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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGATATTGGGCAATTCCACCCTGATGGATGTCTTGAAATCATAGATAGGAAGAAAGATATTGTCAAACTTCAACATGGAGAATATATCTCTCTCGGAAAGgtaactcaaaccataccttgttcgttttggagtctggataaagtacttacaccagatccacagtaactttttctgggccttacgtagtgttttaattatgacttacttgcag

Basic information

species Glycine max
transcript GLYMA20G07280.1
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA20G07280.1 (Glycine max), 5'ss of exon 9
lower sequence: LOC_Os05g25310.1 (Oryza sativa), 5'ss of exon 10
TGATATTGGGCAATTCCACCCTGATGGATGTCTTGAAATCATAGATAGGAAGAAAGATATTGTCAAACTTCAACATGGAGAATATATCTCTCTCGGAAAGgt--aactcaaaccataccttgttcgttttggag----tctggataaagtacttacaccagatccacagtaactttttctgggccttacgtagtgttttaattatgacttacttgcag
 |||||||| || ||||| |||||||| || || || ||||| ||||| || || ||||| || |||||||| |||||||||||| | ||||| || |||||     |  ||   | |||    | || |||      | |   ||   || ||| |  | | || |     || | ||| |  ||  | | |  |||  |                 
AGATATTGGCCAGTTCCATCCTGATGGGTGCCTCGAGATCATTGATAGAAAAAAGGATATAGTAAAACTTCAGCATGGAGAATATGTGTCTCTTGGCAAGgtttggttacaatagtgcctcaaccattatgggtattctttttgtattataattatattaaaccccct----ctctctctcgttctctc-tggcctttacag----------------

upper sequence: GLYMA20G07280.1 (Glycine max), 5'ss of exon 9
lower sequence: GRMZM5G840955_T01 (Zea mays), 5'ss of exon 4
TGATATTGGGCAATTCCACCCTGATGGATGTCTTGAAATCATAGATAGGAAGAAAGATATTGTCAAACTTCAACATGGAGAATATATCTCTCTCGGAAAGgtaactcaaaccataccttgttcgttttggagtctggataaagtacttacaccagatccacagtaactttttctgggccttacgtagtgttttaattatgacttacttgcag
||||||||| || ||||| |||||||| || ||||| || || || ||||| |||||||| || || ||||| |||||||||||| | ||||| || |||||           |   ||||| |||||    | |  | ||| | | |||     ||          ||||  ||  |       |||| ||||    |  ||   ||||||
TGATATTGGTCAGTTCCATCCTGATGGGTGCCTTGAGATTATTGACAGGAAAAAAGATATAGTAAAGCTTCAGCATGGAGAATATGTGTCTCTTGGCAAGgt-----------ttgtttgttagttttt---tttaaaaaaaattcctactgtgaata---------ttttgttgaacg------agtgattta-ccgtctctc-tttgcag

upper sequence: GLYMA20G07280.1 (Glycine max), 5'ss of exon 9
lower sequence: AT2G04350.2 (Arabidopsis thaliana), 5'ss of exon 10
TGATATTGGGCAATTCCACCCTGATGGATGTCTTGAAATCATAGATAGGAAGAAAGATATTGTCAAACTTCAACATGGAGAATATATCTCTCTCGGAAAGgtaactcaaaccataccttgttcgttttggagtctggataaagtacttacaccagatccacagtaactttttctgggccttacgtagtgttttaattatgacttacttgcag
 |||||||||  ||||||||||||||||||||| ||| |||| ||||| |||||||||||||| |||||||||||||| |||||  | || || ||||||||           |  | | |     ||  | |||  ||| || |         | |  |   |||  | |  |    ||     | ||  |  || |      | |  |||
AGATATTGGGAGATTCCACCCTGATGGATGTCTCGAAGTCATCGATAGAAAGAAAGATATTGTTAAACTTCAACATGGGGAATACGTATCCCTTGGAAAGgt-----------ttgcctatagaacttaaattctacatagaggatg-----gtggtatatgataaaatctcatcatgctctttcattgcctggatcaca--caattcacag

upper sequence: GLYMA20G07280.1 (Glycine max), 5'ss of exon 9
lower sequence: Vv12s0057g01270.t01 (Vitis vinifera), 5'ss of exon 10
TGATATTGGGCAATTCCACCCTGATGGATGTCTTGAAATCATAGATAGGAAGAAAGATATTGTCAAACTTCAACATGGAGAATATATCTCTCTCGGAAAGgtaact-caaaccataccttgttcgttttggagtctggataaagtacttacaccagat----ccacagtaactttttctgggccttacgtagtgttttaattatgacttacttgcag
||| ||||| || || || ||| |||| || |||||||| || || |||||||| |||||||| ||||| || ||||||||||||||||| || || |||||   | |      |  || || | || | || |  |||||      |  || ||||        | ||||   ||| |||   | ||    | | ||  |     |||   |||||
TGACATTGGACAGTTTCAACCTAATGGTTGCCTTGAAATAATTGACAGGAAGAAGGATATTGTTAAACTACAGCATGGAGAATATATCTCCCTTGGGAAGgtttgtactggatttgactagtac-ttcttgattgaggatacc-ccttctcatcagaagggatagctgtaatcgtttttggaagtcactctttatgtttgtccatgctt---tgcag

upper sequence: GLYMA20G07280.1 (Glycine max), 5'ss of exon 9
lower sequence: PP1S475_12V6.1 (Physcomitrella patens), 5'ss of exon 9
TGATATTGGGCAATTCCACCCTGATGGATGTCTTGAAATCATAGATAGGAAGAAAGATATTGTCAAACTTCAACATGGAGAATATATCTCTCTCGGAAAGgtaactc---aaaccatacctt--gttcgttttggagtctggataaagtacttacaccagatccacagtaactttttctgggccttacgtagtgttttaattatgacttacttgcag
 || ||||| |  || ||    || |||||| | ||||| || ||| | ||||| |||||||| ||| | ||||||||||||||||| || || ||||||||    |   || | ||||||   |||  | |     |   |  ||  |  ||        |    ||||   || |   | |   || | |||||  ||                 
AGACATTGGCCGCTTTCATGAAGACGGATGTATAGAAATTATTGATCGTAAGAAGGATATTGTGAAATTGCAACATGGAGAATATATATCACTGGGAAAGgtgctgctgtaatctatacctcacgttactgtcctcatgctgtcaagtttttttgtttcactgtggagtatgcttcttatgaca--acctggtgttggaacag--------------

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|192298315|gb|FG992105.1|FG992105
EST:     GAATATATCTCTCTCGGAAAG                         GTTGAGGCAGCACTATCATCATGTGATTATGTGGACAATATAATGGTTTAT
genomic: GAATATATCTCTCTCGGAAAGgtaactcaaa ... ttacttgcagGTTGAGGCAGCACTATCATCATGTGATTATGTGGACAATATAATGGTTTAT
EST: gi|193351723|gb|FK318405.1|FK318405
EST:     ATGGAGAATATATCTCTCTCGGAAAG                         GTTGAGGCAGCACTAATCATCATGTGATTATGTGGACAATATAATGGTTTA
genomic: ATGGAGAATATATCTCTCTCGGAAAGgtaactcaaa ... ttacttgcagGTTGAGGCAGCACT-ATCATCATGTGATTATGTGGACAATATAATGGTTTA
EST: gi|11687916|gb|BF595592.1|BF595592
EST:     AGAAAGATATTGTCAAACTTCAACATGGAGAATATATCTCTCTCGGAAAG                         GTTGAGGCAGCACTATCATCATGTGATTATGTGGACAATATAATGGTTTAT
genomic: AGAAAGATATTGTCAAACTTCAACATGGAGAATATATCTCTCTCGGAAAGgtaactcaaa ... ttacttgcagGTTGAGGCAGCACTATCATCATGTGATTATGTGGACAATATAATGGTTTAT
EST: gi|9820665|gb|BE556175.1|BE556175
EST:     AGAAAGATATTGTCAAACTTCAACATGGAGAATATATCTCTCTCGGAAAG                         GTTGAGGCAGCACTATCATCATGTGATTATGTGGACAATATAATGGTTTAT
genomic: AGAAAGATATTGTCAAACTTCAACATGGAGAATATATCTCTCTCGGAAAGgtaactcaaa ... ttacttgcagGTTGAGGCAGCACTATCATCATGTGATTATGTGGACAATATAATGGTTTAT
EST: gi|6069481|gb|AW099161.1|AW099161
EST:     AGAAAGATATTGTCAAACTTCAACATGGAGAATATATCTCTCTCGGAAAG                         GTTGAGGCAGCACTATCATCATGTGATTATGTGGACAATATAATGGTTTAT
genomic: AGAAAGATATTGTCAAACTTCAACATGGAGAATATATCTCTCTCGGAAAGgtaactcaaa ... ttacttgcagGTTGAGGCAGCACTATCATCATGTGATTATGTGGACAATATAATGGTTTAT
EST: gi|120529641|gb|EH257775.1|EH257775
EST:     AGAAAGATATTGTCAAACTTCAACATGGAGAATATATCTCTCTCGGAAAG                         GTTGAGGCAGCACTATCATCATGTGATTATGTGGACAATATAATGGTTTAT
genomic: AGAAAGATATTGTCAAACTTCAACATGGAGAATATATCTCTCTCGGAAAGgtaactcaaa ... ttacttgcagGTTGAGGCAGCACTATCATCATGTGATTATGTGGACAATATAATGGTTTAT
EST: gi|22929083|gb|BU546222.1|BU546222
EST:     AGAAAGATATTGTCAAACTTCAACATGGAGAATATATCTCTCTCGGAAAG                         GTTGAGGCAGCACTATCATCATGTGATTATGTGGACAATATAATGGTTTAT
genomic: AGAAAGATATTGTCAAACTTCAACATGGAGAATATATCTCTCTCGGAAAGgtaactcaaa ... ttacttgcagGTTGAGGCAGCACTATCATCATGTGATTATGTGGACAATATAATGGTTTAT
EST: gi|10234151|gb|BE803039.1|BE803039
EST:     AGAAAGATATTGTCAAACTTCAACATGGAGAATATATCTCTCTCGGAAAG                         GTTGAGGCAGCACTATCATCATGTGATTATGTGGACAATATAATGGTTTAT
genomic: AGAAAGATATTGTCAAACTTCAACATGGAGAATATATCTCTCTCGGAAAGgtaactcaaa ... ttacttgcagGTTGAGGCAGCACTATCATCATGTGATTATGTGGACAATATAATGGTTTAT
EST: gi|192326437|gb|FK017709.1|FK017709
EST:     AGAAAGATATTGTCAAACTTCAACATGGAGAATATATCTCTCTCGGAA-G                         GTTGAGGCAGCACTATCATCATGTGATTATGTGGACAATATAATGGTTTAT
genomic: AGAAAGATATTGTCAAACTTCAACATGGAGAATATATCTCTCTCGGAAAGgtaactcaaa ... ttacttgcagGTTGAGGCAGCACTATCATCATGTGATTATGTGGACAATATAATGGTTTAT
EST: gi|7796660|gb|AW782055.1|AW782055
EST:     AGAAAGATATTGTCAAACTTCAACATGGAGAATATATCTCTCTCGGAAAG                         GTTGAGGCAGCACTATCATCATGTGATTATGTGGACAATATAATGGTTTAT
genomic: AGAAAGATATTGTCAAACTTCAACATGGAGAATATATCTCTCTCGGAAAGgtaactcaaa ... ttacttgcagGTTGAGGCAGCACTATCATCATGTGATTATGTGGACAATATAATGGTTTAT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGATATTGGGCAATTCCACCCTGATGGATGTCTTGAAATCATAGATAGGAAGAAAGATATTGTCAAACTTCAACATGGAGAATATATCTCTCTCGGAAAGgtaactcaaaccataccttgttcgttttggagtctggataaagtacttacaccagatccacagtaactttttctgggccttacgtagtgttttaattatgacttacttgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA