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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATAGCAGTTTGTGCTGATGACCCTGAGTTCCGCCATTACACAGACATCAAGGAGCTTCCTCCACATCGGCTTGCTGAAATCAGAAGATTCTTTGAGGACTgtatcctgttatttgcacttatacataaaccacatgcatctctgtacgagttattgacaattaatgattagtttcttttacaataaagcctatagaacgt...

Basic information

species Glycine max
transcript GLYMA11G07530.4
intron # 6
splice site 5'
intron type U12 (go to U12 genes for details)

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA11G07530.1 (Glycine max), 5'ss of exon 7
lower sequence: LOC_Os02g47600.2 (Oryza sativa), 5'ss of exon 7
ATAGCAGTTTGTGCTGATGACCCTGAGTTCCGCCATTACACAGACATCAAGGAGCTTCCTCCACATCGGCTTGCTGAAATCAGAAGATTCTTTGAGGACTgtatcctgttatt-tgcacttatacataaacc---acatgcatctctgtacgagttattgacaattaatgattagtttcttttacaataaagcctatagaacgt------
||||| |||||||||||||||||||| | |||||| | ||  |||||||||||  | || || || || |||   || ||| |  | |||||||| ||||||||  | ||||| |  |   ||   |         ||    |     |     |  |||||     || | |||     | || ||| || | | |     ||      
ATAGCTGTTTGTGCTGATGACCCTGAATACCGCCACTTCAGGGACATCAAGGAAATCCCCCCTCACCGCCTTCAAGAGATCCGCCGCTTCTTTGAAGACTgtatattcttattctatatccatgtcttcctttttccaaatgttataatgtagatagttgactgcagat-actagaac--tgtataattaaacttctgtggtgttgacag

upper sequence: GLYMA11G07530.1 (Glycine max), 5'ss of exon 7
lower sequence: GRMZM2G046587_T03 (Zea mays), 5'ss of exon 4
ATAGCAGTTTGTGCTGATGACCCTGAGTTCCGCCATTACACAGACATCAAGGAGCTTCCTCCACATCGGCTTGCTGAAATCAGAAGATTCTTTGAGGACTgtatcctgttat-ttgcacttatacataaaccacatgcatctctgtacgagttattgacaattaatgattagtttcttttacaataaagcctatagaacgt------
|||||||| ||||||||||||||||| ||||| || ||||| ||||||| ||| || || || ||||| |||   || ||| |  | || ||||| || |||||  | |||   || |   | |  |   || || |  |  |  | |   | ||  | |   | | | |||  ||    |   | | |  | |     ||      
ATAGCAGTCTGTGCTGATGACCCTGAATTCCGTCACTACACGGACATCACGGACCTCCCACCGCATCGCCTTCAAGAGATCCGCCGCTTTTTTGAAGATTgtatgttcttaaactgtatccacagcttgtcccca-gtgttacaatccagatcataaa-atgcagtaactagagtcca--atcgttatgtttctgccgtgttgacag

upper sequence: GLYMA11G07530.1 (Glycine max), 5'ss of exon 7
lower sequence: AT2G18230.1 (Arabidopsis thaliana), 5'ss of exon 7
ATAGCAGTTTGTGCTGATGACCCTGAGTTCCGCCATTACACAGACATCAAGGAGCTTCCTCCACATCGGCTTGCTGAAATCAGAAGATTCTTTGAGGACTgtatcctgttatttgcacttatacataaaccacatgcatctctgtacgagttattgacaattaatgattagtttct--tttacaa-taaagcctatagaacgt
|| ||||| ||||||||||| || |||||||| || |||| ||||||||| |||||||| || || || || ||||||||| |  | ||||||||||||||||||||   |    ||  | | |||  |  || |  |  | |||     |   | |  |||  |  | |||||    || ||||  || |  | |||     
ATTGCAGTATGTGCTGATGATCCCGAGTTCCGTCACTACAGAGACATCAAAGAGCTTCCCCCTCACCGTCTAGCTGAAATCCGTCGCTTCTTTGAGGACTgtatcctac-agagacatgt-tgcattta--acgtataattttgttt---tcgcttatgatttgttttcagttttcacttaacaaacaatgtttttag-----

upper sequence: GLYMA11G07530.1 (Glycine max), 5'ss of exon 7
lower sequence: Vv04s0023g02050.t01 (Vitis vinifera), 5'ss of exon 6
ATAGCAGTTTGTGCTGATGACCCTGAGTTCCGCCATTACACAGACATCAAGGAGCTTCCTCCACATCGGCTTGCTGAAATCAGAAGATTCTTTGAGGACTgtatcctgttatttgcacttatacataaaccacatgcatctctgtacgagttattgacaattaatgattagtttcttt-tacaataaagcctatagaacgt----------------------------------------------------------------------------
|||||||| |||||||||||||||||||||||||| |||| ||||||||| ||| |||| |||||||| |||||||| ||| |  | |||||||||||||||||||  | |  |||  |||  | |     | ||  | ||   | | ||| || |||    ||| |||   | || |  | ||       |    |  |                                                                             
ATAGCAGTGTGTGCTGATGACCCTGAGTTCCGCCACTACAAAGACATCAAAGAGATTCCCCCACATCGCCTTGCTGAGATCCGCCGCTTCTTTGAGGACTgtatccattcacatgcctttactcct--tttatatataacttgttgctagtcatagactcacaattatttaatactatacataaattgttttcctaagtgctaccaaattgacatgttttttggtgaatttacattatctattactggataaccttcactccccatgaatgacaaag

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|22928719|gb|BU545858.1|BU545858
EST:     GGAGCTTCCTCCACATCGGCTTGCTGAAATCAGAAGATTCTTTGAGGACT                         ACAAGAAGAATGAGAACAAAATAGTTGATGTTGAAGACTTTCTACCAGCTG
genomic: GGAGCTTCCTCCACATCGGCTTGCTGAAATCAGAAGATTCTTTGAGGACTgtatcctgtt ... gtcacactagACAAGAAGAATGAGAACAAAATAGTTGATGTTGAAGACTTTCTACCAGCTG
EST: gi|254328447|gb|GR835412.1|GR835412
EST:     GGAGCTTCCTCCACATCGGCTTGCTGAAATCAGAAGATTCTTTGAGGACT                         ACAAGAAGAATGAGAACAAAATAGTTGATGTTGAAGACTTTCTACCAGCTG
genomic: GGAGCTTCCTCCACATCGGCTTGCTGAAATCAGAAGATTCTTTGAGGACTgtatcctgtt ... gtcacactagACAAGAAGAATGAGAACAAAATAGTTGATGTTGAAGACTTTCTACCAGCTG
EST: gi|192310086|gb|FK000650.1|FK000650
EST:     GGAGCTTCCTCCACATCGGCTTGCTGAAATCAGAAGATTCTTTGAGGACT                         ACAAGAAGAATGAGAACAAAATAGTTGATGTTGAAGACTTTCTACCAGCTG
genomic: GGAGCTTCCTCCACATCGGCTTGCTGAAATCAGAAGATTCTTTGAGGACTgtatcctgtt ... gtcacactagACAAGAAGAATGAGAACAAAATAGTTGATGTTGAAGACTTTCTACCAGCTG
EST: gi|151397849|gb|EV267722.1|EV267722
EST:     TTCCTCCACATCGGCTTGCTGAAATCAGAAGATTCTTTGAGGACT                         ACAAGAAGAATGAGAACAAAATAGTTGATGTTGAAGACTTTCTACCAGCTG
genomic: TTCCTCCACATCGGCTTGCTGAAATCAGAAGATTCTTTGAGGACTgtatcctgtt ... gtcacactagACAAGAAGAATGAGAACAAAATAGTTGATGTTGAAGACTTTCTACCAGCTG
EST: gi|10254828|gb|BE822594.1|BE822594
EST:     GGAGCTTCCTCCACATCGGCTTGCTGAAATCAGAAGATTCTTTGAGGACT                         ACAAGAAGAATGAGAACAAAATAGTTGATGTTGAAGACTTTCTACCAGCTG
genomic: GGAGCTTCCTCCACATCGGCTTGCTGAAATCAGAAGATTCTTTGAGGACTgtatcctgtt ... gtcacactagACAAGAAGAATGAGAACAAAATAGTTGATGTTGAAGACTTTCTACCAGCTG
EST: gi|31469770|gb|CD411798.1|CD411798
EST:     GGAGCTTCCTCCACATCGGCTTGCTGAAATCAGAAGATTCTTTGAGGACT                         ACAAGAAGAATGAGAACCAAATAGTTGATGTTGAAGACTTTCTACCAGCTG
genomic: GGAGCTTCCTCCACATCGGCTTGCTGAAATCAGAAGATTCTTTGAGGACTgtatcctgtt ... gtcacactagACAAGAAGAATGAGAACAAAATAGTTGATGTTGAAGACTTTCTACCAGCTG
EST: gi|192333274|gb|FK026155.1|FK026155
EST:     GGAGCTTCCTCCACATCGGCTTGCTGAAATCAGAAGATTCTTTGAGGACT                         ACAAGAAGAATGAGAACAAAATAGTTGATGTTGAAGACTTTCTACCAGCTG
genomic: GGAGCTTCCTCCACATCGGCTTGCTGAAATCAGAAGATTCTTTGAGGACTgtatcctgtt ... gtcacactagACAAGAAGAATGAGAACAAAATAGTTGATGTTGAAGACTTTCTACCAGCTG
EST: gi|58022382|gb|CX709123.1|CX709123
EST:     GGAGCTTCCTCCACATCGGCTTGCTGAAATCAGAAGATTCTTTGAGGACT                         ACAAGAAGAATGAGAACAAAATAGTTGATGTTGAAGACTTTCTACCAGCTG
genomic: GGAGCTTCCTCCACATCGGCTTGCTGAAATCAGAAGATTCTTTGAGGACTgtatcctgtt ... gtcacactagACAAGAAGAATGAGAACAAAATAGTTGATGTTGAAGACTTTCTACCAGCTG
EST: gi|22930561|gb|BU547700.1|BU547700
EST:     GGAGCTTCCTCCACATCGGCTTGCTGAAATCAGAAGATTCTTTGAGGACT                         ACAAGAAGAATGAGAACAAAATAGTTGATGTTGAAGACTTTCTACCAGCTG
genomic: GGAGCTTCCTCCACATCGGCTTGCTGAAATCAGAAGATTCTTTGAGGACTgtatcctgtt ... gtcacactagACAAGAAGAATGAGAACAAAATAGTTGATGTTGAAGACTTTCTACCAGCTG
EST: gi|192323914|gb|FK015665.1|FK015665
EST:     GGAGCTTCCTCCACATCGGCTTGCTGAAATCAGAAGATTCTTTGAGGACT                         ACAAGAAGAATGAGAACAAAATAGTTGATGTTGAAGACTTTCTACCAGCTG
genomic: GGAGCTTCCTCCACATCGGCTTGCTGAAATCAGAAGATTCTTTGAGGACTgtatcctgtt ... gtcacactagACAAGAAGAATGAGAACAAAATAGTTGATGTTGAAGACTTTCTACCAGCTG
EST: gi|192321262|gb|FK014352.1|FK014352
EST:     GGAGCTTCCTCCACATCGGCTTGCTGAAATCAGAAGATTCTTTGAGGACT                         ACAAGAAGAATGAGAACAAAATAGTTGATGTTGAAGACTTTTTACCAGCTG
genomic: GGAGCTTCCTCCACATCGGCTTGCTGAAATCAGAAGATTCTTTGAGGACTgtatcctgtt ... gtcacactagACAAGAAGAATGAGAACAAAATAGTTGATGTTGAAGACTTTCTACCAGCTG
EST: gi|192325458|gb|FK018399.1|FK018399
EST:     GGAGCTTCCTCCACATCGGCTTGCTGAAATCAGAAGATTCTTTGAGGACT                         ACAAGAAGAATGAGAACAAAATAGTTGATGTTGAAGACTTTCTACCAGCTG
genomic: GGAGCTTCCTCCACATCGGCTTGCTGAAATCAGAAGATTCTTTGAGGACTgtatcctgtt ... gtcacactagACAAGAAGAATGAGAACAAAATAGTTGATGTTGAAGACTTTCTACCAGCTG
EST: gi|58018488|gb|CX705230.1|CX705230
EST:     GGAGCTTCCTCCACATCGGCTTGCTGAAATCAGAAGATTCTTTGAGGACT                         ACAAGAAGAATGAGAACAAAATAGTTGATGTTGAAGACTTTCTACCAGCTG
genomic: GGAGCTTCCTCCACATCGGCTTGCTGAAATCAGAAGATTCTTTGAGGACTgtatcctgtt ... gtcacactagACAAGAAGAATGAGAACAAAATAGTTGATGTTGAAGACTTTCTACCAGCTG
EST: gi|192316544|gb|FK009313.1|FK009313
EST:     GGAGCTTCCTCCACATCGGCTTGCTGAAATCAGAAGATTCTTTGAGGACT                         ACAAGAAGAATGAGAACAAAATAGTTGATGTTGAAGACTTTCTACCAGCTG
genomic: GGAGCTTCCTCCACATCGGCTTGCTGAAATCAGAAGATTCTTTGAGGACTgtatcctgtt ... gtcacactagACAAGAAGAATGAGAACAAAATAGTTGATGTTGAAGACTTTCTACCAGCTG
EST: gi|151401645|gb|EV271458.1|EV271458
EST:     AGATTCTTTGAGGACT                         ACAAGAAGAATGAGAACAAAATAGTTGATGTTGAAGACTTTCTACCAGCTG
genomic: AGATTCTTTGAGGACTgtatcctgtt ... gtcacactagACAAGAAGAATGAGAACAAAATAGTTGATGTTGAAGACTTTCTACCAGCTG
EST: gi|19934354|gb|BQ079393.1|BQ079393
EST:     GGAGCTTCCTCCACATCGGCTTGCTGAAATCAGAAGATTCTTTGAGGACT                         ACAAGAAGAATGAGAACAAAATAGTTGATGTTGAAGACTTTCTACCAGCTG
genomic: GGAGCTTCCTCCACATCGGCTTGCTGAAATCAGAAGATTCTTTGAGGACTgtatcctgtt ... gtcacactagACAAGAAGAATGAGAACAAAATAGTTGATGTTGAAGACTTTCTACCAGCTG
EST: gi|193553113|gb|FK507748.1|FK507748
EST:     GGAGCTTCCTCCACATCGGCTTGCTGAAATCAGAAGATTCTTTGAGGACT                         ACAAGAAGAATGAGAACAAAATAGTTGATGTTGAAGACTTTCTACCAGCTG
genomic: GGAGCTTCCTCCACATCGGCTTGCTGAAATCAGAAGATTCTTTGAGGACTgtatcctgtt ... gtcacactagACAAGAAGAATGAGAACAAAATAGTTGATGTTGAAGACTTTCTACCAGCTG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATAGCAGTTTGTGCTGATGACCCTGAGTTCCGCCATTACACAGACATCAAGGAGCTTCCTCCACATCGGCTTGCTGAAATCAGAAGATTCTTTGAGGACTgtatcctgttatttgcacttatacataaaccacatgcatctctgtacgagttattgacaattaatgattagtttcttttacaataaagcctatagaacgt

- - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - -  GAGCTT