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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AATTGACCCAAGTGTTACCATGATGACAGTTGAAGAGAAGCCTGATGTGACATATAATGATGTTGGTGGTTGTAAGGAGCAGATTGAAAAGATGCGAGAAgttagtgattggaagttcccttgatttttaatctgttataattgcggatgtaagttacatggtgctaattttatttatttatattttatctgctag

Basic information

species Glycine max
transcript GLYMA03G42370.2
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA03G42370.2 (Glycine max), 5'ss of exon 6
lower sequence: LOC_Os02g54340.1 (Oryza sativa), 5'ss of exon 6
AATTGACCCAAGTGTTACCATGATGACAGTTGAAGAGAAGCCTGATGTGACATATAATGATGTTGGTGGTTGTAAGGAGCAGATTGAAAAGATGCGAGAAgt-tagtgat----tggaagt-----tcccttgatttttaatctg--ttataattgcggatgtaagttacatggtgctaattttatttatttatattttatctgctag-----------------
||||||||||||||||||||||||||||||||| || || ||||||||||||||||||||||| |||||||| ||||| ||||||||||| ||||| || || || | ||    |   |||     |||||||   |  || ||   | ||  ||| | ||  | | ||  | ||  |    ||||||   ||| |  | | |||||                  
AATTGACCCAAGTGTTACCATGATGACAGTTGAGGAAAAACCTGATGTGACATATAATGATGTGGGTGGTTGCAAGGAACAGATTGAAAAAATGCGGGAGgtatactaatcttttttcagttcatatcccttgtcgtgcaaacttgctcatccttgtgcat-caggctagttagttttggacttattttgctatttactgtttgctaattattgtttgttcatag

upper sequence: GLYMA03G42370.2 (Glycine max), 5'ss of exon 6
lower sequence: GRMZM2G110185_T04 (Zea mays), 5'ss of exon 5
AATTGACCCAAGTGTTACCATGATGACAGTTGAAGAGAAGCCTGATGTGACATATAATGATGTTGGTGGTTGTAAGGAGCAGATTGAAAAGATGCGAGAAgttagtgattggaagttcccttgatttttaatctgttataattgcggatgtaagttacatggtgctaattttatttatttatattttatctgctag
||||||||||||||||||||||||||| || || || ||||| |||||||| || |||||||| ||||| || |||||||||||||| |||||||| |||||  ||| |      | |   |||  |   |  |  |  | |  | | |     |       |  |  ||    ||   | || | | | |||   
AATTGACCCAAGTGTTACCATGATGACTGTGGAGGAAAAGCCAGATGTGACGTACAATGATGTCGGTGGCTGCAAGGAGCAGATTGAGAAGATGCGTGAAgtatgtggtccttcttccttgtgagctgggaaatactgca-tcacagttagtgatggatctattttgtttactatttgctgtactatttttgcag-

upper sequence: GLYMA03G42370.2 (Glycine max), 5'ss of exon 6
lower sequence: GRMZM2G181359_T01 (Zea mays), 5'ss of exon 6
AATTGACCCAAGTGTTACCATGATGACAGTTGAAGAGAAGCCTGATGTGACATATAATGATGTTGGTGGTTGTAAGGAGCAGATTGAAAAGATGCGAGAAgttagtgattggaagttcccttgatttttaatctgttataattgcggatgtaagtta--catggtgctaattttatttatttatattt-tatctgctag----
||||||||||||||||||||||||||| || || || ||||| |||||||| || |||||||||||||| || |||||||||||||| || ||||| |||||  |||||      ||   |    || | | |||  | | |   | ||   |||||   | ||  ||| |||  ||  | | |  || || ||  |      
AATTGACCCAAGTGTTACCATGATGACCGTGGAGGAAAAGCCAGATGTGACGTACAATGATGTTGGTGGCTGCAAGGAGCAGATTGAGAAAATGCGTGAAgtatgtgatcc----ttttttcttcttgtgagctggcaca-tactgcatcatagttagttacgggactagtttggttactctgtgcttgtaccttttttgcag

upper sequence: GLYMA03G42370.2 (Glycine max), 5'ss of exon 6
lower sequence: Vv09s0002g00170.t01 (Vitis vinifera), 5'ss of exon 6
AATTGACCCAAGTGTTACCATGATGACAGTTGAAGAGAAGCCTGATGTGACATATAATGATGTTGGTGGTTGTAAGGAGCAGATTGAAAAGATGCGAGAAgttagtgattggaagttcccttgatttttaatctgttataattgcggatgtaagttacatggtgctaattttattta----tttatattttatctgctag-----------------------------------------------
 ||||| |||||||| |||||||||||||| |||||||| || |||||||||||||||||||||||||| || |||||||||||||||||||||||||||||       || |  |||  || |  |||  | |  |   ||     ||| |  |||||  |||    | ||  |||     |  | ||| |||   |                                                 
GATTGATCCAAGTGTAACCATGATGACAGTAGAAGAGAAACCGGATGTGACATATAATGATGTTGGTGGATGCAAGGAGCAGATTGAAAAGATGCGAGAAgtg------tgtatattctttttacatttttttttgtcagatcatatatgcat-ttacaccgtgtctttcttgattaacagctagtttttgatcctgtgaacttctgtccttctcttgtttgctgatatttataactttggctctag

upper sequence: GLYMA03G42370.2 (Glycine max), 5'ss of exon 6
lower sequence: PP1S152_13V6.2 (Physcomitrella patens), 5'ss of exon 6
AATTGACCCAAGTGTTACCATGATGACAGTTGAAGAGAAGCCTGATGTGACATATAATGATGTTGGTGGTTGTAAGGAGCAGATTGAAAAGATGCGAGAAgttagtgattggaagttcccttgatttt-taatctgttataattgcggatgtaagttacatggtgctaatt------ttatttatttatattttatctgctag
 |||||||| ||||| || ||||||||||| ||||| ||||| ||||| || || |||||| |||| || |||||||| || || ||||||||||| || ||||||||    || ||    |  |||  |||| ||  ||  ||| |  ||| |  |   |||| ||  ||        |  || ||||   |  | |  |  
GATTGACCCGAGTGTCACTATGATGACAGTAGAAGAAAAGCCAGATGTTACGTACAATGATATTGGAGGCTGTAAGGAACAAATAGAAAAGATGCGTGAGgttagtgaaaccaacttgttattttttcgtaatttga-atgcttg-gtttgtgaagtttctggtcctttttggcgagcaacatacttatgcatgttgtattg-

upper sequence: GLYMA03G42370.2 (Glycine max), 5'ss of exon 6
lower sequence: PP1S49_256V6.1 (Physcomitrella patens), 5'ss of exon 6
AATTGACCCAAGTGTTACCATGATGACAGTTGAAGAGAAGCCTGATGTGACATATAATGATGTTGGTGGTTGTAAGGAGCAGATTGAAAAGATGCGAGAAgttagtgattggaagttcccttgatttttaatctgttataattgcggatgtaagttacatggtgctaattttatttatttatattttatct-gctag-----
 |||||||| || ||||| ||||||||||| || || ||||| ||||| || || |||||| ||||||| ||||| ||||| || ||||||||||| || || | |||     |  |   ||| |||   || | || |||| ||     |    |||||| |  | |||| ||    |  ||   |||   |||       
GATTGACCCCAGCGTTACAATGATGACAGTGGAGGAAAAGCCAGATGTCACCTACAATGATATTGGTGGCTGTAAAGAGCAAATAGAAAAGATGCGTGAGgtaaatgaa-accaactttattgctttcacatattttctaat-gctttgttcgactacatgtttgtgatttgatgcgatattacgatatgaagctcaccccg

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|208025660|gb|GD822014.1|GD822014
EST:     CATATAATGATGTTGGTGGTTGTAAGGAGCAGATTGAAAAGATGCGAGAA                         GTTGTTGAGCTTCCCATGCTCCACCCTGAGAAATTCGTTAAGCTAGGAATT
genomic: CATATAATGATGTTGGTGGTTGTAAGGAGCAGATTGAAAAGATGCGAGAAgttagtgatt ... tatctgctagGTTGTTGAGCTTCCCATGCTCCACCCTGAGAAATTCGTTAAGCTAGGAATT
EST: gi|16277955|gb|BI942651.1|BI942651
EST:     TGATGTTGGTGGTTGTAAGGAGCAGATTGAAAAGATGCGAGAA                         GTTGTTGAGCTTCCCATGCTCCACCCTGAGAAATTCGTTAAGCTAGGAATT
genomic: TGATGTTGGTGGTTGTAAGGAGCAGATTGAAAAGATGCGAGAAgttagtgatt ... tatctgctagGTTGTTGAGCTTCCCATGCTCCACCCTGAGAAATTCGTTAAGCTAGGAATT
EST: gi|193364388|gb|FK328893.1|FK328893
EST:     CATATAATGATGTTGGTGGTTGTAAGGAGCAGATTGAAAAGATGCGAGAA                         GTTGTTGAGCTTCCCATGCTCCACCCTGAGAAATTCGTTAAGCTAGGAATT
genomic: CATATAATGATGTTGGTGGTTGTAAGGAGCAGATTGAAAAGATGCGAGAAgttagtgatt ... tatctgctagGTTGTTGAGCTTCCCATGCTCCACCCTGAGAAATTCGTTAAGCTAGGAATT
EST: gi|193323486|gb|FK289148.1|FK289148
EST:     CATATAATGATGTTGGTGGTTGTAAGGAGCAGATTGAAAAGATGCGAGAA                         GTTGTTGAGCTTCCCATGCTCCACCCTGAGAAATTCGTTAAGCTAGGAATT
genomic: CATATAATGATGTTGGTGGTTGTAAGGAGCAGATTGAAAAGATGCGAGAAgttagtgatt ... tatctgctagGTTGTTGAGCTTCCCATGCTCCACCCTGAGAAATTCGTTAAGCTAGGAATT
EST: gi|207796307|gb|GD770244.1|GD770244
EST:     TGTTGGTGGTTGTAAGGAGCAGATTGAAAAGATGCGAGAA                         GTTGTTGAGCTTCCCATGCTCCACCCTGAGAAATTCGTTAAGCTAGGAATT
genomic: TGTTGGTGGTTGTAAGGAGCAGATTGAAAAGATGCGAGAAgttagtgatt ... tatctgctagGTTGTTGAGCTTCCCATGCTCCACCCTGAGAAATTCGTTAAGCTAGGAATT
EST: gi|207686291|gb|GD667873.1|GD667873
EST:     CATATAATGATGTTGGTGGTTGTAAGGAGCAGATTGAAAAGATGCGAGAA                         GTTGTTGAGCTTCCCATGCTCCACCCTGAGAAATTCGTTAAGCTAGGAATT
genomic: CATATAATGATGTTGGTGGTTGTAAGGAGCAGATTGAAAAGATGCGAGAAgttagtgatt ... tatctgctagGTTGTTGAGCTTCCCATGCTCCACCCTGAGAAATTCGTTAAGCTAGGAATT
EST: gi|193335921|gb|FK300621.1|FK300621
EST:     GATGTTGGTGGTTGTAAGGAGCAGATTGAAAAGATGCGAGAA                         GTTGTTGAGCTTCCCATGCTCCACCCTGAGAAATTCGTTAAGCTAGGAATT
genomic: GATGTTGGTGGTTGTAAGGAGCAGATTGAAAAGATGCGAGAAgttagtgatt ... tatctgctagGTTGTTGAGCTTCCCATGCTCCACCCTGAGAAATTCGTTAAGCTAGGAATT
EST: gi|37994041|gb|CF805787.1|CF805787
EST:     CATATAATGATGTTGGTGGTTGTAAGGAGCAGATTGAAAAGATGCGAGAA                         GTTGTTGAGCTTCCCATGCTCCACCCTGAGAAATTCGTTAAGCTAGGAATT
genomic: CATATAATGATGTTGGTGGTTGTAAGGAGCAGATTGAAAAGATGCGAGAAgttagtgatt ... tatctgctagGTTGTTGAGCTTCCCATGCTCCACCCTGAGAAATTCGTTAAGCTAGGAATT
EST: gi|207688315|gb|GD672164.1|GD672164
EST:     CATATAATGATGTTGGTGGTTGTAAGGAGCAGATTGAAAAGATGCGAGAA                         GTTGTTGAGCTTCCCATGCTCCACCCTGAGAAATTCGTTAAGCTAGGAAAT
genomic: CATATAATGATGTTGGTGGTTGTAAGGAGCAGATTGAAAAGATGCGAGAAgttagtgatt ... tatctgctagGTTGTTGAGCTTCCCATGCTCCACCCTGAGAAATTCGTTAAGCTAGGAA-T
EST: gi|193632616|gb|FK583292.1|FK583292
EST:     TTGGTGGTTGTAAGGAGCAGATTGAAAAGATGCGAGAA                         GTTGTTGAGCTTCCCATGCTCCACCCTGAGAAATTCGTTAAGCTAGGAATT
genomic: TTGGTGGTTGTAAGGAGCAGATTGAAAAGATGCGAGAAgttagtgatt ... tatctgctagGTTGTTGAGCTTCCCATGCTCCACCCTGAGAAATTCGTTAAGCTAGGAATT
EST: gi|193637984|gb|FK586220.1|FK586220
EST:     ATTGAAAAGATGCGAGAA                         GTTGTTGAGCTTCCCATGCTCCACCCTGAGAAATTCGTTAAGCTAGGAATT
genomic: ATTGAAAAGATGCGAGAAgttagtgatt ... tatctgctagGTTGTTGAGCTTCCCATGCTCCACCCTGAGAAATTCGTTAAGCTAGGAATT
EST: gi|208158165|gb|GD955174.1|GD955174
EST:     TATAATGATGTTGGTGGTTGTAAGGAGCAGATTGAAAAGATGCGAGAA                         GTTGTTGAGCTTCCCATGCTCCACCCTGAGAAATTCGTTAAGCTAGGAATT
genomic: TATAATGATGTTGGTGGTTGTAAGGAGCAGATTGAAAAGATGCGAGAAgttagtgatt ... tatctgctagGTTGTTGAGCTTCCCATGCTCCACCCTGAGAAATTCGTTAAGCTAGGAATT
EST: gi|208127872|gb|GD924022.1|GD924022
EST:     CATATAATGATGTTGGTGGTTGTAAGGAGCAGATTGAAAAGATGCGAGAA                         GTTGTTGAGCTTCCCATGCTCCACCCTGAGAAA
genomic: CATATAATGATGTTGGTGGTTGTAAGGAGCAGATTGAAAAGATGCGAGAAgttagtgatt ... tatctgctagGTTGTTGAGCTTCCCATGCTCCACCCTGAGAAA
EST: gi|208077302|gb|GD876961.1|GD876961
EST:     CATATAATGATGTAGGTGGTTGTAAGGAGCAGATTGAAAAGATGCGAGAA                         GTTGTTGAGCTTCCCATGCTCCACCCTGAGAAATTCGTTAAGCTAGGAATT
genomic: CATATAATGATGTTGGTGGTTGTAAGGAGCAGATTGAAAAGATGCGAGAAgttagtgatt ... tatctgctagGTTGTTGAGCTTCCCATGCTCCACCCTGAGAAATTCGTTAAGCTAGGAATT
EST: gi|209702899|gb|BW667434.1|BW667434
EST:     CATATAATGATGTTGGTGGTTGTAAGGAGCAGATTGAAAAGATGCGAGAA                         GTTGTTGAGCTTCCCATGCTCCACCCTGAGAAATTCGTTAAGCTAGGAATT
genomic: CATATAATGATGTTGGTGGTTGTAAGGAGCAGATTGAAAAGATGCGAGAAgttagtgatt ... tatctgctagGTTGTTGAGCTTCCCATGCTCCACCCTGAGAAATTCGTTAAGCTAGGAATT
EST: gi|208135507|gb|GD937948.1|GD937948
EST:     CATATAATGATGTTGGTGGTTGTAAGGAGCAGATTGAAAAGATGCGAGAA                         GTTGTTGAGCTTCCCATGCTCCACCCTGAGAAATTCGTTAAGCTAGGAATT
genomic: CATATAATGATGTTGGTGGTTGTAAGGAGCAGATTGAAAAGATGCGAGAAgttagtgatt ... tatctgctagGTTGTTGAGCTTCCCATGCTCCACCCTGAGAAATTCGTTAAGCTAGGAATT
EST: gi|207688552|gb|GD671743.1|GD671743
EST:     CATATAATGATGTTGGTGGTTGTAAGGAACAGATTGAAAAAATGCGAGAA                         GTTGTTGAGCTTCCCATGCTCCACCCAGAGAAATTCGTTAAGCTAGGAATT
genomic: CATATAATGATGTTGGTGGTTGTAAGGAGCAGATTGAAAAGATGCGAGAAgttagtgatt ... tatctgctagGTTGTTGAGCTTCCCATGCTCCACCCTGAGAAATTCGTTAAGCTAGGAATT
EST: gi|193528836|gb|FK483596.1|FK483596
EST:     CATATAATGATGTTGGTGGTTGTAAGGAGCAGATTGAAAAGATGCGAGAA                         GTTGTTGAGCTTCCCATGCTCCACCCTGAGAAATTCGTTAAGCTAGGAATT
genomic: CATATAATGATGTTGGTGGTTGTAAGGAGCAGATTGAAAAGATGCGAGAAgttagtgatt ... tatctgctagGTTGTTGAGCTTCCCATGCTCCACCCTGAGAAATTCGTTAAGCTAGGAATT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AATTGACCCAAGTGTTACCATGATGACAGTTGAAGAGAAGCCTGATGTGACATATAATGATGTTGGTGGTTGTAAGGAGCAGATTGAAAAGATGCGAGAAgttagtgattggaagttcccttgatttttaatctgttataattgcggatgtaagttacatggtgctaattttatttatttatattttatctgctag

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