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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGTGGATGTCTGGAGCTGTGGTGTAATTTTATATGCCCTTCTTTGTGGCACCCTTCCTTTTGATGATGAAAATATTCCAAATCTCTTCAAGAAAATAAAGgtattgttaatttaattttatttatttaattaattgagtgatcggctgttgactacattcaaacatcccaggccttggacatgtggataattttccagct...

Basic information

species Glycine max
transcript GLYMA18G49770.1
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA18G49770.1 (Glycine max), 5'ss of exon 6
lower sequence: LOC_Os05g45420.3 (Oryza sativa), 5'ss of exon 5
AGTGGATGTCTGGAGCTGTGGTGTAATTTTATATGCCCTTCTTTGTGGCACCCTTCCTTTTGATGATGAAAATATTCCAAATCTCTTCAAGAAAATAAAGgtattgttaatttaattttatttatttaattaattgagtgatcggctgttgactacattcaaacatc----ccaggccttggacatgtggataattttccagct
||| ||||| ||||| |||||||| ||| | ||||| ||||||||||| |||||||| |||||||| || |||||||| || || || |||||||||||||| | |  ||    || | || |||   | | ||  ||     | ||  |  || | || | |  |       |  |  ||  | | | |||    ||| ||  
AGTTGATGTGTGGAGTTGTGGTGTTATTCTTTATGCTCTTCTTTGTGGTACCCTTCCATTTGATGACGAGAATATTCCCAACCTTTTTAAGAAAATAAAGgt-tagcaaa---gatgtgatatatcctactgataaaggtgctgcctcat--ctccttttatatgttaaagtaaaactctgtccgttttgatg---ttctag--

upper sequence: GLYMA18G49770.1 (Glycine max), 5'ss of exon 6
lower sequence: LOC_Os03g17980.2 (Oryza sativa), 5'ss of exon 5
AGTGGATGTCTGGAGCTGTGGTGTAATTTTATATGCCCTTCTTTGTGGCACCCTTCCTTTTGATGATGAAAATATTCCAAATCTCTTCAAGAAAATAAAGgtattgttaatttaattttatttatttaattaattgagtgatcggctgttgactacat------tcaaacatcccag-----------gccttggacatgtggataattttccagct---------------
 || ||||| ||||||||||| || ||  | ||||| || |||||||| || ||||| ||||||||||| ||||| || || || ||||| || ||||||||    |  |||||  |    |      |    |||     ||   ||||||||| ||      | ||| |||  ||               || | || ||  || ||  || | |               
GGTTGATGTATGGAGCTGTGGAGTGATCCTTTATGCTCTCCTTTGTGGTACTCTTCCATTTGATGATGAGAATATCCCCAACCTATTCAAAAAGATAAAGgtgagatagatttatgtaggctagccagacc--ttgtaaactcttatgttgactagatggtccttaaaatatctaagtttttattattattctgtatatttgagtatttgacctgtttgtttggtgttccag

upper sequence: GLYMA18G49770.1 (Glycine max), 5'ss of exon 6
lower sequence: GRMZM2G077278_T01 (Zea mays), 5'ss of exon 5
AGTGGATGTCTGGAGCTGTGGTGTAATTTTATATGCCCTTCTTTGTGGCACCCTTCCTTTTGATGATGAAAATATTCCAAATCTCTTCAAGAAAATAAAGgtattgttaatttaattttatttatttaattaattgagtgatcggctgttgactacattcaa-acatcccaggccttggacatgtggataattttccagct
||| || |||||||||||||| || ||| | ||||| |||||||||||||| || || ||||| ||||| ||||||||||| || |||||||||||||||||   | ||   |||| | | | |||| |       |    ||   | |    ||  || || |    | |    ||     | |   ||||| |      
AGTTGACGTCTGGAGCTGTGGAGTTATTCTTTATGCTCTTCTTTGTGGCACTCTCCCATTTGACGATGAGAATATTCCAAACCTTTTCAAGAAAATAAAGgtga-gcta---taatctcagtgattttacctgaaaaagattcctttatattttatttttaatatgctcaataaattctttttatatctaattgtag----

upper sequence: GLYMA18G49770.1 (Glycine max), 5'ss of exon 6
lower sequence: GRMZM2G107867_T02 (Zea mays), 5'ss of exon 5
AGTGGATGTCTGGAGCTGTGGTGTAATTTTATATGCCCTTCTTTGTGGCACCCTTCCTTTTGATGATGAAAATATTCCAAATCTCTTCAAGAAAATAAAGgtattgttaatttaattttatttatttaattaattgagtgatcggctgttgactacattcaaacatcccaggccttggacatgtggataattttccagct----
 || ||||| ||||| ||||| || ||| | ||||| ||||||||||| || ||||| ||||||||||| |||||||| ||||| ||||| ||||| |||||   |  ||   | || | |  | |  |  ||    |  | |   |   || |   |||     |      |  |    || |||    |||| | | |    
GGTCGATGTATGGAGTTGTGGGGTGATTCTTTATGCTCTTCTTTGTGGAACTCTTCCATTTGATGATGAGAATATTCCCAATCTGTTCAAAAAAATTAAGgt---gagaaagcacttatgtggaat--acaaaccttgcaa-caatta--gattctgttctggagttatgaccactctctatctgg----ttttacggttttag

upper sequence: GLYMA18G49770.1 (Glycine max), 5'ss of exon 6
lower sequence: AT3G29160.3 (Arabidopsis thaliana), 5'ss of exon 5
AGTGGATGTCTGGAGCTGTGGTGTAATTTTATATGCCCTTCTTTGTGGCACCCTTCCTTTTGATGATGAAAATATTCCAAATCTCTTCAAGAAAATAAAGgtattgttaatttaattttatttatttaattaattgagtgatcggctgttgactacattcaaacatcccaggccttggacatgtggataattttccagct-----
||| ||||| ||||| || || || || || || || ||  | || || || |||||||||||||||||||| ||||| || || ||||||||||| |||||| |||   ||  | |||    ||| |  |||  || |  ||     || | |  ||||| |  |    |   |     ||   | |  ||||           
AGTAGATGTATGGAGTTGCGGAGTTATATTGTACGCTCTATTATGCGGTACTCTTCCTTTTGATGATGAAAACATTCCCAACCTTTTCAAGAAAATTAAGgtactgtacgttatactttg---attcagctaaaagactcttc-----ttaaatggattcatatgtatgtgaagtaacttatcaaggtgttttttttctctttag

upper sequence: GLYMA18G49770.1 (Glycine max), 5'ss of exon 6
lower sequence: AT3G01090.2 (Arabidopsis thaliana), 5'ss of exon 5
AGTGGATGTCTGGAGCTGTGGTGTAATTTTATATGCCCTTCTTTGTGGCACCCTTCCTTTTGATGATGAAAATATTCCAAATCTCTTCAAGAAAATAAAGgtattgttaatttaattttatttatttaattaattgagtgatcggctgttgactacattcaaacatcc---caggccttggacatgtggataattttccagct---------------
||| |||||||||||||||||||| ||  | || || ||||| ||||| || ||||| |||||||||||||| ||||| || || || ||||| |||||||||   |  ||| | |  |  |  ||    || ||||   |  |  ||     |  |||  |   | |       |||| ||| |||      ||||    ||               
AGTAGATGTCTGGAGCTGTGGTGTGATACTCTACGCTCTTCTCTGTGGGACGCTTCCATTTGATGATGAAAACATTCCCAACCTTTTTAAGAAGATAAAGgtacattctatt-actcctcctctttcgtctatttgaactaatgcttgaattttttattttatttttcgtatcacccttcgac-tgtaaccttttttttttctcttttcgtcctatag

upper sequence: GLYMA18G49770.1 (Glycine max), 5'ss of exon 6
lower sequence: Vv14s0108g01230.t01 (Vitis vinifera), 5'ss of exon 5
AGTGGATGTCTGGAGCTGTGGTGTAATTTTATATGCCCTTCTTTGTGGCACCCTTCCTTTTGATGATGAAAATATTCCAAATCTCTTCAAGAAAATAAAGgtattgttaatttaattttattta-tttaattaattgagtgatcggctgttgactacattcaaacatcccaggccttggacatgtggataattt-tccagct
 |||||||| |||||||| ||||| ||||| || || ||||||||||| || ||||| |||||||||||||| ||||| || || ||||||||||||||||||||  ||| || | || | | | ||| |  |  ||   | |  ||||    || ||||    | |    | ||||  || | |   |  ||| |  ||  
GGTGGATGTATGGAGCTGCGGTGTTATTTTGTACGCTCTTCTTTGTGGTACTCTTCCATTTGATGATGAAAACATTCCCAACCTTTTCAAGAAAATAAAGgtatttctaaatttacttcactaacttttagcatgtgccagcttagctgg-atctgcatt-gctcttttttgtccttttactttttatttttttgtttagaa

upper sequence: GLYMA18G49770.1 (Glycine max), 5'ss of exon 6
lower sequence: EFJ16445 (Selaginella moellendorffii), 5'ss of exon 4
AGTGGATGTCTGGAGCTGTGGTGTAATTTTATATGCCCTTCTTTGTGGCACCCTTCCTTTTGATGATGAAAATATTCCAAATCTCTTCAAGAAAATAAAGgtattgttaatttaattttatttatttaattaattgagtgatcggctgttgactacattcaaacatcccaggccttggacatgtggataattttccagct
||| || || ||||||||||| || ||  |||| || ||||| ||||||| |||||| ||||| || ||||| ||||||||||| ||||||||||| |||||    | | |   |    |   | |   |||| ||  |  ||   | |||  ||    ||                                       
AGTAGACGTATGGAGCTGTGGGGTGATACTATACGCACTTCTCTGTGGCAGCCTTCCCTTTGACGACGAAAACATTCCAAATCTATTCAAGAAAATCAAGgtga-atcagtcagacaacaagaagtc--ttaaatgttttttcttttcttgtttattcccag--------------------------------------

upper sequence: GLYMA18G49770.1 (Glycine max), 5'ss of exon 6
lower sequence: EFJ17922 (Selaginella moellendorffii), 5'ss of exon 4
AGTGGATGTCTGGAGCTGTGGTGTAATTTTATATGCCCTTCTTTGTGGCACCCTTCCTTTTGATGATGAAAATATTCCAAATCTCTTCAAGAAAATAAAGgtattgttaatttaattttatttatttaattaattgagtgatcggctgttgactacattcaaacatcccaggccttggacatgtggataattttccagct
||| || || ||||||||||| || ||  |||| || ||||| ||||||| |||||| ||||| || ||||| ||||||||||| ||||||||||| |||||    | | |   |    |   | |   |||| ||  |  |    | |||  ||    ||                                       
AGTAGACGTATGGAGCTGTGGGGTGATACTATACGCACTTCTCTGTGGCAGCCTTCCCTTTGACGACGAAAACATTCCAAATCTATTCAAGAAAATCAAGgtga-atcagtcagacaacaagaagtc--ttaaatgtttttttt-ttcttgtttattcccag--------------------------------------

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|23731437|gb|BU763843.1|BU763843
EST:     CCCTTCCTTTTGATGATGAAAATATTCCAAATCTCTTCAAGAAAATAAAG                         GGTGGGATTTACACTCTTCCCAGTCATCTATCACCCGGTGCTAGAGATTTG
genomic: CCCTTCCTTTTGATGATGAAAATATTCCAAATCTCTTCAAGAAAATAAAGgtattgttaa ... tttcatgtagGGTGGGATTTACACTCTTCCCAGTCATCTATCACCCGGTGCTAGAGATTTG
EST: gi|193414561|gb|FK379283.1|FK379283
EST:     ATGAAAATATTCCTAATTCTCTTCAAGAAAATAAAG                         GGTGGGATTTACACTCTTCCCAGTCATCTATCACCCGGTGCTAGAGATTTG
genomic: ATGAAAATATTCC-AAATCTCTTCAAGAAAATAAAGgtattgttaa ... tttcatgtagGGTGGGATTTACACTCTTCCCAGTCATCTATCACCCGGTGCTAGAGATTTG
EST: gi|208161964|gb|GD962751.1|GD962751
EST:     TTCCAAATCTCTTCTAAGAAAATAAAG                         GGTGGGATTTACACTCTTCCCAGTCATCTATCACCCGGTGCTAGAGATTTG
genomic: TTCCAAATCTCTTC-AAGAAAATAAAGgtattgttaa ... tttcatgtagGGTGGGATTTACACTCTTCCCAGTCATCTATCACCCGGTGCTAGAGATTTG
EST: gi|254336679|gb|GR842858.1|GR842858
EST:     CCCTTCCTTTTGATGATGAAAATATTCCAAATCTCTTCAAGAAAATAAAG                         GGTGGGATTTACACTCTTCCCAGTCATCTATCACCCGGTGCTAGAGATTTG
genomic: CCCTTCCTTTTGATGATGAAAATATTCCAAATCTCTTCAAGAAAATAAAGgtattgttaa ... tttcatgtagGGTGGGATTTACACTCTTCCCAGTCATCTATCACCCGGTGCTAGAGATTTG
EST: gi|208263578|gb|GE063376.1|GE063376
EST:     TCTCTTCAAGAAAATAAAG                         GGTGGGATTTACACTCTTCCCAGTCATCTATCACCCGGTGCTAGAGATTTG
genomic: TCTCTTCAAGAAAATAAAGgtattgttaa ... tttcatgtagGGTGGGATTTACACTCTTCCCAGTCATCTATCACCCGGTGCTAGAGATTTG
EST: gi|151395613|gb|EV265490.1|EV265490
EST:     CCCTTCCTTTTGATGATGAAAATATTCCAAATCTCTTCAAGAAAATAAAG                         GGTGGGATTTACACTCTTCCCAGTCATCTATCACCCGGTGCTAGAGATTTG
genomic: CCCTTCCTTTTGATGATGAAAATATTCCAAATCTCTTCAAGAAAATAAAGgtattgttaa ... tttcatgtagGGTGGGATTTACACTCTTCCCAGTCATCTATCACCCGGTGCTAGAGATTTG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGTGGATGTCTGGAGCTGTGGTGTAATTTTATATGCCCTTCTTTGTGGCACCCTTCCTTTTGATGATGAAAATATTCCAAATCTCTTCAAGAAAATAAAGgtattgttaatttaattttatttatttaattaattgagtgatcggctgttgactacattcaaacatcccaggccttggacatgtggataattttccagct

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA