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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTAACTGTTGGAGCTTCTTTTTTGTCACAAACAATAGCTCTGCAAGACTCTACAACAGTCAAGTTTGAAATATGGGATACTGCTGGTCAAGAGAGgtgactctcatttatctttccagattaatcataatctattgtacaaaccattcttttttcaacaaaaaatgatttttgaaataaaatttgtttgctaattctctatttcag

Basic information

species Glycine max
transcript GLYMA20G32320.1
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA20G32320.1 (Glycine max), 5'ss of exon 4
lower sequence: LOC_Os10g30520.1 (Oryza sativa), 5'ss of exon 4
GTAACTGTTGGAGCTTCTTTTTTGTCACAAACAATAGCTCTGCAAGACTCTACAACAGTCAAGTTTGAAATATGGGATACTGCTGGTCAAGAGAGgtgactctcatttatctttccagattaatcataatctattgtacaaaccattcttttttcaacaaaaaatgatttttgaaataaaatttgtttgctaattctctatttcag-----------------------------------------------------------------------------
|| |||||||| || || ||||||||||||||| | ||  || | || || |||||||| ||||||||||||||||||||||||||||| ||||||||  |     |||        ||||||  ||  ||    || ||  |     ||   ||   |  |    |||| || |  |   |||| ||   |  | |||  ||||                                                                              
GTGACTGTTGGTGCATCATTTTTGTCACAAACATTGGCGTTGGAGGATTCCACAACAGTAAAGTTTGAAATATGGGATACTGCTGGTCAGGAGAGgtgcataaatattagaagctttgattaactattttcccaagtgcatccttgcattaactctgtactatggaatttctgtaccatcttttgcttcacatatgtcttcttcacccttgatttacattgtttgcaagcatatgtgttgctattcgttaccaaagaagtcacgagaactggttaattttcag

upper sequence: GLYMA20G32320.1 (Glycine max), 5'ss of exon 4
lower sequence: LOC_Os03g05740.1 (Oryza sativa), 5'ss of exon 4
GTAACTGTTGGAGCTTCTTTTTTGTCACAAACAATAGCTCTGCAAGACTCTACAACAGTCAAGTTTGAAATATGGGATACTGCTGGTCAAGAGAGgtg-actctcatt--tatctttccagattaatcataatctattgtacaaaccattctttt--ttcaacaaaaa-atgatttttgaaataaaatttgtttgcta---attctctatttcag-----------------------------------------------------------------------------
|||||||| || || || ||||| ||||||||| | ||| || | ||||| |||| ||| || ||||||||||||||||| ||||| ||||||||||  ||   ||    |||  ||  || ||  ||  |||||   |   |   ||| || ||  | ||  | ||  ||   |||||  | ||| ||    |  ||    ||    ||||                                                                                
GTAACTGTCGGTGCATCATTTTTATCACAAACATTGGCTTTGGAGGACTCAACAATAGTGAAATTTGAAATATGGGATACCGCTGGACAAGAGAGgtacacatacagcactatggttttagcttcttc-caatcttgggataatggcatgctgttggtgcattagaagcattggttttgtgagaaagttctagtagtatgtgttactgatttttacaattgatccatcttacgtgccacacatgcatatggtttttctcaatcaagaactcattggtaccagccaattttag

upper sequence: GLYMA20G32320.1 (Glycine max), 5'ss of exon 4
lower sequence: GRMZM2G362088_T02 (Zea mays), 5'ss of exon 5
GTAACTGTTGGAGCTTCTTTTTTGTCACAAACAATAGCTCTGCAAGACTCTACAACAGTCAAGTTTGAAATATGGGATACTGCTGGTCAAGAGAGgtgactctcatttatctttccagattaatcataatctattgtacaaaccattcttttttcaacaaaaaatgatttttga-aataaaatttgtttgctaattctctatttcag-------------------------------------------------------------------------
||||||||||| || |||||||| ||||||||| | ||  || | || || |||| ||| ||||||||||| |||||||||||||| |||||||||| | |      |    |      ||| |    ||   |  |    |   ||       |      | | ||||| ||| | ||   ||||     |   ||  | ||||                                                                           
GTAACTGTTGGCGCATCTTTTTTATCACAAACATTGGCATTGGAGGATTCAACAATAGTGAAGTTTGAAATTTGGGATACTGCTGGGCAAGAGAGgtaatttggtgctgagatcagtacttattttggatacctaattgggatactttgccgcacgtacccacaggatttctgatagtattctttgcacatttgatccatctttctttgcaagcacaacagcacatgcatgtttttgcctgaatcaagagtcatgagaattgagagcttgtcaatttcag

upper sequence: GLYMA20G32320.1 (Glycine max), 5'ss of exon 4
lower sequence: AT3G54840.2 (Arabidopsis thaliana), 5'ss of exon 4
GTAACTGTTGGAGCTTCTTTTTTGTCACAAACAATAGCTCTGCAAGACTCTACAACAGTCAAGTTTGAAATATGGGATACTGCTGGTCAAGAGAGgtgactctcatttatctttccagattaatcataatctattgtacaaaccattcttttttcaacaaaaaatgatttttgaaataaaatttgtttgctaattctctatttcag
|||||||||||||| || || ||||| ||||| |||||  ||||||||||||| ||||| |||||||||||||||||||| || || || |||||||     | |    |   | ||||||  | ||    |||| ||  |   |  |  ||| |||          ||  |   ||  ||  ||     | | | | | ||| ||
GTAACTGTTGGAGCCTCGTTCTTGTCCCAAACTATAGCATTGCAAGACTCTACCACAGTGAAGTTTGAAATATGGGATACAGCAGGACAGGAGAGgta---ttaaacccttcatgcagatttgt-attgcttattttattagataaacgctttgcaa--------acttactaggatttaacctgc--attcactttat-ttttag

upper sequence: GLYMA20G32320.1 (Glycine max), 5'ss of exon 4
lower sequence: Vv13s0019g04680.t01 (Vitis vinifera), 5'ss of exon 4
GTAACTGTTGGAGCTTCTTTTTTGTCACAAACAATAGCTCTGCAAGACTCTACAACAGTCAAGTTTGAAATATGGGATACTGCTGGTCAAGAGAGgtgactctcat-------ttatctttccagattaatcat--aatctattgtacaaaccattcttttttcaacaaaaaatgatttttga---aataaaatttgtttgctaat-tctctatttcag---------------------------------------------
|| ||||| |||||||| || |||||||||||||| ||  ||||||| ||||| ||||| ||||||||||||||||| |||||||||||||||||||  |  |          || | ||||| | | |   ||   |  |  |  |   |  |    |   |||||  | | |  | ||      | | ||||   | |     | ||||| || ||                                              
GTGACTGTAGGAGCTTCATTCTTGTCACAAACAATTGCCTTGCAAGATTCTACGACAGTTAAGTTTGAAATATGGGACACTGCTGGTCAAGAGAGgtatcattggccaacccattttttttcctgttcacctatctgactttctaaattcaatagaaataactcaacttatagtcttcttgagtctattgaaatggatctagagctctctctcttccatgaaaacccatttgagaaaattacagaggataacttcattcctcag

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|298188274|gb|HO034967.1|HO034967
EST:     GACTCTACAACAGTCAAGTTTGAAATATGGGATACTGCTGGTCAAGAGAG                         GTACGCTGCGTTAGCACCACTCTATTACCGTGGTGCAGCAGTTGCAGTTAT
genomic: GACTCTACAACAGTCAAGTTTGAAATATGGGATACTGCTGGTCAAGAGAGgtgactctca ... tctatttcagGTACGCTGCGTTAGCACCACTCTATTACCGTGGTGCAGCAGTTGCAGTTAT
EST: gi|8670136|gb|BE191243.1|BE191243
EST:     CTGGTCAAGAGAG                         GTACGCTGCGTTAGCACCACTCTATTACCGTGGTGCAGCAGTTGCAGTTAT
genomic: CTGGTCAAGAGAGgtgactctca ... tctatttcagGTACGCTGCGTTAGCACCACTCTATTACCGTGGTGCAGCAGTTGCAGTTAT
EST: gi|151401597|gb|EV271411.1|EV271411
EST:     GACTCTACAACAGTCAAGTTTGAAATATGGGATACTGCTGGTCAAGAGAG                         GTACGCTGCGTTAGCACCACTCTATTACCGTGGTGCAGCAGTTGCAGTTAT
genomic: GACTCTACAACAGTCAAGTTTGAAATATGGGATACTGCTGGTCAAGAGAGgtgactctca ... tctatttcagGTACGCTGCGTTAGCACCACTCTATTACCGTGGTGCAGCAGTTGCAGTTAT
EST: gi|14009240|gb|BG725844.1|BG725844
EST:     GACTCTACAACAGTCAAGTTTGAAATATGGGATACTGCTGGTCAAGAGAG                         GTACGCTGCGTTAGCACCACTCTATTACCGTGGTGCAGCAGTTGCAGTTAT
genomic: GACTCTACAACAGTCAAGTTTGAAATATGGGATACTGCTGGTCAAGAGAGgtgactctca ... tctatttcagGTACGCTGCGTTAGCACCACTCTATTACCGTGGTGCAGCAGTTGCAGTTAT
EST: gi|21887641|gb|BQ740854.1|BQ740854
EST:     GACTCTACAACAGTCAAGTTTGAAATATGGGATACTGCTGGTCAAGAGAG                         GTACGCTGCGTTAGCACCACTCTATTACCGTGGTGCAGCAGTTGC
genomic: GACTCTACAACAGTCAAGTTTGAAATATGGGATACTGCTGGTCAAGAGAGgtgactctca ... tctatttcagGTACGCTGCGTTAGCACCACTCTATTACCGTGGTGCAGCAGTTGC
EST: gi|120530730|gb|EH258863.1|EH258863
EST:     GACTCTACAACAGTCAAGTTTGAAATATGGGATACTGCTGGTCAAGAGAG                         GTACGCTGCGTTAGCACCACTCTATTACCGTGGTGCAGCAGTTGCAGTTAT
genomic: GACTCTACAACAGTCAAGTTTGAAATATGGGATACTGCTGGTCAAGAGAGgtgactctca ... tctatttcagGTACGCTGCGTTAGCACCACTCTATTACCGTGGTGCAGCAGTTGCAGTTAT
EST: gi|33388034|gb|CA851241.1|CA851241
EST:     GACTCTACAACAGTCAAGTTTGAAATATGGGATACTGCTGGTCAAGAGAG                         GTACGCTGCGTTAGCACCACTCTATTACCGTGGTGCAGCAGTTGCAGTTAT
genomic: GACTCTACAACAGTCAAGTTTGAAATATGGGATACTGCTGGTCAAGAGAGgtgactctca ... tctatttcagGTACGCTGCGTTAGCACCACTCTATTACCGTGGTGCAGCAGTTGCAGTTAT
EST: gi|208062999|gb|GD860901.1|GD860901
EST:     TTTGAAATATGGGATACTGCTGGTCAAGAGAG                         GTACGCTGCGTTAGCACCACTCTATTACCGTGGTGCAGCAGTTGCAGTTAT
genomic: TTTGAAATATGGGATACTGCTGGTCAAGAGAGgtgactctca ... tctatttcagGTACGCTGCGTTAGCACCACTCTATTACCGTGGTGCAGCAGTTGCAGTTAT
EST: gi|8670147|gb|BE191254.1|BE191254
EST:     CTGGTCAAGAGAG                         GTACGCTGCGTTAGCACCACTCTATTACCGTGGTGCAGCAGTTGCAGTTAT
genomic: CTGGTCAAGAGAGgtgactctca ... tctatttcagGTACGCTGCGTTAGCACCACTCTATTACCGTGGTGCAGCAGTTGCAGTTAT
EST: gi|120530900|gb|EH259033.1|EH259033
EST:     GACTCTACAACAGTCAAGTTTGAAATATGGGATACTGCTGGTCAAGAGAG                         GTACGCTGCGTTAGCACCACTCTATTACCGTGGTGCAGCAGTTGCAGTTAT
genomic: GACTCTACAACAGTCAAGTTTGAAATATGGGATACTGCTGGTCAAGAGAGgtgactctca ... tctatttcagGTACGCTGCGTTAGCACCACTCTATTACCGTGGTGCAGCAGTTGCAGTTAT
EST: gi|208127836|gb|GD924910.1|GD924910
EST:     TTTGAAATATGGGATACTGCTGGTCAAGAGAG                         GTATGCTGCGTTAGCACCGCTATATTACCGTGGTGCAGCAGTTGCAGTTAT
genomic: TTTGAAATATGGGATACTGCTGGTCAAGAGAGgtgactctca ... tctatttcagGTACGCTGCGTTAGCACCACTCTATTACCGTGGTGCAGCAGTTGCAGTTAT
EST: gi|213603351|gb|DB966610.1|DB966610
EST:     GACTCTACAACAGTCAAGTTTGAAATATGGGATACTGCTGGTCAAGAGAG                         GTACGCTGCGTTAGCACCACTCTATTACCGTGGTGCAGCAGTTGCAGTTAT
genomic: GACTCTACAACAGTCAAGTTTGAAATATGGGATACTGCTGGTCAAGAGAGgtgactctca ... tctatttcagGTACGCTGCGTTAGCACCACTCTATTACCGTGGTGCAGCAGTTGCAGTTAT
EST: gi|14126037|gb|BG790475.1|BG790475
EST:     GACTCTACAACAGTCAAGTTTGAAATATGGGATACTGCTGGTCAAGAGAG                         GTACGCTGCGTTAGCACCACTCTATTACCGTGGTGCAGCAGTTGCAGTTAT
genomic: GACTCTACAACAGTCAAGTTTGAAATATGGGATACTGCTGGTCAAGAGAGgtgactctca ... tctatttcagGTACGCTGCGTTAGCACCACTCTATTACCGTGGTGCAGCAGTTGCAGTTAT
EST: gi|11687687|gb|BF595363.1|BF595363
EST:     GACTCTACAACAGTCAAGTTTGAAATATGGGATACTGCTGGTCAAGAGAG                         GTACGCTGCGTTAGCACCACTCTATTACCGTGGTGCAGCAGTTGCAGTTAT
genomic: GACTCTACAACAGTCAAGTTTGAAATATGGGATACTGCTGGTCAAGAGAGgtgactctca ... tctatttcagGTACGCTGCGTTAGCACCACTCTATTACCGTGGTGCAGCAGTTGCAGTTAT
EST: gi|58017129|gb|CX703871.1|CX703871
EST:     GACTCTACAACAGTCAAGTTTGAAATATGGGATACTGCTGGTCAAGAGAG                         GTACGCTGCGTTAGCACCACTCTATTACCGTGGTGCAGCAGTTGCAGTTAT
genomic: GACTCTACAACAGTCAAGTTTGAAATATGGGATACTGCTGGTCAAGAGAGgtgactctca ... tctatttcagGTACGCTGCGTTAGCACCACTCTATTACCGTGGTGCAGCAGTTGCAGTTAT
EST: gi|151409251|gb|EV279059.1|EV279059
EST:     GACTCTACAACAGTCAAGTTTGAAATATGGGATACTGCTGGTCAAGAGAG                         GTACGCTGCGTTAGCACCACTCTATTACCGTGGTGCAGCAGTTGCAGTTAT
genomic: GACTCTACAACAGTCAAGTTTGAAATATGGGATACTGCTGGTCAAGAGAGgtgactctca ... tctatttcagGTACGCTGCGTTAGCACCACTCTATTACCGTGGTGCAGCAGTTGCAGTTAT
EST: gi|192303625|gb|FG998635.1|FG998635
EST:     GACTCTACAACAGTCAAGTTTGAAATATGGGATACTGCTGGTCAAGAGAG                         GTACGCTGCGTTAGCACCACTCTATTACCGTGGTGCAGCAGTTGCAGTTAT
genomic: GACTCTACAACAGTCAAGTTTGAAATATGGGATACTGCTGGTCAAGAGAGgtgactctca ... tctatttcagGTACGCTGCGTTAGCACCACTCTATTACCGTGGTGCAGCAGTTGCAGTTAT
EST: gi|208141217|gb|GD934383.1|GD934383
EST:     GACTCTACAACAGTCAAGTTTGAAATATGGGATACTGCTGGTCAAGAGAG                         GTACGCTGCGTTAGCACCACTCTATTACCGTGGTGCAGCAGTTGCAGTTAT
genomic: GACTCTACAACAGTCAAGTTTGAAATATGGGATACTGCTGGTCAAGAGAGgtgactctca ... tctatttcagGTACGCTGCGTTAGCACCACTCTATTACCGTGGTGCAGCAGTTGCAGTTAT
EST: gi|151399728|gb|EV269599.1|EV269599
EST:     GACTCTACAACAGTCAAGTTTGAAATATGGGATACTGCTGGTCAAGAGAG                         GTACGCTGCGTTAGCACCACTCTATTACCGTGGTGCAGCAGTTGCAGTTAT
genomic: GACTCTACAACAGTCAAGTTTGAAATATGGGATACTGCTGGTCAAGAGAGgtgactctca ... tctatttcagGTACGCTGCGTTAGCACCACTCTATTACCGTGGTGCAGCAGTTGCAGTTAT
EST: gi|13478097|gb|BG507714.1|BG507714
EST:     GACTCTACAACAGTCAAGTTTGAAATATGGGATACTGCTGGTCAAGAGAG                         GTACGCTGCGTTAGCACCACTCTATTACCGTGGTGCAGCAGTTGCAGTTAT
genomic: GACTCTACAACAGTCAAGTTTGAAATATGGGATACTGCTGGTCAAGAGAGgtgactctca ... tctatttcagGTACGCTGCGTTAGCACCACTCTATTACCGTGGTGCAGCAGTTGCAGTTAT
EST: gi|19053755|gb|BM732422.1|BM732422
EST:     GACTCTACAACAGTCAAGTTTGAAATATGGGATACTGCTGGTCAAGAGAG                         GTACGCTGCGTTAGCACCACTCTATTACCGTGGTGCAGCAGTTGCAGTTAT
genomic: GACTCTACAACAGTCAAGTTTGAAATATGGGATACTGCTGGTCAAGAGAGgtgactctca ... tctatttcagGTACGCTGCGTTAGCACCACTCTATTACCGTGGTGCAGCAGTTGCAGTTAT
EST: gi|6912828|gb|AW394312.1|AW394312
EST:     GACTCTACAACAGTCAAGTTTGAAATATGGGATACTGCTGGTCAAGAGAG                         GTACGCTGCGTTAGCACCACTCTATTACCGTGGTGCAGCAGTTGCAGTTAT
genomic: GACTCTACAACAGTCAAGTTTGAAATATGGGATACTGCTGGTCAAGAGAGgtgactctca ... tctatttcagGTACGCTGCGTTAGCACCACTCTATTACCGTGGTGCAGCAGTTGCAGTTAT
EST: gi|6665996|gb|AW277455.1|AW277455
EST:     GACTCTACAACAGTCAAGTTTGAAATATGGGATACTGCTGGTCAAGAGAG                         GTACGCTGCGTTAGCACCACTCTATTACCGTGGTGCAGCAGTTGCAGTTAT
genomic: GACTCTACAACAGTCAAGTTTGAAATATGGGATACTGCTGGTCAAGAGAGgtgactctca ... tctatttcagGTACGCTGCGTTAGCACCACTCTATTACCGTGGTGCAGCAGTTGCAGTTAT
EST: gi|6667685|gb|AW279136.1|AW279136
EST:     GGGATACTGCTGGTCAAGAGAG                         GTACGCTGCGTTAGCACCACTCTATTACCGTGGTGCAGCAGTTGCAGTTAT
genomic: GGGATACTGCTGGTCAAGAGAGgtgactctca ... tctatttcagGTACGCTGCGTTAGCACCACTCTATTACCGTGGTGCAGCAGTTGCAGTTAT
EST: gi|6455577|gb|AW186260.1|AW186260
EST:     GACTCTACAACAGTCAAGTTTGAAATATGGGATACTGCTGGTCAAGAGAG                         GTACGCTGCGTTAGCACCACTCTATTACCGTGGTGCAGCAGTTGCAGTTAT
genomic: GACTCTACAACAGTCAAGTTTGAAATATGGGATACTGCTGGTCAAGAGAGgtgactctca ... tctatttcagGTACGCTGCGTTAGCACCACTCTATTACCGTGGTGCAGCAGTTGCAGTTAT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTAACTGTTGGAGCTTCTTTTTTGTCACAAACAATAGCTCTGCAAGACTCTACAACAGTCAAGTTTGAAATATGGGATACTGCTGGTCAAGAGAGgtgactctcatttatctttccagattaatcataatctattgtacaaaccattcttttttcaacaaaaaatgatttttgaaataaaatttgtttgctaattctctatttcag

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