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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATGAGAGCAAGCTGAATGATCTTTTGAACAGCTCTGATTATGTCCCAACCTATGAGGACAAGGATGGTGACTGGATGCTTGTCGGTGATGTCCCATGGGAgtaagtctttcacctctactcaaaatcaatttggccgcgataattgaactttgcaatattatggggataaactttaacatatgtttaccaaacttcacgt...

Basic information

species Glycine max
transcript GLYMA03G31530.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA03G31530.1 (Glycine max), 5'ss of exon 3
lower sequence: LOC_Os12g40890.1 (Oryza sativa), 5'ss of exon 3
ATGAGAGCAAGCTGAATGATCTTTTGAACAGCTCTGATTATGTCCCAACCTATGAGGACAAGGATGGTGACTGGATGCTTGTCGGTGATGTCCCATGGGAgtaagt--ctttcacctctactcaaaatcaatttggccgcgataattgaactttg-----caatattatggggataaactttaac----atatgtttaccaaacttcacgt----------------------------------------------
| ||||||||| |   ||||||  | ||| ||||||| ||||| |||||||| ||||||||||| || ||||||||||| ||||| || ||||||||||||| |||    |  || |  | |    || |  |        |   || || |||      |   |||| ||   ||  ||  | |    |||||  | |||  ||   | |                                              
ACGAGAGCAAGATTGCTGATCTGCTCAACGGCTCTGAATATGTGCCAACCTACGAGGACAAGGACGGCGACTGGATGCTCGTCGGCGACGTCCCATGGGAgtcagtaatctctacttaaattttctattatctaatatctaagtgtttaattttaataacctgaattaaggtactagtctgaatctctgatatgagt-ccatgctctgcatctgtgttctgaattctgaccattttgtttggaaatggaaatttcag

upper sequence: GLYMA03G31530.1 (Glycine max), 5'ss of exon 3
lower sequence: LOC_Os03g53150.1 (Oryza sativa), 5'ss of exon 3
ATGAGAGCAAGCTGAATGATCTTTTGAACAGCTCTGATTATGTCCCAACCTATGAGGACAAGGATGGTGACTGGATGCTTGTCGGTGATGTCCCATGGGAgtaagtctttcacctctactcaaaatcaatttggccgcgataattgaactttgcaatattatggggataaactttaac-atatgtttaccaaacttcacgt------------------------
    || |||  |||||||  |   |||  ||||||||  |||  |||| ||||| |||||||||||||||||||||||||| || |||||||| ||| |||| ||   | || ||          |   ||  | |   |  ||    |   |   || ||  | ||    |||| | |||       |||  ||| ||                         
---GGAACAATATGAATGAGGT---GAATGGCTCTGATGCTGTTACAACTTATGAAGACAAGGATGGTGACTGGATGCTTGTTGGAGATGTCCCGTGGCAgtatgttact-acttcattcttgtgcccccttaactgttttccttattttccacctcatgattagaatgcggtttagcgataccacgttcaagtttctcgcattagctgattggttactctgcag

upper sequence: GLYMA03G31530.1 (Glycine max), 5'ss of exon 3
lower sequence: LOC_Os03g43400.1 (Oryza sativa), 5'ss of exon 3
--ATGAGAGCAAGCTGAATGATCTTTTGAACAGCTCTGATTATGTCCCAACCTATGAGGACAAGGATGGTGACTGGATGCTTGTCGGTGATGTCCCATGGGAgtaagtctttcacctctactcaaaatcaatttggccgcgataattgaactttgcaatattatggggataaactttaacatatgtttaccaaacttcacgt-
   |||  |  |||  ||| | ||     |   |   || || || || || || ||||||||||| || ||||||||||| ||||| || ||||| |||||||||| ||  |        | |  || |     |     |||||| | |      |   || |     | |    |      | |     ||||   |   
AGCTGAAGGAGAGC--AATAAGCTGAGAGATGACCTGGAGTACGTGCCGACGTACGAGGACAAGGACGGCGACTGGATGCTCGTCGGCGACGTCCCGTGGGAgtaagcctcgccgtcgcgataagcataatcccagttctaataattaatccccatca-gctaagctagcagatcggatggatcgatcgagtaactgatcaac

upper sequence: GLYMA03G31530.1 (Glycine max), 5'ss of exon 3
lower sequence: GRMZM2G077356_T01 (Zea mays), 5'ss of exon 3
ATGAGAGCAAGCTGAATGATCTTTTGAACAGCTCTGATTAT---GTCCCAACCTATGAGGACAAGGATGGTGACTGGATGCTTGTCGGTGATGTCCCATGGGAgtaagtctttcacctctactcaaaatcaatt-tggccgcgataattgaactttgcaatattatggggataaactttaacatat--gtttaccaaacttcacgt--------
   || | |   ||  |||||       |    ||||| ||   ||| | || || || ||||||||||||||||||||||| ||||| || ||||| |||||||| ||  | |       |     |||   |     ||   | | ||| |  ||    |||| |     |   | |   || |    || |  |  |||  ||        
---AGGGGAGATTGGTTGATCCGGCCGGCGATGCTGATGATGTGGTCACTACTTACGAAGACAAGGATGGTGACTGGATGCTGGTCGGCGACGTCCCGTGGGAgtatgttctccgttctagcgtgccatcgtctgctttcgtatttactgacccatg----attaggactccagtgtcttgtatgtcgccttgctgattttctggtccctgcag

upper sequence: GLYMA03G31530.1 (Glycine max), 5'ss of exon 3
lower sequence: GRMZM2G138268_T01 (Zea mays), 5'ss of exon 3
ATGAGAGCAAGCTGAATGATCTTTTGAACAGCTCTGATTATGTCCCAACCTATGAGGACAAGGATGGTGACTGGATGCTTGTCGGTGATGTCCCATGGGAgtaagtctttcacctctactcaaaatc----aatttggccgcgataattgaactttgcaatattatggggataaactttaacatatgtttaccaaacttcacgt
| ||||||||||||   |||||  | ||| |||| || || || || ||||| ||||||||||| || ||||||||||| ||||| ||||| || ||||||| ||   | ||    | | |    ||    | | |   |   || ||   | |    |||   |     ||||   ||  ||| |  ||  ||          
ACGAGAGCAAGCTGGTGGATCTGCTCAACGGCTCCGAGTACGTGCCGACCTACGAGGACAAGGACGGGGACTGGATGCTCGTCGGCGATGTGCCGTGGGAgtgagcactgcatgcatgcgcttcttcctgcactatactccttattatattattgcctaatcggaaaataataataatttccatttcattttcag---------

upper sequence: GLYMA03G31530.1 (Glycine max), 5'ss of exon 3
lower sequence: Vv07s0141g00290.t01 (Vitis vinifera), 5'ss of exon 3
ATGAGAGCAAGCTGAATGATCTTTTGAACAGCTCTGATTATGTCCCAACCTATGAGGACAAGGATGGTGACTGGATGCTTGTCGGTGATGTCCCATGGGAgtaagtctttc--------acctctactcaaaatcaatttggccgcgataattgaactttgcaatattatggggataaactttaacatatgtttaccaaacttcacgt
||||||||||| |||  |||||||||||  | | |||| |||| ||||| || || ||||| ||||| || |||||||| || || ||||||||||||||||||||  |||        |  | |     ||||||              |||   |     |||| | |  | |  || | ||| | ||| ||| |||         
ATGAGAGCAAGTTGATGGATCTTTTGAATGGTTTTGATCATGTTCCAACATACGAAGACAAAGATGGGGATTGGATGCTCGTTGGAGATGTCCCATGGGAgtaagttcttccaaccatgagttttggcttaaatcaccaaaaatatatatattaggcagaaaaatagtttttgaaataattctaaaaaatgattatcaat--------

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|151394543|gb|EV264414.1|EV264414
EST:     TATGAGGACAAGGATGGTGACTGGATGCTTGTCGGTGATGTCCCATGGGA                         GATGTTTGTTGAATCATGCAAGCGTTTACGCATCATGAAAGGAAAGGAG-C
genomic: TATGAGGACAAGGATGGTGACTGGATGCTTGTCGGTGATGTCCCATGGGAgtaagtcttt ... tgtcaaccagGATGTTTGTTGAATCATGCAAGCGTTTACGCATCATGAAAGGAAAGGAGGC
EST: gi|193722765|gb|FK656669.1|FK656669
EST:     TATGAGGACAAGGATGGTGACTGGATGCTTGTCGGTGATGTCCCATGGGA                         GATGTTTGTTGAATCATGCAAGCGTTTACGCATCATGAAAGGAAAGGAGGC
genomic: TATGAGGACAAGGATGGTGACTGGATGCTTGTCGGTGATGTCCCATGGGAgtaagtcttt ... tgtcaaccagGATGTTTGTTGAATCATGCAAGCGTTTACGCATCATGAAAGGAAAGGAGGC
EST: gi|31455938|gb|CD397966.1|CD397966
EST:     TATGAGGACAAGGATGGTGACTGGATGCTTGTCGGTGATGTCCCATGGGA                         GATGTTTGTTGAATCATGCAAGCGTTTACGCATCATGAAAGGAAAGGAGGC
genomic: TATGAGGACAAGGATGGTGACTGGATGCTTGTCGGTGATGTCCCATGGGAgtaagtcttt ... tgtcaaccagGATGTTTGTTGAATCATGCAAGCGTTTACGCATCATGAAAGGAAAGGAGGC
EST: gi|9987128|gb|BE661236.1|BE661236
EST:     TGANGACCAAGGATGGTGACTGGATGCCTTGTCGGTGATGTCCCATGGGA                         A
genomic: TGAGGAC-AAGGATGGTGACTGGATGC-TTGTCGGTGATGTCCCATGGGAgtaagtcttt ... tgtcaaccag-
EST: gi|9987128|gb|BE661236.1|BE661236
EST:     TGANGACCAAGGATGGTGACTGGATGCCTTGTCGGTGATGTCCCATGGGA                         A
genomic: TGAGGAC-AAGGATGGTGACTGGATGC-TTGTCGGTGATGTCCCATGGGAgtaagtcttt ... tgtcaaccag-
EST: gi|14126060|gb|BG790498.1|BG790498
EST:     TATGAGGACAAGGATGGTGACTGGATGCTTGTCGGTGATGTCCCATGGGA                         GATGTTTGTTGAATCATGCAAGCGTTTACGCATCATGAAAGGAAAGGAGGC
genomic: TATGAGGACAAGGATGGTGACTGGATGCTTGTCGGTGATGTCCCATGGGAgtaagtcttt ... tgtcaaccagGATGTTTGTTGAATCATGCAAGCGTTTACGCATCATGAAAGGAAAGGAGGC
EST: gi|192295217|gb|FG986936.1|FG986936
EST:     TATGAGGACAAGGATGGTGACTGGATGCTTGTCGGTGATGTCCCATGGGA                         GATGTTTGTTGAATCATGCAAGCGTTTACGCATCATGAAAGGAAAGGAGGC
genomic: TATGAGGACAAGGATGGTGACTGGATGCTTGTCGGTGATGTCCCATGGGAgtaagtcttt ... tgtcaaccagGATGTTTGTTGAATCATGCAAGCGTTTACGCATCATGAAAGGAAAGGAGGC
EST: gi|22930383|gb|BU547522.1|BU547522
EST:     TATGAGGACAAGGATGGTGACTGGATGCNNNTCGGTGATGTCCCATGGGA                         GATGTTTGTTGAATCATGCAAGCGTTTACGCATCATGAAAGGAAAGGAGGC
genomic: TATGAGGACAAGGATGGTGACTGGATGCTTGTCGGTGATGTCCCATGGGAgtaagtcttt ... tgtcaaccagGATGTTTGTTGAATCATGCAAGCGTTTACGCATCATGAAAGGAAAGGAGGC
EST: gi|209699150|gb|BW652893.1|BW652893
EST:     TATGAGGACAAGGATGGTGACTGGATGCTTGTCGGTGATGTCCCATGGGA                         GATGTTTGTTGAATCATGCAAGCGTTTACGCATCATGAAAGGAAAGGAGGC
genomic: TATGAGGACAAGGATGGTGACTGGATGCTTGTCGGTGATGTCCCATGGGAgtaagtcttt ... tgtcaaccagGATGTTTGTTGAATCATGCAAGCGTTTACGCATCATGAAAGGAAAGGAGGC
EST: gi|10255026|gb|BE822792.1|BE822792
EST:     TATGAGGACAAGGATGGTGACTGGATGCTTGTCGGTGATGTCCCATGGGA                         GATGTTTGTTGAATCATGCAAGCGTTTACGCATCATGAAAGGAAAGGAGGC
genomic: TATGAGGACAAGGATGGTGACTGGATGCTTGTCGGTGATGTCCCATGGGAgtaagtcttt ... tgtcaaccagGATGTTTGTTGAATCATGCAAGCGTTTACGCATCATGAAAGGAAAGGAGGC
EST: gi|209699149|gb|BW652892.1|BW652892
EST:     TATGAGGACAAGGATGGTGACTGGATGCTTGTCGGTGATGTCCCATGGGA                         GATGTTTGTTGAATCATGCAAGCGTTTACGCATCATGAAAGGAAAGGAGGC
genomic: TATGAGGACAAGGATGGTGACTGGATGCTTGTCGGTGATGTCCCATGGGAgtaagtcttt ... tgtcaaccagGATGTTTGTTGAATCATGCAAGCGTTTACGCATCATGAAAGGAAAGGAGGC
EST: gi|213604392|gb|DB983480.1|DB983480
EST:     TATGAGGACAAGGATGGTGACTGGATGCTTGTCGGTGATGTCCCATGGGA                         GATGTTTGTTGAATCATGCAAGCGTTTACGCATCATGAAAGGAAAGGAGGC
genomic: TATGAGGACAAGGATGGTGACTGGATGCTTGTCGGTGATGTCCCATGGGAgtaagtcttt ... tgtcaaccagGATGTTTGTTGAATCATGCAAGCGTTTACGCATCATGAAAGGAAAGGAGGC
EST: gi|151406946|gb|EV276761.1|EV276761
EST:     TATGAGGACAAGGATGGTGACTGGATGCCTGTCGGTGATGTCCCATGGGA                         GATGTTTGTTGAATCATGCAAGCGTTTACGCATCATGAAAGGAAAGGAGGC
genomic: TATGAGGACAAGGATGGTGACTGGATGCTTGTCGGTGATGTCCCATGGGAgtaagtcttt ... tgtcaaccagGATGTTTGTTGAATCATGCAAGCGTTTACGCATCATGAAAGGAAAGGAGGC
EST: gi|193480258|gb|FK445866.1|FK445866
EST:     TATGAGGACAAGGATGGTGACTGGATGCTTGTCGGTGATGTCCCATGGGA                         GATGTTTGTTGAATCATGCAAG
genomic: TATGAGGACAAGGATGGTGACTGGATGCTTGTCGGTGATGTCCCATGGGAgtaagtcttt ... tgtcaaccagGATGTTTGTTGAATCATGCAAG
EST: gi|193648481|gb|FK596178.1|FK596178
EST:     TATGAGGACAAGGATGGTGACTGGATGCTTGTCGGTGATGTCCCATGGGA                         GATGTTTGTTGAATCATGCAAGCGTTTACGCATCATGAAAGGAAAGGAGGC
genomic: TATGAGGACAAGGATGGTGACTGGATGCTTGTCGGTGATGTCCCATGGGAgtaagtcttt ... tgtcaaccagGATGTTTGTTGAATCATGCAAGCGTTTACGCATCATGAAAGGAAAGGAGGC
EST: gi|208084448|gb|GD884930.1|GD884930
EST:     ATAGAGGACAAGGATGGTGACTGGATGCTTGTCGGTGATGTCCCATGGGA                         GATGTTTGTTGAATCATGCAAGCGTTTACGCATCATGAAAGGAAAGGAGGC
genomic: AT-GAGGACAAGGATGGTGACTGGATGCTTGTCGGTGATGTCCCATGGGAgtaagtcttt ... tgtcaaccagGATGTTTGTTGAATCATGCAAGCGTTTACGCATCATGAAAGGAAAGGAGGC
EST: gi|151394747|gb|EV264618.1|EV264618
EST:     TATGAGGACAAGGATGGTGACTGGATGCTTGTCGGTGATGTCCCATGGGA                         GATGTTTGTTGAATCATGCAAGCGTTTACGCATCATGAAAGGAAAGGAGGC
genomic: TATGAGGACAAGGATGGTGACTGGATGCTTGTCGGTGATGTCCCATGGGAgtaagtcttt ... tgtcaaccagGATGTTTGTTGAATCATGCAAGCGTTTACGCATCATGAAAGGAAAGGAGGC
EST: gi|6667635|gb|AW279086.1|AW279086
EST:     TATGAGGACAAGGATGGTGACTGGATGCTTGTCGGTGATGTCCCATGGGA                         GATGTTTGTTGAATCATGCAAGCGTTTACGCATCATGAAAGGAAAGGAGGC
genomic: TATGAGGACAAGGATGGTGACTGGATGCTTGTCGGTGATGTCCCATGGGAgtaagtcttt ... tgtcaaccagGATGTTTGTTGAATCATGCAAGCGTTTACGCATCATGAAAGGAAAGGAGGC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATGAGAGCAAGCTGAATGATCTTTTGAACAGCTCTGATTATGTCCCAACCTATGAGGACAAGGATGGTGACTGGATGCTTGTCGGTGATGTCCCATGGGAgtaagtctttcacctctactcaaaatcaatttggccgcgataattgaactttgcaatattatggggataaactttaacatatgtttaccaaacttcacgt

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG