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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgtggattatcattgtgttattttcaaattttgatttcatgacctgtatgaaggaactgatcattaaaattctctcttttgttgctgtgattcattatagGCAAATGATCCTACAATTGAGCGTATCATCACTCCTCGTATTGCTCTTACTACTGCTGAATATTTGGCATATGAATGTGGCAAGCATGTTCTTGTGATAC

Basic information

species Glycine max
transcript GLYMA09G38110.1
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA09G38110.2 (Glycine max), 3'ss of exon 8
lower sequence: LOC_Os06g37180.1 (Oryza sativa), 3'ss of exon 8
---------------------------------------------------------------tgtggattatcattgtgttattttcaa----attttgatttcatgacctgta--tgaag--gaactgatcattaaaattc-----tctcttttgttgctgtgattca----ttatagGCAAATGATCCTACAATTGAGCGTATCATCACTCCTCGTATTGCTCTTACTACTGCTGAATATTTGGCATATGAATGTGGCAAGCATGTTCTTGTGATAC
                                                               ||    |    ||    ||||||||       || |   | ||| |  | ||   ||||  || |||||  |||||  |      | | || |    |   | | |     ||| ||||||||||||| || ||||| ||||||||||| ||||| ||||| || || ||||| ||||||||||||||||||||||| ||||| || ||||| ||  
gtacatatagcagacttttgaagttctgattcataccaatttgttatgcatggaaactaattctgctagtgtatatgtgcttattttctgtatggttatatatgcatcatttttaacagaagttgacctgattgttaaaggtagaacatattttctaacaccaggctactctgtttacagGCAAATGATCCCACCATTGAACGTATCATCACCCCTCGAATTGCACTGACAACTGCAGAATATTTGGCATATGAATGTGGGAAGCACGTGCTTGTCATCT

upper sequence: GLYMA09G38110.2 (Glycine max), 3'ss of exon 8
lower sequence: GRMZM2G181151_T02 (Zea mays), 3'ss of exon 8
-tgtggattatcattgtgttattttcaaattttgatttcatgacctgtatgaaggaactgat-cattaaaattctctcttttgttgctgtgattca-ttatagGCAAATGATCCTACAATTGAGCGTATCATCACTCCTCGTATTGCTCTTACTACTGCTGAATATTTGGCATATGAATGTGGCAAGCATGTTCTTGTGATAC
 | |    |  |  ||  | |   | |       | |  ||      | |||   ||    |  ||   |   |    ||||    |  |||| |  ||| |||| |||||||| || ||||| ||||| ||||| ||||| |||||||| || || || ||||||||||||||||||||||| |||||||| ||||| ||  
ctatcctctggccctgcataacgatgag---ccaaatatattctacatgtgacataatcagtgtatagcacagcatatttttaacaccttgatcctcttacagGCTAATGATCCCACCATTGAACGTATTATCACCCCTCGGATTGCTCTAACAACAGCAGAATATTTGGCATATGAATGTGGGAAGCATGTACTTGTCATCT

upper sequence: GLYMA09G38110.2 (Glycine max), 3'ss of exon 8
lower sequence: GRMZM2G094497_T01 (Zea mays), 3'ss of exon 8
------tgtggattatcattgt---gttattttcaaattttgatttcatgacctgtatgaaggaactgatcattaaaattctctcttttgttgctgtgattcattatagGCAAATGATCCTACAATTGAGCGTATCATCACTCCTCGTATTGCTCTTACTACTGCTGAATATTTGGCATATGAATGTGGCAAGCATGTTCTTGTGATAC
           || |||||       | |||||| || |||||  | || |  ||||| |   | |  ||  |||| |       | |   || |        ||| |||| || || || || ||||| ||||| ||||| ||||| |||||||| || || || ||||||||||||||||||||||| |||||||| ||||| ||  
cccctgcacacataatcatgagccaatcattttctaaatttgacataattag-tgtataatacagcatatttttaacacctcaattctctctgtt--------ttacagGCTAACGACCCCACCATTGAACGTATTATCACCCCTCGGATTGCTCTAACAACAGCGGAATATTTGGCATATGAATGTGGGAAGCATGTACTTGTTATCT

upper sequence: GLYMA09G38110.2 (Glycine max), 3'ss of exon 8
lower sequence: AT4G38510.4 (Arabidopsis thaliana), 3'ss of exon 9
tgtggattatcattgtgttattttcaaattttgatttcatgacctgtatgaaggaactgatcattaaaat-tctctct-----tttgttgctgtgattcat-tatagGCAAATGATCCTACAATTGAGCGTATCATCACTCCTCGTATTGCTCTTACTACTGCTGAATATTTGGCATATGAATGTGGCAAGCATGTTCTTGTGATAC
                |  | | ||  | |   | | || ||| | | ||||| || |  |  ||  ||| | | |||     ||| |   | || ||     | ||||||| || || || |||||||||||||||||||||||||| || ||||| |||||||| || |||||||||||||||||||||||||| ||||| || |
----------------gcaagtctcgcaatcacactaca-gacatct-tgaagcaaattttagttccaatgtttttctgaaggtttctcattctgttttccgcacagGCAAACGACCCCACTATTGAGCGTATCATCACTCCTCGTATCGCACTTACAACTGCTGAGTACTTGGCATATGAATGTGGCAAGCATGTCCTTGTCATTC

upper sequence: GLYMA09G38110.2 (Glycine max), 3'ss of exon 8
lower sequence: Vv03s0038g02760.t01 (Vitis vinifera), 3'ss of exon 8
-----------------------tgtggattatcattgtgttattttcaaattttgatttcatgacctg--tatgaaggaactgatcattaaaattctctcttttgttgctgtgattcattatagGCAAATGATCCTACAATTGAGCGTATCATCACTCCTCGTATTGCTCTTACTACTGCTGAATATTTGGCATATGAATGTGGCAAGCATGTTCTTGTGATAC
                       ||    |||| ||||| |    |  ||||| | | ||    ||| |  |    |  |  ||    | || | | |||  | || |   |||       | |||| || || || || ||||| || |||||||||||||| |||||||| || |||||||||||||| ||||||||||||||||| ||||||||||| ||||
gtatttatattaaattaatatagtggtatttattattgtttgtggtgtaaattctaaattttaaaccaggcttcagaatagttggctttgaatagtttctgatatgctcaagtgg------acagGCCAACGACCCCACCATTGAACGCATCATCACTCCTCGAATTGCTCTCACCACTGCTGAATATTTAGCATATGAATGTGGCAAACATGTTCTTGTCATAC

upper sequence: GLYMA09G38110.2 (Glycine max), 3'ss of exon 8
lower sequence: PP1S425_12V6.1 (Physcomitrella patens), 3'ss of exon 7
tgtggattatcattgtgttattttcaaattttgatttc----atgacctgtatgaaggaactgatcattaaaattctctcttttgttgctgtgattcattatagGCAAATGATCCTACAATTGAGCGTATCATCACTCCTCGTATTGCTCTTACTACTGCTGAATATTTGGCATATGAATGTGGCAAGCATGTTCTTGTGATAC
     || |   || |   |||  |   || |  || |    |  |  | | ||      || ||  ||| ||||     |    |  || |    | ||  |||| |||||||| || ||||| || || ||||||||||| || || ||||||||||||||||| |  || ||||||||||| |||||||| || || || |
---aaatcaatgttcttccattccctctttctttttcctcgaacaatttctgtggtaagtcttatatttagaatttaagttcgaatctctcttgggc-ttgcagGCTAATGATCCAACGATTGAACGGATTATCACTCCTCGAATCGCCCTTACTACTGCTGAATACTACGCTTATGAATGTGGGAAGCATGTCCTGGTCATCC

upper sequence: GLYMA09G38110.2 (Glycine max), 3'ss of exon 8
lower sequence: PP1S100_117V6.1 (Physcomitrella patens), 3'ss of exon 8
--tgtggattatcattgtgttattttcaaattttgatttcatgacctgtatgaaggaactgatcattaaaattctctcttttgttgctgtgattcattatagGCAAATGATCCTACAATTGAGCGTATCATCACTCCTCGTATTGCTCTTACTACTGCTGAATATTTGGCATATGAATGTGGCAAGCATGTTCTTGTGATAC
  |||     | | |    |  || ||    |   ||||| | |      ||  ||||| || ||||     | |   |||||    | |  |   ||  |||| |||||||| |||||||||||||||||||||||||| ||||| || ||||||||||||||||  || ||||| ||||| ||||||||  | || ||||
catgtttccaaccctctcttcgttctcggtatcaaatttcgtaaatca-gtgctggaac-gaacatttcgtgttttaattttgaatttatactgatttgcagGCTAATGATCCAACAATTGAGCGTATCATCACTCCTCGAATTGCACTCACTACTGCTGAATATTATGCTTATGAGTGTGGGAAGCATGTGTTGGTCATAC

upper sequence: GLYMA09G38110.2 (Glycine max), 3'ss of exon 8
lower sequence: PP1S85_75V6.1 (Physcomitrella patens), 3'ss of exon 7
-------------------------------------------------------------------------------------------------------tgtggattatcattgtgttattttcaaattttgatttcatgacctgtatgaaggaactgatcattaaaattctctcttttgttgctgtgattcattatagGCAAATGATCCTACAATTGAGCGTATCATCACTCCTCGTATTGCTCTTACTACTGCTGAATATTTGGCATATGAATGTGGCAAGCATGTTCTTGTGATAC
                                                                                                       | ||     |||    || | |||      |  | | | ||   | | |    | | | |    |  |||| | | ||  | |  | |    | ||  |||| |||||||| |||||||||||||| ||||| ||||| ||||| ||||| |||||||| || |  || ||||| ||||| ||||| ||||| || || |
gtatgtacatcttcagttttcttttatcgtcgattttcaccacatttttggattatatatggaacttcatccagtttcttttcgtaatggaagagtcgtctgttttgagacttcacaaagtcaatttt---cctccagtccttgcgtttttttcctggattaagttctggaattttattttaggatcgtcttgggcttt-cagGCTAATGATCCAACAATTGAGCGTATTATCACACCTCGAATTGCACTTACAACTGCTGAGTACTACGCTTATGAGTGTGGAAAGCACGTTCTGGTCATCC

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|18734533|gb|BM528238.1|BM528238
EST:     ACTTTGAGGAGAATGGCTCGATGGAGAGAGTGACCCTTTTCCTTAATCTG                         GCAAATGATCCTACAATTGAGCGTATCATCACTCCTCGTATTGCTCTTACT
genomic: ACTTTGAGGAGAATGGCTCGATGGAGAGAGTGACCCTTTTCCTTAATCTGgtagtcttta ... ttcattatagGCAAATGATCCTACAATTGAGCGTATCATCACTCCTCGTATTGCTCTTACT
EST: gi|22931741|gb|BU548880.1|BU548880
EST:     ACTTTGAGGAGAATGGCTCGATGGNNAGAGTGACCCTTTTCCTTAATCTG                         GCAAATGATCCTANNNTTGAGCGTATCATCACTCCTCGTATTGCTCTTACT
genomic: ACTTTGAGGAGAATGGCTCGATGGAGAGAGTGACCCTTTTCCTTAATCTGgtagtcttta ... ttcattatagGCAAATGATCCTACAATTGAGCGTATCATCACTCCTCGTATTGCTCTTACT
EST: gi|14259630|gb|BG882538.1|BG882538
EST:     ACTTTGAGGAGAATGGCTCGATGGAGAGAGTGACCCTTTTCCTTAATCTG                         GCAAATGATCCTACAATTGAGCGTATCATCACTCCTCGTATTGCTCTTACT
genomic: ACTTTGAGGAGAATGGCTCGATGGAGAGAGTGACCCTTTTCCTTAATCTGgtagtcttta ... ttcattatagGCAAATGATCCTACAATTGAGCGTATCATCACTCCTCGTATTGCTCTTACT
EST: gi|8285807|gb|BE023366.1|BE023366
EST:     ACTTTGAGGAAAATGGCTCGATGGAGAGAGTGACCCTTTTCCTTAATCTG                         GCAAATGATCCTACGATTGAGCGTATCATCACTCCTCGTATTGCTCTTACT
genomic: ACTTTGAGGAGAATGGCTCGATGGAGAGAGTGACCCTTTTCCTTAATCTGgtagtcttta ... ttcattatagGCAAATGATCCTACAATTGAGCGTATCATCACTCCTCGTATTGCTCTTACT
EST: gi|208232106|gb|GE031831.1|GE031831
EST:     ACCCTTTTCCTTAATCTG                         GCAAATGATCCTACAATTGAGCGTATCATCACT
genomic: ACCCTTTTCCTTAATCTGgtagtcttta ... ttcattatagGCAAATGATCCTACAATTGAGCGTATCATCACT
EST: gi|16279376|gb|BI943404.1|BI943404
EST:     ACTTTGAGGAGAATGGCTCGATGGAGAGAGTGACCCTTTTCCTTAATCTG                         GCAAATGATCCTACAATTGAGCGTATCATCACTCCTCGTATTGCTCTTACT
genomic: ACTTTGAGGAGAATGGCTCGATGGAGAGAGTGACCCTTTTCCTTAATCTGgtagtcttta ... ttcattatagGCAAATGATCCTACAATTGAGCGTATCATCACTCCTCGTATTGCTCTTACT
EST: gi|193510698|gb|FK467196.1|FK467196
EST:     ACTTTGAGGAAAATGGCTCGATGGAGAGAGTGACCCTTTTCCTTAATCTG                         GCAAATGATCCTACGATTGAGCGTATCATCACTCCTCGTATTGCTCTTACT
genomic: ACTTTGAGGAGAATGGCTCGATGGAGAGAGTGACCCTTTTCCTTAATCTGgtagtcttta ... ttcattatagGCAAATGATCCTACAATTGAGCGTATCATCACTCCTCGTATTGCTCTTACT
EST: gi|16283538|gb|BI945603.1|BI945603
EST:     ACTTTGAGGAGAATGGCTCGATGGAGAGAGTGACCCTTTTCCTTAATCTG                         GCAAATGATCCTACAATTGAGCGTATCATCACCTCTT-GTATTGCTCTTAC
genomic: ACTTTGAGGAGAATGGCTCGATGGAGAGAGTGACCCTTTTCCTTAATCTGgtagtcttta ... ttcattatagGCAAATGATCCTACAATTGAGCGTATCATCAC-TCCTCGTATTGCTCTTAC
EST: gi|208116661|gb|GD917183.1|GD917183
EST:     ACTTTGAGGAGAATGGCTCGATGGAGAGAGTGACCCTTTTCCTTAATCTG                         GCAAATGATCCTACAATTGAGCGTATCATCACTCCTCGTATTGCTCTTACT
genomic: ACTTTGAGGAGAATGGCTCGATGGAGAGAGTGACCCTTTTCCTTAATCTGgtagtcttta ... ttcattatagGCAAATGATCCTACAATTGAGCGTATCATCACTCCTCGTATTGCTCTTACT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtatgaaggaactgatcattaaaattctctcttttgttgctgtgattcattatagGCAAATGATCCTACAATTGAGCGTATCATCACTCCTCGTATTGCTCTTACTACTGCTGAATATTTGGCATATGAATGTGGCAAGCATGTTCTTGTGATAC
         aactgat  putative branch site (score: 3)
            tgatcattaaaatt  TA-rich tract