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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATATGAAAAGCGGCATTCAAATATTCCTTCACACATATCACCTTGTTTCCGTGTTAAGGAAGGAGATCATGTTATTATTGGCCAATGCAGgttagactttcataggagaaaccttttctgggattactaatgtgagaatttattgttgtctactctattgtatagatttaaccatctgattgcctttatttgtgccatatgtatag

Basic information

species Glycine max
transcript GLYMA09G12430.1
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA09G12430.1 (Glycine max), 5'ss of exon 5
lower sequence: LOC_Os04g42380.1 (Oryza sativa), 5'ss of exon 5
ATATGAAAAGCGGCATTCAAATATTCCTTCACACATATCACCTTGTTTCCGTGTTAAGGAAGGAGATCATGTTATTATTGGCCAATGCAGgttagactt-tcataggag--aaaccttttctgggattactaa-tgtgagaatttattgttgtctactctattg--tatagatttaaccatctga--ttgcctttatttgtgcca--tatgtatag-----------------------------------------------------------------
 || || ||| |||| || ||||||||| | ||||| ||||| || ||||||||||||||||||||||| || || |||||||| ||||||| |  ||| ||||         |   ||| || ||   || | | |||    | | |||||| |||   | ||  || | |  | |   | |||   ||  |||  |  |   |   | ||| ||                                                                 
GTACGAGAAGAGGCACTCCAATATTCCTGCTCACATTTCACCGTGCTTCCGTGTTAAGGAAGGAGATCACGTGATCATTGGCCAGTGCAGgtaaagcttgtcatgttcctttgaatgtttttgtgacggctcactttgacctgtgaatgttgtgtacctcagtgaatacaaacctgaatgtttgagcatgaattttctaatcttagccaagtaaagtacagttattttgtgtgcttcatcccagaaatccacaaattactcaactatctgtttaatatcag

upper sequence: GLYMA09G12430.1 (Glycine max), 5'ss of exon 5
lower sequence: LOC_Os08g10608.1 (Oryza sativa), 5'ss of exon 5
ATATGAAAAGCGGCATTCAAATATTCCTTCACACATATCACCTTGTTTCCGTGTTAAGGAAGGAGATCATGTTATTATTGGCCAATGCAGgttagactttcataggagaaaccttttctgggattactaatgtgagaatttattgttgtctactctattgtatagatttaaccatctgattgcctttatttgtgccatatgtatag
|||||||||| |||| || || |||||  | ||||| || || || ||||||||||||||||| || ||||| || |||||||| ||||||| |   | || |||  ||  |  |   | |   |||   | |     ||| ||  ||  |||   | | |   ||||  |  |  |||  |  ||    ||    |         
ATATGAAAAGAGGCACTCCAACATTCCAGCTCACATTTCTCCATGCTTCCGTGTTAAGGAAGGTGACCATGTCATCATTGGCCAGTGCAGgtaatgttctc-tagctgatgctgtacttag---tacatgttttctgttttgtt-ctgcatacctgaatattgggattacatgacttgaaag--ttccactgaatta---------

upper sequence: GLYMA09G12430.1 (Glycine max), 5'ss of exon 5
lower sequence: GRMZM2G086486_T02 (Zea mays), 5'ss of exon 7
ATATGAAAAGCGGCATTCAAATATTCCTTCACACATATCACCTTGTTTCCGTGTTAAGGAAGGAGATCATGTTATTATTGGCCAATGCAGgttagactt------tcataggagaaaccttttctgggattactaatgtgagaatttattgttgtct--actctattgtatagatttaac----catctgattgcctttatttg---tgccatatgtatag-------------------------------------------------------------------
 ||||| ||| | || || || || ||| | ||||| ||||| || || ||||| ||||||||||||||||| || |||||||| ||||||| |  |||      || |    | | |   || | | | | ||       ||    || |||      || | |||    |   | ||     |   |  || ||| | || |   ||  |||| |||                                                                     
GTATGAGAAGAGACACTCCAACATCCCTGCGCACATTTCACCATGCTTTCGTGTCAAGGAAGGAGATCATGTGATCATTGGCCAGTGCAGgtaaagcttgctatatctttcctggacctgctttttgtaatgctgtacctggatggcatggtttctgaaacgcaattagcaaagctcaatataacccgtccttccctctgttggacatgaaatatctatcttggctttttttggcactgtgctctattccgtagatgcacttatgttgtactcctgttttaatttcag

upper sequence: GLYMA09G12430.1 (Glycine max), 5'ss of exon 5
lower sequence: Vv11s0118g00680.t01 (Vitis vinifera), 5'ss of exon 5
ATATGAAAAGCGGCATTCAAATATTCCTTCACACATATCACCTTGTTTCCGTGTTAAGGAAGGAGATCATGTTATTATTGGCCAATGCAGgttagactttcataggagaaacctttt-ctgggattactaatgtgagaatttatt------gttgtctactctattgtatagatttaaccatctgattgcctttatttgtgccatatgtatag--
|||||| ||| |||| ||||| |||||| | |||| ||| || || |||||||| ||||||||||||||||||||||||||||| ||||||| |  |||  || | |   ||||     | |   | | |||   | | || |||      || ||  ||||| | || |     | | |||    |||  | | | | |    |   |||    
ATATGAGAAGAGGCACTCAAACATTCCTGCTCACACATCGCCATGCTTCCGTGTGAAGGAAGGAGATCATGTTATTATTGGCCAGTGCAGgtaaatcttcaattgaaactacctccagtttgtccttccaata-aaaagttgatttagagggtggtgaactctgt-gtttgttactgaacataatgttgtttctttctatattttccttattcag

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|58021442|gb|CX708183.1|CX708183
EST:     CCTTGTTTCCGTGTTAAGGAAGGAGATCATGTTATTATTGGCCAATGCAG                         GCCAATCTCAAAGACAGTGAGGTTCAATGTGTTGAAAGTGATCCCCGCTGG
genomic: CCTTGTTTCCGTGTTAAGGAAGGAGATCATGTTATTATTGGCCAATGCAGgttagacttt ... atatgtatagGCCAATCTCAAAGACAGTGAGGTTCAATGTGTTGAAAGTGATCCCCGCTGG
EST: gi|298185405|gb|HO030618.1|HO030618
EST:     CCTTGTTTCCGTGTTAAGGAAGGAGATCATGTTATTATTGGCCAATGCAG                         GCCAATCTCAAA
genomic: CCTTGTTTCCGTGTTAAGGAAGGAGATCATGTTATTATTGGCCAATGCAGgttagacttt ... atatgtatagGCCAATCTCAAA
EST: gi|58025331|gb|CX712072.1|CX712072
EST:     CCTTGTTTCCGTGTTAAGGAAGGAGATCATGTTATTATTGGCCAATGCAG                         GCCAATCTCAAAGACAGTGAGGTTCAATGTGTTGAAAGTGATCCCCGCTGG
genomic: CCTTGTTTCCGTGTTAAGGAAGGAGATCATGTTATTATTGGCCAATGCAGgttagacttt ... atatgtatagGCCAATCTCAAAGACAGTGAGGTTCAATGTGTTGAAAGTGATCCCCGCTGG
EST: gi|7926332|gb|AW832358.1|AW832358
EST:     CCTTGTTTCCGTGTTAAGGAAGGAGATCATGTTATTATTGGCCAATGCAA                         GCCAATCTCAAAGACAGTGAGGTTCAATGTGTTGAAAGTGATCCCCGCTGG
genomic: CCTTGTTTCCGTGTTAAGGAAGGAGATCATGTTATTATTGGCCAATGCAGgttagacttt ... atatgtatagGCCAATCTCAAAGACAGTGAGGTTCAATGTGTTGAAAGTGATCCCCGCTGG
EST: gi|31466051|gb|CD408079.1|CD408079
EST:     CCTTGTTTCCGTGTTAAGGAAGGAGATCATGTTATTATTGGCCAATGCAG                         GCCAATCTCTAAGACAGTGAGGTTCAATGTGTTGAAAGTGTATCCCCGCTG
genomic: CCTTGTTTCCGTGTTAAGGAAGGAGATCATGTTATTATTGGCCAATGCAGgttagacttt ... atatgtatagGCCAATCTCAAAGACAGTGAGGTTCAATGTGTTGAAAGTG-ATCCCCGCTG
EST: gi|298198041|gb|HO039580.1|HO039580
EST:     CCTTGTTTCCGTGTTAAGGAAGGAGATCATGTTATTATTGGCCAATGCAG                         GCCAATCTCAAAGACAGTGAGGTTCAATGTGTTGAAAGTGATCCCCGCTGG
genomic: CCTTGTTTCCGTGTTAAGGAAGGAGATCATGTTATTATTGGCCAATGCAGgttagacttt ... atatgtatagGCCAATCTCAAAGACAGTGAGGTTCAATGTGTTGAAAGTGATCCCCGCTGG
EST: gi|298199106|gb|HO042469.1|HO042469
EST:     CCTTGTTTCCGTGTTAAGGAAGGAGATCATGTTATTATTGGCCAATGCAG                         GCCAATCTCAAAGACAGTGAGGTTCAATGTGTTGAAAGTGATCCCCGCTGG
genomic: CCTTGTTTCCGTGTTAAGGAAGGAGATCATGTTATTATTGGCCAATGCAGgttagacttt ... atatgtatagGCCAATCTCAAAGACAGTGAGGTTCAATGTGTTGAAAGTGATCCCCGCTGG
EST: gi|31476512|gb|CD418540.1|CD418540
EST:     CCTTGTTTCCGTGTTAAGGAAGGAGATCATGTTATTATTGGCCAATGCAG                         GCCAATCTCAAAGACAGTGAGGTTCAATGTGTTGAAAGTGATCCCCGCTGG
genomic: CCTTGTTTCCGTGTTAAGGAAGGAGATCATGTTATTATTGGCCAATGCAGgttagacttt ... atatgtatagGCCAATCTCAAAGACAGTGAGGTTCAATGTGTTGAAAGTGATCCCCGCTGG
EST: gi|13181115|gb|BG352455.1|BG352455
EST:     CCTTGTTTCCGTGTTAAGGAAGGAGATCATGTTATTATTGGCCAATGCAG                         GCCAATCTCAAAGACAGTGAGGTTCAATGTGTTGAAAGTGATCCCCGCTGG
genomic: CCTTGTTTCCGTGTTAAGGAAGGAGATCATGTTATTATTGGCCAATGCAGgttagacttt ... atatgtatagGCCAATCTCAAAGACAGTGAGGTTCAATGTGTTGAAAGTGATCCCCGCTGG
EST: gi|192303094|gb|FG994212.1|FG994212
EST:     CCTTGTTTCCGTGTTAAGGAAGGAGATCATGTTATTATTGGCCAATGCAG                         GCCAATCTCAAAGACAGTGAGGTTCAATGTGTTGAAAGTGATCCCCGCTGG
genomic: CCTTGTTTCCGTGTTAAGGAAGGAGATCATGTTATTATTGGCCAATGCAGgttagacttt ... atatgtatagGCCAATCTCAAAGACAGTGAGGTTCAATGTGTTGAAAGTGATCCCCGCTGG
EST: gi|31309567|gb|CD394770.1|CD394770
EST:     CCTTGTTTCCGTGTTAAGGAAGGAGATCATGTTATTATTGGCCAATGCAG                         GCCAATCTCAAAGACAGTGAGGTTCAATGTGTTGAAAGTGATCCCCGCTGG
genomic: CCTTGTTTCCGTGTTAAGGAAGGAGATCATGTTATTATTGGCCAATGCAGgttagacttt ... atatgtatagGCCAATCTCAAAGACAGTGAGGTTCAATGTGTTGAAAGTGATCCCCGCTGG
EST: gi|298171592|gb|HO021184.1|HO021184
EST:     CCTTGTTTCCGTGTTAAGGAAGGAGATCATGTTATTATTGGCCAATGCAG                         GCCAATCTCAAAGACAGTGAGGTTCAATGTGTTGAAAGTGATCCCCGCTGG
genomic: CCTTGTTTCCGTGTTAAGGAAGGAGATCATGTTATTATTGGCCAATGCAGgttagacttt ... atatgtatagGCCAATCTCAAAGACAGTGAGGTTCAATGTGTTGAAAGTGATCCCCGCTGG
EST: gi|120532484|gb|EH260617.1|EH260617
EST:     CCTTGTTTCCGTGTTAAGGAAGGAGATCATGTTATTATTGGCCAATGCAG                         GCCAATCTCAAAGACAGTGAGGTTCAATGTGTTGAAAGTGATCCCCGCTGG
genomic: CCTTGTTTCCGTGTTAAGGAAGGAGATCATGTTATTATTGGCCAATGCAGgttagacttt ... atatgtatagGCCAATCTCAAAGACAGTGAGGTTCAATGTGTTGAAAGTGATCCCCGCTGG
EST: gi|31461828|gb|CD403856.1|CD403856
EST:     CCTTGTTTCCGTGTTAAGGAAGGAGATCATGTTATTATTGGCCAATGCAG                         GCCAATCTCAAAGACAGTGAGGTTCAATGTGTTGAAAGTGATCCCCGCTGG
genomic: CCTTGTTTCCGTGTTAAGGAAGGAGATCATGTTATTATTGGCCAATGCAGgttagacttt ... atatgtatagGCCAATCTCAAAGACAGTGAGGTTCAATGTGTTGAAAGTGATCCCCGCTGG
EST: gi|298195925|gb|HO044316.1|HO044316
EST:     CCTTGTTTCCGTGTTGAGGAAGGAGATCATGTTATTATTGGCCAATGCAG                         GCCAATCTCAAAGACAGTGAGGTTCAATGTGTTGAAAGTGATCCCCGCTGG
genomic: CCTTGTTTCCGTGTTAAGGAAGGAGATCATGTTATTATTGGCCAATGCAGgttagacttt ... atatgtatagGCCAATCTCAAAGACAGTGAGGTTCAATGTGTTGAAAGTGATCCCCGCTGG
EST: gi|15336926|gb|BI497582.1|BI497582
EST:     CCTTGTTTCCGTGTTAAGGAAGGAGATCATGTTATTATTGGCCAATGCAG                         GCCAATCTCAAAGACAGTGAGGTTCAATGTGTTGAAAGTGATCCCCGCTGG
genomic: CCTTGTTTCCGTGTTAAGGAAGGAGATCATGTTATTATTGGCCAATGCAGgttagacttt ... atatgtatagGCCAATCTCAAAGACAGTGAGGTTCAATGTGTTGAAAGTGATCCCCGCTGG
EST: gi|58014715|gb|CX701457.1|CX701457
EST:     CCTTGTTTCCGTGTTAAGGAAGGAGATCATGTTATTATTGGCCAATGCAG                         GCCAATCTCAAAGACAGTGAGGTTCAATGTGTTGAAAGTGATCCCCGCTGG
genomic: CCTTGTTTCCGTGTTAAGGAAGGAGATCATGTTATTATTGGCCAATGCAGgttagacttt ... atatgtatagGCCAATCTCAAAGACAGTGAGGTTCAATGTGTTGAAAGTGATCCCCGCTGG
EST: gi|298163527|gb|HO012260.1|HO012260
EST:     CCTTGTTTCCGTGTTAAGGAAGGAGATCATGTTATTATTGACCAATGCAG                         GCCAATCTCAAAGACAGTGAGGTTCAATGTGTTGAAAGTGATCCCCGCTGG
genomic: CCTTGTTTCCGTGTTAAGGAAGGAGATCATGTTATTATTGGCCAATGCAGgttagacttt ... atatgtatagGCCAATCTCAAAGACAGTGAGGTTCAATGTGTTGAAAGTGATCCCCGCTGG
EST: gi|151404874|gb|EV274688.1|EV274688
EST:     CCTTGTTTCCGTGTTAAGGAAGGAGATCATGTTATTATTGGCCAATGCAG                         GCCAATCTCAAAGACAGTGAGGTTCAATGTGTTGAAAGTGATCCCCGCTGG
genomic: CCTTGTTTCCGTGTTAAGGAAGGAGATCATGTTATTATTGGCCAATGCAGgttagacttt ... atatgtatagGCCAATCTCAAAGACAGTGAGGTTCAATGTGTTGAAAGTGATCCCCGCTGG
EST: gi|31464691|gb|CD406704.1|CD406704
EST:     CCTTGTTTCCGTGTTAAGGAAGGAGATCATGTTATTATTGGCCNATGCAG                         GCCAATCTCAAAGACAGTGAGGTTCAATGTGTTGAAAGTGATCCCCGCTGG
genomic: CCTTGTTTCCGTGTTAAGGAAGGAGATCATGTTATTATTGGCCAATGCAGgttagacttt ... atatgtatagGCCAATCTCAAAGACAGTGAGGTTCAATGTGTTGAAAGTGATCCCCGCTGG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATATGAAAAGCGGCATTCAAATATTCCTTCACACATATCACCTTGTTTCCGTGTTAAGGAAGGAGATCATGTTATTATTGGCCAATGCAGgttagactttcataggagaaaccttttctgggattactaatgtgagaatttattgttgtctactctattgtatagatttaaccatctgattgcctttatttgtgccatatgtatag

- - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGATCA