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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aaagcaaaatttaaatgaggctttttgatttcctgacttgcatgaaggagctaatccctaaaatgttctcttgctaatgtgaatatgtgatttactgcagGCAAATGATCCTACAATTGAGCGTATTATCACTCCTCGTATTGCTCTTACTACTGCTGAATATTTGGCTTATGAATGTGGCAAGCACGTTCTTGTGATAC

Basic information

species Glycine max
transcript GLYMA20G24070.1
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA20G24070.1 (Glycine max), 3'ss of exon 9
lower sequence: LOC_Os06g37180.1 (Oryza sativa), 3'ss of exon 8
---------------------------------------------------------------------------aaagcaaaatttaaatgaggctttttgatttcctgacttgcatgaag--gagctaatccctaaaa----tgttctcttgctaatgtgaatatgtgatttactgcagGCAAATGATCCTACAATTGAGCGTATTATCACTCCTCGTATTGCTCTTACTACTGCTGAATATTTGGCTTATGAATGTGGCAAGCACGTTCTTGTGATAC
                                                                              ||  | |||   |  || | | |      |    ||    ||||  || || ||   ||||            || ||||    |   |    | |  | |||||||||||||| || ||||| ||||| ||||| ||||| ||||| || || ||||| ||||||||||| ||||||||||| |||||||| ||||| ||  
gtacatatagcagacttttgaagttctgattcataccaatttgttatgcatggaaactaattctgctagtgtatatgtgcttattttctgtatggttatatatgcatcatttttaacagaagttgacctgattgttaaaggtagaacatattttctaacaccaggctactctgt-ttacagGCAAATGATCCCACCATTGAACGTATCATCACCCCTCGAATTGCACTGACAACTGCAGAATATTTGGCATATGAATGTGGGAAGCACGTGCTTGTCATCT

upper sequence: GLYMA20G24070.1 (Glycine max), 3'ss of exon 9
lower sequence: GRMZM2G181151_T02 (Zea mays), 3'ss of exon 8
---aaagcaaaatttaaatgaggcttt-ttgatttcctgacttgcatgaaggagctaatccctaaaatgttctcttgctaatgtgaatatgtgatttactgcagGCAAATGATCCTACAATTGAGCGTATTATCACTCCTCGTATTGCTCTTACTACTGCTGAATATTTGGCTTATGAATGTGGCAAGCACGTTCTTGTGATAC
       |      |  || | | |      | |   |        |||   |   | |   ||  |     | ||  |||       ||      |  | ||||| |||||||| || ||||| ||||||||||| ||||| |||||||| || || || ||||||||||| ||||||||||| ||||| || ||||| ||  
ctatcctctggccctgcataacgatgagccaaatatattctacatgtgacataatcagtgtatagcacagcatatttttaacaccttgat----cctcttacagGCTAATGATCCCACCATTGAACGTATTATCACCCCTCGGATTGCTCTAACAACAGCAGAATATTTGGCATATGAATGTGGGAAGCATGTACTTGTCATCT

upper sequence: GLYMA20G24070.1 (Glycine max), 3'ss of exon 9
lower sequence: GRMZM2G094497_T01 (Zea mays), 3'ss of exon 8
--aaagcaaaatttaaatgaggctttttgatttcctgacttgcatgaaggagctaatccctaaaatgttctcttgctaatg--tgaatatgtgatttactgcagGCAAATGATCCTACAATTGAGCGTATTATCACTCCTCGTATTGCTCTTACTACTGCTGAATATTTGGCTTATGAATGTGGCAAGCACGTTCTTGTGATAC
     ||| |   |||    |      | |||| || | ||   |||   |  || |   ||| |     | ||  |||    | |||      | |  | ||||| || || || || ||||| ||||||||||| ||||| |||||||| || || || ||||||||||| ||||||||||| ||||| || ||||| ||  
cccctgcaca-cataatcatgagccaatcattttctaaatt---tgacataattagtgtataatacagcatatttttaacacctcaattctctctgttttacagGCTAACGACCCCACCATTGAACGTATTATCACCCCTCGGATTGCTCTAACAACAGCGGAATATTTGGCATATGAATGTGGGAAGCATGTACTTGTTATCT

upper sequence: GLYMA20G24070.1 (Glycine max), 3'ss of exon 9
lower sequence: AT4G38510.4 (Arabidopsis thaliana), 3'ss of exon 9
aaagcaaaatttaaatgaggctttttgatttcctgacttgcatgaaggagctaatccc---taaaatgttctcttgctaatgtgaatatgtgatttac-tgcagGCAAATGATCCTACAATTGAGCGTATTATCACTCCTCGTATTGCTCTTACTACTGCTGAATATTTGGCTTATGAATGTGGCAAGCACGTTCTTGTGATAC
                 | |  |    ||  |   ||   |||   | ||| |||      |  |||||| |  ||    | |     | || ||| |   |||||||| || || || ||||||||||| |||||||||||||| || ||||| |||||||| || ||||| ||||||||||||||||| || ||||| || |
---------------gcaagtctcgcaatcacactacagacatcttgaagcaaattttagttccaatgtttttctgaaggtttctcattctgttttccgcacagGCAAACGACCCCACTATTGAGCGTATCATCACTCCTCGTATCGCACTTACAACTGCTGAGTACTTGGCATATGAATGTGGCAAGCATGTCCTTGTCATTC

upper sequence: GLYMA20G24070.1 (Glycine max), 3'ss of exon 9
lower sequence: Vv03s0038g02760.t01 (Vitis vinifera), 3'ss of exon 8
-----aaagcaaaatttaaatgaggctttttgatttcctgacttgcatgaag----------gagctaatccctaaaatgttctcttgctaatg--tgaatatgtgatttactg--cagGCAAATGATCCTACAATTGAGCGTATTATCACTCCTCGTATTGCTCTTACTACTGCTGAATATTTGGCTTATGAATGTGGCAAGCACGTTCTTGTGATAC
      |    ||||| | ||   | | |||  | |  |   | |  | ||            | | |  |   | |||  |    |   |||   |    || || |  | ||  ||||| || || || || ||||| || || ||||||||||| |||||||| || |||||||||||||| || |||||||||||||| || |||||||| ||||
gtatttatattaaattaatatagtggtatttattattgtttgtggtgtaaattctaaattttaaaccaggcttcagaatagttggctttgaatagtttctgatatgctcaagtggacagGCCAACGACCCCACCATTGAACGCATCATCACTCCTCGAATTGCTCTCACCACTGCTGAATATTTAGCATATGAATGTGGCAAACATGTTCTTGTCATAC

upper sequence: GLYMA20G24070.1 (Glycine max), 3'ss of exon 9
lower sequence: PP1S425_12V6.1 (Physcomitrella patens), 3'ss of exon 7
aaagcaaaatttaaatgaggctttttgatttcctgacttgca-tgaaggagctaatccctaaaatgttctcttgctaatgtgaatatgtgatttact-gcagGCAAATGATCCTACAATTGAGCGTATTATCACTCCTCGTATTGCTCTTACTACTGCTGAATATTTGGCTTATGAATGTGGCAAGCACGTTCTTGTGATAC
||| |||  ||         | | ||  |||     |   || |    | | |||  | || | |      ||   | |  |||| | |  |   || |||||| |||||||| || ||||| || |||||||||||||| || || ||||||||||||||||| |  |||||||||||||| ||||| || || || || |
aaatcaatgttcttccattccctctttctttttcctcgaacaatttctgtggtaagtcttatatttagaattta--agttcgaatctctcttgggcttgcagGCTAATGATCCAACGATTGAACGGATTATCACTCCTCGAATCGCCCTTACTACTGCTGAATACTACGCTTATGAATGTGGGAAGCATGTCCTGGTCATCC

upper sequence: GLYMA20G24070.1 (Glycine max), 3'ss of exon 9
lower sequence: PP1S100_117V6.1 (Physcomitrella patens), 3'ss of exon 8
aaagcaaaatttaaatgaggctttttgatttc----ctgacttgcatgaaggagc-taatccctaaaatgttctcttgctaatgtgaatatgtgatttactgcagGCAAATGATCCTACAATTGAGCGTATTATCACTCCTCGTATTGCTCTTACTACTGCTGAATATTTGGCTTATGAATGTGGCAAGCACGTTCTTGTGATAC
    ||   ||  ||     || || | | ||       | || | | ||  ||        | || || |  | ||   | | ||||| | |  |    ||||||| |||||||| |||||||||||||| ||||||||||| ||||| || ||||||||||||||||  |||||||| ||||| ||||| ||  | || ||||
----catgtttccaaccct-ctcttcgttctcggtatcaaatttcgtaaatcagtgctggaacgaacatttcgtgttttaattttgaatttatactgatttgcagGCTAATGATCCAACAATTGAGCGTATCATCACTCCTCGAATTGCACTCACTACTGCTGAATATTATGCTTATGAGTGTGGGAAGCATGTGTTGGTCATAC

upper sequence: GLYMA20G24070.1 (Glycine max), 3'ss of exon 9
lower sequence: PP1S85_75V6.1 (Physcomitrella patens), 3'ss of exon 7
----------------------------------------------------------------------------------------------------------aaagcaaaatttaaatgaggctttttgatttcctgacttgcatgaaggagctaatccctaaaatgttctcttgctaatgtgaatatgtgatttactgcagGCAAATGATCCTACAATTGAGCGTATTATCACTCCTCGTATTGCTCTTACTACTGCTGAATATTTGGCTTATGAATGTGGCAAGCACGTTCTTGTGATAC
                                                                                                           |  |   |   |    |   |  |  | | | ||  ||   |    |   |||   ||  ||| || | ||   |  ||     || | |||    ||||| |||||||| |||||||||||||||||||| ||||| ||||| ||||| |||||||| || |  |||||||| ||||| ||||||||||| || || |
gtatgtacatcttcagttttcttttatcgtcgattttcaccacatttttggattatatatggaacttcatccagtttcttttcgtaatggaagagtcgtctgttttgagacttcacaaagtcaattttcctccagtccttgcgtttttttcctggattaagttctggaattttattttaggatcgt---cttgggcttt----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|16279439|gb|BI943437.1|BI943437
EST:     ACTTTGAGGAGAATGGATCAATGGAGAGAGTGACTCTTTTCCTTAATTTG                         GCAAATGATCCTACAATTGAGCGTATTATCACTCCTCGTATTGCTCTTACT
genomic: ACTTTGAGGAGAATGGATCAATGGAGAGAGTGACTCTTTTCCTTAATTTGgtaattcttt ... tttactgcagGCAAATGATCCTACAATTGAGCGTATTATCACTCCTCGTATTGCTCTTACT
EST: gi|151411391|gb|EV281202.1|EV281202
EST:     ACTTTGAGGAGAATGGATCAATGGAGAGAGTGACTCTTTTCCTTAATTTG                         GCAAATGATCCTACAATTGAGCGTATTATCACTC
genomic: ACTTTGAGGAGAATGGATCAATGGAGAGAGTGACTCTTTTCCTTAATTTGgtaattcttt ... tttactgcagGCAAATGATCCTACAATTGAGCGTATTATCACTC
EST: gi|23729967|gb|BU763089.1|BU763089
EST:     ACTTTGAGGAGAATGGATCAATGGAGAGAGTGACTCTTTTCCTTAATTTG                         GCAAATGATCCTACAATTGAACGTATTATCACTCCTCGTATTGCTCTTACT
genomic: ACTTTGAGGAGAATGGATCAATGGAGAGAGTGACTCTTTTCCTTAATTTGgtaattcttt ... tttactgcagGCAAATGATCCTACAATTGAGCGTATTATCACTCCTCGTATTGCTCTTACT
EST: gi|16279488|gb|BI943462.1|BI943462
EST:     ACTTTGAGGAGAATGGATCAATGGAGAGAGTGACTCTTTTCCTTAATTTG                         GCAAATGATCCTACAATTGAGCGTATTATCACTCCTCGTATTGCTCTTACT
genomic: ACTTTGAGGAGAATGGATCAATGGAGAGAGTGACTCTTTTCCTTAATTTGgtaattcttt ... tttactgcagGCAAATGATCCTACAATTGAGCGTATTATCACTCCTCGTATTGCTCTTACT
EST: gi|16278548|gb|BI942962.1|BI942962
EST:     ACTTTGAGGAGAATGGATCAATGGAGAGAGTGACTCTTTTCCTTAATTTG                         GCAAATGATCCTACAATTGAGCGTATTATCACTCCTCGTATTGCTCTTACT
genomic: ACTTTGAGGAGAATGGATCAATGGAGAGAGTGACTCTTTTCCTTAATTTGgtaattcttt ... tttactgcagGCAAATGATCCTACAATTGAGCGTATTATCACTCCTCGTATTGCTCTTACT
EST: gi|19346883|gb|BM891771.1|BM891771
EST:     ACTTTGAGGAGAATGGATCAATGGAGAGAGTGACTCTTTTCCTTAATTTG                         GCAAATGATCCTACAATTGAGCGTATTATCACTCCTCGTATTGCTCTTACT
genomic: ACTTTGAGGAGAATGGATCAATGGAGAGAGTGACTCTTTTCCTTAATTTGgtaattcttt ... tttactgcagGCAAATGATCCTACAATTGAGCGTATTATCACTCCTCGTATTGCTCTTACT
EST: gi|16279486|gb|BI943461.1|BI943461
EST:     ACTTTGAGGAGAATGGATCAATGGAGAGAGTGACTCTTTTCCTTAATTTG                         GCAAATGATCCTACAATTGAGCGTATTATCACTCCTCGTATTGCTCTTACT
genomic: ACTTTGAGGAGAATGGATCAATGGAGAGAGTGACTCTTTTCCTTAATTTGgtaattcttt ... tttactgcagGCAAATGATCCTACAATTGAGCGTATTATCACTCCTCGTATTGCTCTTACT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aggagctaatccctaaaatgttctcttgctaatgtgaatatgtgatttactgcagGCAAATGATCCTACAATTGAGCGTATTATCACTCCTCGTATTGCTCTTACTACTGCTGAATATTTGGCTTATGAATGTGGCAAGCACGTTCTTGTGATAC
                          tgctaat  putative branch site (score: 2)
             taaaatgtt  TA-rich tract