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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGTATCGAAGGGCGCAACTTGCTCTTCAGAAGGGAGACGAGGAACTTGCCCGTGAGGCACTTAAGAGAAGAAAGTCTTATGCggtacgtcatttgactatctaaaagctttgttgtatttgagttttatgcatcataaatgtgaataatatgcattacatataggtcttgatatgagattat...

Basic information

species Glycine max
transcript GLYMA18G47890.1
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA18G47890.1 (Glycine max), 5'ss of exon 5
lower sequence: LOC_Os01g67000.1 (Oryza sativa), 5'ss of exon 5
GGTATCGAAGGGCGCAACTTGCTCTTCAGAAGGGAGACGAGGAACTTGCCCGTGAGGCACTTAAGAGAAGAAAGTCTTATGCggtacgtcatttgactatctaaaagctttgttgtatttgagttttatgcatcataaatgtgaataa-tatgc-attacatataggtcttgatatgagattat----
 |||||| ||||| |||||||||||||||||||| || ||||| ||||| ||||| || |||||| |  | || || ||||| ||| ||    ||   |||||||     |  || ||   || | |   |||   | || ||| ||| ||  | ||||  | ||    ||  ||     |  |    
-GTATCGGAGGGCTCAACTTGCTCTTCAGAAGGGTGATGAGGATCTTGCTCGTGAAGCCCTTAAGCGGCGTAAATCATATGCTgtaggtatcatgcaaatctaaag----ttctggatcaaagatctgcccatatcatat-tgagtaactacacgattagttttaaaatttcttactctttcgtgtgc

upper sequence: GLYMA18G47890.1 (Glycine max), 5'ss of exon 5
lower sequence: GRMZM2G017077_T01 (Zea mays), 5'ss of exon 5
GGTATCGAAGGGCGCAACTTGCTCTTCAGAAGGGAGACGAGGAACTTGCCCGTGAGGCACTTAAGAGAAGAAAGTCTTATGCggtacgt-catttgactatctaaa----agctttgttgtatttgagttttatgcatcataaatgtgaat--aatatgcattacatataggtcttg-atatgagattat-----------------------------------------------
 |||||| ||||| |||||||||||||| ||||| |||||||| ||||| ||||| || |||||| |  | || || ||||| ||| ||    ||||  || |  |    |   |  |||| || |  |    | |  |||  ||  ||||  ||| |   ||||||||   | |   || |   || |                                                
-GTATCGGAGGGCTCAACTTGCTCTTCAAAAGGGTGACGAGGATCTTGCTCGTGAAGCCCTTAAGCGGCGTAAATCATATGCTgtatgtgtccttgatgatgtgtagtacaatgtgcttgttttaggatcccttaccacattgattggaatagaatgtatgttacatatctatgtgacatgttgaatcaacatatcgaagtcctaatatagacttactatttgtgtggtttgtttag

upper sequence: GLYMA18G47890.1 (Glycine max), 5'ss of exon 5
lower sequence: GRMZM2G024607_T01 (Zea mays), 5'ss of exon 5
GGTATCGAAGGGCGCAACTTGCTCTTCAGAAGGGAGACGAGGAACTTGCCCGTGAGGCACTTAAGAGAAGAAAGTCTTATGCggtacgt-catttgactatcta----aaagctttgttgtatttgagttttatgcatcataaatgtgaataatatgcattacatataggtcttgatatgagattat-------------------------------------------------------------
 |||||||||||| |||||||||||||| ||||| |||||||| ||||| || || || |||||| |  | || || ||||| ||| ||    ||||  || |     | |   |  |||| || |  |||  | |  |||  ||  |||||  ||  ||   | ||      ||  |   | || |                                                             
-GTATCGAAGGGCTCAACTTGCTCTTCAAAAGGGTGACGAGGATCTTGCTCGCGAAGCCCTTAAGCGGCGTAAATCATATGCTgtatgtgtcattgatgatgtgtagtacaatgtgcttgttttaggttttcttaccacattgattcgaatagaatttatgttacattatctatgcgacatgttttttttcaacagtctatgctgttgaatcaacatatcaaattgtattgcgtgattgtttgcttag

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|192306186|gb|FG995036.1|FG995036
EST:     GGAGACGAGGAACTTGCCCGTGAGGCACTTAAGAGAAGAAAGTCTTATGC                         GGATAATGCAACTGCTTTGAAGATGCAGCTTGATCAGCAAAAGAATGTTGC
genomic: GGAGACGAGGAACTTGCCCGTGAGGCACTTAAGAGAAGAAAGTCTTATGCggtacgtcat ... ggtatgtacaGGATAATGCAACTGCTTTGAAGATGCAGCTTGATCAGCAAAAGAATGTTGC
EST: gi|151412234|gb|EV282046.1|EV282046
EST:     GGAGACGAGGAACTTGCCCGTGAGGCACTTAAGAGAAGAAAGTCTTATGC                         GGATAATGCCACTGCTTTTGAAGATGCAGCTTGATCAGCAAAAGAATGTTG
genomic: GGAGACGAGGAACTTGCCCGTGAGGCACTTAAGAGAAGAAAGTCTTATGCggtacgtcat ... ggtatgtacaGGATAATGCAACTGCTTT-GAAGATGCAGCTTGATCAGCAAAAGAATGTTG
EST: gi|192294504|gb|FG987433.1|FG987433
EST:     GGAGACGAGGAACTTGCCCGTGAGGCACTTAAGAGAAGAAAGTCTTATGC                         GGATAATGCAACTGCTTTGAAGATGCAGCTTGATCAGCAAAAGAATGTTGC
genomic: GGAGACGAGGAACTTGCCCGTGAGGCACTTAAGAGAAGAAAGTCTTATGCggtacgtcat ... ggtatgtacaGGATAATGCAACTGCTTTGAAGATGCAGCTTGATCAGCAAAAGAATGTTGC
EST: gi|151398835|gb|EV268706.1|EV268706
EST:     GGAGACGAGGAACTTGCCCGTGAGGCACTTAAGAGAAGAAAGTCTTATGC                         GGATAATGCAACTGCTTTGAAGATGCAGCTTGATCAGCAAAAGAATGTTGC
genomic: GGAGACGAGGAACTTGCCCGTGAGGCACTTAAGAGAAGAAAGTCTTATGCggtacgtcat ... ggtatgtacaGGATAATGCAACTGCTTTGAAGATGCAGCTTGATCAGCAAAAGAATGTTGC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGTATCGAAGGGCGCAACTTGCTCTTCAGAAGGGAGACGAGGAACTTGCCCGTGAGGCACTTAAGAGAAGAAAGTCTTATGCggtacgtcatttgactatctaaaagctttgttgtatttgagttttatgcatcataaatgtgaataatatgcattacatataggtcttgatatgagattat

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA