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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CGCAAAATCAAACTACATGTCTGCTGGGCAAATATCTGTGCCTATTGTCTTTAGAGGACCCAATGGTGCCGCTGCTGGAGTTGGTGCTCAGCATTCTCAAgtatggttctcctagctgctttcttttaaagacaaactttatttaactatttgagaactgataaataattcaggtttcgtctttgtatgcccaacaactttgcctttatgcag

Basic information

species Glycine max
transcript GLYMA02G46380.1
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA02G46380.2 (Glycine max), 5'ss of exon 7
lower sequence: LOC_Os09g33500.1 (Oryza sativa), 5'ss of exon 7
CGCAAAATCAAACTACATGTCTGCTGGGCAAATATCTGTGCCTATTGTCTTTAGAGGACCCAATGGTGCCGCTGCTGGAGTTGGTGCTCAGCATTCTCAAgtatggttctcctagctgctttcttttaaagacaaactttatttaactatttgagaactgataaataattcaggtttcgtctttgtatgcccaacaactttgcctttatgcag
 || || |||||||||||||| || || || |||||||| |||||||| || |||||||| ||||| || |||||||||||||| ||||| || || || || ||           ||  || |     ||   | | |  |   ||    |   |  |  ||||   |    ||||| | ||  | ||     | ||               
TGCCAAGTCAAACTACATGTCAGCGGGTCAGATATCTGTCCCTATTGTTTTCAGAGGACCTAATGGAGCTGCTGCTGGAGTTGGCGCTCAACACTCGCAGgtttgtgatcagggaatggcttatgaattagtttatcatcctaggaccccattgaactttgtaaaagttcattgtttccttttgttgtgttgttctaccc-------------

upper sequence: GLYMA02G46380.2 (Glycine max), 5'ss of exon 7
lower sequence: LOC_Os08g42410.2 (Oryza sativa), 5'ss of exon 5
CGCAAAATCAAACTACATGTCTGCTGGGCAAATATCTGTGCCTATTGTCTTTAGAGGACCCAATGGTGCCGCTGCTGGAGTTGGTGCTCAGCATTCTCAAgtatggttctcctagctgctttcttttaaagacaaactttattta--actatttgagaactgataaataattcaggtttcgtctttgtatgcccaacaactttgcctttatgcag
 || || || ||||||||||| ||||| || |||   || |||||||| |||||||| || || ||||| |||||||| |||||||||||||| ||||| || ||   |    |  || |      ||      |   |  | ||  | ||||        |  ||||||   |  |||     | || |    ||||  |||||          
TGCCAAGTCGAACTACATGTCAGCTGGTCAGATAAACGTTCCTATTGTTTTTAGAGGGCCAAACGGTGCTGCTGCTGGTGTTGGTGCTCAGCACTCTCAGgtttgtgacagaaacttgttaatgcctatctgttattctattctattattattgtttggacggcaaataaccaatatttg----tggtgttttgaaca-ttttgc----------

upper sequence: GLYMA02G46380.2 (Glycine max), 5'ss of exon 7
lower sequence: GRMZM2G043198_T03 (Zea mays), 5'ss of exon 7
CGCAAAATCAAACTACATGTCTGCTGGGCAAATATCTGTGCCTATTGTCTTTAGAGGACCCAATGGTGCCGCTGCTGGAGTTGGTGCTCAGCATTCTCAAgtatggttctcctagctgctttcttttaaagacaaactttatttaactatttgagaactgataaataattcaggtttcgtctttgtatgcccaacaactttgcctttatgcag
 || || || |||||||||||||||||||| |||||||| |||||||||||||| || || |||||||| ||||||||||||||||| || || || || || |  | | |  || | | |     |     |    ||  |     ||||    |   || ||||  || | |   | |  ||  ||   |   || | |            
TGCCAAGTCGAACTACATGTCTGCTGGGCAGATATCTGTTCCTATTGTCTTTAGGGGTCCAAATGGTGCTGCTGCTGGAGTTGGTGCCCAACACTCACAGgtttt-tgcacaaagtttcctctacatgggtgctctgttgctgctgttattctttagaggacaaattgtt-atgccacatgatttaattttctgaaagtctt-----------

upper sequence: GLYMA02G46380.2 (Glycine max), 5'ss of exon 7
lower sequence: GRMZM2G097226_T02 (Zea mays), 5'ss of exon 7
CGCAAAATCAAACTACATGTCTGCTGGGCAAATATCTGTGCCTATTGTCTTTAGAGGACCCAATGGTGCCGCTGCTGGAGTTGGTGCTCAGCATTCTCAAgtatggttctcctagctgctttcttttaaagacaaactttatttaactatttgagaactgataaataattcaggtttcgtctttgtatgcccaacaactttgcctttatgcag
 || || ||||| || ||||| ||||| || |||||||| |||||||| ||||||||||| || || || |||||||||||||||||||| || || || || ||        |  ||||    |    |   ||   |||| |  ||  ||   | |     | |   | |  |||| ||||| | |      || | ||            
TGCCAAGTCAAATTATATGTCAGCTGGTCAGATATCTGTTCCTATTGTTTTTAGAGGACCAAACGGAGCTGCTGCTGGAGTTGGTGCTCAACACTCACAGgtttgtcagatggaattgctcatgtagttatgtaa---ttatgtgtctgattatcatccttctacttcctaatttttcatctttatgttattgccatcctttt----------

upper sequence: GLYMA02G46380.2 (Glycine max), 5'ss of exon 7
lower sequence: GRMZM2G128121_T01 (Zea mays), 5'ss of exon 1
CGCAAAATCAAACTACATGTCTGCTGGGCAAATATCTGTGCCTATTGTCTTTAGAGGACCCAATGGTGCCGCTGCTGGAGTTGGTGCTCAGCATTCTCAAgtatggttctcctagctgctttcttttaaagacaaactttatttaactatttgagaac-tgataaataattcaggtttcgtctttgtatgcc-caacaactttgcctttatgcag
                                   |||| |||||||| ||||||||||| ||||| || |||||||||||||||||||| || || || || ||        || ||||  | | ||   |   |||| |  |  ||  || | | | |  ||  |  |     ||||  |||| ||||      | ||  |            
-----------------------------------CTGTTCCTATTGTTTTTAGAGGACCAAATGGAGCTGCTGCTGGAGTTGGTGCTCAACACTCACAGgtttgtcagatggagttgct--catgtagttatgtactt-acgtgtctgattaacatccttctacttcctatttttttccactttttatgttattgcgaccct------------

upper sequence: GLYMA02G46380.2 (Glycine max), 5'ss of exon 7
lower sequence: AT5G50850.1 (Arabidopsis thaliana), 5'ss of exon 8
CGCAAAATCAAACTACATGTCTGCTGGGCAAATATCTGTGCCTATTGTCTTTAGAGGACCCAATGGTGCCGCTGCTGGAGTTGGTGCTCAGCATTCTCAAgtatg-gttctcctagctgctttcttttaaagacaaactttatttaactatttgagaactgataaataattcaggtttcgtctttgtatgcccaacaactttgcctttatgcag
 ||||| ||||| |||||||||||||| || |||  ||| || || ||||||||||||||||||||||| |||||||| ||||| ||||| |||||||| |||   | || || |       |   | ||  |     |   ||  | | ||| | ||  ||       ||||| |       |  ||     |   |  | |  |        
TGCAAAGTCAAATTACATGTCTGCTGGACAGATAAATGTACCCATCGTCTTTAGAGGACCCAATGGTGCTGCTGCTGGTGTTGGAGCTCAACATTCTCAGgtaaacgctcacccaaaaaaaat---tgaataatttgttactttgcattctttcaaaagagacc-----ttcagctactaaactgataaagatattcatataggatga------

upper sequence: GLYMA02G46380.2 (Glycine max), 5'ss of exon 7
lower sequence: Vv17s0000g00690.t01 (Vitis vinifera), 5'ss of exon 7
CGCAAAATCAAACTACATGTCTGCTGGGCAAATATCTGTGCCTATTGTCTTTAGAGGACCCAATGGTGCCGCTGCTGGAGTTGGTGCTCAGCATTCTCAAgtatggttctcctagctgctttcttttaaagacaaactttatttaactatttgagaactgataaataattcaggtttcgtctt-tgtatgcccaacaactttgcctttatgcag
 ||||| |||||||| ||||||||||| || ||||||||||| ||||| || ||||| || ||||| || ||||| ||||||||||| ||||||||||| || | ||    | |  | || |||  ||   |     |||||   | | |   |  |   ||   || |     | |   ||| |  |||| |  |   ||| ||         
TGCAAAGTCAAACTATATGTCTGCTGGTCAGATATCTGTGCCAATTGTTTTCAGAGGGCCAAATGGGGCTGCTGCAGGAGTTGGTGCCCAGCATTCTCAGgtgtagt----ccaaattctgtctgatacttattg--tttatgcgattttgccatcatatatggttagtctccttctaaccttctagatgctctgcttattttccc--------

upper sequence: GLYMA02G46380.2 (Glycine max), 5'ss of exon 7
lower sequence: EFJ19158 (Selaginella moellendorffii), 5'ss of exon 5
CGCAAAATCAAACTACATGTCTGCTGGGCAAATATCTGTGCCTATTGTCTTTAGAGGACCCAATGGTGCCGCTGCTGGAGTTGGTGCTCAGCATTCTCAAgtatggttctcctagctgctttcttttaaagacaaactttatttaactatttgagaactgataaataattcaggtttcgtctttgtatgcccaacaactttgcctttatgcag
 |||||  || |||| ||||| |  |||||||||||||| || ||||| ||| | || ||||||||||| ||||| || ||||||||||| || || || ||   |  |||    ||||     ||      ||   ||  ||| |   ||| ||                                                          
AGCAAAGACATACTATATGTCCGGAGGGCAAATATCTGTTCCCATTGTATTTCGGGGTCCCAATGGTGCAGCTGCCGGTGTTGGTGCTCAACACTCACAGgtg-agcgctctgttctgcgagagtt-ggctccatttttattttcatcctttcag----------------------------------------------------------

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|7041702|gb|AW471543.1|AW471543
EST:     TTAGAGGACCCAATGGTGCCGCTGCTGGAGTTGGTGCTCAGCATTCTCAA                         TGTTATGCATCTTGGTATGGTTCATGCCCTGGGTTGAAAGTCTTGTCACCA
genomic: TTAGAGGACCCAATGGTGCCGCTGCTGGAGTTGGTGCTCAGCATTCTCAAgtatggttct ... ctttatgcagTGTTATGCATCTTGGTATGGTTCATGCCCTGGGTTGAAAGTCTTGTCACCA
EST: gi|192295237|gb|FG986956.1|FG986956
EST:     TTAGAGGACCCAATGGTGCCGCTGCTGGAGTTGGTGCTCAGCATTCTCAA                         TGTTATGCATCTTGGTATGGTTCATGCCCTGGGTTGAAAGTCTTGTCACCA
genomic: TTAGAGGACCCAATGGTGCCGCTGCTGGAGTTGGTGCTCAGCATTCTCAAgtatggttct ... ctttatgcagTGTTATGCATCTTGGTATGGTTCATGCCCTGGGTTGAAAGTCTTGTCACCA
EST: gi|21887778|gb|BQ740991.1|BQ740991
EST:     TTAGAGGACCCAATGGTGCCGCTGCTGGAGTTGGTGCTCAGCATTCTCAA                         TGTTATGCATCTTGGTATGGTTCATGCCCTGGGTTGAAAGTCTTGTCACCA
genomic: TTAGAGGACCCAATGGTGCCGCTGCTGGAGTTGGTGCTCAGCATTCTCAAgtatggttct ... ctttatgcagTGTTATGCATCTTGGTATGGTTCATGCCCTGGGTTGAAAGTCTTGTCACCA
EST: gi|8826851|gb|BE210581.1|BE210581
EST:     ATAGAGGACCCAATGGTGCCGCTGCTGGAGTTGGTGCTCAGCATTCTCGA                         TGTTATGCATCTTCGG-ATGGTTCATGCCCTGGG
genomic: TTAGAGGACCCAATGGTGCCGCTGCTGGAGTTGGTGCTCAGCATTCTCAAgtatggttct ... ctttatgcagTGTTATGCATCTT-GGTATGGTTCATGCCCTGGG
EST: gi|209708509|gb|BW668119.1|BW668119
EST:     TTAGAGGACCCAATGGTGCCGCTGCTGGAGTTGGTGCTCAGCATTCTCAA                         TGTTATGCATCTTGGTATG
genomic: TTAGAGGACCCAATGGTGCCGCTGCTGGAGTTGGTGCTCAGCATTCTCAAgtatggttct ... ctttatgcagTGTTATGCATCTTGGTATG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CGCAAAATCAAACTACATGTCTGCTGGGCAAATATCTGTGCCTATTGTCTTTAGAGGACCCAATGGTGCCGCTGCTGGAGTTGGTGCTCAGCATTCTCAAgtatggttctcctagctgctttcttttaaagacaaactttatttaactatttgagaactgataaataattcaggtttcgtctttgtatgcccaacaactttgcctttatgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGGA