGAAAGGTGGATGTCAGCATGCGAAGAAGAGAGCTGGCTTGAAGACTATAGCCAGgtaataaaaagtatacag-tatgtaacttcttcattg--tttgatc------tcattaacagtcatacatctttacattga-tattctgataatggcag-

upper sequence: GLYMA02G46450.3 (Glycine max), 5'ss of exon 7
lower sequence: GRMZM2G112337_T04 (Zea mays), 5'ss of exon 7
AGCAAAAGAAGAAGCTTTAAGCCGAAAAGATATATTGGACAAGGTTGAGAAATGGATGTCAGCATGTGAAGAAGAAAGTTGGCTTGAAGATTATAATCGGgtacttaaaatctcgcttctgctttattttttttctgagtttgaatgattggttgtgcacagtcgtggatagagaggtgaagtagtattatgatcagaac----------------------------------------------------------------------
|||||| || ||  | |||||| |||| || |||||||| | |||||| |  |||||||||||||||||||||||||| ||||||||||| || |  ||||||       | |   || |  | |  ||| | ||| |      |||    |  || |     |        |    |||| | | |||||  |    |                                                                       
AGCAAATGAGGAGTCCTTAAGCAGAAAGGACATATTGGAGAGGGTTGATAGGTGGATGTCAGCATGTGAAGAAGAAAGCTGGCTTGAAGACTACAGCCGGgtatgctgcttattcatttt--tgtgatttgtgtctcatggaagatgccaagccgtactttagctcctggcaattcttgaaattgcattattttttatatacttgctgttgtcttcacttcgtgtcctatcacaaggttctgacgtctatgctatcttaattaaccgcag

upper sequence: GLYMA02G46450.3 (Glycine max), 5'ss of exon 7
lower sequence: GRMZM2G465169_T01 (Zea mays), 5'ss of exon 7
AGCAAAAGAAGAAGCTTTAAGCCGAAAAGATATATTGGACAAGGTTGAGAAATGGATGTCAGCATGTGAAGAAGAAAGTTGGCTTGAAGATTATAATCGGgtacttaaaatctcgcttctgc---tttattttttttctgagtttga---atgattggttgtgc----acagtcgtggatagagag--gtgaagtag-tattatgatcagaac-----------------
|||||| |||||||| || ||  ||||||||||  | || || || || | ||||||||| || |||||||||||||| ||||||||||||||||| ||||||    ||   | | ||| ||   |  |  ||  | |||  | |      | |    || |||    | |     | ||||   |  ||| ||||| | |||    || |||                 
AGCAAAGGAAGAAGCATTGAGTAGAAAAGATATCCTTGATAAAGTAGAAAGATGGATGTCTGCGTGTGAAGAAGAAAGCTGGCTTGAAGATTATAACCGGgtatggcaataattggttcggcaagtcaaagttactgctgcatgtatcctgtaaccatttatgcgataataccaacgcatagctggctgtggagtagcttttaaccacaaaactaaaataccttctgcag

upper sequence: GLYMA02G46450.3 (Glycine max), 5'ss of exon 7
lower sequence: GRMZM2G101874_T01 (Zea mays), 5'ss of exon 8
AGCAAAAGAAGAAGCTTTAAGCCGAAAAGATATATTGGACAAGGTTGAGAAATGGATGTCAGCATGTGAAGAAGAAAGTTGGCTTGAAGATTATAATCGGgtacttaaaatctcgcttctgc----tttattttttttctgagt-ttgaatgattggttgtgc-acagt--cgtggatagagaggtgaagtagta--ttatgatcagaac-------------------
|||||| |||||||| || ||  ||||||| ||  | || || || || | ||||||||| || ||||||||||| || ||||||||||||||||| ||||||    ||   | | ||| ||       | ||  |   |  || |    ||||   |||||| | | |  |   |  |    ||    | || |  || | | || ||                    
AGCAAAGGAAGAAGCATTGAGTAGAAAAGACATCCTTGATAAAGTAGAAAGATGGATGTCTGCGTGTGAAGAAGAGAGCTGGCTTGAAGATTATAACCGGgtatgacaataattggttcggcaagtcaaaattactgcttatgtatcctgtgatcatttgtgcgataataccaaagccatgctggctgtgcagcagcttttaaccacaaaattaaaataccttctgcag

upper sequence: GLYMA02G46450.3 (Glycine max), 5'ss of exon 7
lower sequence: AT5G55230.2 (Arabidopsis thaliana), 5'ss of exon 6
AGCAAAAGAAGAAGCTTTAAGCCGAAAAGATATATTGGACAAGGTTGAGAAATGGATGTCAGCATGTGAAGAAGAAAGTTGGCTTGAAGATTATAATCGGgtacttaaaatctcgcttctgctttattttttttctgagtttgaatgattggttgtgcacagtcgtggatagagaggtgaagtagtattatgatcagaac----
 || || |||||||| || ||  |||||||||||||||||   || ||||||||||||||||| ||||| ||||| || ||||| ||||| || ||||||||| |  | |  |    || |        | |     |   | |   |||   | |    | | |    | |||   |    | || || |  || ||      
GGCTAAGGAAGAAGCATTTAGTAGAAAAGATATATTGGACCGAGTCGAGAAATGGATGTCAGCTTGTGAGGAAGAGAGCTGGCTAGAAGACTACAATCGGgtaatgcataatttctctcagtcactcactatgatacatcataagacattaacttta---aattggatcttgagctttttcatggttttgttttctgagagcag

upper sequence: GLYMA02G46450.3 (Glycine max), 5'ss of exon 7
lower sequence: AT4G26760.1 (Arabidopsis thaliana), 5'ss of exon 7
AGCAAAAGAAGAAGCTTTAAGCCGAAAAGATATATTGGACAAGGTTGAGAAATGGATGTCAGCATGTGAAGAAGAAAGTTGGCTTGAAGATTATAATCGGgtacttaaaatctcgcttctgctttattttttttctgagtttgaatgattggttgtgcacagtcgtggatagagaggtgaagtagtattatgatcagaac
 || || || ||||| || ||  ||||||| || || |||   || ||||||||||||||||| ||||| ||||| || ||||| |||||||| ||||| |||        ||  | |  ||| | ||  |   |  | |    || |    | | |  || | |  |||      | |   | ||  |   |  | |  
GGCCAAGGAGGAAGCCTTTAGTAGAAAAGAAATTTTAGACCGTGTAGAGAAATGGATGTCAGCTTGTGAGGAAGAGAGCTGGCTCGAAGATTACAATCGAgtatg------ctaacattggctatgttaataaacacattacttattaagcatagagttcaattgatgattcttttgggtttttgttctggaaaaacag-

upper sequence: GLYMA02G46450.3 (Glycine max), 5'ss of exon 7
lower sequence: Vv19s0090g01230.t01 (Vitis vinifera), 5'ss of exon 6
AGCAAAAGAAGAAGCTTTAAGCCGAAAAGATATATTGGACAAGGTTGAGAAATGGATGTCAGCATGTGAAGAAGAAAGTTGGCTTGAAGATTATAATCGGgtacttaaaatctcgcttctgctttattttttttctgagtttgaatgattggttgtgcacagtcgtggatagagaggtgaagtagtattatgatcagaac--
|||||| ||||| ||||| ||| |||| |||||||| |||||||||||||||||||||||||| ||||||||||| |||||||||||||| || |||||||||       |||| ||    ||     |   | |   | ||   ||  ||| |  |  |   | ||  |||  | |   | | ||  | |   ||      
AGCAAAGGAAGAGGCTTTCAGCAGAAAGGATATATTAGACAAGGTTGAGAAATGGATGTCAGCTTGTGAAGAAGAGAGTTGGCTTGAAGACTACAATCGGgtatcctctctctctctctctctccccctccctccctggattcgttg--tggattagatccaccttgattaggaatgctcatttgtgctctctgcaatgttg

upper sequence: GLYMA02G46450.3 (Glycine max), 5'ss of exon 7
lower sequence: EFJ24960 (Selaginella moellendorffii), 5'ss of exon 7
AGCAAAAGAAGAAGCTTTAAGCCGAAAAGATATATTGGACAAGGTTGAGAAATGGATGTCAGCATGTGAAGAAGAAAGTTGGCTTGAAGATTATAATCGGgtacttaaaatctcgcttctgctttattttttttctgagtttgaatgattggttgtgcacagtcgtggatagagaggtgaagtagtattatgatcagaac
 || || |||||| |  |  |  || |||||||| |||| |   | ||   ||||||    ||||||||||||||||||||||||||||| || |||  |||| | |   |  ||||  | |  |  ||  |||  || | |                                                          
GGCGAAGGAAGAATCACTCGGTAGACAAGATATAATGGAAAGAATGGAACGATGGATTAGTGCATGTGAAGAAGAAAGTTGGCTTGAAGAATACAATAAGgta-tgagcgttacgctatttcacttattcattttcgattgtag--------------------------------------------------------

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|208073566|gb|GD872775.1|GD872775
EST:     AATGGATGTCAGCATGTGAAGAAGAAAGTTGGCTTGAAGATTATAATCGG                         GATGATAACAGGTATAATGCAAGCAGAGGTGCACACTTAAACCTCAAACGT
genomic: AATGGATGTCAGCATGTGAAGAAGAAAGTTGGCTTGAAGATTATAATCGGgtacttaaaa ... tgtaaaacagGATGATAACAGGTATAATGCAAGCAGAGGTGCACACTTAAACCTCAAACGT
EST: gi|208259220|gb|GE055470.1|GE055470
EST:     AAAGTTGGCTTGAAGATTATAATCGG                         GATGATAACAGGTATAATGCAAGCAGAGGTGCACACTTAAACCTCAAACGT
genomic: AAAGTTGGCTTGAAGATTATAATCGGgtacttaaaa ... tgtaaaacagGATGATAACAGGTATAATGCAAGCAGAGGTGCACACTTAAACCTCAAACGT
EST: gi|207682351|gb|GD665338.1|GD665338
EST:     AATGGATGTCAGCATGTGAAGAAGAAAGTTGGCTTGAAGATTATAATCGG                         GATGATAACAGGTA
genomic: AATGGATGTCAGCATGTGAAGAAGAAAGTTGGCTTGAAGATTATAATCGGgtacttaaaa ... tgtaaaacagGATGATAACAGGTA
EST: gi|207735001|gb|GD712532.1|GD712532
EST:     TGTCAGCATGTGAAGAAGAAAGTTGGCTTGAAGATTATAATCGG                         GATGATAACAGGTATAATGCAAGCAGAGGTGCACACTTAAACCTCAAACGT
genomic: TGTCAGCATGTGAAGAAGAAAGTTGGCTTGAAGATTATAATCGGgtacttaaaa ... tgtaaaacagGATGATAACAGGTATAATGCAAGCAGAGGTGCACACTTAAACCTCAAACGT
EST: gi|51334691|gb|CO978557.1|CO978557
EST:     AATGGATGTCAGCATGTGAAGAAGAAAGTTGGCTTGAAGATTATAATCGG                         GATGATAACAGGTATAATGCAAGCAGAGGTGCACACTTAAACCTCAAACGT
genomic: AATGGATGTCAGCATGTGAAGAAGAAAGTTGGCTTGAAGATTATAATCGGgtacttaaaa ... tgtaaaacagGATGATAACAGGTATAATGCAAGCAGAGGTGCACACTTAAACCTCAAACGT
EST: gi|26048331|gb|CA784835.1|CA784835
EST:     GAAGATTATAATCGG                         GATGATAACAGGTATAATGCAAGCAGAGGTGCACACTTAAACCTCAAACGT
genomic: GAAGATTATAATCGGgtacttaaaa ... tgtaaaacagGATGATAACAGGTATAATGCAAGCAGAGGTGCACACTTAAACCTCAAACGT
EST: gi|193511966|gb|FK471418.1|FK471418
EST:     GCATGTGAAGAAGAAAGTTGGCTTGAAGATTATAATCGG                         GATGATAACAGGTATAATGCAAGCAGAGGTGCACACTTAAACCTCAAACGT
genomic: GCATGTGAAGAAGAAAGTTGGCTTGAAGATTATAATCGGgtacttaaaa ... tgtaaaacagGATGATAACAGGTATAATGCAAGCAGAGGTGCACACTTAAACCTCAAACGT
EST: gi|10843940|gb|BF067293.1|BF067293
EST:     AATGGATGTCAGCATGTGAAGAAGAAAGTTGGCTTGAAGATTATAATCGG                         GATGATAACAGGTATAATGCAAGCAGAGGTGCACACTTAAACCTCAAACGT
genomic: AATGGATGTCAGCATGTGAAGAAGAAAGTTGGCTTGAAGATTATAATCGGgtacttaaaa ... tgtaaaacagGATGATAACAGGTATAATGCAAGCAGAGGTGCACACTTAAACCTCAAACGT
EST: gi|193539636|gb|FK498606.1|FK498606
EST:     AATGGATGTCAGCATGTGAAGAAGAAAGTTGGCTTGAAGATTATAATCGG                         GATGATAACAGGTATAATGCAAGCAGAGGTGCACACTTAAACCTCAAACGT
genomic: AATGGATGTCAGCATGTGAAGAAGAAAGTTGGCTTGAAGATTATAATCGGgtacttaaaa ... tgtaaaacagGATGATAACAGGTATAATGCAAGCAGAGGTGCACACTTAAACCTCAAACGT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGCAAAAGAAGAAGCTTTAAGCCGAAAAGATATATTGGACAAGGTTGAGAAATGGATGTCAGCATGTGAAGAAGAAAGTTGGCTTGAAGATTATAATCGGgtacttaaaatctcgcttctgctttattttttttctgagtttgaatgattggttgtgcacagtcgtggatagagaggtgaagtagtattatgatcagaac

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA