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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATACAATGGCGCGCACTTGATGAGATAAATGCTGGTGTGTGTGATGGGATGACGTATGAAGAAATCAAGAAGAACATGCCAGAGGAGTATGAgtatgtcacaagcttgtaatctgtcttatttccagttgaatgcaaatggtacattagatataaaagcaagtgcttgttgggagcacaatgctgtctaaaaatgtttaaacactattcttattttattttattttgttgcag

Basic information

species Glycine max
transcript GLYMA02G39390.1
intron # 19
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA02G39390.1 (Glycine max), 5'ss of exon 19
lower sequence: LOC_Os05g07130.2 (Oryza sativa), 5'ss of exon 19
ATACAATGGCGCGCACTTGATGAGATAAATGCTGGTGTGTGTGATGGGATGACGTATGAAGAAATCAAGAAGAACATGCCAGAGGAGTATGAgtatgtcacaagcttgtaatctgtcttatttccagttgaatgcaaatggtacattagata--taaaagcaagtgcttgttgggagcacaatgctgtctaaaaatgtttaaacactattcttattttattttattttgttgcag
||||||||||| || ||||||||||||||  |||| |||||||||||||||||||||||||| || |||||    ||||| ||||| | |||||||||   |   |||| ||||   || ||| || |||  ||  | |  |   ||   ||  | | |  | ||||   |  |    ||  |||||  |   ||| | |                                   
ATACAATGGCGTGCTCTTGATGAGATAAACTCTGGGGTGTGTGATGGGATGACGTATGAAGAGATAAAGAAAGTTATGCCCGAGGAATTTGAgtatgtgcta---ttgttatct---ttgtttacatttgtttgggagttctttctttagtagtttacatgatgtgcccatctgctagac--tgctgattgtcaatttgt-----------------------------------

upper sequence: GLYMA02G39390.1 (Glycine max), 5'ss of exon 19
lower sequence: LOC_Os03g18310.2 (Oryza sativa), 5'ss of exon 18
ATACAATGGCGCGCACTTGATGAGATAAATGCTGGTGTGTGTGATGGGATGACGTATGAAGAAATCAAGAAGAACATGCCAGAGGAGTATGAgtatgtcacaagcttgt-aatctgtcttatttccagttgaatgcaaatggtacattagatataaaagcaagtgcttgttggg--agcaca-atgctgtctaaaaatgtttaaacactattcttattttattttattttgttgcag
||||||||||| ||||||||||| ||||| |||||  | |||||||||||||||||||| ||||| ||||| |  |  || || || |||||||| |   |||  |  |  || |  ||| | |   |||   | ||  ||   |  ||  | |    |||  || |  ||| |  ||| ||  | ||| | |  ||                                        
ATACAATGGCGTGCACTTGATGAAATAAACGCTGGCATCTGTGATGGGATGACGTATGATGAAATAAAGAAAATTAAACCTGAAGAATATGAgtacg---caaattcattgattttccttttgttttgtttttttcat-tgaagc--tatcttttgttgcatttgttctttgagtaagcccatgtcctgccaagtaaa---------------------------------------

upper sequence: GLYMA02G39390.1 (Glycine max), 5'ss of exon 19
lower sequence: GRMZM2G021846_T01 (Zea mays), 5'ss of exon 19
ATACAATGGCGCGCACTTGATGAGATAAATGCTGGTGTGTGTGATGGGATGACGTATGAAGAAATCAAGAAGAACATGCCAGAGGAGTATGAgtatgtcacaagcttgtaatctgtcttatttccagttg---aatgcaaatggtacattagatataaaa---gcaagtgcttgttgggagcacaatgctgtctaaaaatgtt-taaacactattcttat-tttattttattttgttgcag------------------------------------
||||||||||| || ||||||||||| ||| |||| ||||||||||||||||| |||||||| || ||||| | |||||| ||||| | |||||| ||   |||    |  |   |  |  ||  |||||    |||   |||| | ||  | ||   |     ||  |    | ||  ||  ||||| |   |    ||| | || | | ||     |     |  | |  ||    ||                                     
ATACAATGGCGTGCTCTTGATGAGATCAATTCTGGAGTGTGTGATGGGATGACTTATGAAGAGATAAAGAAAATCATGCCCGAGGAATTTGAgtacgtataaagaaaattttgctttattgttgtagttgcaccatgtgcatggaatatccgttacttaccattcatatatgaggtgttagaccaatgtttcatttccatgctgtacaaattaggaaaaaacagaaatgaaattaacacaaatccttttggcacttgtgaatgcttgtttcaaccag

upper sequence: GLYMA02G39390.1 (Glycine max), 5'ss of exon 19
lower sequence: GRMZM2G021846_T02 (Zea mays), 5'ss of exon 18
--------ATACAATGGCGCGCACTTGATGAGATAAATGCTGGTGTGTGTGATGGGATGACGTATGAAGAAATCAAGAAGAACATGCCAGAGGAGTATGAgtatgtcacaagcttgtaatctgtcttatttccagttga---atgcaaatggtacattagatataaaag---caagtgcttgttgggagcacaatgctgtctaaaaatgtt-taaacactattcttatttt-attttattttgttgcag------------------------------------
        ||||||||||| || ||||||||||| ||| |||| ||||||||||||||||| |||||||| || ||||| | |||||| ||||| | |||||| ||   |||    |  |   |  |  ||  |||||    |||   |||| | ||  | ||   |     ||  |    | ||  ||  ||||| |   |    ||| | || | | ||     |     |  | |  ||    ||                                     
ATTTGTAGATACAATGGCGTGCTCTTGATGAGATCAATTCTGGAGTGTGTGATGGGATGACTTATGAAGAGATAAAGAAAATCATGCCCGAGGAATTTGAgtacgtataaagaaaattttgctttattgttgtagttgcaccatgtgcatggaatatccgttacttaccattcatatatgaggtgttagaccaatgtttcatttccatgctgtacaaattaggaaaaaacagaaatgaaattaacacaaatccttttggcacttgtgaatgcttgtttcaaccag

upper sequence: GLYMA02G39390.1 (Glycine max), 5'ss of exon 19
lower sequence: GRMZM5G824405_T02 (Zea mays), 5'ss of exon 17
ATACAATGGCGCGCACTTGATGAGATAAATGCTGGTGTGTGTGATGGGATGACGTATGAAGAAATCAAGAAGAACATGCCAGAGGAGTATGAgtatgtcacaagcttgtaatctgtcttatttccagttgaatgcaaatggtac--attagatataaaagcaagtgcttgttgggagcacaatgctgtctaaaaatgtttaaacactattcttattttattttattttgttgcag
||||||||||| || ||||||||||| |||||||| || |||||||||||||| || || ||||| ||||| |  |  || || || |||||||| || |      ||  |||  |   ||||    || ||   ||||    |  || |       |  ||     |||||  |        | ||| |     || |                                    
ATACAATGGCGTGCTCTTGATGAGATCAATGCTGGGGTCTGTGATGGGATGACATACGATGAAATAAAGAAAAGTAAACCTGAAGAATATGAgtacgtgaattcactgatatc-atgacattttatattaaa---aaatccccctgatcactctgtcactcagaattttgttcagc---tgtgggtgtgtgttggtgct------------------------------------

upper sequence: GLYMA02G39390.1 (Glycine max), 5'ss of exon 19
lower sequence: AT1G07110.1 (Arabidopsis thaliana), 5'ss of exon 19
ATACAATGGCGCGCACTTGATGAGATAAATGCTGGTGTGTGTGATGGGATGACGTATGAAGAAATCAAGAAGAACATGCCAGAGGAGTATGAgtatgtcacaagcttgtaatctgtcttatttccagttgaatgcaaatggtacattagatataaaagcaagtgcttgttgggagcacaatgctgtctaaaaatgtttaaacactattcttattttattttattttgttgcag
 | |||||||| || || || ||||| |||||||| || |||||||||||||| ||||||||  | ||||||||||||||||| || || ||||| || ||  | |   |||| ||   || |  | | | |   || || |||  |||      |   |    || || |     | |||    ||| | | |  |  | |     || | || |  |  || |   |||||
GTGCAATGGCGTGCCCTGGACGAGATCAATGCTGGAGTTTGTGATGGGATGACATATGAAGAGGTAAAGAAGAACATGCCAGAAGAATACGAgtaagtgacttgatca-aatccgt---atatgtaat-gtaaaaaagtgttac--tagc-----agctatcccctcgtagaacagaaaataaactctcagacttctctacc-----tcatcttgtggtgcatatgactgcag

upper sequence: GLYMA02G39390.1 (Glycine max), 5'ss of exon 19
lower sequence: Vv06s0004g06920.t01 (Vitis vinifera), 5'ss of exon 19
ATACAATGGCGCGCACTTGATGAGATAAATGCTGGTGTGTGTGATGGGATGACGTATGAAGAAATCAAGAAGAACATGCCAGAGGAGTATGAgtatgtcacaagcttgtaatctgtcttatttccagttgaatgcaaatggtacattagatataaaagcaagtgcttgttgggagcacaatgctgtctaaaaatgtttaaacactattcttattttattttattttgttgcag
||||||||||| ||||||||||||||||||||||| ||||||||||| ||||| |||||||| || |||||||||||||| ||||| || |||||||            |   | | ||||||   ||| ||    ||   | |||  ||| |||       |  || ||    ||| |    ||   | |  |  ||| |||   || | || |||                
ATACAATGGCGTGCACTTGATGAGATAAATGCTGGAGTGTGTGATGGAATGACATATGAAGAGATAAAGAAGAACATGCCTGAGGAATACGAgtatg------------agcattttttattt---gtttaa---gaaattttcat--gatgtaa-------tttttcttccatgcatacacatgatgatagcttattagacatacttgtcatattaca--------------

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|208125843|gb|GD925955.1|GD925955
EST:     GAAGAAATCAAGAAGAACATGCCAGAGGAGTATGA                         ATCCCGCAATAAGGACAAACTTAGGTATCGTTATCCTCGTGGAGAGTCTTA
genomic: GAAGAAATCAAGAAGAACATGCCAGAGGAGTATGAgtatgtcaca ... tttgttgcagATCCCGCAATAAGGACAAACTTAGGTATCGTTATCCTCGTGGAGAGTCTTA
EST: gi|17024057|gb|BM095091.1|BM095091
EST:     GATGGGAAGACATATGAAGAAATCAAGAAGAACATGCCAGAGGAGTACGA                         ATCCCGCAATAAGGACAAACTTAGGTATCGTTATCCTCGTGGAGAGTCTTA
genomic: GATGGGATGACGTATGAAGAAATCAAGAAGAACATGCCAGAGGAGTATGAgtatgtcaca ... tttgttgcagATCCCGCAATAAGGACAAACTTAGGTATCGTTATCCTCGTGGAGAGTCTTA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATACAATGGCGCGCACTTGATGAGATAAATGCTGGTGTGTGTGATGGGATGACGTATGAAGAAATCAAGAAGAACATGCCAGAGGAGTATGAgtatgtcacaagcttgtaatctgtcttatttccagttgaatgcaaatggtacattagatataaaagcaagtgcttgttgggagcacaatgctgtctaaaaatgtttaaacactattcttattttattttattttgttgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG