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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tcatacacattaaaccggataacagatgtactcattgctctcttgctattagttgtaatttattcctgatacgactgaacttgagttttaaatggtgtagGTTAAAAATCCATGGCCTAATGTTGATGCTCACAGTGGAGTGCTACTGAACTATTATGGTCTAACTGAGGAAAA

Basic information

species Glycine max
transcript GLYMA08G16770.1
intron # 17
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA08G16770.1 (Glycine max), 3'ss of exon 17
lower sequence: LOC_Os02g10070.1 (Oryza sativa), 3'ss of exon 17
---------tcatacacattaaaccggataacagatgtactcattgctctcttgctattagttgtaatttattcctgatacgactgaacttgagttttaaatggtgtagGTTAAAAATCCATGGCCTAATGTTGATGCTCACAGTGGAGTGCTACTGAACTATTATGGTCTAACTGAGGAAAA
           | |   || ||     ||  |   | || | |  ||||  |   | ||| ||  |  | |||    | |  | | |        || | ||  |  |||| ||||| |||||||||||||||||||||||||| ||||| ||||||||| | | |||  || |||| |    
gtaatgctactagattgatcaataattattgctcctttaattacggctccttcagt-ttacttccatctcattggcta-agaaataagaacatccttcacatttt-cagGTCAAAAACCCATGGCCTAATGTTGATGCTCACAGCGGAGTTCTACTGAACCACTTTGGATTATCTGAAGCTCG

upper sequence: GLYMA08G16770.1 (Glycine max), 3'ss of exon 17
lower sequence: LOC_Os11g33240.2 (Oryza sativa), 3'ss of exon 17
tcatacacattaaaccggataacagatgtactcattgctctcttgctattagttgtaatttattcctgatacgactgaacttgagttttaaatggtgtagGTTAAAAATCCATGGCCTAATGTTGATGCTCACAGTGGAGTGCTACTGAACTATTATGGTCTAACTGAGGAAAA
         | |  ||     |  |||    | ||||||  | |  |||    |  |  |||||   | ||  |    ||   | | |  |    |  |||| ||||| |||||||||||||||||||||||||||||||| || |||||| | | |||  || |||| |    
--------gtaatgccactagattgatca--tgattgctaccgttttatg---tccatcttattg--gctaaaaagtgacaacattgtccatatttccagGTCAAAAACCCATGGCCTAATGTTGATGCTCACAGTGGAGTTCTGCTGAACCACTTTGGATTATCTGAAGCTCG

upper sequence: GLYMA08G16770.1 (Glycine max), 3'ss of exon 17
lower sequence: GRMZM2G063851_T05 (Zea mays), 3'ss of exon 3
--tcatacacattaaaccggataacagatgtactcattgctctcttgctattagttgtaatttattcctgatacgactg--aacttgagttttaaatggtgtagGTTAAAAATCCATGGCCTAATGTTGATGCTCACAGTGGAGTGCTACTGAACTATTATGGTCTAACTGAGGAAAA
  || ||   |||       | | |  ||  | ||  || | | |||  | ||   | |    |  |||| |  ||     |   |  |       |     |||| || || |||||||| |||||||||||||||||||||||  | |||||| | | ||| ||| |||| | |  
cttcttaagaatttttttcca-atctcatccaatccatg-tgtattgggaataaccgaa--caaagcctggtgtgaacactattctttgcccatgttttctcagGTCAAGAACCCATGGCCAAATGTTGATGCTCACAGTGGAGTTTTGCTGAACCACTTTGGACTATCTGAAGCACG

upper sequence: GLYMA08G16770.1 (Glycine max), 3'ss of exon 17
lower sequence: GRMZM2G064023_T01 (Zea mays), 3'ss of exon 18
tcatacacattaaaccggataacagatgtactcattgctctcttgctattagttgtaatttattcctgatacgactgaacttgagttttaaatggtgtagGTTAAAAATCCATGGCCTAATGTTGATGCTCACAGTGGAGTGCTACTGAACTATTATGGTCTAACTGAGGAAAA
            ||   | || |||||  |        | ||   |  || |||  |   || |  | ||       |   |  |       |     |||| || || || ||||| |||||||||||||||||||||||  | |||||| | | ||| ||| |||| | |  
----------gtaatgtggtaccagattgatcacaatttttcactcctttggtttcagcctactggttatgaacaccactctttgcccatgttttctcagGTCAAGAACCCGTGGCCGAATGTTGATGCTCACAGTGGAGTTTTGCTGAACCACTTTGGACTATCTGAAGCACG

upper sequence: GLYMA08G16770.1 (Glycine max), 3'ss of exon 17
lower sequence: AT3G60100.1 (Arabidopsis thaliana), 3'ss of exon 16
tcatacacattaaaccggataacagatgtactcattgctctcttg--ctattag---ttgtaatttattcctgatacgactgaacttgagttttaaatggtgtagGTTAAAAATCCATGGCCTAATGTTGATGCTCACAGTGGAGTGCTACTGAACTATTATGGTCTAACTGAGGAAAA
                   ||  |  | ||||||||  | || ||  |||  ||   || | |||| |  ||| |   |   | |||||  ||    ||    |||| || || || |||||||| ||||||||||| || |||||||| |||||||| ||||||||||| || | || 
------------------gtactacttatactcattcatttcatgtgctaccagattttctgattt-tctctggttttatgaatcttgaaatt--gctgtatcagGTCAAGAACCCGTGGCCTAACGTTGATGCTCATAGCGGAGTGCTTCTGAACTACTATGGTCTAACCGAAGCAAG

upper sequence: GLYMA08G16770.1 (Glycine max), 3'ss of exon 17
lower sequence: Vv13s0156g00180.t01 (Vitis vinifera), 3'ss of exon 17
tcatacacattaaaccggataacagatgtactcattgctctcttgctattagttgtaatt-tattcctgata-cgactgaacttgagttttaaatgg--tgtagGTTAAAAATCCATGGCCTAATGTTGATGCTCACAGTGGAGTGCTACTGAACTATTATGGTCTAACTGAGGAAAA
   |   ||  |  ||   ||  |  | |    | |   || | ||| | |||  ||  | |     | | |  || ||   ||| | |||        ||||||||||||| |||||||| ||||| |||||||||||||| ||  | |||||| ||| |||| ||   || | |  
--ttctgcaacatgcctactag-aattctgtaaaataaactttggct-tcagtgatacctgtggagttaacagtgattgtttttgggatttgggacacttgtagGTTAAAAACCCATGGCCCAATGTCGATGCTCACAGTGGGGTCTTGCTGAACCATTTTGGTTTACACGAAGCACG

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|37995119|gb|CF806708.1|CF806708
EST:     AGAGGTTGTGCCTCCCATTCTTACCAAGTTAGGCAAG                         GTTAAAAATCCATGGCCTAATGTTGATGCTCACAGTGGAGTGCTACTGAAC
genomic: AGAGGTTGTGCCTCCCATTCTTACCAAGTTAGGCAAGgtattgttta ... aatggtgtagGTTAAAAATCCATGGCCTAATGTTGATGCTCACAGTGGAGTGCTACTGAAC
EST: gi|213604400|gb|DB983488.1|DB983488
EST:     CTCAAAAGATAAAAGAGGTTGTGCCTCCCATTCGTACCAAGTTAGGCAAG                         GTTAAAAATCCATGGCCTAATGTTGATGCTCACAGTGGAGTGCTACTGAAC
genomic: GTC-TAAGATAAAAGAGGTTGTGCCTCCCATTCTTACCAAGTTAGGCAAGgtattgttta ... aatggtgtagGTTAAAAATCCATGGCCTAATGTTGATGCTCACAGTGGAGTGCTACTGAAC
EST: gi|22934201|gb|BU551340.1|BU551340
EST:     AGATAAAAGAGGTTGTGCCTCCCATTCTTACCAAGTTAGGCAAG                         GTTAAAAATCCATGGCCTAATGTTGATGCTCACAGTGGAGTGCTACTGAAC
genomic: AGATAAAAGAGGTTGTGCCTCCCATTCTTACCAAGTTAGGCAAGgtattgttta ... aatggtgtagGTTAAAAATCCATGGCCTAATGTTGATGCTCACAGTGGAGTGCTACTGAAC
EST: gi|23057280|gb|BU577954.1|BU577954
EST:     TGTCTAAGATAAAAGAGGTTGTGCCTCCCATTCTTACCAAGTTAGGCAAG                         GTTAAAAATCCATGGCCTAATGTTGATGCTCACAGTGGAGTGCTACTGAAC
genomic: TGTCTAAGATAAAAGAGGTTGTGCCTCCCATTCTTACCAAGTTAGGCAAGgtattgttta ... aatggtgtagGTTAAAAATCCATGGCCTAATGTTGATGCTCACAGTGGAGTGCTACTGAAC
EST: gi|31460126|gb|CD402154.1|CD402154
EST:     AGAGGTTGTGCCTCCCATTCTTACCAAGTTAGGCAAG                         GTTAAAAATCCATGGCCTAATGTTGATGCTCACAGTGGAGTGCTACTGAAC
genomic: AGAGGTTGTGCCTCCCATTCTTACCAAGTTAGGCAAGgtattgttta ... aatggtgtagGTTAAAAATCCATGGCCTAATGTTGATGCTCACAGTGGAGTGCTACTGAAC
EST: gi|9440345|gb|BE440851.1|BE440851
EST:     TGTCTAAGATAAAAGAGGTTGTGCCTCCCATTCTTACCAAGTTAGGCAAG                         GTTAAAAATCCATGGCCTAATGTTGATGCTCACAGTGGAGTGCTACTGAAC
genomic: TGTCTAAGATAAAAGAGGTTGTGCCTCCCATTCTTACCAAGTTAGGCAAGgtattgttta ... aatggtgtagGTTAAAAATCCATGGCCTAATGTTGATGCTCACAGTGGAGTGCTACTGAAC
EST: gi|15287775|gb|BI471666.1|BI471666
EST:     TGTCTAAGATAAAAGAGGTTGTGCCTCCCATTCTTACCAAGTTAGGCAAG                         GTTAAAAATCCATGGCCTAATGTTGATGCTCACAGTGGAGTGCTACTGAAC
genomic: TGTCTAAGATAAAAGAGGTTGTGCCTCCCATTCTTACCAAGTTAGGCAAGgtattgttta ... aatggtgtagGTTAAAAATCCATGGCCTAATGTTGATGCTCACAGTGGAGTGCTACTGAAC
EST: gi|21994889|gb|BQ786417.1|BQ786417
EST:     TGTCTAAGATAAAAGAGGTTGTGCCTCCCATTCTTACCAAGTTAGGCAAG                         GTTAAAAATCCATGGCCTAATGTTGATGCTCACAGTGGAGTGCTACTGAAC
genomic: TGTCTAAGATAAAAGAGGTTGTGCCTCCCATTCTTACCAAGTTAGGCAAGgtattgttta ... aatggtgtagGTTAAAAATCCATGGCCTAATGTTGATGCTCACAGTGGAGTGCTACTGAAC
EST: gi|15664905|gb|BI702276.1|BI702276
EST:     TGTCTAAGATAAAAGAGGTTGTGCCTCCCATTCTTACCAAGTTAGGCAAG                         GTTAAAAATCCATGGCCTAATGTTGATGCTCACAGTGGAGTGCTACTGAAC
genomic: TGTCTAAGATAAAAGAGGTTGTGCCTCCCATTCTTACCAAGTTAGGCAAGgtattgttta ... aatggtgtagGTTAAAAATCCATGGCCTAATGTTGATGCTCACAGTGGAGTGCTACTGAAC
EST: gi|9820752|gb|BE556262.1|BE556262
EST:     ACCAGGTTAGGCAAG                         GTTAAAAATCCATGGCCTAATGTTGATGCTCACAGTGGAGTGCTACTGAAC
genomic: ACCAAGTTAGGCAAGgtattgttta ... aatggtgtagGTTAAAAATCCATGGCCTAATGTTGATGCTCACAGTGGAGTGCTACTGAAC
EST: gi|23733765|gb|BU765093.1|BU765093
EST:     TGTCTAAGATAAAAGAGGTTGTGCCTCCCATTCTTACCAAGTTAGGCAAG                         GTTAAAAATCCATGGCCTAATGTTGATGCTCACAGTGGAGTGCTACTGAAC
genomic: TGTCTAAGATAAAAGAGGTTGTGCCTCCCATTCTTACCAAGTTAGGCAAGgtattgttta ... aatggtgtagGTTAAAAATCCATGGCCTAATGTTGATGCTCACAGTGGAGTGCTACTGAAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctattagttgtaatttattcctgatacgactgaacttgagttttaaatggtgtagGTTAAAAATCCATGGCCTAATGTTGATGCTCACAGTGGAGTGCTACTGAACTATTATGGTCTAACTGAGGAAAA
                  tcctgat  putative branch site (score: 3)
     agttgtaatttatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tcatacacattaaaccggataacagatgtactcattgctctcttgctattagttgtaatttattcctgatacgactgaacttgagttttaaatggtgtagGTTAAAAATCCATGGCCTAATGTTGATGCTCACAGTGGAGTGCTACTGAACTATTATGGTCTAACTGAGGAAAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG