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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATACAATGGCGTGCACTTGATGAGATAAATGCAGGGGTGTGTGATGGTATGACATACGCAGAAATCAAGAAAAACATGCCAGAGGAGTATGAgtatgtttgcagacttgtaatttctctcttatttgcaagttgaatgcaactaatatggcagataacaaagaagcacaatgtgaaacatcttttggttttggggttagaagatgctgtttaaactcagtagttattatttccctcccctattgtcttattgcag

Basic information

species Glycine max
transcript GLYMA11G27870.1
intron # 20
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA11G27870.1 (Glycine max), 5'ss of exon 20
lower sequence: LOC_Os05g07130.2 (Oryza sativa), 5'ss of exon 19
ATACAATGGCGTGCACTTGATGAGATAAATGCAGGGGTGTGTGATGGTATGACATACGCAGAAATCAAGAAAAACATGCCAGAGGAGTATGAgtatgtttgcagacttgtaatttctctct-tatttgcaagttgaatgcaactaatatggcagataacaaagaagcacaatgtgaaacatcttttggttttggggttagaagatgctgtttaaactcagtagttattatttccctcccctattgtcttattgcag
|||||||||||||| ||||||||||||||  | |||||||||||||| ||||| || | ||| || ||||||   ||||| ||||| | |||||||||  ||    |||| || | | | |  |||||    |||   |    |  | | | || | |||        | || ||  | | ||  || || |    ||                                                          
ATACAATGGCGTGCTCTTGATGAGATAAACTCTGGGGTGTGTGATGGGATGACGTATGAAGAGATAAAGAAAGTTATGCCCGAGGAATTTGAgtatgt--gcta--ttgttatctttgtttacatttgt---ttgggagttctttctttagtagtttacatgatgtgcccatctgctaga-ctgctgattgtcaatttgt--------------------------------------------------------

upper sequence: GLYMA11G27870.1 (Glycine max), 5'ss of exon 20
lower sequence: LOC_Os03g18310.2 (Oryza sativa), 5'ss of exon 18
ATACAATGGCGTGCACTTGATGAGATAAATGCAGGGGTGTGTGATGGTATGACATACGCAGAAATCAAGAAAAACATGCCAGAGGAGTATGAgtatgtttgcagacttgt-aatttctctcttatttgcaagttgaatgcaactaatatggcagataacaaagaagcacaatgtgaaacatcttttggttttggggttagaagatgctgtttaaactcagtagttattatttccctcccctattgtcttattgcag
||||||||||||||||||||||| ||||| || ||  | |||||||| ||||| || |  ||||| |||||||  |  || || || |||||||| |    || | |  |  ||||  || || |||    |||   | ||   ||  |  |   |     |   |  |  || | ||   | | |  |     |  || |                                                       
ATACAATGGCGTGCACTTGATGAAATAAACGCTGGCATCTGTGATGGGATGACGTATGATGAAATAAAGAAAATTAAACCTGAAGAATATGAgtacg----caaattcattgattttccttttgtttt---gtttttttcattgaagctatcttttgttgcatttgttctttgagtaagcccatgtcctgccaag--taaa-------------------------------------------------------

upper sequence: GLYMA11G27870.1 (Glycine max), 5'ss of exon 20
lower sequence: GRMZM5G824405_T02 (Zea mays), 5'ss of exon 17
ATACAATGGCGTGCACTTGATGAGATAAATGCAGGGGTGTGTGATGGTATGACATACGCAGAAATCAAGAAAAACATGCCAGAGGAGTATGAgtatgtttgcagacttgtaatttctc-tcttat-ttgcaagttgaatgcaactaatatggcagataacaaagaagcacaatgtgaaacatcttttggttttggggttagaagatgctgtttaaactcagtagttattatttccctcccctattgtcttattgcag
|||||||||||||| ||||||||||| ||||| ||||| |||||||| ||||||||||  ||||| |||||||  |  || || || |||||||| ||      |||  ||   |  | | |||| ||  ||  |       |  | | || ||   |  ||    |  ||          | | |||||  |                                                                
ATACAATGGCGTGCTCTTGATGAGATCAATGCTGGGGTCTGTGATGGGATGACATACGATGAAATAAAGAAAAGTAAACCTGAAGAATATGAgtacgtgaattcactgatatcatgacattttatattaaaaaatccccctgatcactctgtcactcag-aattttgttcagctgtgggtgtgtgttggtgct----------------------------------------------------------------

upper sequence: GLYMA11G27870.1 (Glycine max), 5'ss of exon 20
lower sequence: GRMZM2G021846_T01 (Zea mays), 5'ss of exon 19
ATACAATGGCGTGCACTTGATGAGATAAATGCAGGGGTGTGTGATGGTATGACATACGCAGAAATCAAGAAAAACATGCCAGAGGAGTATGAgtatgtttgcaga--cttgtaatttctc-tcttatttgca--agttgaatgcaactaatatggcagataacaaagaagcacaatgtgaaac--atcttttggttttggggttagaagatgctgtttaaactcagtagttattatttccctcccctattgtcttattgcag---------------
|||||||||||||| ||||||||||| ||| | || ||||||||||| ||||| || | ||| || ||||||| |||||| ||||| | |||||| || |  |||   || |  ||| |  |  || |||||  |  || ||| ||      |  |  |  |   | |       ||| | ||  || |||   ||    | |    | ||   |   ||||  |   |  ||||   |    || | | |   |  || |                
ATACAATGGCGTGCTCTTGATGAGATCAATTCTGGAGTGTGTGATGGGATGACTTATGAAGAGATAAAGAAAATCATGCCCGAGGAATTTGAgtacgtataaagaaaattttgctttattgttgtagttgcaccatgtgcatggaatatccgttacttaccattcatatatgaggtgttagaccaatgtttcatttccatgctgtacaaattaggaaaaaacagaaatgaaattaacacaaatccttttggcacttgtgaatgcttgtttcaaccag

upper sequence: GLYMA11G27870.1 (Glycine max), 5'ss of exon 20
lower sequence: GRMZM2G021846_T02 (Zea mays), 5'ss of exon 18
--------ATACAATGGCGTGCACTTGATGAGATAAATGCAGGGGTGTGTGATGGTATGACATACGCAGAAATCAAGAAAAACATGCCAGAGGAGTATGAgtatgtttgcaga--cttgtaatttctc-tcttatttgca--agttgaatgcaactaatatggcagataacaaagaagcacaatgtgaaac--atcttttggttttggggttagaagatgctgtttaaactcagtagttattatttccctcccctattgtcttattgcag---------------
        |||||||||||||| ||||||||||| ||| | || ||||||||||| ||||| || | ||| || ||||||| |||||| ||||| | |||||| || |  |||   || |  ||| |  |  || |||||  |  || ||| ||      |  |  |  |   | |       ||| | ||  || |||   ||    | |    | ||   |   ||||  |   |  ||||   |    || | | |   |  || |                
ATTTGTAGATACAATGGCGTGCTCTTGATGAGATCAATTCTGGAGTGTGTGATGGGATGACTTATGAAGAGATAAAGAAAATCATGCCCGAGGAATTTGAgtacgtataaagaaaattttgctttattgttgtagttgcaccatgtgcatggaatatccgttacttaccattcatatatgaggtgttagaccaatgtttcatttccatgctgtacaaattaggaaaaaacagaaatgaaattaacacaaatccttttggcacttgtgaatgcttgtttcaaccag

upper sequence: GLYMA11G27870.1 (Glycine max), 5'ss of exon 20
lower sequence: Vv06s0004g06920.t01 (Vitis vinifera), 5'ss of exon 19
ATACAATGGCGTGCACTTGATGAGATAAATGCAGGGGTGTGTGATGGTATGACATACGCAGAAATCAAGAAAAACATGCCAGAGGAGTATGAgtatgtttgcagacttgtaatttctctcttatttgcaagttg-aatgcaactaatatggcagataacaaagaagcacaatgtgaaacat-cttttggttttggggttagaagatgctgtttaaactcagtagttattatttccctcccctattgtcttattgcag
|||||||||||||||||||||||||||||||| || ||||||||||| |||||||| | ||| || ||||| |||||||| ||||| || |||||||   |||   ||    | | |     |||| || | || |||    ||   ||| || | | ||       |   | | | |||| ||| |  | ||                                                                
ATACAATGGCGTGCACTTGATGAGATAAATGCTGGAGTGTGTGATGGAATGACATATGAAGAGATAAAGAAGAACATGCCTGAGGAATACGAgtatg--agcattttttatttgtttaagaaattttcatgatgtaatttttcttccatg-cataca-catgatgatagcttattagacatacttgtcatattaca-------------------------------------------------------------

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|51336524|gb|CO980390.1|CO980390
EST:     GATGGTATGACATACGCAGAAATCAAGAAAAACATGCCAGAGGAGTATGA                         ATCGCGCAAGAAGGACAAGCTTAGGTATCGTTATCCTCGTGGTGAGTCATA
genomic: GATGGTATGACATACGCAGAAATCAAGAAAAACATGCCAGAGGAGTATGAgtatgtttgc ... cttattgcagATCGCGCAAGAAGGACAAGCTTAGGTATCGTTATCCTCGTGGTGAGTCATA
EST: gi|51336471|gb|CO980337.1|CO980337
EST:     GATGGTATGACATACGCAGAAATCAAGAAAAACATGCCAGAGGAGTATGA                         ATCGCGCAAGAAGGACAAGCTTAGGTATCGTTATCCTCGTGGTGAGTCATA
genomic: GATGGTATGACATACGCAGAAATCAAGAAAAACATGCCAGAGGAGTATGAgtatgtttgc ... cttattgcagATCGCGCAAGAAGGACAAGCTTAGGTATCGTTATCCTCGTGGTGAGTCATA
EST: gi|9564592|gb|BE474101.1|BE474101
EST:     GATGGTATGACATACGCAGAAATCAAGAAAAACATGCCAGAGGAGTATGA                         ATCGCGCAAGAAGGACAAGCTTAGGTATCGTTATCCTCGTGGTGAGTCATA
genomic: GATGGTATGACATACGCAGAAATCAAGAAAAACATGCCAGAGGAGTATGAgtatgtttgc ... cttattgcagATCGCGCAAGAAGGACAAGCTTAGGTATCGTTATCCTCGTGGTGAGTCATA
EST: gi|22930234|gb|BU547373.1|BU547373
EST:     GATGGTATGACATACGCAGAAATCAAGAAAAACATGCCAGAGGAGTATGA                         ATCGCGCAAGAAGGACAAGCTTAGGTATCGTTATCCTCGTGGTGAGTCATA
genomic: GATGGTATGACATACGCAGAAATCAAGAAAAACATGCCAGAGGAGTATGAgtatgtttgc ... cttattgcagATCGCGCAAGAAGGACAAGCTTAGGTATCGTTATCCTCGTGGTGAGTCATA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATACAATGGCGTGCACTTGATGAGATAAATGCAGGGGTGTGTGATGGTATGACATACGCAGAAATCAAGAAAAACATGCCAGAGGAGTATGAgtatgtttgcagacttgtaatttctctcttatttgcaagttgaatgcaactaatatggcagataacaaagaagcacaatgtgaaacatcttttggttttggggttagaagatgctgtttaaactcagtagttattatttccctcccctattgtcttattgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG