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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCTACGCGCCGACGGGGAGCGTGAGTTCATGTTCTACCGGAACCCCAGCGCCGACATGCTCCTCAAGCCCGAAGAACTCAACCTTGAACTCATCAGATCTgtatgcatcttttccctctctctcgctctctctactttctcggaaaatatttaaccttttcccggaaaacgaagtctttgtttcgtgattccatgtatga...

Basic information

species Glycine max
transcript GLYMA15G03430.1
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA15G03430.1 (Glycine max), 5'ss of exon 1
lower sequence: LOC_Os01g66940.1 (Oryza sativa), 5'ss of exon 1
CCTACGCGCCGACGGGGAGCGTGAGTTCATGTTCTACCGGAACCCCAGCGCCGACATGCTCCTCAAGCCCGAAGAACTCAACCTTGAACTCATCAGATCTgtatgcatcttttccctctctctcgctctctctactttctcggaaaatatttaaccttttcccggaaaacgaagtctttgtttcgtgattccat-gtatga-
||| ||||||||||||||||| ||||||||||||||||| |||||||||||||||||||||||||  | ||  || |||||| | || |||||||     ||| ||  |       |||| ||    | | || | |  ||     || |      | | |   | |  | |  ||  |    |  ||| || | |   |  
CCTCCGCGCCGACGGGGAGCGCGAGTTCATGTTCTACCGCAACCCCAGCGCCGACATGCTCCTCACCCACGCCGAGCTCAACGTCGAGCTCATCAAGAGGgtaagccccccgctgatctc-cttatcccccctccgtgttcttctcatctccgcgatctgcggaggaggc-agttccgttccacccgatcccgtcgcgcgcg

upper sequence: GLYMA15G03430.1 (Glycine max), 5'ss of exon 1
lower sequence: GRMZM2G086845_T02 (Zea mays), 5'ss of exon 1
CCTACGCGCCGACGGGGAGCGTGAGTTCATGTTCTACCGGAACCCCAGCGCCGACATGCTCCTCAAGCCCGAAGAACTCAACCTTGAACTCATCAGATCTgtatgcatcttttccctctctctcgctctctctactt-tctcggaaaatatttaaccttttcccggaaaacgaagtctttgtttcgtgattccatgtatga
||| ||||||||||||||||| ||||||||||||||||| ||||||||||| |||||||||||||   |||| || |||||| | || |||||||     ||| |        | |     | |||       ||   ||   |   ||  |   ||   | ||   |  |   |   |              ||   || 
CCTGCGCGCCGACGGGGAGCGCGAGTTCATGTTCTACCGCAACCCCAGCGCTGACATGCTCCTCACCGCCGACGAGCTCAACGTCGAGCTCATCAAGAGGgtaagttaagccacgccacgccacgccacggtaacccatccttggtgatcctcgcccccgtgccttcacgccccgcgatctgcggacagccttattgctg-

upper sequence: GLYMA15G03430.1 (Glycine max), 5'ss of exon 1
lower sequence: GRMZM2G026969_T01 (Zea mays), 5'ss of exon 1
CCTACGCGCCGACGGGGAGCGTGAGTTCATGTTCTACCGGAACCCCAGCGCCGACATGCTCCTCAAGCCCGAAGAACTCAACCTTGAACTCATCAGATCTgtatg------catcttttccctctctct-cgctctctctactttctcggaaaatatttaaccttttcccggaaaacgaagtctttgtttcgtgattccatgtatga
||| ||||||||||| ||||| ||||||||||||||||| |||||||||||||||||||||||||   |||| || |||||| | |  |||||| |    ||| |      |  | |  ||||  ||   || || |  | | ||| ||  |       |      | | | ||      | |   || | |||    ||       
CCTGCGCGCCGACGGCGAGCGCGAGTTCATGTTCTACCGCAACCCCAGCGCCGACATGCTCCTCACTGCCGACGAGCTCAACGTCGGGCTCATCCGGAGGgtaagtcaagccgccctggcccttgcttggcgatccccgtgccttcccgtgatccgcggacagccatactgtaactgattgaccccgtctagtggcagca-------

upper sequence: GLYMA15G03430.1 (Glycine max), 5'ss of exon 1
lower sequence: AT1G06030.1 (Arabidopsis thaliana), 5'ss of exon 1
CCTACGCGCCGACGGGGAGCGTGAGTTCATGTTCTACCGGAACCCCAGCGCCGACATGCTCCTCAAGCCCGAAGAACTCAACCTTGAACTCATCAGATCTgtatgcatcttttccctctctctcgctctctctactttctcggaaaatatttaaccttttcccggaaaacgaagtctttgtttcgtgattccatgtatga
 || ||  | ||||| || || ||||| ||||| |||||||| ||||||||||| ||||| |||  ||| || ||||||||||| ||||| |||||||| ||| | |   | |   |       | | ||   | ||        || |||| || | ||   |  |   || |  | | |||| | |||          
TCTGCGTTCTGACGGAGAACGAGAGTTTATGTTTTACCGGAATCCCAGCGCCGATATGCTTCTCCGGCCAGATGAACTCAACCTCGAACTAATCAGATCCgtacgtaaaatctttatgatctctgttttcaagatttc-------aagattttacttgttttggagatttgatgaatatttttctttatttggcag----

upper sequence: GLYMA15G03430.1 (Glycine max), 5'ss of exon 1
lower sequence: AT1G06020.1 (Arabidopsis thaliana), 5'ss of exon 1
CCTACGCGCCGACGGGGAGCGTGAGTTCATGTTCTACCGGAACCCCAGCGCCGACATGCTCCTCAAGCCCGAAGAACTCAACCTTGAACTCATCAGATCTgtatgca---tcttttccctctctctcgctctctctact--ttctcggaaaatattta--accttttcccggaaaacgaagtctttgtttcgtgattccatgtatga
  | ||  | ||||| || || ||||| ||||| |||||||| ||||||||||| ||||| |||  ||| || ||||| || |||||||| |||||||| ||| | |   |||||  | |   | ||    |   ||||  ||||       ||||||  || |||| |    | | |   | ||  ||||   |   |        
TTTGCGTTCTGACGGAGAACGAGAGTTTATGTTTTACCGGAATCCCAGCGCCGATATGCTTCTCCGGCCAGATGAACTGAATCTTGAACTTATCAGATCCgtacgtaaaatctttctctttgttttcaagattgttactcgttctatctttttatttattacatttttctcttacaaggttttttaatttctaaaacacg-------

upper sequence: GLYMA15G03430.1 (Glycine max), 5'ss of exon 1
lower sequence: AT3G59480.1 (Arabidopsis thaliana), 5'ss of exon 1
CCTACGCGCCGACGGGGAGCGTGAGTTCATGTTCTACCGGAACCCCAGCGCCGACATGCTCCTCAAGCCCGAAGAACTCAACCTTGAACTCATCAGATCTgtatgcatcttttccctctctctcgctctctctac-------------tttctcggaaaatatttaaccttttcccggaaaacgaagtc------tttgtttcgtgattccatgtatga----------------------------------------------------------
 ||| |  | || || || |||||||||||||||||||||||||| || ||||| |||||||||   ||||| || ||||| |||||  |||||||||||||| |    ||||   | |   |          ||             ||| | ||    | | | || |||     |  ||||  |        ||    |   | ||    ||||                                                            
ACTAAGATCTGATGGAGAACGTGAGTTCATGTTCTACCGGAACCCTAGTGCCGATATGCTCCTCCGTCCCGACGAGCTCAATCTTGATGTCATCAGATCTgtacgttatttttatttttaattaatatatgacacgtaggcaaattcttttttgggtccgtgtctcacatttaattagcgaacggtgctacatcattaacgtaacggttgttggtatacgtaacgtagatgtcaagttaggttaatgagtgctctgttttgtttttgttttacacag

upper sequence: GLYMA15G03430.1 (Glycine max), 5'ss of exon 1
lower sequence: Vv05s0102g00710.t01 (Vitis vinifera), 5'ss of exon 1
CCTACGCGCCGACGGGGAGCGTGAGTTCATGTTCTACCGGAACCCCAGCGCCGACATGCTCCTCAAGCCCGAAGAACTCAACCTTGAACTCATCAGATCTgtatgcatcttttccctctctctcgctctctctactttctcggaaaatatttaaccttttcccggaaaacgaagtctttgtttcgtgat--tccatgtatga--------
 || ||||||||||| ||||||||||||||||||||||||||||| |||||||||||||| || ||||| || || |||||||| || |||||  |||| ||| |  |||| | | |||  |||      ||| ||     |  || | | |  | ||| ||   | ||   ||    |  |  | |||  |||||| ||          
GCTCCGCGCCGACGGAGAGCGTGAGTTCATGTTCTACCGGAACCCTAGCGCCGACATGCTGCTGAAGCCGGAGGAGCTCAACCTCGAGCTCATTCGATCCgtacgtttcttcttcttcttactc-----ttctgct-----gcgaactctctctcttttccctttagaattgagaagattctcggagatcttccatggatttctctcttt

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|16997210|gb|BM086582.1|BM086582
EST:     CCGACATGCTCCTCAAGCCCGAAGAACTCAACCTCGAACTCATCAGATCT                         GCAAAAGTTTTCCATTATGGATCAATAAGTTTGATCGTGGAGCCATGCAGA
genomic: CCGACATGCTCCTCAAGCCCGAAGAACTCAACCTTGAACTCATCAGATCTgtatgcatct ... ctttcttcagGCAAAAGTTTTCCATTACGGATCAATAAGTTTGATCGTGGAGCCATGCAGA
EST: gi|254326084|gb|GR840676.1|GR840676
EST:     CCGACATGCTCCTCAAGCCCGAAGAACTCAACCTTGAACTCATCAGATCT                         GCAAAAGTTTTCCATTACGGATCAATAAGTTTGATCGTGGAGCCATGCAGA
genomic: CCGACATGCTCCTCAAGCCCGAAGAACTCAACCTTGAACTCATCAGATCTgtatgcatct ... ctttcttcagGCAAAAGTTTTCCATTACGGATCAATAAGTTTGATCGTGGAGCCATGCAGA
EST: gi|26058519|gb|CA801433.1|CA801433
EST:     CCGACATGCTCCTCGAGCCCGAAGAACTCAACCTCGAACTCATCAGATCT                         GCAAAAGTTTTCCATTATGGATCAATAAGTTTGATCGTGGAGCCATGCAGA
genomic: CCGACATGCTCCTCAAGCCCGAAGAACTCAACCTTGAACTCATCAGATCTgtatgcatct ... ctttcttcagGCAAAAGTTTTCCATTACGGATCAATAAGTTTGATCGTGGAGCCATGCAGA
EST: gi|298190704|gb|HO032825.1|HO032825
EST:     CCGACATGCTCCTCAAGCCCGAAGAACTCAACCTTGAACTCATCAGATCT                         GCAAAAGTTTTCCATTACGGATCAATAAGTTTGATCGTGGAGCCATGCAGA
genomic: CCGACATGCTCCTCAAGCCCGAAGAACTCAACCTTGAACTCATCAGATCTgtatgcatct ... ctttcttcagGCAAAAGTTTTCCATTACGGATCAATAAGTTTGATCGTGGAGCCATGCAGA
EST: gi|207764007|gb|GD738872.1|GD738872
EST:     CCGACATGCTCCTCAAGCCCGAAGAACTCAACCTTGAACTCATCAGATCT                         GCAAAAGTTTTCCATTACGGATCAATAAGTTTGATCGTGGAGCCATGCAGA
genomic: CCGACATGCTCCTCAAGCCCGAAGAACTCAACCTTGAACTCATCAGATCTgtatgcatct ... ctttcttcagGCAAAAGTTTTCCATTACGGATCAATAAGTTTGATCGTGGAGCCATGCAGA
EST: gi|15813034|gb|BI785309.1|BI785309
EST:     CCGACATGCTCCTCAAGCCCGAAGAACTCAACCTTGAACTCATCAGATCT                         GCAAAAGTTTTCCATTACGGATCAATAAGTTTGATCGGGGAGCCATGCAGA
genomic: CCGACATGCTCCTCAAGCCCGAAGAACTCAACCTTGAACTCATCAGATCTgtatgcatct ... ctttcttcagGCAAAAGTTTTCCATTACGGATCAATAAGTTTGATCGTGGAGCCATGCAGA
EST: gi|17022021|gb|BM093055.1|BM093055
EST:     CCGACATGCTCCTCAAGCCCGAAGAACTCAACCTTGAACTCATCAGATCT                         GCAAAAGTTTTTCATTACGGATCAATAAGTTTGATCGTGGAGCCATGCAGA
genomic: CCGACATGCTCCTCAAGCCCGAAGAACTCAACCTTGAACTCATCAGATCTgtatgcatct ... ctttcttcagGCAAAAGTTTTCCATTACGGATCAATAAGTTTGATCGTGGAGCCATGCAGA
EST: gi|10231806|gb|BE800694.1|BE800694
EST:     CCGACATGCTCCTCAAGCCCGAAGAACTCAACCTTGAACTCATCAGATCT                         GCAAAAGTTTTCCATTACGGATCAATAAGTTTGATCGTGGAGCCATGCAGA
genomic: CCGACATGCTCCTCAAGCCCGAAGAACTCAACCTTGAACTCATCAGATCTgtatgcatct ... ctttcttcagGCAAAAGTTTTCCATTACGGATCAATAAGTTTGATCGTGGAGCCATGCAGA
EST: gi|9204266|gb|BE330490.1|BE330490
EST:     CCGACATGCTCCTCAAGCCCGAAGAACTCAACCTTGAACTCATCAGATCT                         GCAAAAGTTTTCCATTACGGATCAATAAGTTTGATCGTGGAGCCATGCAGA
genomic: CCGACATGCTCCTCAAGCCCGAAGAACTCAACCTTGAACTCATCAGATCTgtatgcatct ... ctttcttcagGCAAAAGTTTTCCATTACGGATCAATAAGTTTGATCGTGGAGCCATGCAGA
EST: gi|193483959|gb|FK452390.1|FK452390
EST:     CCGACATGCTCCTCAAGCCCGAAGAACTCAACCTTGAACTCATCAGATCT                         GCAAAAGTTTTCCATTACGGATCAATAAGTTTGATCGTGGAGCCATGCAGA
genomic: CCGACATGCTCCTCAAGCCCGAAGAACTCAACCTTGAACTCATCAGATCTgtatgcatct ... ctttcttcagGCAAAAGTTTTCCATTACGGATCAATAAGTTTGATCGTGGAGCCATGCAGA
EST: gi|26048304|gb|CA784817.1|CA784817
EST:     CCGACATGCTCCTCAAGCCCGAAGAACTCAACCTCGAACTCATCAGATCT                         GCAAAAGTTTTCCATTATGGATCAATAAGTTTGATCGTGGAGCCATGCAGA
genomic: CCGACATGCTCCTCAAGCCCGAAGAACTCAACCTTGAACTCATCAGATCTgtatgcatct ... ctttcttcagGCAAAAGTTTTCCATTACGGATCAATAAGTTTGATCGTGGAGCCATGCAGA
EST: gi|208241907|gb|GE040639.1|GE040639
EST:     CTCCTCAAGCCCGAAGAACTCAACCTTGAACTCATCAGATCT                         GCAAAAGTTTTCCATTACGGATCAATAAATTTGATCGTGGAGCCATGCAGA
genomic: CTCCTCAAGCCCGAAGAACTCAACCTTGAACTCATCAGATCTgtatgcatct ... ctttcttcagGCAAAAGTTTTCCATTACGGATCAATAAGTTTGATCGTGGAGCCATGCAGA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CCTACGCGCCGACGGGGAGCGTGAGTTCATGTTCTACCGGAACCCCAGCGCCGACATGCTCCTCAAGCCCGAAGAACTCAACCTTGAACTCATCAGATCTgtatgcatcttttccctctctctcgctctctctactttctcggaaaatatttaaccttttcccggaaaacgaagtctttgtttcgtgattccatgtatga

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ttccctc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctctctc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ggaaaata
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ccttttcc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gaaaacga