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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AATTGATCCAAGTGTGACCATGATGACTGTTGAAGAGAAGCCAGATGTAACATATAATGATGTTGGCGGTTGTAAGGAGCAGATTGAAAAGATGCGAGAAgtaagtcattggaatttttacttattttacatttataatgaagtagataagtcacgtgtcactaatttgtaatttcactgcaag

Basic information

species Glycine max
transcript GLYMA07G05220.1
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA07G05220.1 (Glycine max), 5'ss of exon 6
lower sequence: LOC_Os02g54340.1 (Oryza sativa), 5'ss of exon 6
AATTGATCCAAGTGTGACCATGATGACTGTTGAAGAGAAGCCAGATGTAACATATAATGATGTTGGCGGTTGTAAGGAGCAGATTGAAAAGATGCGAGAAgtaagtcattggaatttttacttattttacatttataatgaagtagataagtcacgtgtcactaatttgtaatttcactgcaag----------------------------------------
|||||| |||||||| ||||||||||| ||||| || || || ||||| |||||||||||||| || ||||| ||||| ||||||||||| ||||| || |||    | |    |||    | || |  | | |      || | | | |  |  |||   |    | || | ||     |                                           
AATTGACCCAAGTGTTACCATGATGACAGTTGAGGAAAAACCTGATGTGACATATAATGATGTGGGTGGTTGCAAGGAACAGATTGAAAAAATGCGGGAGgtatactaatcttttttcagttcatatcccttgtcgtgcaaacttgctcatccttgtgcatcaggctagttagttttggacttattttgctatttactgtttgctaattattgtttgttcatag

upper sequence: GLYMA07G05220.1 (Glycine max), 5'ss of exon 6
lower sequence: GRMZM2G110185_T04 (Zea mays), 5'ss of exon 5
AATTGATCCAAGTGTGACCATGATGACTGTTGAAGAGAAGCCAGATGTAACATATAATGATGTTGGCGGTTGTAAGGAGCAGATTGAAAAGATGCGAGAAgtaagtcattggaatttttacttattttacatttataatgaagtagataagtcacgtgtcactaatttgtaat-ttcactgcaag----------
|||||| |||||||| |||||||||||||| || || ||||||||||| || || |||||||| || || || |||||||||||||| |||||||| |||||| ||  |     ||  |  | |  |   |  ||         || || || | |  ||  |  | | || | ||  ||| |            
AATTGACCCAAGTGTTACCATGATGACTGTGGAGGAAAAGCCAGATGTGACGTACAATGATGTCGGTGGCTGCAAGGAGCAGATTGAGAAGATGCGTGAAgtatgtggtccttcttccttgtgagctgggaaatactgcatcacagtta-gtgatggatctattttgtttactatttgctgtactatttttgcag

upper sequence: GLYMA07G05220.1 (Glycine max), 5'ss of exon 6
lower sequence: GRMZM2G181359_T01 (Zea mays), 5'ss of exon 6
AATTGATCCAAGTGTGACCATGATGACTGTTGAAGAGAAGCCAGATGTAACATATAATGATGTTGGCGGTTGTAAGGAGCAGATTGAAAAGATGCGAGAAgtaagtcattggaatttttacttat---tttacatttataatgaagtagataagtcacgtgtcactaatttgtaatttcactgcaag--------------
|||||| |||||||| ||||||||||| || || || ||||||||||| || || ||||||||||| || || |||||||||||||| || ||||| |||||| || ||     ||| | ||| |    |  ||  ||        ||| || || ||| |  |||| ||||     ||  |||  |              
AATTGACCCAAGTGTTACCATGATGACCGTGGAGGAAAAGCCAGATGTGACGTACAATGATGTTGGTGGCTGCAAGGAGCAGATTGAGAAAATGCGTGAAgtatgtgatccttttttcttcttgtgagctggcacatactgcatcatagtta-gttacggg--actagtttggttactctgtgcttgtaccttttttgcag

upper sequence: GLYMA07G05220.1 (Glycine max), 5'ss of exon 6
lower sequence: Vv09s0002g00170.t01 (Vitis vinifera), 5'ss of exon 6
AATTGATCCAAGTGTGACCATGATGACTGTTGAAGAGAAGCCAGATGTAACATATAATGATGTTGGCGGTTGTAAGGAGCAGATTGAAAAGATGCGAGAAgtaagtcattggaatttttacttattttacatttataatgaa-gtagataagtcacgtgtcact-aatttgtaatttcactgcaag------------------------------------------------------
 |||||||||||||| ||||||||||| || |||||||| || ||||| ||||||||||||||||| || || |||||||||||||||||||||||||||||  ||   |    |||  | || ||||      || ||  | | |  ||   |  || |  ||  |||   |  |    |   |                                                       
GATTGATCCAAGTGTAACCATGATGACAGTAGAAGAGAAACCGGATGTGACATATAATGATGTTGGTGGATGCAAGGAGCAGATTGAAAAGATGCGAGAAgtgtgtatattctttttacatttttttttgtcagatcatatatgcatttacaccgtgtctttcttgattaacagctagtttttgatcctgtgaacttctgtccttctcttgtttgctgatatttataactttggctctag

upper sequence: GLYMA07G05220.1 (Glycine max), 5'ss of exon 6
lower sequence: PP1S152_13V6.2 (Physcomitrella patens), 5'ss of exon 6
AATTGATCCAAGTGTGACCATGATGACTGTTGAAGAGAAGCCAGATGTAACATATAATGATGTTGGCGGTTGTAAGGAGCAGATTGAAAAGATGCGAGAAgtaagtcattggaatttttacttattttacatttataatg---aagtagataagtcacgtgtcact---aatttgtaatttcactgcaag----------
 ||||| || ||||| || |||||||| || ||||| ||||||||||| || || |||||| |||| || |||||||| || || ||||||||||| || || ||| |    || || |  || |||   | ||  ||||      | |  ||||  |  |||  |        | ||  |   |               
GATTGACCCGAGTGTCACTATGATGACAGTAGAAGAAAAGCCAGATGTTACGTACAATGATATTGGAGGCTGTAAGGAACAAATAGAAAAGATGCGTGAGgttagtgaaaccaacttgttattttttcgtaatttgaatgcttggtttgtgaagtttctggtcctttttggcgagcaacatacttatgcatgttgtattg

upper sequence: GLYMA07G05220.1 (Glycine max), 5'ss of exon 6
lower sequence: PP1S49_256V6.1 (Physcomitrella patens), 5'ss of exon 6
AATTGATCCAAGTGTGACCATGATGACTGTTGAAGAGAAGCCAGATGTAACATATAATGATGTTGGCGGTTGTAAGGAGCAGATTGAAAAGATGCGAGAAgtaagtcattggaatttttacttattttacatttataatgaag--tagataagtcacgtgtcactaatttgtaatttcactgcaag---------------
 ||||| || || || || |||||||| || || || ||||||||||| || || |||||| |||| || ||||| ||||| || ||||||||||| || |||| | |    || ||| | |  ||| |||| | |  | | |  | | |     || |||   | |||||       | | | |                
GATTGACCCCAGCGTTACAATGATGACAGTGGAGGAAAAGCCAGATGTCACCTACAATGATATTGGTGGCTGTAAAGAGCAAATAGAAAAGATGCGTGAGgtaaatgaaaccaacttt-attgctttcacatattttctaatgctttgttcgactacatgtttgtgatttgatgcgatattacgatatgaagctcaccccg

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|207733086|gb|GD710938.1|GD710938
EST:     CATATAATGATGTTGGCGGTTGTAAGGAGCAGATTGAAAAGNTGCGAGAA                         GTTGTTGAACTT
genomic: CATATAATGATGTTGGCGGTTGTAAGGAGCAGATTGAAAAGATGCGAGAAgtaagtcatt ... tcactgcaagGTTGTTGAACTT
EST: gi|19937368|gb|BQ081261.1|BQ081261
EST:     GCAGATTGAAAAGATGCGAGAA                         GTTGTTGAACTTCCCATGCTTCATCCAGAGAAATTTGTCAAGCTTGGGATT
genomic: GCAGATTGAAAAGATGCGAGAAgtaagtcatt ... tcactgcaagGTTGTTGAACTTCCCATGCTTCATCCAGAGAAATTTGTCAAGCTTGGGATT
EST: gi|192302201|gb|FG997281.1|FG997281
EST:     CATATAATGATGTTGGCGGTTGTAAGGAGCAGATTGAAAAGATGCGAGAA                         GTTGTTGAACTTCCCATGCTTCATCCAGAGAAATTTGTCAAGCTTGGGATT
genomic: CATATAATGATGTTGGCGGTTGTAAGGAGCAGATTGAAAAGATGCGAGAAgtaagtcatt ... tcactgcaagGTTGTTGAACTTCCCATGCTTCATCCAGAGAAATTTGTCAAGCTTGGGATT
EST: gi|16277271|gb|BI942294.1|BI942294
EST:     CATATAATGATGTTGGCGGTTGTAAGGAGCAGATTGAAAAGATGCGAGAA                         GTTGTTGAACTTCCCATGCTTCATCCAGAGAAATTTGTCAAGCTTGGGATT
genomic: CATATAATGATGTTGGCGGTTGTAAGGAGCAGATTGAAAAGATGCGAGAAgtaagtcatt ... tcactgcaagGTTGTTGAACTTCCCATGCTTCATCCAGAGAAATTTGTCAAGCTTGGGATT
EST: gi|57575942|gb|CX548913.1|CX548913
EST:     TTGTAAGGAGCAGATTGAAAAGATGCGAGAA                         GTTGTTG-ACTTTCCCATGTTTCATCCAGAGAAATTGGTCAAGCTTGGGAT
genomic: TTGTAAGGAGCAGATTGAAAAGATGCGAGAAgtaagtcatt ... tcactgcaagGTTGTTGAAC-TTCCCATGCTTCATCCAGAGAAATTTGTCAAGCTTGGGAT
EST: gi|208236095|gb|GE030659.1|GE030659
EST:     CATATAATGATGTTGGCGGTTGTAAGGAGCAGATTGAAAAGATGCGAGAA                         GTTGTTGAACTTCCCATGCTTCATCCAGAGAAATTTGTCAAG
genomic: CATATAATGATGTTGGCGGTTGTAAGGAGCAGATTGAAAAGATGCGAGAAgtaagtcatt ... tcactgcaagGTTGTTGAACTTCCCATGCTTCATCCAGAGAAATTTGTCAAG
EST: gi|16346898|gb|BI972493.1|BI972493
EST:     CATATAATGATGTTGGCGGTTGTAAGGAGCAGATTGAAAAGATGCGAGAA                         GTTGTTGAACTTCCCATGCTTCATCCAGAGAAATTTGTCAAGCTTGGGATT
genomic: CATATAATGATGTTGGCGGTTGTAAGGAGCAGATTGAAAAGATGCGAGAAgtaagtcatt ... tcactgcaagGTTGTTGAACTTCCCATGCTTCATCCAGAGAAATTTGTCAAGCTTGGGATT
EST: gi|58024535|gb|CX711276.1|CX711276
EST:     CATATAATGATGTTGGCGGTTGTAAGGAGCAGATTGAAAAGATGCGAGAA                         GTTGTTGAACTTCCCATGCTTCATCCAGAGAAATTTGTCAAGCTTGGGATT
genomic: CATATAATGATGTTGGCGGTTGTAAGGAGCAGATTGAAAAGATGCGAGAAgtaagtcatt ... tcactgcaagGTTGTTGAACTTCCCATGCTTCATCCAGAGAAATTTGTCAAGCTTGGGATT
EST: gi|193407658|gb|FK374476.1|FK374476
EST:     CATATAATGATGTTGGCGGTTGTAAGGAGCAGATTGAAAAGATGCGAGAA                         GTTGTTGAACTTCCCATGCTTCATCCAGAGAAATTTGTCAAGCTTGGGATT
genomic: CATATAATGATGTTGGCGGTTGTAAGGAGCAGATTGAAAAGATGCGAGAAgtaagtcatt ... tcactgcaagGTTGTTGAACTTCCCATGCTTCATCCAGAGAAATTTGTCAAGCTTGGGATT
EST: gi|209717333|gb|BW659036.1|BW659036
EST:     CATATAATGATGTTGGCGGTTGTAAGGAGCAGATTGAAAAGATGCGAGAA                         GTTGTTGAACTTCCCATGCTTCATCCAGAGAAATTTGTCAAGCTTGGGATT
genomic: CATATAATGATGTTGGCGGTTGTAAGGAGCAGATTGAAAAGATGCGAGAAgtaagtcatt ... tcactgcaagGTTGTTGAACTTCCCATGCTTCATCCAGAGAAATTTGTCAAGCTTGGGATT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AATTGATCCAAGTGTGACCATGATGACTGTTGAAGAGAAGCCAGATGTAACATATAATGATGTTGGCGGTTGTAAGGAGCAGATTGAAAAGATGCGAGAAgtaagtcattggaatttttacttattttacatttataatgaagtagataagtcacgtgtcactaatttgtaatttcactgcaag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG