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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTGCAAATTTGGAGCCACATGCAGGTTTCATCATCCTAGAGACAAGGCTGGGATTGCTGGAAGAGTTGCCATGAATATTTTAGGCTATCCTCTCCGCCCAgttagtattgaatatttacctcttgtttatagctaaatacagctgaggcagtagttttttgtcaatttgtggccatctagtttgattgcttgtttggttt...

Basic information

species Glycine max
transcript GLYMA09G38650.2
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA09G38650.2 (Glycine max), 5'ss of exon 4
lower sequence: AT3G02830.1 (Arabidopsis thaliana), 5'ss of exon 4
TTGCAAATTTGGAGCCACATGCAGGTTTCATCATCCTAGAGACAAGGCTGGGATTGCTGGAAGAGTTGCCATGAATATTTTAGGCTATCCTCTCCGCCCAgttagtattgaatatttacctcttgtttatagctaaatacagctgaggcagtagttttttgtcaatttgtggccatctagtttgattgcttgtttggttt
 ||||| |||||||  ||||| | |||||||||||| ||  |||| ||||||||||||||||||||  |  | ||||| |||||||||||||| ||| | ||   ||||  |  |||    |||| | ||   | | |||  ||    || |  ||  |  ||  || |||    ||| ||    |    | |   |   
CTGCAAGTTTGGAGTAACATGTAAGTTTCATCATCCAAGGAACAAAGCTGGGATTGCTGGAAGAGTCTCTCTCAATATGTTAGGCTATCCTCTACGCTCGgt--atatttgac-tttttgacttgctgat--ttcattacttct----cattgtttcatcatc--ttagtgattctct-gtaatgtcatatatgcag---

upper sequence: GLYMA09G38650.2 (Glycine max), 5'ss of exon 4
lower sequence: Vv04s0023g00370.t01 (Vitis vinifera), 5'ss of exon 4
TTGCAAATTTGGAGCCACATGCAGGTTTCATCATCCTAGAGACAAGGCTGGGATTGCTGGAAGAGTTGCCATGAATATTTTAGGCTATCCTCTCCGCCCAgttagtattgaatatttacctcttgtttatagctaaatacagctgaggcagtagttttttgtcaatttgtggccatctagtttgattgcttgtttggttt---------
|||||| |||||||||||||||| ||||||||||||||||||||||||||| ||||||||||||||| |  | ||||||||||||||||| || || || ||| | |||   ||||| |   ||  | ||   | | |  |  |||      | | |     | || |  |||  |  | ||      |  |||||| ||         
TTGCAAGTTTGGAGCCACATGCAAGTTTCATCATCCTAGAGACAAGGCTGGAATTGCTGGAAGAGTTTCTTTAAATATTTTAGGCTATCCACTGCGGCCGgttcg-attttttattt-ctctttactcatg--ttactggaattgatttg--aatgtgccaaccatgttaggcttttcatttc---ccccagtttggattcaccaaatt
















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|20813953|gb|BQ298431.1|BQ298431
EST:     CCATGAATATTTTAGGCTATCCTCTCCGCCCA                         AATGAGCCTGAATGTGCTTATTATTTAAGAACTGGACAATGTAAATTTGGG
genomic: CCATGAATATTTTAGGCTATCCTCTCCGCCCAgttagtattg ... tttgatacagAATGAGCCTGAATGTGCTTATTATTTAAGAACTGGACAATGTAAATTTGGG
EST: gi|15814048|gb|BI786323.1|BI786323
EST:     GGATTGCTGGAAGAGTTGCCATGAATATTTTAGGCTATCCTCTCCGCCCA                         AATGAGCCTGAATGTGCTTATTATTTAAGA
genomic: GGATTGCTGGAAGAGTTGCCATGAATATTTTAGGCTATCCTCTCCGCCCAgttagtattg ... tttgatacagAATGAGCCTGAATGTGCTTATTATTTAAGA
EST: gi|26057548|gb|CA800462.1|CA800462
EST:     GGATTGCTGGAAGAGTTGCCATGAATATTTTAGGCTATCCTCTCCGCCCA                         AATGAGCCTGAATGTGCTTATTATTTAAGAACTGGACAATGTAAATTTGGG
genomic: GGATTGCTGGAAGAGTTGCCATGAATATTTTAGGCTATCCTCTCCGCCCAgttagtattg ... tttgatacagAATGAGCCTGAATGTGCTTATTATTTAAGAACTGGACAATGTAAATTTGGG
EST: gi|207770523|gb|GD742879.1|GD742879
EST:     GGATTGCTGGAAGAGTTGCCATGAATATTTTAGGCTATCCTCTCCGCCCA                         AATGAGCCTGAATGTGCTTATTATTTAAGAACTGGAACAATGTAAATTTGG
genomic: GGATTGCTGGAAGAGTTGCCATGAATATTTTAGGCTATCCTCTCCGCCCAgttagtattg ... tttgatacagAATGAGCCTGAATGTGCTTATTATTTAAGAACTGGA-CAATGTAAATTTGG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTGCAAATTTGGAGCCACATGCAGGTTTCATCATCCTAGAGACAAGGCTGGGATTGCTGGAAGAGTTGCCATGAATATTTTAGGCTATCCTCTCCGCCCAgttagtattgaatatttacctcttgtttatagctaaatacagctgaggcagtagttttttgtcaatttgtggccatctagtttgattgcttgtttggttt

- - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA