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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTCTTAGCAACACAATTAAGCAAAAGAGGAAGGAGAAGGCGGGAAAATGGGATGTTCCTCTACCTAAGgtgaaattacgttcaatactttgtgcattatgttaaatgatatcttttgcaatgtgtatcttattgctatttcatgtttgttttatgtttccctgtgaatggaagggagcgaacttggtaattaaatgaatgtatgctttctcatttcttcag

Basic information

species Glycine max
transcript GLYMA10G10000.1
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA10G10000.1 (Glycine max), 5'ss of exon 5
lower sequence: LOC_Os07g47580.1 (Oryza sativa), 5'ss of exon 5
GTTCTTAGCAACACAATTAAGCAAAAGAGGAAGGAGAAGGCGGGAAAATGGGATGTTCCTCTACCTAAGgtgaaattacgttcaatactttgtgcatta--tgttaaatgatatcttttgcaatgtgtatcttattgctatttcatgtttgttttatgtttccctgtgaatggaagggagcgaacttggtaattaaatgaatgtatgctttctcatttcttcag
||||| ||||||||||||||||||||||||| ||| ||||| || |||||||| |||||| | || |||||||  ||     ||| ||| | |  | ||  ||  ||   ||   |||   |   ||   || |   || |  ||  ||| ||   |                                                                   
GTTCTCAGCAACACAATTAAGCAAAAGAGGATGGAAAAGGCTGGCAAATGGGAGGTTCCTTTGCCAAAGgtgattttcaacacaa-actgtttctagtacctggcaatcaatggttttcctaccttga--ctaagcactgtcacaattttcttcctttcag---------------------------------------------------------------

upper sequence: GLYMA10G10000.1 (Glycine max), 5'ss of exon 5
lower sequence: GRMZM2G009876_T01 (Zea mays), 5'ss of exon 5
GTTCTTAGCAACACAATTAAGCAAAAGAGGAAGGAGAAGGCGGGAAAATGGGATGTTCCTCTACCTAAGgtgaaattacgttcaatactttgtgcattatgttaaatgatatcttttgcaatgtgtatcttattgctatttcatgtttgttttatgtttccctgtgaatggaagggagcgaacttggtaattaaatgaatgtatgctttctcatttcttcag
||||| ||||||||||| ||||||||||||||||| ||||| || ||||||||||||||||| || |||||||        |||| ||     ||    |  |   || |    |  |  |  | |  || |  | | | || | |  |                                                                         
GTTCTCAGCAACACAATAAAGCAAAAGAGGAAGGAAAAGGCTGGCAAATGGGATGTTCCTCTGCCAAAGgtga-----ttctcaacacagcacgcccatttctggttgcttcaatgggttagtttttactcacagttttatcctttcag-------------------------------------------------------------------------

upper sequence: GLYMA10G10000.1 (Glycine max), 5'ss of exon 5
lower sequence: GRMZM2G174204_T02 (Zea mays), 5'ss of exon 1
-------------------------------GTTCTTAGCAACACAATTAAGCAAAAGAGGAAGGAGAAGGCGGGAAAATGGGATGTTCCTCTACCTAAGgtgaaattacgttcaatactttgtgcattatgttaaatgatatcttttgcaatgtgtatcttattgctatttcatgtttgttttatgtttccctgtgaatggaagggagcgaacttggtaattaaatgaatgtatgctttctcatttcttcag
                               || || ||||||||||| ||||||||||||||||| ||||| || |||||||||||||| || || ||||||    |  ||  ||| ||     ||  |     | |  |   |  | ||||| ||  | |||| || | || | |  |                                                                         
GCATTGATCACTGATTTCTGGTGAAGCGTAGGTACTCAGCAACACAATCAAGCAAAAGAGGAAGGAAAAGGCTGGCAAATGGGATGTTCCGCTGCCAAAGgtg----tttgtcaaat-ctgaacacagcaaacctatttctggttgattcaatgagttacatatttct-tgtcctttcag-------------------------------------------------------------------------

upper sequence: GLYMA10G10000.1 (Glycine max), 5'ss of exon 5
lower sequence: GRMZM2G174204_T01 (Zea mays), 5'ss of exon 5
GTTCTTAGCAACACAATTAAGCAAAAGAGGAAGGAGAAGGCGGGAAAATGGGATGTTCCTCTACCTAAGgtgaaattacgttcaatactttgtgcattatgttaaatgatatcttttgcaatgtgtatcttattgctatttcatgtttgttttatgtttccctgtgaatggaagggagcgaacttggtaattaaatgaatgtatgctttctcatttcttcag
|| || ||||||||||| ||||||||||||||||| ||||| || |||||||||||||| || || ||||||    |  ||  ||| ||     ||  |     | |  |   |  | ||||| ||  | |||| || | || | |  |                                                                         
GTACTCAGCAACACAATCAAGCAAAAGAGGAAGGAAAAGGCTGGCAAATGGGATGTTCCGCTGCCAAAGgtg----tttgtcaaat-ctgaacacagcaaacctatttctggttgattcaatgagttacatatttct-tgtcctttcag-------------------------------------------------------------------------

upper sequence: GLYMA10G10000.1 (Glycine max), 5'ss of exon 5
lower sequence: AT5G06360.1 (Arabidopsis thaliana), 5'ss of exon 5
GTTCTTAGCAACACAATTAAGCAAAAGAGGAAGGAGAAGGCGGGAAAATGGGATGTTCCTCTACCTAAGgtgaaattacgttcaatactttgtgcattatgttaaatgatatcttttgcaatgtgtatcttattgctatttcatgtttgttttatgtttccctgtgaatggaagggagcgaacttggtaattaaatgaatgtatgctttctcatttcttcag
|||||||||||||| ||||| ||||||||||| ||||| || || |||||||| || ||||| || ||||||||||  |  ||  | |||| || |||   | |     |    | |   |  ||        |   |||  |    |||  |    ||  | |                                                          
GTTCTTAGCAACACCATTAAACAAAAGAGGAAAGAGAAAGCTGGCAAATGGGAGGTCCCTCTTCCAAAGgtgaaatctctctctctgcttt-tgtattccttcagtgtttgaactctaacaaatgggcaaagcttaaattcaagccctgtcct----tttacag----------------------------------------------------------

upper sequence: GLYMA10G10000.1 (Glycine max), 5'ss of exon 5
lower sequence: Vv08s0105g00280.t01 (Vitis vinifera), 5'ss of exon 5
GTTCTTAGCAACACAATTAAGCAAAAGAGGAAGGAGAAGGCGGGAAAATGGGATGTTCCTCTACCTAAGgtgaaattacgttcaatactttgtgcattatgttaaatgatatcttttgcaatgtgtatcttattgctatttcatg---tttgttttatgtttccctgtgaatggaagggagcgaacttggtaattaaatgaatgtatgctttctcatttcttcag
||||||||||| || || |||||||| ||||| ||||| || || |||||||| || |||||||| || || | || || ||  | | | |||    ||| || |    || | ||| || | | | ||| |||    |||| ||   ||| | | ||| | |  |     |                                                     
GTTCTTAGCAATACTATAAAGCAAAAAAGGAAAGAGAAAGCTGGGAAATGGGAAGTCCCTCTACCCAAAgtaagatcacatttgacattgtgt----tat-ttcagcattaaccttttcagtat-tttctgatttgagtttcctgcactttttctaatggtacttttcccttttt--------------------------------------------------

upper sequence: GLYMA10G10000.1 (Glycine max), 5'ss of exon 5
lower sequence: PP1S136_220V6.1 (Physcomitrella patens), 5'ss of exon 5
GTTCTTAGCAACACAATTAAGCAAAAGAGGAAGGAGAAGGCGGGAAAATGGGATGTTCCTCTACCTAAGgtgaaattacgttcaatactttgtgcattatgttaaatgatatcttttgcaatgtgtatcttattgctatttcatgtttgttttatgtttccctgtgaatggaagggagcgaacttggtaattaaatgaatgtatgctttctcatttcttcag
||||| |||||||| || ||||| ||  | ||||||||||| || |||||||| || ||||| ||||||||||    |  |   |    |  || |   ||| |||     ||||    |||             | |  |||  |   || |    | |   ||||| ||| | ||      ||                                     
GTTCTCAGCAACACCATCAAGCAGAAACGTAAGGAGAAGGCTGGTAAATGGGAGGTGCCTCTTCCTAAGgtgagccgatatcgtacgaatgctgtagcttgtgaaac----tcttgaataat----------ccaccacatcacttaaattgtgaagtac---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|298196961|gb|HO041704.1|HO041704
EST:     AGCAAAAGAGGAAGGAGAAGGCGGGAAAATGGGATGTTCCTCTACCTAAG                         GTACGTCCAGTGGCTGAAGATGAAATGTTCAAAGTGGTCCGTACTGGTAAA
genomic: AGCAAAAGAGGAAGGAGAAGGCGGGAAAATGGGATGTTCCTCTACCTAAGgtgaaattac ... atttcttcagGTACGTCCAGTGGCTGAAGATGAAATGTTCAAAGTGGTCCGTACTGGTAAA
EST: gi|9987770|gb|BE661878.1|BE661878
EST:     AGCAAAAGAGGAAGGAGAAGGCGGGAAAATGGGATGTTCCTCTACCTAAG                         GTACGTCCAGTGGCTGAAGATGAAATGTTCAAGGTGGTCCGTACTGGTAAA
genomic: AGCAAAAGAGGAAGGAGAAGGCGGGAAAATGGGATGTTCCTCTACCTAAGgtgaaattac ... atttcttcagGTACGTCCAGTGGCTGAAGATGAAATGTTCAAAGTGGTCCGTACTGGTAAA
EST: gi|15813808|gb|BI786083.1|BI786083
EST:     AGCAAAAGAGGAAGGAGAAGGCGGGAAAATGGGATGTTCCTCTACCTAAG                         GTACGTCCGGTGGCTGAAGATGAAATGTTCAAAGTGGTCCGTACTGGTAAA
genomic: AGCAAAAGAGGAAGGAGAAGGCGGGAAAATGGGATGTTCCTCTACCTAAGgtgaaattac ... atttcttcagGTACGTCCAGTGGCTGAAGATGAAATGTTCAAAGTGGTCCGTACTGGTAAA
EST: gi|208085267|gb|GD884055.1|GD884055
EST:     AGCAAAAGAGGAAGGAGAAGGCGGGAAAATGGGATGTTCCTCTACCTAAG                         GTACGTCCAGTGGCTGAAGATGAAATGTTCAAAGTGGTCCGTACTGGTAAA
genomic: AGCAAAAGAGGAAGGAGAAGGCGGGAAAATGGGATGTTCCTCTACCTAAGgtgaaattac ... atttcttcagGTACGTCCAGTGGCTGAAGATGAAATGTTCAAAGTGGTCCGTACTGGTAAA
EST: gi|14205367|gb|BG839045.1|BG839045
EST:     AGCAAAAGAGGAAGGAGAAGGCGGGAAAATGGGATGTTCCTCTACCTAAG                         GTACGTCCAGTGGCTGAAGATGAAATGTTCAAAGTGGTCCGTACTGGTAAA
genomic: AGCAAAAGAGGAAGGAGAAGGCGGGAAAATGGGATGTTCCTCTACCTAAGgtgaaattac ... atttcttcagGTACGTCCAGTGGCTGAAGATGAAATGTTCAAAGTGGTCCGTACTGGTAAA
EST: gi|208277056|gb|GE077465.1|GE077465
EST:     AGCAAAAGAGGAAGGAGAAGGCGGGAAAATGGGATGTTCCTCTACCTAAG                         GTACGTCCGGTGGCTGAAGAT
genomic: AGCAAAAGAGGAAGGAGAAGGCGGGAAAATGGGATGTTCCTCTACCTAAGgtgaaattac ... atttcttcagGTACGTCCAGTGGCTGAAGAT
EST: gi|151397650|gb|EV267523.1|EV267523
EST:     AGCAAA-GAGGAAGGAGAAGGCGGGAAAATGGGATGTTCCTCTACCTAAG                         GTACGTCCAGTGGCTGAAGATGAAATGTTCAAAGTGGTCCGTACTGGTAAA
genomic: AGCAAAAGAGGAAGGAGAAGGCGGGAAAATGGGATGTTCCTCTACCTAAGgtgaaattac ... atttcttcagGTACGTCCAGTGGCTGAAGATGAAATGTTCAAAGTGGTCCGTACTGGTAAA
EST: gi|151408011|gb|EV277826.1|EV277826
EST:     AGCAAAAGAGGAAGGAGAAGGCGGGAAAATGGGATGTTCCTCTACCTAAG                         GTACGTCCGGTGGCTGAAGATGAAATGTTCAAAGTGGTCCGTACTGGTAAA
genomic: AGCAAAAGAGGAAGGAGAAGGCGGGAAAATGGGATGTTCCTCTACCTAAGgtgaaattac ... atttcttcagGTACGTCCAGTGGCTGAAGATGAAATGTTCAAAGTGGTCCGTACTGGTAAA
EST: gi|24205496|gb|BU964749.1|BU964749
EST:     AGCAAAAGAGGAAGGAGAAGGCGGGAAAATGGGATGTTCCTCTACCTAAG                         GTACGTCCGGTGGCTGAAGATGAAATGTTCAAAGTGGTCCGTACTGGTAAA
genomic: AGCAAAAGAGGAAGGAGAAGGCGGGAAAATGGGATGTTCCTCTACCTAAGgtgaaattac ... atttcttcagGTACGTCCAGTGGCTGAAGATGAAATGTTCAAAGTGGTCCGTACTGGTAAA
EST: gi|298177257|gb|HO023504.1|HO023504
EST:     AGCAAAAGAGGAAGGAGAAGGCGGGAAAATGGGATGTTCCTCTACCTAAG                         GTACGTCCAGTGGCTGAAGATGAAATGTTCAAAGTGGTCCGTACTGGTAAA
genomic: AGCAAAAGAGGAAGGAGAAGGCGGGAAAATGGGATGTTCCTCTACCTAAGgtgaaattac ... atttcttcagGTACGTCCAGTGGCTGAAGATGAAATGTTCAAAGTGGTCCGTACTGGTAAA
EST: gi|14206051|gb|BG839729.1|BG839729
EST:     AGCAAAAGAGGAAGGAGAAGGCGGGAAAATGGGATGTTCCTCTACCTAAG                         GTACGTCCAGTGGCTGAAAGATGAAATGTTCAAAGTGGTCCGTACTGGGTA
genomic: AGCAAAAGAGGAAGGAGAAGGCGGGAAAATGGGATGTTCCTCTACCTAAGgtgaaattac ... atttcttcagGTACGTCCAGTGGCTGAA-GATGAAATGTTCAAAGTGGTCCGTACTGG-TA
EST: gi|9899604|gb|BE608572.1|BE608572
EST:     CGGGAAAATGGGATGTTCCTCTACCTAAG                         GTACGTCCAGTGGCTGAAGATGAAATGTTCAAAGTGGTCCGTACTGGTAAA
genomic: CGGGAAAATGGGATGTTCCTCTACCTAAGgtgaaattac ... atttcttcagGTACGTCCAGTGGCTGAAGATGAAATGTTCAAAGTGGTCCGTACTGGTAAA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTTCTTAGCAACACAATTAAGCAAAAGAGGAAGGAGAAGGCGGGAAAATGGGATGTTCCTCTACCTAAGgtgaaattacgttcaatactttgtgcattatgttaaatgatatcttttgcaatgtgtatcttattgctatttcatgtttgttttatgtttccctgtgaatggaagggagcgaacttggtaattaaatgaatgtatgctttctcatttcttcag

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