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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagtactactttgagatattttaatttgttctgttttttgtcattagtagaagtagaaatgcactttttgaatactgattgtacaatgagaggtttatatagaattgaggtgcattgaatatttgaagcacaactgatgatgacaattgtttttctccatggttgtagGTTGTCAGATGGGGGCGGTCTGTATATGCAAATATTCAGAAATTTATCCAGTTTCAGCTTACAGTAAATGTGGCCGCTCTAGTGATAAATGTTGTTGCTG

Basic information

species Glycine max
transcript GLYMA15G18180.1
intron # 25
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA15G18180.1 (Glycine max), 3'ss of exon 25
lower sequence: LOC_Os04g51610.3 (Oryza sativa), 3'ss of exon 26
gttagtactactttgagatattttaatttgttctgttttttgtcattagtagaagtagaaatgcactttttgaatactgattgtacaatgagaggtttatatagaattgaggtgcattgaatatttgaagcacaactgatgatgacaattgtttttctccatggttgtagGTTGTCAGATGGGGGCGGTCTGTATATGCAAATATTCAGAAATTTATCCAGTTTCAGCTTACAGTAAATGTGGCCGCTCTAGTGATAAATGTTGTTGCTG
                                                                                                 ||| || |  || | |   ||       |    ||  ||||    | | | |  | |||   |  | || ||||||||||||||||| || || || |||||||| |||||||||||||| ||||||||| | || || || || || ||  |  | || || ||||||||||
------------------------------------------------------------------------------------------------gtatgtaca-ctgtgttctgttattggccttc--catgactgcaacttatagtattcttttctctcgcttttagGTTGTCAGATGGGGTCGCTCGGTTTATGCAAACATTCAGAAATTTATACAGTTTCAGTTAACCGTCAACGTTGCAGCCTTGATTATTAACGTTGTTGCTG

upper sequence: GLYMA15G18180.1 (Glycine max), 3'ss of exon 25
lower sequence: GRMZM5G893864_T01 (Zea mays), 3'ss of exon 5
gttagtactactttgagatattttaatttgttctgttttttgtcattagtagaagtagaaatgcactttttgaatactgattgtacaatgagaggtttatatagaattgaggtgcattgaatatttgaagcacaactgatgatgacaattgtttttctccatggttgtagGTTGTCAGATGGGGGCGGTCTGTATATGCAAATATTCAGAAATTTATCCAGTTTCAGCTTACAGTAAATGTGGCCGCTCTAGTGATAAATGTTGTTGCTG
                                                                    ||||    ||  || || |||   ||| |  |  | |||  | | |||    ||   | |  ||    ||      |   |  || |  |  ||  || ||||| ||  | ||||| || ||||| ||||||||||| || || ||||| ||||| |||||||| |||||||| || ||||| || || |||||||||||||
-------------------------------------------------------------------gtttggc--ctatttttagaatctaaggatcttg-ataat--acgcgcac---atgcctaatacaacgttgtcttacatgttctttatcttttata-ttctagGTGGTTCGCTGGGGTCGCTCTGTTTATGCAAATATCCAAAAGTTTATTCAGTTCCAGCTTACCGTAAATGTTGCAGCTCTTGTCATCAATGTTGTTGCTG

upper sequence: GLYMA15G18180.1 (Glycine max), 3'ss of exon 25
lower sequence: AT4G29900.1 (Arabidopsis thaliana), 3'ss of exon 27
gttagtactactttgagat-----attttaatttgttctg--------ttttttgtcattagtagaagtagaaatgcactttttgaatactgattgtacaatgagaggtttatatagaattgaggtgcatt---gaatatttgaagcacaactgat--gatgacaattgtttttctc----catggttgtagGTTGTCAGATGGGGGCGGTCTGTATATGCAAATATTCAGAAATTTATCCAGTTTCAGCTTACAGTAAATGTGGCCGCTCTAGTGATAAATGTTGTTGCTG
||| ||| | ||| || |      |||  ||||| || |         |  ||| | ||        || |      |||||| ||||     ||   |    |     |  | | |  ||  ||   |||   ||   ||| ||  |      ||  |||  | ||| |  |  ||    |||   | ||||||||| | ||||| || ||||| ||||| |||||||| || || |||||||||||||| || || ||||| || ||||| || || ||||| || ||||
gtttgta-tccttagaaaccaaggattcaaatttcttataaaagaagctcctttttgatactcttctgttgcgtgatacttttggaatttcttttcctcgtaaatgtcctcctttgggctttggggctatttgtgatctttttaattatcctgaattagatatccattttaataatcgtctcattcctatagGTTGTCCGTTGGGGTCGATCTGTGTATGCGAATATTCAAAAGTTCATCCAGTTTCAGCTCACGGTTAATGTCGCAGCTCTTGTCATCAATGTGGTGGCTG

upper sequence: GLYMA15G18180.1 (Glycine max), 3'ss of exon 25
lower sequence: Vv11s0052g00320.t01 (Vitis vinifera), 3'ss of exon 28
gttagtactactttgagatattttaatttgttctgttttttgtcattagtagaagtagaaatgcactttttgaatactgattgtacaatgagaggtttatatagaattgaggtgcattgaatatttgaagcacaactgatgatgacaattg-tttttctccatggttgtagGTTGTCAGATGGGGGCGGTCTGTATATGCAAATATTCAGAAATTTATCCAGTTTCAGCTTACAGTAAATGTGGCCGCTCTAGTGATAAATGTTGTTGCTG
                                                              |   || ||||  |  | ||   |  |  || |  || |  | |||  | |   |||||     |||||     |  |  | ||  ||| ||| |||   ||  | ||||||||||||||||| || ||||||||||||||||| |||||||| |||||||||||||| ||||| ||||| || |||||| | || ||||| || || |
-------------------------------------------------------------cgagtttgttgatcaaagttt---cccttcgatgcctaca--gcatttggataagttgaa-----gaagctgggatctttgtaactgttgatttctcttgttgcatttagGTTGTCAGATGGGGACGATCTGTATATGCAAATATACAGAAATTCATCCAGTTTCAGCTCACAGTTAATGTTGCAGCTCTAATAATTAATGTCGTGGCAG

upper sequence: GLYMA15G18180.1 (Glycine max), 3'ss of exon 25
lower sequence: EFJ22392 (Selaginella moellendorffii), 3'ss of exon 22
gttagtactactttgagatattttaatttgttctgttttttgtcattagtagaagtagaaatgcactttttgaatactgattgtacaatgagaggtttatatagaattgaggtgcattgaatatttgaagcacaactgatgatgacaatt--gtttttctccatggttgtagGTTGTCAGATGGGGGCGGTCTGTATATGCAAATATTCAGAAATTTATCCAGTTTCAGCTTACAGTAAATGTGGCCGCTCTAGTGATAAATGTTGTTGCTG
                                                                                                                            |   |  ||| ||  || ||  | |        ||   ||  ||| |||||||  | ||||| ||||| || ||||| ||||||||||| ||||||||||| ||||| || |||||||| |  || || ||  | || || || || |
---------------------------------------------------------------------------------------------------------------------------gtaagataacagcttttggtgcgagtctgaaggatcgaaattcttgcagGTTGTACGCTGGGGTCGGTCCGTGTATGCCAATATTCAGAAGTTTATCCAGTTCCAGCTGACTGTAAATGTTGTTGCGCTGGTTCTCAACGTCGTGGCCG

upper sequence: GLYMA15G18180.1 (Glycine max), 3'ss of exon 25
lower sequence: EFJ25508 (Selaginella moellendorffii), 3'ss of exon 23
gttagtactactttgagatattttaatttgttctgttttttgtcattagtagaagtagaaatgcactttttgaatactgattgtacaatgagaggtttatatagaattgaggtgcattgaatatttgaagcacaactgatgatgacaatt--gtttttctccatggttgtagGTTGTCAGATGGGGGCGGTCTGTATATGCAAATATTCAGAAATTTATCCAGTTTCAGCTTACAGTAAATGTGGCCGCTCTAGTGATAAATGTTGTTGCTG
                                                                                                                            |   |  ||| ||  || ||  | |        ||   ||  ||| |||||||  | ||||| ||||| || ||||| ||||||||||| ||||||||||| ||||| || |||||||| |  || || ||  | || || || || |
---------------------------------------------------------------------------------------------------------------------------gtaagataacagcttttggtgcgagtctgaaggatcgaaattcttgcagGTTGTACGCTGGGGTCGGTCCGTGTATGCCAATATTCAGAAGTTTATCCAGTTCCAGCTGACTGTAAATGTAGTTGCGCTGGTTCTCAACGTCGTGGCCG

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|23729217|gb|BU762697.1|BU762697
EST:     AGAGCTCCGATATCATTATTTTGGATGACAATTTTGCTTCAGTTGTGAAG                         GTTGTCAGATGGGGGCGGTCTGTATATGCAAATATTCAGAAATTTATCCAG
genomic: AGAGCTCCGATATCATTATTTTGGATGACAATTTTGCTTCAGTTGTGAAGgttagtacta ... atggttgtagGTTGTCAGATGGGGGCGGTCTGTATATGCAAATATTCAGAAATTTATCCAG






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attgaatatttgaagcacaactgatgatgacaattgtttttctccatggttgtagGTTGTCAGATGGGGGCGGTCTGTATATGCAAATATTCAGAAATTTATCCAGTTTCAGCTTACAGTAAATGTGGCCGCTCTAGTGATAAATGTTGTTGCTG
                  aactgat  putative branch site (score: 3)
                                 ttgtttttctccat  putative PPT
                               aattgttttt  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttagtactactttgagatattttaatttgttctgttttttgtcattagtagaagtagaaatgcactttttgaatactgattgtacaatgagaggtttatatagaattgaggtgcattgaatatttgaagcacaactgatgatgacaattgtttttctccatggttgtagGTTGTCAGATGGGGGCGGTCTGTATATGCAAATATTCAGAAATTTATCCAGTTTCAGCTTACAGTAAATGTGGCCGCTCTAGTGATAAATGTTGTTGCTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TCAGCT