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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAAGAACGTCGCCTTGTATCAGTTCCGTAACGGCATCCCTCTTACCACCGCCGCCGCCGCCAATTTCACGCGTGGCGAACTCGCCACTGCTCTCCGCAAGgtatcttctaaaccctatctcccatatatcatctcctttctcacttttaggaaaacaaattgagaagctaaaatcaatttatgcatttgctccaatttag...

Basic information

species Glycine max
transcript GLYMA20G38970.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA20G38970.1 (Glycine max), 5'ss of exon 2
lower sequence: LOC_Os03g48930.1 (Oryza sativa), 5'ss of exon 2
GAAGAACGTCGCCTTGTATCAGTTCCGTAACGGCATCCCTCTTACCACCGCCGCCGCCGCCAATTTCACGCGTGGCGAACTCGCCACTGCTCTCCGCAAGgtatct-tctaaaccctatctcccatatatcatctcctttctcacttttaggaaaacaaattgagaagctaaa--atcaatttatgcatttgctccaatttag
||||||  ||  | ||||||||||||| |||  |||||| || | |||||||||| ||||||||||||| || ||||| |||||||| || || || |||||| |  ||   |     |   |      |  ||   | |   | | |        |  |  |    |    |  | | |||||  |  |||   |  |||  
GAAGAATCTCCACCTGTATCAGTTCCGCAACAACATCCCGCTCAGCACCGCCGCCACCGCCAATTTCACCCGCGGCGAGCTCGCCACCGCCCTGCGGAAGgtaccgatccggattggcttctctccccgttttccagtgttctattgtcgattgcgcccaggggttggtctgatcagctatttac-cgattgtggcgtttt--

upper sequence: GLYMA20G38970.1 (Glycine max), 5'ss of exon 2
lower sequence: GRMZM2G097164_T02 (Zea mays), 5'ss of exon 2
GAAGAACGTCGCCTTGTATCAGTTCCGTAACGGCATCCCTCTTACCACCGCCGCCGCCGCCAATTTCACGCGTGGCGAACTCGCCACTGCTCTCCGCAAGgtatcttctaaaccctatctcccatatatcatc-tcctttctcacttttaggaaaacaaattgagaagctaaaatcaatttatg--catttgctccaatttag
||||||| ||  | |||| |||||||| |||  |||||| ||  | ||||||||||||||||| ||||| || |||||||||||||| || || |||||||||        |    ||||    | | || |  | |  | |     ||   |      ||||    | ||  || || |   |  || ||  |  | |    
GAAGAACCTCCACCTGTACCAGTTCCGGAACACCATCCCGCTCTCAACCGCCGCCGCCGCCAACTTCACACGCGGCGAACTCGCCACAGCCCTTCGCAAGgtactaatccgaattaatcttgtttctctctttgtgcgatttgggcgttccaaggttccattggatggatattattaaatggcgttcaatttttttagtc---
















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|27426852|gb|CA938372.1|CA938372
EST:     CCGCCGCCGCCAATTTCACGCGTGGCGAACTCGCCACTGCTCTCCGCAAG                         AACCCATACTCTGTGAACATCCTTCTTGCTGGTTATGACAAAGAGACGGGC
genomic: CCGCCGCCGCCAATTTCACGCGTGGCGAACTCGCCACTGCTCTCCGCAAGgtatcttcta ... ttttctacagAACCCATACTCTGTGAACATCCTTCTTGCTGGTTATGACAAAGAGACGGGC
EST: gi|9901547|gb|BE610515.1|BE610515
EST:     CCGCCGCCGCCAATTTCACGCGTGGCGAACTCGCCACTGCTCTCCGCAAG                         AACCCATACTCTGTGAACATCCTTCTTGCTGGTTATGACAAAGAGACGGGC
genomic: CCGCCGCCGCCAATTTCACGCGTGGCGAACTCGCCACTGCTCTCCGCAAGgtatcttcta ... ttttctacagAACCCATACTCTGTGAACATCCTTCTTGCTGGTTATGACAAAGAGACGGGC
EST: gi|298196926|gb|HO041669.1|HO041669
EST:     CCGCCGCCGCCAATTTCACGCGTGGCGAACTCGCCACTGCTCTCCGCAAG                         AACCCATACTCTGTGAACATCCTTCTTGCTGGTTATGACAAAGAGACGGGC
genomic: CCGCCGCCGCCAATTTCACGCGTGGCGAACTCGCCACTGCTCTCCGCAAGgtatcttcta ... ttttctacagAACCCATACTCTGTGAACATCCTTCTTGCTGGTTATGACAAAGAGACGGGC
EST: gi|254335231|gb|GR846728.1|GR846728
EST:     CCGCCGCCGCCAATTTCACGCGTGGCGAACTCGCCACTGCTCTCCGCAAG                         AACCCATACTCTGTGAACATCCTTCTTGCTGGTTATGACAAAGAGACGGGC
genomic: CCGCCGCCGCCAATTTCACGCGTGGCGAACTCGCCACTGCTCTCCGCAAGgtatcttcta ... ttttctacagAACCCATACTCTGTGAACATCCTTCTTGCTGGTTATGACAAAGAGACGGGC
EST: gi|58025147|gb|CX711888.1|CX711888
EST:     CCGCCGCCGCCAATTTCACGCGTGGCGAACTCGCCACTGCTCTCCGCAAG                         AACCCATACTCTGTGAACATCCTTCTTGCTGGTTATGACAAAGAGACGGGC
genomic: CCGCCGCCGCCAATTTCACGCGTGGCGAACTCGCCACTGCTCTCCGCAAGgtatcttcta ... ttttctacagAACCCATACTCTGTGAACATCCTTCTTGCTGGTTATGACAAAGAGACGGGC
EST: gi|192300124|gb|FG992232.1|FG992232
EST:     CCGCCGCCGCCAATTTCACGCGTGGCGAACTCGCCGCTGCTCTCCGCAAG                         AACCCATACTCTGTGAACATCCTTCTTGCTGGTTATGACAAAGAGACGGGC
genomic: CCGCCGCCGCCAATTTCACGCGTGGCGAACTCGCCACTGCTCTCCGCAAGgtatcttcta ... ttttctacagAACCCATACTCTGTGAACATCCTTCTTGCTGGTTATGACAAAGAGACGGGC
EST: gi|208197371|gb|GD997136.1|GD997136
EST:     CAATTTCACGCGTTGGCGAACTCGCCACTGCTCTCCGCAAG                         AACCCATACTCTGTGAACATCCTTCTTGCTGGCTATGACAAAGAGACGGGC
genomic: CAATTTCACGCG-TGGCGAACTCGCCACTGCTCTCCGCAAGgtatcttcta ... ttttctacagAACCCATACTCTGTGAACATCCTTCTTGCTGGTTATGACAAAGAGACGGGC
EST: gi|9259295|gb|BE347372.1|BE347372
EST:     CCGCCGCCGCCAATTTCACGCGTGGCGAACTCGCCACTGCTCTCCGCAAG                         AACCCATACTCTGTGAACATCCTTCTTGCTGGTTATGACAAAGAGACGGGC
genomic: CCGCCGCCGCCAATTTCACGCGTGGCGAACTCGCCACTGCTCTCCGCAAGgtatcttcta ... ttttctacagAACCCATACTCTGTGAACATCCTTCTTGCTGGTTATGACAAAGAGACGGGC
EST: gi|208047019|gb|GD846020.1|GD846020
EST:     CCGCCGCCGCCAATTTCACGCGTGGCGAACTCGCCACTGCTCTCCGCAAG                         AACCCATACTCTGTGAACATCCTTCTTGTCTGGTTATGACAAAGAGACAGG
genomic: CCGCCGCCGCCAATTTCACGCGTGGCGAACTCGCCACTGCTCTCCGCAAGgtatcttcta ... ttttctacagAACCCATACTCTGTGAACATCCTTCTTG-CTGGTTATGACAAAGAGACGGG
EST: gi|208215837|gb|GE008563.1|GE008563
EST:     CCGCCGCCGCCAATTTCACGCGTGGCGAACTCGCCACTGCTCTCCGCAAG                         AACCCATACTCTGTGAACATCCTTCTTGCTGGTTATGACAAAGAGACGGGC
genomic: CCGCCGCCGCCAATTTCACGCGTGGCGAACTCGCCACTGCTCTCCGCAAGgtatcttcta ... ttttctacagAACCCATACTCTGTGAACATCCTTCTTGCTGGTTATGACAAAGAGACGGGC
EST: gi|13480010|gb|BG509353.1|BG509353
EST:     CCGCCGCCGCCAATTTCACGCGTGGCGAACTCGCCACTGCTCTCCGCAAG                         AACCCATACTCTGTGAACATCCTTCTTGCTGGTTATGACAAAGAGACGGGC
genomic: CCGCCGCCGCCAATTTCACGCGTGGCGAACTCGCCACTGCTCTCCGCAAGgtatcttcta ... ttttctacagAACCCATACTCTGTGAACATCCTTCTTGCTGGTTATGACAAAGAGACGGGC
EST: gi|298177460|gb|HO023593.1|HO023593
EST:     CCGCCGCCGCCAATTTCACGCGTGGCGAACTCGCCACTGCTCTCCGCAAG                         AACCCATACTCTGTGAACATCCTTCTTGCTGGTTATGACAAAGAGACGGGC
genomic: CCGCCGCCGCCAATTTCACGCGTGGCGAACTCGCCACTGCTCTCCGCAAGgtatcttcta ... ttttctacagAACCCATACTCTGTGAACATCCTTCTTGCTGGTTATGACAAAGAGACGGGC
EST: gi|254325949|gb|GR838830.1|GR838830
EST:     CCGCCGCCGCCAATTTCACGCGTGGCGAACTCGCCACTGCTCTCCGCAAG                         AACCCATACTCTGTGAACATCCTTCTTGCTGGTTATGACAAAGAGACGGGC
genomic: CCGCCGCCGCCAATTTCACGCGTGGCGAACTCGCCACTGCTCTCCGCAAGgtatcttcta ... ttttctacagAACCCATACTCTGTGAACATCCTTCTTGCTGGTTATGACAAAGAGACGGGC
EST: gi|151397676|gb|EV267549.1|EV267549
EST:     CCGCCGCCGCCAATTTCACGCGTGGCGAACTCGCCACTGCTCTCCGCAAG                         AACCCATACTCTGTGAACATCCTTCTTGCTGGTTATGACAAAGAGACGGGC
genomic: CCGCCGCCGCCAATTTCACGCGTGGCGAACTCGCCACTGCTCTCCGCAAGgtatcttcta ... ttttctacagAACCCATACTCTGTGAACATCCTTCTTGCTGGTTATGACAAAGAGACGGGC
EST: gi|15813614|gb|BI785889.1|BI785889
EST:     CCGCCGCCGCCAATTTCACGCGTGGCGAACTCGCCACTGCTCTCCGCAAG                         AACCCATACTCTGTGAACATCCTTCTTGCTGGTTATGACAAAGAGACGGGC
genomic: CCGCCGCCGCCAATTTCACGCGTGGCGAACTCGCCACTGCTCTCCGCAAGgtatcttcta ... ttttctacagAACCCATACTCTGTGAACATCCTTCTTGCTGGTTATGACAAAGAGACGGGC
EST: gi|9902807|gb|BE611775.1|BE611775
EST:     CCGCCGCCGCCAATTTCACGCGTGGCGAACTCGCCACTGCTCTCCGCAAG                         AACCCATACTCTGTGAACATCCTTCTTGCTGGTTATGACAAAGAGACGGGC
genomic: CCGCCGCCGCCAATTTCACGCGTGGCGAACTCGCCACTGCTCTCCGCAAGgtatcttcta ... ttttctacagAACCCATACTCTGTGAACATCCTTCTTGCTGGTTATGACAAAGAGACGGGC
EST: gi|298195591|gb|HO043982.1|HO043982
EST:     CCGCCGCCGCCAATTTCACGCGTGGCGAACTCGCCACTGCTCTCCGCAAG                         AACCCATACTCTGTGAACATCCTTCTTGCTGGTTATGACAAAGAGACGGGC
genomic: CCGCCGCCGCCAATTTCACGCGTGGCGAACTCGCCACTGCTCTCCGCAAGgtatcttcta ... ttttctacagAACCCATACTCTGTGAACATCCTTCTTGCTGGTTATGACAAAGAGACGGGC
EST: gi|21285827|gb|BQ473698.1|BQ473698
EST:     CCGCCGCCGCCAATTTCACGCGTGGCGAACTCGCCACTGCTCTCCGCAAG                         AACCCATACTCTGTGAACATCCTTCTTGCTGGTTATGACAAAGAGACGGGC
genomic: CCGCCGCCGCCAATTTCACGCGTGGCGAACTCGCCACTGCTCTCCGCAAGgtatcttcta ... ttttctacagAACCCATACTCTGTGAACATCCTTCTTGCTGGTTATGACAAAGAGACGGGC
EST: gi|192300108|gb|FG992231.1|FG992231
EST:     CCGCCGCCGCCAATTTCACGCGTGGCGAACTCGCCGCTGCTCTCCGCAAG                         AACCCATACTCTGTGAACATCCTTCTTGCTGGTTATGACAAAGAGACGGGC
genomic: CCGCCGCCGCCAATTTCACGCGTGGCGAACTCGCCACTGCTCTCCGCAAGgtatcttcta ... ttttctacagAACCCATACTCTGTGAACATCCTTCTTGCTGGTTATGACAAAGAGACGGGC
EST: gi|8402648|gb|BE058282.1|BE058282
EST:     GCCAATTTCACGCGTGGCGAACTCGCCACTGCTCTCCGCAAG                         AACCCATACTCTGTGAACATCCTTCTTGCTGGTTATGACAAAGAGACGGGC
genomic: GCCAATTTCACGCGTGGCGAACTCGCCACTGCTCTCCGCAAGgtatcttcta ... ttttctacagAACCCATACTCTGTGAACATCCTTCTTGCTGGTTATGACAAAGAGACGGGC
EST: gi|298172982|gb|HO019981.1|HO019981
EST:     CCGCCGCCGCCAATTTCACGCGTGGCGAACTCGCCACTGCTCTCCGCAAG                         AACCCATACTCTGTGAACATCCTTCTTGCTGGTTATGACAAAGAGACGGGC
genomic: CCGCCGCCGCCAATTTCACGCGTGGCGAACTCGCCACTGCTCTCCGCAAGgtatcttcta ... ttttctacagAACCCATACTCTGTGAACATCCTTCTTGCTGGTTATGACAAAGAGACGGGC
EST: gi|298165711|gb|HO008682.1|HO008682
EST:     CCGCCGCCGCCAATTTCACGCGTGGCGAACTCGCCACTGCTCTCCGCAAG                         AACCCATACTCTGTGAACATCCTTCTTGCTGGTTATGACAAAGAGACGGGC
genomic: CCGCCGCCGCCAATTTCACGCGTGGCGAACTCGCCACTGCTCTCCGCAAGgtatcttcta ... ttttctacagAACCCATACTCTGTGAACATCCTTCTTGCTGGTTATGACAAAGAGACGGGC
EST: gi|58019270|gb|CX706012.1|CX706012
EST:     CCGCCGCCGCCAATTTCACGCGTGGCGAACTCGCCACTGCTCTCCGCAAG                         AACCCATACTCTGTGAACATCCTTCTTGCTGGTTATGACAAAGAGACGGGC
genomic: CCGCCGCCGCCAATTTCACGCGTGGCGAACTCGCCACTGCTCTCCGCAAGgtatcttcta ... ttttctacagAACCCATACTCTGTGAACATCCTTCTTGCTGGTTATGACAAAGAGACGGGC
EST: gi|298194947|gb|HO043419.1|HO043419
EST:     CCGCCGCCGCCAATTTCACGCGTGGCGAACTCGCCACTGCTCTCCGCAAG                         AACCCATACTCTGTGAACATCCTTCTTGCTGGTTATGACAAAGAGACGGGC
genomic: CCGCCGCCGCCAATTTCACGCGTGGCGAACTCGCCACTGCTCTCCGCAAGgtatcttcta ... ttttctacagAACCCATACTCTGTGAACATCCTTCTTGCTGGTTATGACAAAGAGACGGGC
EST: gi|4437057|gb|AI522922.1|AI522922
EST:     CCGCCGCCGCCAATTTCACGCGTGGCGAACTCGCCACTGCTCTCCGCAAG                         AACCCATACTCTGTGAACATCCTTCTTGCTGGTTATGACAAAGAGACGGGC
genomic: CCGCCGCCGCCAATTTCACGCGTGGCGAACTCGCCACTGCTCTCCGCAAGgtatcttcta ... ttttctacagAACCCATACTCTGTGAACATCCTTCTTGCTGGTTATGACAAAGAGACGGGC
EST: gi|192305778|gb|FG995720.1|FG995720
EST:     CCGCCGCCGCCAATTTCACGCGTGGCGAACTCGCCGCTGCTCTCCGCAAG                         AACCCATACTCTGTGAACATCCTTCTTGCTGGTTATGACAAAGAGACGGGC
genomic: CCGCCGCCGCCAATTTCACGCGTGGCGAACTCGCCACTGCTCTCCGCAAGgtatcttcta ... ttttctacagAACCCATACTCTGTGAACATCCTTCTTGCTGGTTATGACAAAGAGACGGGC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAAGAACGTCGCCTTGTATCAGTTCCGTAACGGCATCCCTCTTACCACCGCCGCCGCCGCCAATTTCACGCGTGGCGAACTCGCCACTGCTCTCCGCAAGgtatcttctaaaccctatctcccatatatcatctcctttctcacttttaggaaaacaaattgagaagctaaaatcaatttatgcatttgctccaatttag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctatctcc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ggaaaaca