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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATTAGAAAAGAAGACATGAATAAATTGGTAATGAATTTCCTTGTCACCGAAGGCTATGTTGAAGCTGCTGAGAAATTTCGAATGGAGTCTGGAACTGAACgcatcctttttattaatttatttatttatttatttatttttgggtctatgagtgcaagagattgtattctttatccagctatgattttccttattgatctacag

Basic information

species Glycine max
transcript GLYMA13G31720.1
intron # 2
splice site 5'
intron type U12 (go to U12 genes for details)

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA13G31720.1 (Glycine max), 5'ss of exon 2
lower sequence: AT1G61150.2 (Arabidopsis thaliana), 5'ss of exon 4
ATTAGAAAAGAAGACATGAATAAATTGGTAATGAATTTCCTTGTCACCGAAGGCTATGTTGAAGCTGCTGAGAAATTTCGAATGGAGTCTGGAACTGAACgcatcctttttattaatttatttatttatttatttatttttgggtctatgagtgcaagagattgtattctttatccagctatgattttccttattgatctacag
 |||| |||||||| |||||||  ||||| |||||||| ||||| || ||||| ||||||||||||||||||||||| | || ||||||||||||  |||| ||||||||| | | | |  ||  ||   | ||| ||| |||   |  | |||   ||  ||    |  |   |    | |||  |||||||| ||   ||||
CTTAGGAAAGAAGATATGAATACTTTGGTGATGAATTTTCTTGTGACTGAAGGATATGTTGAAGCTGCTGAGAAATTCCAAAGGGAGTCTGGAACCAAACgtatcctttttctgattctggtt--ttgagtttttgtttatggaattg-gtgtgtttgatgtttagcttatctactccttttgaacttccttatcgagaaacag

upper sequence: GLYMA13G31720.1 (Glycine max), 5'ss of exon 2
lower sequence: PP1S379_20V6.1 (Physcomitrella patens), 5'ss of exon 2
ATTAGAAAAGAAGACATGAATAAATTGGTAATGAATTTCCTTGTCACCGAAGGCTATGTTGAAGCTGCTGAGAAATTTCGAATGGAGTCTGGAACTGAACgcatcctttttattaatttatttatttatttatttatttttgggtctatgagtgcaagagatt-gtattctttatccagctatgattttcc--ttattgatctacag
||| | |||||||| ||||| | |||||| ||||||||  | ||||| ||||||||||| || || |||||||||||||     |||||||| ||| |||| ||||| |  |   || | |  ||| || |  |||  |||      ||   ||   ||| || ||      ||||  |   ||  ||| |  ||   ||| |    
ATTCGGAAAGAAGATATGAACAGATTGGTGATGAATTTTTTGGTCACTGAAGGCTATGTCGAGGCAGCTGAGAAATTTCAGCACGAGTCTGGGACTCAACgtatcctctgca--gatgt-tgcattgatcttattacctttataataatcgctggttgaggtttgtcgggagtatcttgtcttgtcttttcctttgccgattt----

upper sequence: GLYMA13G31720.1 (Glycine max), 5'ss of exon 2
lower sequence: PP1S268_9V6.1 (Physcomitrella patens), 5'ss of exon 3
ATTAGAAAAGAAGACATGAATAAATTGGTAATGAATTTCCTTGTCACCGAAGGCTATGTTGAAGCTGCTGAGAAATTTCGAATGGAGTCTGGAACTGAACgcatcctttttattaatttatttatttatttatttatttttgggtctatgagtgcaagagattgtattctttatccagctatgattttccttattgatctacag-----
||| |||| ||||||||||| | | | |||||||||||  | ||||||||||| ||||| || || |||||||||||||     |||||||| ||| |||| ||||| |     | ||  |   |||||||  |||  |         | |    ||  |||||    || |   | | | ||  |||  ||  ||  | |  |     
ATTCGAAAGGAAGACATGAACAGACTCGTAATGAATTTTTTGGTCACCGAAGGGTATGTCGAGGCAGCTGAGAAATTTCAGCACGAGTCTGGGACTCAACgtatcctctgc---agttcttgcgtttatttcattacctcca---tcgtaacaataaccgattgagaactgt-cgctgttgtg--ttttatttctgggccatcgctgat

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|193686312|gb|FK625999.1|FK625999
EST:     AGGCTATGTTGAAGCTGCTGAGAAATTTCGAATGGAGTCTGGAACTGAAC                         CAGACATAGATCTTGCAACAATAACAGATCGCATGGCTGTTAAGAAAGCAG
genomic: AGGCTATGTTGAAGCTGCTGAGAAATTTCGAATGGAGTCTGGAACTGAACgcatcctttt ... tgatctacagCAGACATAGATCTTGCAACAATAACAGATCGCATGGCTGTTAAGAAAGCAG
EST: gi|193384825|gb|FK353183.1|FK353183
EST:     AGGCTATGTTGAAGCTGCTGAGAAATTTCGAATGGAGTCTGGAACTGAAC                         CAGACATAGATCTTGCAACAATAACAGATCGCATGGCTGTTAAGAAAGCAG
genomic: AGGCTATGTTGAAGCTGCTGAGAAATTTCGAATGGAGTCTGGAACTGAACgcatcctttt ... tgatctacagCAGACATAGATCTTGCAACAATAACAGATCGCATGGCTGTTAAGAAAGCAG
EST: gi|298195085|gb|HO043613.1|HO043613
EST:     AGGCAATGTTGAAGCTGCTGAGAAATTTCGAATGGAGTCTGGAACTGAAC                         CAGACATAGATCTTGCAACAATAACAGATCGCATGGCTGTTAAGAAAGCAG
genomic: AGGCTATGTTGAAGCTGCTGAGAAATTTCGAATGGAGTCTGGAACTGAACgcatcctttt ... tgatctacagCAGACATAGATCTTGCAACAATAACAGATCGCATGGCTGTTAAGAAAGCAG
EST: gi|21285801|gb|BQ473672.1|BQ473672
EST:     AGGCTATGTTGAAGCTGCTGAGAAATTTCGAATGGAGTCTGGAACTGAAC                         CAGACATAGATCTTGCAACAATAACAGATCGCATGGCTGTTAAGAAAGCAG
genomic: AGGCTATGTTGAAGCTGCTGAGAAATTTCGAATGGAGTCTGGAACTGAACgcatcctttt ... tgatctacagCAGACATAGATCTTGCAACAATAACAGATCGCATGGCTGTTAAGAAAGCAG
EST: gi|7029731|gb|AW459514.1|AW459514
EST:     TCTGGAACTGAAC                         CAGACATAGATCTTGCAACAATAACAGATCGCATGGCTGTTAAGAAAGCAG
genomic: TCTGGAACTGAACgcatcctttt ... tgatctacagCAGACATAGATCTTGCAACAATAACAGATCGCATGGCTGTTAAGAAAGCAG
EST: gi|18039280|gb|BM307574.1|BM307574
EST:     AGGCTATGTTGAAGCTGCTGAGAAATTTCGAATGGAGTCTGGAACTGAAC                         CAGACATAGATCTTGCAACAATAACAGATCGCATGGCTGTTAAGAAAGCAG
genomic: AGGCTATGTTGAAGCTGCTGAGAAATTTCGAATGGAGTCTGGAACTGAACgcatcctttt ... tgatctacagCAGACATAGATCTTGCAACAATAACAGATCGCATGGCTGTTAAGAAAGCAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATTAGAAAAGAAGACATGAATAAATTGGTAATGAATTTCCTTGTCACCGAAGGCTATGTTGAAGCTGCTGAGAAATTTCGAATGGAGTCTGGAACTGAACgcatcctttttattaatttatttatttatttatttatttttgggtctatgagtgcaagagattgtattctttatccagctatgattttccttattgatctacag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT