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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGATGGCCTTGGAGCCGAGATTGTTGGCACTTTTATTCTTGTTTACACTGTCTTCTCCGCCACTGATGCCAAGAGAAACGCTAGAGACTCTCACGTCCCGgtacctatttatcatctttattctctcttctcattcgtgcaactttaagccaaagtgtgtaaacaggtttattagctaggtagaagagagagactaaact...

Basic information

species Glycine max
transcript GLYMA11G02530.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA11G02530.1 (Glycine max), 5'ss of exon 2
lower sequence: LOC_Os02g44630.2 (Oryza sativa), 5'ss of exon 3
TGATGGCCTTGGAGCCGAGATTGTTGGCACTTTTATTCTTGTTTACACTGTCTTCTCCGCCACTGATGCCAAGAGAAACGCTAGAGACTCTCACGTCCCGgtacctatttatcatctttattctctcttctcattcgtgcaactttaa-gccaaagtgtgtaaacaggtttattagctaggtagaagagagagactaaact--
||| || ||||| || |||||||||||||| || || || || ||||| |||||||| ||||||||||||||||| || || || ||||| || || || |||  |||   ||  |||| | |  | |    ||  ||| || || |     |    ||||   |   |   |||   |    ||  |   |  |   ||   
TGACGGTCTTGGTGCTGAGATTGTTGGCACCTTCATCCTGGTCTACACCGTCTTCTCAGCCACTGATGCCAAGAGGAATGCCAGGGACTCACATGTTCCTgtaagtatccttctcctttttgcagtgtg---atatgtgaaagttcagtagtagttagtgtggtctaatgagttatgcactgtgataactaattcatcaccaa

upper sequence: GLYMA11G02530.1 (Glycine max), 5'ss of exon 2
lower sequence: LOC_Os04g47220.1 (Oryza sativa), 5'ss of exon 1
TGATGGCCTTGGAGCCGAGATTGTTGGCACTTTTATTCTTGTTTACACTGTCTTCTCCGCCACTGATGCCAAGAGAAACGCTAGAGACTCTCACGTCCCGgt--acctatttatcatctttattctctcttctcattcgtgcaact--ttaagccaaagtgtgtaaacaggtttattagctaggtagaagagagagactaaact
 || ||||| || |||||||| || ||||| || || || || ||||| |||||||||||||| || |||||||| ||||| || ||||| ||||| |||||     ||   |  |    |    |      |||    || || |  ||   |     | ||       | || ||   |   |    | ||    | | |  
CGACGGCCTCGGCGCCGAGATCGTCGGCACCTTCATCCTCGTCTACACCGTCTTCTCCGCCACCGACGCCAAGAGGAACGCCAGGGACTCCCACGTTCCGgttagtataccaactactactgcagtaaagattcagagatggaagtatttttactgttttctgagtgattgatttttgttttaatttgcgcgatcttccacag-

upper sequence: GLYMA11G02530.1 (Glycine max), 5'ss of exon 2
lower sequence: AC209208.3_FGT002 (Zea mays), 5'ss of exon 2
TGATGGCCTTGGAGCCGAGATTGTTGGCACTTTTATTCTTGTTTACACTGTCTTCTCCGCCACTGATGCCAAGAGAAACGCTAGAGACTCTCACGTCCCGgtacctatttatcatctttattctctcttctcattcgtgcaactttaagccaaagtgtgtaaacaggttta--ttagc-taggtagaagagagagactaaact-
|||||||||||| || |||||||||||||| || || || || ||||| |||||||| ||||| ||||||||||| || || || ||||| || || || |||  || |  ||  |||    |  | | ||  || || ||  | | |       ||  |  |   ||||   |||||  |  || | |  |  || | |||| 
TGATGGCCTTGGCGCTGAGATTGTTGGCACCTTCATCCTAGTCTACACCGTCTTCTCAGCCACCGATGCCAAGAGGAATGCCAGGGACTCCCATGTTCCTgtaagtactcttccacttc---ccttttcctagtttgttcagttgtta-tagttctgcttggattagtttggcttagcacacatatatgtaattgaatcaactt

upper sequence: GLYMA11G02530.1 (Glycine max), 5'ss of exon 2
lower sequence: GRMZM2G392975_T03 (Zea mays), 5'ss of exon 2
TGATGGCCTTGGAGCCGAGATTGTTGGCACTTTTATTCTTGTTTACACTGTCTTCTCCGCCACTGATGCCAAGAGAAACGCTAGAGACTCTCACGTCCCGgtacctatttatcatctttattctctcttctcattcgtgcaact-ttaagccaaagtgtgtaaacaggtttat-tagctagg-tagaagagagagactaaact
 || |||||||| || ||||| |||||||| || || || || ||||| |||||||| ||||| ||||||||||| ||||| || ||||| || ||||| |||  || |  || || ||  ||  | | ||  || || || || ||| |     |  || |  ||  |||   || |||   || ||||    |  |  |  
GGACGGCCTTGGCGCAGAGATCGTTGGCACCTTCATCCTAGTCTACACCGTCTTCTCGGCCACCGATGCCAAGAGGAACGCCAGGGACTCCCATGTCCCCgtaagtactcttcgtcctt--tcgttttcctagtttgttcagctgttagggttctgcttgaattcacatttgcatatctaaaatataagatgacggttgtaa-

upper sequence: GLYMA11G02530.1 (Glycine max), 5'ss of exon 2
lower sequence: GRMZM2G174807_T01 (Zea mays), 5'ss of exon 2
TGATGGCCTTGGAGCCGAGATTGTTGGCACTTTTATTCTTGTTTACACTGTCTTCTCCGCCACTGATGCCAAGAGAAACGCTAGAGACTCTCACGTCCCGgtacctatt-tatcatctttattctctcttctcattcgtgcaactttaagccaaagtgtgtaaaca-ggtttattagctaggtagaagagagagactaaact-
 || ||||| || |||||||| || ||||| || || || || ||||| |||||||||||||| || |||||||| ||||| || ||||| || || |||||   ||   ||||| | ||    || || || |||||     ||    | |     ||| || |  |  ||||        |    | |   || | |||  
CGACGGCCTAGGCGCCGAGATCGTCGGCACCTTCATCCTCGTCTACACCGTCTTCTCCGCCACCGACGCCAAGAGGAACGCCAGGGACTCCCATGTGCCGgtgagtacagtatcagccttgccttc-ctgcttattcgc----ctc---gtccgtccgtgcaagctcgacttatcgatggtttctttgtggacgaatgaacag

upper sequence: GLYMA11G02530.1 (Glycine max), 5'ss of exon 2
lower sequence: Vv15s0046g02420.t01 (Vitis vinifera), 5'ss of exon 2
TGATGGCCTTGGAGCCGAGATTGTTGGCACTTTTATTCTTGTTTACACTGTCTTCTCCGCCACTGATGCCAAGAGAAACGCTAGAGACTCTCACGTCCCGgtacctatttatcatcttt--attctctcttctcattcgtgcaactttaagccaaagtgtgtaaac--aggtttattagctaggtagaagagagagactaaact--
 ||||| ||||| || ||||| |||||||||||| ||||||| |||||||| ||||| || ||||||||||||||||| || |||||||| || ||||| |||  |||||  | || ||  ||  |||||    ||   ||||  | |  |      | | || |   |  ||| | |  ||||||      || || | |  |  
CGATGGGCTTGGTGCTGAGATAGTTGGCACTTTTGTTCTTGTCTACACTGTTTTCTCTGCAACTGATGCCAAGAGAAATGCCAGAGACTCACATGTCCCTgtaagtattttccctcattgtatcatctctctgtatgtatgcatatgtgtggtttgttttatagatctaactttgtcaa-taggta-----aagcgattgagttct

upper sequence: GLYMA11G02530.1 (Glycine max), 5'ss of exon 2
lower sequence: Vv02s0025g03390.t01 (Vitis vinifera), 5'ss of exon 2
TGATGGCCTTGGAGCCGAGATTGTTGGCACTTTTATTCTTGTTTACACTGTCTTCTCCGCCACTGATGCCAAGAGAAACGCTAGAGACTCTCACGTCCCGgtacctatttatcatctttattctctcttctcattcgtgcaactttaagccaaagtgtgtaaacaggtttattagctaggtagaagagagagactaaact-
|||||||||||| || |||||||||||||| ||  |||||||||||||||||||||| || |||||||||||||||||||| ||||||||||||||||| |||  ||||  || | ||| ||        ||||  |  || | ||    || | | ||     |  ||  || |     ||            |    | 
TGATGGCCTTGGTGCTGAGATTGTTGGCACCTTCGTTCTTGTTTACACTGTCTTCTCTGCTACTGATGCCAAGAGAAACGCCAGAGACTCTCACGTCCCTgtatgtattc-tcttatttctttctcaacttcatgagaccatccttgtttcatattatgattttactttccttggaatcttattttttgttttttctcatt

upper sequence: GLYMA11G02530.1 (Glycine max), 5'ss of exon 2
lower sequence: Vv15s0046g02410.t01 (Vitis vinifera), 5'ss of exon 2
TGATGGCCTTGGAGCCGAGATTGTTGGCACTTTTATTCTTGTTTACACTGTCTTCTCCGCCACTGATGCCAAGAGAAACGCTAGAGACTCTCACGTCCCGgtacctatttatcatctttattctctcttctcattcgtgcaactttaagccaaagtgtgtaa--acaggtttattagctaggtagaagagagagactaaact-
|| ||| ||||| || ||||| |||||||||||| ||||||| ||||||||  |||| || ||||||||||||||||| || |||||||| || || || |||  ||||     ||| | |  | | | |  |    ||    |||      |  | | ||   | |  ||| || |  |  | | | || ||   | | || 
TGCTGGGCTTGGTGCTGAGATAGTTGGCACTTTTGTTCTTGTCTACACTGTTCTCTCTGCAACTGATGCCAAGAGAAATGCCAGAGACTCACATGTTCCAgtaagtattctctctctgtgta-tatatacataaatatgtgggttttgttttacatatctagttatatatttctttgtcaattggtaaagtga--ttgagctg

upper sequence: GLYMA11G02530.1 (Glycine max), 5'ss of exon 2
lower sequence: EFJ18960 (Selaginella moellendorffii), 5'ss of exon 2
TGATGGCCTTGGAGCCGAGATTGTTGGCACTTTTATTCTTGTTTACACTGTCTTCTCCGCCACTGATGCCAAGAGAAACGCTAGAGACTCTCACGTCCCGgtac----------ctatttatcatctttatt--ctctcttctcattc-gtgcaactttaagccaaagtgtgtaaacaggtttattagctaggtagaagagagagactaaact----------------------------------------------------------------------------------
 ||||| |||||||| ||||||||||| || ||  |||| || ||||| ||||||||||||||||||||||||||||  || |||||||| || ||||||||||          | ||  |     ||  ||   || | ||||||   ||    ||||    |    | | |      ||   ||  |||| |      |    |||                                                                                       
AGATGGTCTTGGAGCTGAGATTGTTGGTACCTTCGTTCTCGTCTACACGGTCTTCTCCGCCACTGATGCCAAGAGAAGTGCCAGAGACTCCCATGTCCCGgtacgtttcttcttccatccaaagctttggttgattcccctctcatgaagttttgcttttcttcttcttatcttcttgtgtggttttcctagtttttcttgctgtacttcctcttatcttctccttatctcttctcctcctcatggatagatttaagatatgttccaagctcacaaactttggcgatttctacag

upper sequence: GLYMA11G02530.1 (Glycine max), 5'ss of exon 2
lower sequence: EFJ11572 (Selaginella moellendorffii), 5'ss of exon 2
TGATGGCCTTGGAGCCGAGATTGTTGGCACTTTTATTCTTGTTTACACTGTCTTCTCCGCCACTGATGCCAAGAGAAACGCTAGAGACTCTCACGTCCCGgtac----------ctatttatcatctttattctctcttctcattcgtgcaactttaagccaaagtgtgtaaacaggtttattagctaggtagaagagagagactaaact---------------------------------------------------------------------------------------
 ||||| |||||||| ||||||||||| || ||  |||| || ||||| ||||||||||||||||||||||||||||  || |||||||| || ||||||||||          | ||  |     ||  ||   ||  | |  || || |  ||||          | | | |   ||   | | |                ||  |||                                                                                       
AGATGGTCTTGGAGCTGAGATTGTTGGTACCTTCGTTCTCGTCTACACCGTCTTCTCCGCCACTGATGCCAAGAGAAGTGCCAGAGACTCCCATGTCCCGgtacgtttctccttccatccaaagctttggttgattcccccctctcatgaagttttacttttcttcttcttatcttcttgtgtggttttcctagtttttcttgctgtacttcctcttatcttctccttatctcttctcctcctcatggatagatttaagatatgttccaagctcacaaactttggcgatttctacag

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|7233954|gb|AW569296.1|AW569296
EST:     TCTTCTCCGCCACTGATGCCAAGAGAAACGCTAGAGACTCTCACGTCCCG                         ATTTTGGCTCCTCTTCCAATCGGGTTTGCTGTGTTTTTGGTCCACTTGGCA
genomic: TCTTCTCCGCCACTGATGCCAAGAGAAACGCTAGAGACTCTCACGTCCCGgtacctattt ... aaaattgtagATTTTGGCTCCTCTTCCAATCGGGTTTGCTGTGTTTTTGGTCCACTTGGCA
EST: gi|208295980|gb|GE092230.1|GE092230
EST:     AAACGCTAGAGACTCTCACGTCCCG                         ATTTTGGCTCCTCTTCCAATCGGGTTTGCTGTGTTTTTGGTCCACTTGGCA
genomic: AAACGCTAGAGACTCTCACGTCCCGgtacctattt ... aaaattgtagATTTTGGCTCCTCTTCCAATCGGGTTTGCTGTGTTTTTGGTCCACTTGGCA
EST: gi|6848062|gb|AW350352.1|AW350352
EST:     TCTTCTCCGCCACTGATGCCAAGAGAAACGCTAGAGACTCTCACGTCCCG                         ATTTTGGCTCCTCTTCCAATCGGGTTTGCTGTGTTTTTGGTCCACTTGGCA
genomic: TCTTCTCCGCCACTGATGCCAAGAGAAACGCTAGAGACTCTCACGTCCCGgtacctattt ... aaaattgtagATTTTGGCTCCTCTTCCAATCGGGTTTGCTGTGTTTTTGGTCCACTTGGCA
EST: gi|19270654|gb|BM886910.1|BM886910
EST:     TCTTCTCCGCCACTGATGCCAAGAGAAACGCTAGAGACTCTCACGTCCCG                         ATTTTGGCTCCTCTTCCAATCGGGTTTGCTGTGTTTTTGGTCCACTTGGCA
genomic: TCTTCTCCGCCACTGATGCCAAGAGAAACGCTAGAGACTCTCACGTCCCGgtacctattt ... aaaattgtagATTTTGGCTCCTCTTCCAATCGGGTTTGCTGTGTTTTTGGTCCACTTGGCA
EST: gi|151402404|gb|EV272217.1|EV272217
EST:     TCTTCTCCGCCACTGATGCCAAGAGAAACGCTAGAGACTCTCACGTCCCG                         ATTTTGGCTCCTCTTCCAATCGGGTTTGCTGTGTTTT-GGTCCACTTGGCA
genomic: TCTTCTCCGCCACTGATGCCAAGAGAAACGCTAGAGACTCTCACGTCCCGgtacctattt ... aaaattgtagATTTTGGCTCCTCTTCCAATCGGGTTTGCTGTGTTTTTGGTCCACTTGGCA
EST: gi|192325960|gb|FK016637.1|FK016637
EST:     TCTTCTCCGCCACTGATGCCAAGAGAAACGCTAGAGACTCTCACGTCCCG                         ATTTTGGCTCCTCTTCCAATCGGGTTTGCTGTGTTTTTGGTCCACTTGGCA
genomic: TCTTCTCCGCCACTGATGCCAAGAGAAACGCTAGAGACTCTCACGTCCCGgtacctattt ... aaaattgtagATTTTGGCTCCTCTTCCAATCGGGTTTGCTGTGTTTTTGGTCCACTTGGCA
EST: gi|21601397|gb|BQ611728.1|BQ611728
EST:     TCTTCTCCGCCACTGATGCCAAGAGAAACGCTAGAGACTCTCACGTCCCG                         ATTTTGGCTCCTCTTCCAATCGGGTTTGCTGTGTTTTTGGTCCACTTGGCA
genomic: TCTTCTCCGCCACTGATGCCAAGAGAAACGCTAGAGACTCTCACGTCCCGgtacctattt ... aaaattgtagATTTTGGCTCCTCTTCCAATCGGGTTTGCTGTGTTTTTGGTCCACTTGGCA
EST: gi|10842879|gb|BF066240.1|BF066240
EST:     TCTTCTCCGCCACTGATGCCAAGAGAAACGCTAGAGACTCTCACGTCCCG                         ATTTTGGCTCCTCTTCCAATCGGGTTTGCTGTGTTTTTGGTCCACTTGGCA
genomic: TCTTCTCCGCCACTGATGCCAAGAGAAACGCTAGAGACTCTCACGTCCCGgtacctattt ... aaaattgtagATTTTGGCTCCTCTTCCAATCGGGTTTGCTGTGTTTTTGGTCCACTTGGCA
EST: gi|192317536|gb|FK011298.1|FK011298
EST:     TCTTCTCCGCCACTGATGCCAAGAGAAACGCTAGAGACTCTCACGTCCCG                         ATTTTGGCTCCTCTTCCAATCGGGTTTGCTGTGTTTTTGGTCCACTTGGCA
genomic: TCTTCTCCGCCACTGATGCCAAGAGAAACGCTAGAGACTCTCACGTCCCGgtacctattt ... aaaattgtagATTTTGGCTCCTCTTCCAATCGGGTTTGCTGTGTTTTTGGTCCACTTGGCA
EST: gi|4285014|gb|AI440853.1|AI440853
EST:     TCTTCTCCGCCACTGATGCCAAGAGAAACGCTAGAGACTCTCACGTCCCG                         ATTTTGGCTCCTCTTCCAATCGGGTTTGCTGTGTTTTTGGTCCACTTGGCA
genomic: TCTTCTCCGCCACTGATGCCAAGAGAAACGCTAGAGACTCTCACGTCCCGgtacctattt ... aaaattgtagATTTTGGCTCCTCTTCCAATCGGGTTTGCTGTGTTTTTGGTCCACTTGGCA
EST: gi|192317537|gb|FK011299.1|FK011299
EST:     TCTTCTCCGCCACTGATGCCAAGAGAAACGCTAGAGACTCTCACGTCCCG                         ATTTTGGCTCCTCTTCCAATCGGGTTTGCTGTGTTTTTGGTCCACTTGGCA
genomic: TCTTCTCCGCCACTGATGCCAAGAGAAACGCTAGAGACTCTCACGTCCCGgtacctattt ... aaaattgtagATTTTGGCTCCTCTTCCAATCGGGTTTGCTGTGTTTTTGGTCCACTTGGCA
EST: gi|15663877|gb|BI701248.1|BI701248
EST:     TCTTCTCCGCCACTGATGCCAAGAGAAACGCTAGAGACTCTCACGTCCCG                         ATTTTGGCTCCTCTTCCAATCGGGTTTGCTGTGTTTTTGGTCCACTTGGCA
genomic: TCTTCTCCGCCACTGATGCCAAGAGAAACGCTAGAGACTCTCACGTCCCGgtacctattt ... aaaattgtagATTTTGGCTCCTCTTCCAATCGGGTTTGCTGTGTTTTTGGTCCACTTGGCA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGATGGCCTTGGAGCCGAGATTGTTGGCACTTTTATTCTTGTTTACACTGTCTTCTCCGCCACTGATGCCAAGAGAAACGCTAGAGACTCTCACGTCCCGgtacctatttatcatctttattctctcttctcattcgtgcaactttaagccaaagtgtgtaaacaggtttattagctaggtagaagagagagactaaact

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA