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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTCTTAGCAACACCATTAAGCAAAAGAGGAAGGAGAAGGCAGGGAAATGGGATGTTCCTCTACCTAAGgtgaaattgcgttcaatactttttgcacggattatgttaaacgatatctcttgcaatttgttccttgtttctatttcatgtgtgttttatgtttccctgttaatggaagggagcgagcttgagtaattaaatgaatgtatactttctcatttcttcag

Basic information

species Glycine max
transcript GLYMA02G35500.1
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA02G35500.1 (Glycine max), 5'ss of exon 5
lower sequence: LOC_Os07g47580.1 (Oryza sativa), 5'ss of exon 5
GTTCTTAGCAACACCATTAAGCAAAAGAGGAAGGAGAAGGCAGGGAAATGGGATGTTCCTCTACCTAAGgtgaaattgcgttcaatactttttgcacggattatgttaaacgatatctcttgcaatttgttccttgtttctatttcatgtgtgttttatgtttccctgttaatggaagggagcgagcttgagtaattaaatgaatgtatactttctcatttcttcag
||||| |||||||| |||||||||||||||| ||| ||||| || |||||||| |||||| | || |||||||  ||     ||| ||| |||  |  |    ||  || | ||   | |   |  |||   ||     || |  ||      |||| |   |  | |                                                           
GTTCTCAGCAACACAATTAAGCAAAAGAGGATGGAAAAGGCTGGCAAATGGGAGGTTCCTTTGCCAAAGgtgattttcaacacaa-actgtttcta--gtacctggcaatcaatggttttcctaccttga--ctaagcactgtcaca-----attttcttcctttcag-----------------------------------------------------------

upper sequence: GLYMA02G35500.1 (Glycine max), 5'ss of exon 5
lower sequence: GRMZM2G009876_T01 (Zea mays), 5'ss of exon 5
GTTCTTAGCAACACCATTAAGCAAAAGAGGAAGGAGAAGGCAGGGAAATGGGATGTTCCTCTACCTAAGgtgaaattgcgttcaatactttttgcacggattatgttaa-acgatatctcttgcaatttgttccttgtttctatttcatgtgtgttttatgtttccctgttaatggaagggagcgagcttgagtaattaaatgaatgtatactttctcatttcttcag
||||| |||||||| || ||||||||||||||||| ||||| || ||||||||||||||||| || |||||||   |     ||  ||        | | ||   | ||   | ||  | || |     |||   |  ||  |                                                                                     
GTTCTCAGCAACACAATAAAGCAAAAGAGGAAGGAAAAGGCTGGCAAATGGGATGTTCCTCTGCCAAAGgtgattctcaacacagcacgcccatttctggttgcttcaatgggttagtttttactcacagttttatcctttcag------------------------------------------------------------------------------------

upper sequence: GLYMA02G35500.1 (Glycine max), 5'ss of exon 5
lower sequence: GRMZM2G174204_T02 (Zea mays), 5'ss of exon 1
-------------------------------GTTCTTAGCAACACCATTAAGCAAAAGAGGAAGGAGAAGGCAGGGAAATGGGATGTTCCTCTACCTAAGgtgaaattgcgttcaatactttttgcacggattatgttaaacgatatctcttgcaatttgttccttgtttctatttcatgtgtgttttatgtttccctgttaatggaagggagcgagcttgagtaattaaatgaatgtatactttctcatttcttcag
                               || || |||||||| || ||||||||||||||||| ||||| || |||||||||||||| || || ||||||    |  ||  |||      || ||  |  |     |    |   |  | ||||  ||| | | |||||  | | |                                                                               
GCATTGATCACTGATTTCTGGTGAAGCGTAGGTACTCAGCAACACAATCAAGCAAAAGAGGAAGGAAAAGGCTGGCAAATGGGATGTTCCGCTGCCAAAGgtg----tttgtcaaat-----ctgaacacagcaaacctatttctggttgattcaatgagttacatatttcttgtcctttcag---------------------------------------------------------------------------

upper sequence: GLYMA02G35500.1 (Glycine max), 5'ss of exon 5
lower sequence: GRMZM2G174204_T01 (Zea mays), 5'ss of exon 5
GTTCTTAGCAACACCATTAAGCAAAAGAGGAAGGAGAAGGCAGGGAAATGGGATGTTCCTCTACCTAAGgtgaaattgcgttcaatactttttgcacggattatgttaaacgatatctcttgcaatttgttccttgtttctatttcatgtgtgttttatgtttccctgttaatggaagggagcgagcttgagtaattaaatgaatgtatactttctcatttcttcag
|| || |||||||| || ||||||||||||||||| ||||| || |||||||||||||| || || ||||||    |  ||  |||      || ||  |  |     |    |   |  | ||||  ||| | | |||||  | | |                                                                               
GTACTCAGCAACACAATCAAGCAAAAGAGGAAGGAAAAGGCTGGCAAATGGGATGTTCCGCTGCCAAAGgtg----tttgtcaaat-----ctgaacacagcaaacctatttctggttgattcaatgagttacatatttcttgtcctttcag---------------------------------------------------------------------------

upper sequence: GLYMA02G35500.1 (Glycine max), 5'ss of exon 5
lower sequence: AT5G06360.1 (Arabidopsis thaliana), 5'ss of exon 5
GTTCTTAGCAACACCATTAAGCAAAAGAGGAAGGAGAAGGCAGGGAAATGGGATGTTCCTCTACCTAAGgtgaaattgcgttcaatactttttgcacggattatgttaaacgatatctcttgcaatttgttccttgtttctatttcatgtgtgttttatgtttccctgttaatggaagggagcgagcttgagtaattaaatgaatgtatactttctcatttcttcag
|||||||||||||||||||| ||||||||||| ||||| || || |||||||| || ||||| || ||||||||||  |  ||  | ||||| | |    ||  ||        | ||||  ||| | |  |   | ||  |||  |    |||  |    ||  | |                                                           
GTTCTTAGCAACACCATTAAACAAAAGAGGAAAGAGAAAGCTGGCAAATGGGAGGTCCCTCTTCCAAAGgtgaaatctctctctctgctttt-gtattccttcagt---gtttgaactctaacaaatggg-caaagcttaaattcaagccctgtcct----tttacag-----------------------------------------------------------

upper sequence: GLYMA02G35500.1 (Glycine max), 5'ss of exon 5
lower sequence: Vv08s0105g00280.t01 (Vitis vinifera), 5'ss of exon 5
GTTCTTAGCAACACCATTAAGCAAAAGAGGAAGGAGAAGGCAGGGAAATGGGATGTTCCTCTACCTAAGgtgaaattgcgttcaatact---ttttgcacggattatgttaaacgatatctcttgcaatttgttccttgtttctatttcatgtgtgttttatgtttccctgttaatggaagggagcgagcttgagtaattaaatgaatgtatactttctcatttcttcag
||||||||||| || || |||||||| ||||| ||||| || ||||||||||| || |||||||| || || | ||  | ||  | | |   || |    | ||||   |   |  ||| |  ||   |  ||| | ||    | ||  |   ||  |||    ||                                                                
GTTCTTAGCAATACTATAAAGCAAAAAAGGAAAGAGAAAGCTGGGAAATGGGAAGTCCCTCTACCCAAAgtaagatcacatttgacattgtgttatttcagcattaaccttttcagtattttctgatttgagtttcctgcactttttctaatggtacttttcccttttt-------------------------------------------------------------

upper sequence: GLYMA02G35500.1 (Glycine max), 5'ss of exon 5
lower sequence: PP1S136_220V6.1 (Physcomitrella patens), 5'ss of exon 5
GTTCTTAGCAACACCATTAAGCAAAAGAGGAAGGAGAAGGCAGGGAAATGGGATGTTCCTCTACCTAAGgtgaaattgcgttcaatactttttgcacggattatgttaaacgatatctcttgcaatttgttccttgttt-ctatttcatgtgtgttttatgtttccctgttaatggaagggagcgagcttgagtaattaaatgaatgtatactttctcatttcttcag
||||| ||||||||||| ||||| ||  | ||||||||||| || |||||||| || ||||| ||||||||||         | |||    | | ||| ||  ||        || ||  || || |  |   |  |   | |  |||  |   || |    | |   || || ||| | ||    | ||                                      
GTTCTCAGCAACACCATCAAGCAGAAACGTAAGGAGAAGGCTGGTAAATGGGAGGTGCCTCTTCCTAAGgtgag-------ccgata----tcgtacgaatgctg--------tagcttgtgaaactcttgaataatccaccacatcacttaaattgtgaagtac---gtgaacggaggcgatgtggtttc-------------------------------------

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|192313831|gb|FK007647.1|FK007647
EST:     AGCAA--GAGGAAGGAGAAGGCAGGGAAATGGGATGTTCCTCTACCTAAG                         GTACGTCCCGTGGCTGAAGATGAAATGTTCAAAGTGGTCCGAACTGGTAAA
genomic: AGCAAAAGAGGAAGGAGAAGGCAGGGAAATGGGATGTTCCTCTACCTAAGgtgaaattgc ... atttcttcagGTACGTCCCGTGGCTGAAGATGAAATGTTCAAAGTGGTCCGAACTGGTAAA
EST: gi|15203872|gb|BI426640.1|BI426640
EST:     AGCAAAAGAGGAAGGAGAAGGCAGGGAAATGGGATGTTCCTCTACCTAAG                         GTACGTCCCGTGGCTGAAGATGAAATGTTCAAAGTGGTCCGAACTGGTAAA
genomic: AGCAAAAGAGGAAGGAGAAGGCAGGGAAATGGGATGTTCCTCTACCTAAGgtgaaattgc ... atttcttcagGTACGTCCCGTGGCTGAAGATGAAATGTTCAAAGTGGTCCGAACTGGTAAA
EST: gi|7478670|gb|AW666357.1|AW666357
EST:     AGCAAAAGAGGAAGGAGAAGGCAGGGAAATGGGATGTTCCTCTACCTAAG                         GTACGTCCCGTGGCTGAAGATGAAATGTTCAAAGTGGTCCGAACTGGTAAA
genomic: AGCAAAAGAGGAAGGAGAAGGCAGGGAAATGGGATGTTCCTCTACCTAAGgtgaaattgc ... atttcttcagGTACGTCCCGTGGCTGAAGATGAAATGTTCAAAGTGGTCCGAACTGGTAAA
EST: gi|6071298|gb|AW100685.1|AW100685
EST:     AGCAAAAGAGGAAGGAGAAGGCAGGGAAATGGGATGTTCCTCTACCTAAG                         GTACGTCCCGTGGCTGAAGATGAAATGTTCAAAGTGGTCCGAACTGGTAAA
genomic: AGCAAAAGAGGAAGGAGAAGGCAGGGAAATGGGATGTTCCTCTACCTAAGgtgaaattgc ... atttcttcagGTACGTCCCGTGGCTGAAGATGAAATGTTCAAAGTGGTCCGAACTGGTAAA
EST: gi|23733288|gb|BU764826.1|BU764826
EST:     AGCAAAAGAGGAAGGAGAAGGCAGGGAAATGGGATGTTCCTCTACCTAAG                         GTACGTCCCGTGGCTGAAGATGAAATGTTCAAAGTGGTCCGAACTGG
genomic: AGCAAAAGAGGAAGGAGAAGGCAGGGAAATGGGATGTTCCTCTACCTAAGgtgaaattgc ... atttcttcagGTACGTCCCGTGGCTGAAGATGAAATGTTCAAAGTGGTCCGAACTGG
EST: gi|17519530|gb|BM188572.1|BM188572
EST:     AGCAAAAGAGGAAGGAGAAGGCAGGGAAATGGGATGTTCCTCTACCTAAG                         GTACGTCCCGTGGCTGAAGATGAAATGTTCAAAGTGGTCCGAACTGGTAAA
genomic: AGCAAAAGAGGAAGGAGAAGGCAGGGAAATGGGATGTTCCTCTACCTAAGgtgaaattgc ... atttcttcagGTACGTCCCGTGGCTGAAGATGAAATGTTCAAAGTGGTCCGAACTGGTAAA
EST: gi|298194398|gb|HO041046.1|HO041046
EST:     AGCAAAAGAGGAAGGAGAAGGCAGGGAAATGGGATGTTCCTCTACCTAAG                         GTACGTCCCGTGGCTGAAGATGAAATGTTCAAAGTGGTCCGAACTGGTAAA
genomic: AGCAAAAGAGGAAGGAGAAGGCAGGGAAATGGGATGTTCCTCTACCTAAGgtgaaattgc ... atttcttcagGTACGTCCCGTGGCTGAAGATGAAATGTTCAAAGTGGTCCGAACTGGTAAA
EST: gi|15203893|gb|BI426661.1|BI426661
EST:     AGCAAAAGAGGAAGGAGAAGGCAGGGAAATGGGATGTTCCTCTACCTAAG                         GTACGTCCCGTGGCTGAAGATGAAATGTTCAAAGTGGTCCGAACTGGTAAA
genomic: AGCAAAAGAGGAAGGAGAAGGCAGGGAAATGGGATGTTCCTCTACCTAAGgtgaaattgc ... atttcttcagGTACGTCCCGTGGCTGAAGATGAAATGTTCAAAGTGGTCCGAACTGGTAAA
EST: gi|31310190|gb|CD395393.1|CD395393
EST:     CTCTACCTAAG                         GTACGTCCCGTGGCTGAAGATGAAATGTTCAAAGTGGTCCGAACTGGTAAA
genomic: CTCTACCTAAGgtgaaattgc ... atttcttcagGTACGTCCCGTGGCTGAAGATGAAATGTTCAAAGTGGTCCGAACTGGTAAA
EST: gi|8285802|gb|BE023361.1|BE023361
EST:     AGCAAAAGAGGAAGGAGAAGGCAGGGAAATGGGATGTTCCTCTACCTAAG                         GTACGTCCCGTGGCTGAAGATGAAATGTTCAAAGTGGTCCGAACTGGTAAA
genomic: AGCAAAAGAGGAAGGAGAAGGCAGGGAAATGGGATGTTCCTCTACCTAAGgtgaaattgc ... atttcttcagGTACGTCCCGTGGCTGAAGATGAAATGTTCAAAGTGGTCCGAACTGGTAAA
EST: gi|120491259|gb|EH219426.1|EH219426
EST:     AGCAAAAGAGGAAGGAGAAGGCAGGGAAATGGGATGTTCCTCTACCTAAG                         GTACGTCCCGTGGCTGAAGATGAAATGTTCAAAGTGGTCCGAACTGGTAAA
genomic: AGCAAAAGAGGAAGGAGAAGGCAGGGAAATGGGATGTTCCTCTACCTAAGgtgaaattgc ... atttcttcagGTACGTCCCGTGGCTGAAGATGAAATGTTCAAAGTGGTCCGAACTGGTAAA
EST: gi|192328211|gb|FK020444.1|FK020444
EST:     AGCAAAAGAGGAAGGAGAAGGCAGGGAAATGGGATGTTCCTCTACCTAAG                         GTACGTCCCGTGGCTGAAGATGAAATGTTCAAAGTGGTCCGAACTGGTAAA
genomic: AGCAAAAGAGGAAGGAGAAGGCAGGGAAATGGGATGTTCCTCTACCTAAGgtgaaattgc ... atttcttcagGTACGTCCCGTGGCTGAAGATGAAATGTTCAAAGTGGTCCGAACTGGTAAA
EST: gi|31312274|gb|CD397477.1|CD397477
EST:     GGAAGGAGAAGGCAGGGAAATGGGATGTTCCTCTACCTAAG                         GTACGTCCCGTGGCTGAAGATGAAATGTTCAAAGTGGTCCGAACTGGTAAA
genomic: GGAAGGAGAAGGCAGGGAAATGGGATGTTCCTCTACCTAAGgtgaaattgc ... atttcttcagGTACGTCCCGTGGCTGAAGATGAAATGTTCAAAGTGGTCCGAACTGGTAAA
EST: gi|21995126|gb|BQ786654.1|BQ786654
EST:     AGCAAAAGAGGAAGGAGAAGGCAGGGAAATGGGATGTTCCTCTACCTAAG                         GTACGTCCCGTGGCTGAAGATGAAATGTTCAAAGTGGTCCGAACTGGTAAA
genomic: AGCAAAAGAGGAAGGAGAAGGCAGGGAAATGGGATGTTCCTCTACCTAAGgtgaaattgc ... atttcttcagGTACGTCCCGTGGCTGAAGATGAAATGTTCAAAGTGGTCCGAACTGGTAAA
EST: gi|192313774|gb|FK007646.1|FK007646
EST:     AGCAA--GAGGAAGGAGAAGGCAGGGAAATGGGATGTTCCTCTACCTAAG                         GTACGTCCCGTGGCTGAAGATGAAATGTTCAAAGTGGTCCGAACTGGTAAA
genomic: AGCAAAAGAGGAAGGAGAAGGCAGGGAAATGGGATGTTCCTCTACCTAAGgtgaaattgc ... atttcttcagGTACGTCCCGTGGCTGAAGATGAAATGTTCAAAGTGGTCCGAACTGGTAAA
EST: gi|20811431|gb|BQ295909.1|BQ295909
EST:     AGCAAAAGAGGAAGGAGAAGGCAGGGAAATGGGATGTTCCTCTACCTAAG                         GTACGTCCCGTGGCTGAAGATGAAATGTTCAAAGTGGTCCGAACTGGTAAA
genomic: AGCAAAAGAGGAAGGAGAAGGCAGGGAAATGGGATGTTCCTCTACCTAAGgtgaaattgc ... atttcttcagGTACGTCCCGTGGCTGAAGATGAAATGTTCAAAGTGGTCCGAACTGGTAAA
EST: gi|7588724|gb|AW704513.1|AW704513
EST:     AGCAAAAGAGGAAGGAGAAGGCAGGGAAATGGGATGTTCCTCTACCTAAG                         GTACGTCCCGTGGCTGAAGATGAAATGTTCAAAGTGGTCCGAACTGGTAAA
genomic: AGCAAAAGAGGAAGGAGAAGGCAGGGAAATGGGATGTTCCTCTACCTAAGgtgaaattgc ... atttcttcagGTACGTCCCGTGGCTGAAGATGAAATGTTCAAAGTGGTCCGAACTGGTAAA
EST: gi|151402809|gb|EV272622.1|EV272622
EST:     AGCAAAAGAGGAAGGAGAAGGCAGGGAAATGGGATGTTCCTCTACCTAAG                         GTACGTCCCGTGGCTGAAGATGAAATGTTCAAAGTGGTCCGAACTGGTAAA
genomic: AGCAAAAGAGGAAGGAGAAGGCAGGGAAATGGGATGTTCCTCTACCTAAGgtgaaattgc ... atttcttcagGTACGTCCCGTGGCTGAAGATGAAATGTTCAAAGTGGTCCGAACTGGTAAA
EST: gi|16348558|gb|BI974153.1|BI974153
EST:     GAGGAAGGAGAAGGCAGGGAAATGGGATGTTCCTCTACCTAAG                         GTACGTCCCGTGGCTGAAGATGAAATGTTCAAAGTGGTCCGAACTGGTAAA
genomic: GAGGAAGGAGAAGGCAGGGAAATGGGATGTTCCTCTACCTAAGgtgaaattgc ... atttcttcagGTACGTCCCGTGGCTGAAGATGAAATGTTCAAAGTGGTCCGAACTGGTAAA
EST: gi|6668126|gb|AW279577.1|AW279577
EST:     AGCAAAAGAGGAAGGAGAAGGCAGGGAAATGGGATGTTCCTCTACCTAAG                         GTACGTCCCGTGGCTGAAGATGAAATGTTCAAAGTGGTCCGAACTGGTAAA
genomic: AGCAAAAGAGGAAGGAGAAGGCAGGGAAATGGGATGTTCCTCTACCTAAGgtgaaattgc ... atttcttcagGTACGTCCCGTGGCTGAAGATGAAATGTTCAAAGTGGTCCGAACTGGTAAA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTTCTTAGCAACACCATTAAGCAAAAGAGGAAGGAGAAGGCAGGGAAATGGGATGTTCCTCTACCTAAGgtgaaattgcgttcaatactttttgcacggattatgttaaacgatatctcttgcaatttgttccttgtttctatttcatgtgtgttttatgtttccctgttaatggaagggagcgagcttgagtaattaaatgaatgtatactttctcatttcttcag

- - - - - - - - - - - - AAGAGG
- - - - - - - - - - - -  AGAGGA
- - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - -  AGGAGA
- - - - - - - - - - - - - - - - GGAGAA