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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatgactgtagtgtgatactcctctgtatgctatgcttattctaaaattttcaacttttctcaatgaagatgaccaactattttttgtgttgtgaccgagttttatgctgatcaactccatcagGGACCTAAGTTTCAAGAGATTGTTAATATTCGCTTGGGAGATGGAACTACTCGGCGTGGACAAGTGCTAGAAGTTGATGGTGAAAAGGCTGTTGTTCAG

Basic information

species Glycine max
transcript GLYMA09G38110.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA09G38110.2 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os06g37180.1 (Oryza sativa), 3'ss of exon 3
gtaatgactgtagtgtgatactcctctgtatgctatgcttattcta-aaattttcaacttttctcaatgaagatgaccaactattttttgtgttgtgaccgagttttatgctgatcaactccatcagGGACCTAAGTTTCAAGAGATTGTTAATATTCGCTTGGGAGATGGAACTACTCGGCGTGGACAAGTGCTAGAAGTTGATGGTGAAAAGGCTGTTGTTCAG
                          |   |||||   ||  |||| |||||||||||       |||   | |  | |  |||  |  |  ||     |    || |||      |||| | |||||| || ||||  || || ||||| || || || ||||||||||| || ||||| ||||| ||||| || |||||||| ||||||||||||||||| |||
-------------------------gtacgtgctactgttcctctacaaattttcaacagact--aatctgg-tagcaagttatactgagcatttctttc----ttcatgt-----aacttcttcagGGCCCAAAGTACCAGGAAATTGTAAACATCCGATTGGGAGATGGCACCACTCGCCGTGGCCAAGTTCTGGAAGTTGACGGTGAAAAGGCTGTTGTGCAG

upper sequence: GLYMA09G38110.2 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G181151_T02 (Zea mays), 3'ss of exon 3
gtaatgactgtagtgtgatactcctctgtatgctatgcttattctaaaattttcaacttttctcaatgaagatgaccaactattttttgtgttgtgaccgagttttatgctgatcaactccatcagGGACCTAAGTTTCAAGAGATTGTTAATATTCGCTTGGGAGATGGAACTACTCGGCGTGGACAAGTGCTAGAAGTTGATGGTGAAAAGGCTGTTGTTCAG
            ||||| |||   | | |    |||| | ||    |   | |  | |||   ||    ||    | | |  | || ||  ||||  |   | ||   ||  ||| | || || |||| || ||||  ||||| ||||| || || ||  | |||||||| || ||||| ||||| ||||| || ||||||||||| ||||| |||||||| |||
------------gtgtg-tacagttttctccaatatgatgataactaccatgtagattttgaacagctcagtctgctagcc-tcttatgctttgttcctttgctt---gcatatcca-tctat-agGGCCCAAAGTACCAAGAAATTGTAAACATCCGACTTGGAGATGGCACCACTCGCCGTGGTCAAGTCCTTGAAGTTGATGGAGAAAAAGCTGTTGTGCAG

upper sequence: GLYMA09G38110.2 (Glycine max), 3'ss of exon 3
lower sequence: AT4G38510.5 (Arabidopsis thaliana), 3'ss of exon 4
gtaatgactgtagtgtgatactcctctgtatgctatgcttattctaaaattttcaacttttctcaatgaagatgaccaactattttttgtgttgtgaccgagttttatgctgatcaactccatcagGGACCTAAGTTTCAAGAGATTGTTAATATTCGCTTGGGAGATGGAACTACTCGGCGTGGACAAGTGCTAGAAGTTGATGGTGAAAAGGCTGTTGTTCAG
                                         |  |    ||| ||   ||||||  | |  |||  |     |    || |||    | ||   | || ||| |   |||    |||| ||||| |  ||||| ||||| ||||| ||  | || ||||||||||| || ||||| ||||| || ||||||||||| || || ||||||||||||
----------------------------------------gtattggtgtttcca-tctttctcttttataatgttc--tcgtcccatgggtttc--ctga---tgatactgctttcctct-ctagGGGCCTAAATACCAAGAAATTGTCAATATCCGTCTTGGGGATGGAACTACCCGACGTGGTCAAGTTCTCGAAGTTGATGGAGAGAAAGCTGTTGTTCAG

upper sequence: GLYMA09G38110.2 (Glycine max), 3'ss of exon 3
lower sequence: Vv03s0038g02760.t01 (Vitis vinifera), 3'ss of exon 3
gtaatgactgtagtgtgatactcctctgtatgctatgcttattctaaaattttcaacttttctcaatgaagatgaccaactattttttgtgttgtgaccgagttttatgctgatcaactccatcagGGACCTAAGTTTCAAGAGATTGTTAATATTCGCTTGGGAGATGGAACTACTCGGCGTGGACAAGTGCTAGAAGTTGATGGTGAAAAGGCTGTTGTTCAG
              ||  | |||   | | |  |||  |||||      |||   | |  | |       |||  ||| || ||     | |  ||| | | |  | | ||    || | || |||||||| || | |||||||||||| |||||||| |||||||||||||| ||||| ||||| ||||| ||||||||||||||||| || || ||||| |||
--------------gtattcctcacttatttagtatttttatttattcctttctgattcatat-------gatttccatctgttcagaatctattgatcaa-tgattttctttctaattgcaccagGGACCCAAATATCAAGAGATTGTCAATATTCGTTTGGGAGATGGAACAACTCGACGTGGTCAAGTCCTAGAAGTTGATGGTGAGAAAGCAGTTGTGCAG

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|209723248|gb|BW675195.1|BW675195
EST:     GAACTGTGTCTGGAGTTGCTGGGCCATTGGTCATTCTTGATAAAGTTAAG                         GGACCTAAGTTTCAAGAGATTGTTAATATTCGCTTGGGAGATGGAACTACT
genomic: GAACTGTGTCTGGAGTTGCTGGGCCATTGGTCATTCTTGATAAAGTTAAGgtaatgactg ... actccatcagGGACCTAAGTTTCAAGAGATTGTTAATATTCGCTTGGGAGATGGAACTACT
EST: gi|298183011|gb|HO028274.1|HO028274
EST:     GAACTGTGTCTGGAGTTGCTGGGCCATTGGTCATTCTTGATAAAGTTAAG                         GGACCTAAGTTTCAAGAGATTGTTAATATTCGCTTGGGAGATGGAACTACT
genomic: GAACTGTGTCTGGAGTTGCTGGGCCATTGGTCATTCTTGATAAAGTTAAGgtaatgactg ... actccatcagGGACCTAAGTTTCAAGAGATTGTTAATATTCGCTTGGGAGATGGAACTACT
EST: gi|213617416|gb|DB965231.1|DB965231
EST:     GAACTGTGTCTGGAGTTGCTGGGCCATTGGTCATTCTTGATAAAGTTAAG                         GGACCTAAGTTTCAAGAGATTGTTAATATTCGCTTGGGAGATGGAACTACT
genomic: GAACTGTGTCTGGAGTTGCTGGGCCATTGGTCATTCTTGATAAAGTTAAGgtaatgactg ... actccatcagGGACCTAAGTTTCAAGAGATTGTTAATATTCGCTTGGGAGATGGAACTACT
EST: gi|6567285|gb|AW234896.1|AW234896
EST:     GAACTGTGTCTGGAGTTGCTGGGCCATTGGTCATTCTTGATAAAGTTAAG                         GGACCTAAGTTTCAAGAGATTGTTAATATTCGCTTGGGAGATGGAACTACT
genomic: GAACTGTGTCTGGAGTTGCTGGGCCATTGGTCATTCTTGATAAAGTTAAGgtaatgactg ... actccatcagGGACCTAAGTTTCAAGAGATTGTTAATATTCGCTTGGGAGATGGAACTACT
EST: gi|5342420|gb|AI794704.1|AI794704
EST:     GAACTGTGTCTGGAGTTGCTGGGCCATTGGTCATTCTTGATAAAGTTAAG                         GGACCTAAGTTTCAAGAGATTGTTAATATTCGCTTGGGAGATGGAACTACT
genomic: GAACTGTGTCTGGAGTTGCTGGGCCATTGGTCATTCTTGATAAAGTTAAGgtaatgactg ... actccatcagGGACCTAAGTTTCAAGAGATTGTTAATATTCGCTTGGGAGATGGAACTACT
EST: gi|213607123|gb|DB967000.1|DB967000
EST:     GAACTGTGTCTGGAGTTGCTGGGCCATTGGTCATTCTTGATAAAGTTAAG                         GGACCTAAGTTTCAAGAGATTGTTAATATTCGCTTGGGAGATGGAACTACT
genomic: GAACTGTGTCTGGAGTTGCTGGGCCATTGGTCATTCTTGATAAAGTTAAGgtaatgactg ... actccatcagGGACCTAAGTTTCAAGAGATTGTTAATATTCGCTTGGGAGATGGAACTACT
EST: gi|10709431|gb|BF009155.1|BF009155
EST:     AACTGTGTCTGGAGTTGCTGGGCCATTGGTCATTCTTGATAAAAGTTAAG                         GGACCTAAGTTTCAAGAGATTGTTAATATTCGCTTGGGAGATGGAACTAC
genomic: AACTGTGTCTGGAGTTGCTGGGCCATTGGTCATTCTTGAT-AAAGTTAAGgtaatgactg ... actccatcagGGACCTAAGTTTCAAGAGATTGTTAATATTCGCTTGGGAGATGGAACTAC
EST: gi|213592755|gb|DB957813.1|DB957813
EST:     GAACTGTGTCTGGAGTTGCTGGGCCATTGGTCATTCTTGATAAAGTTAAG                         GGACCTAAGTTTCAAGAGATTGTTAATATTCGCTTGGGAGATGGAACTACT
genomic: GAACTGTGTCTGGAGTTGCTGGGCCATTGGTCATTCTTGATAAAGTTAAGgtaatgactg ... actccatcagGGACCTAAGTTTCAAGAGATTGTTAATATTCGCTTGGGAGATGGAACTACT
EST: gi|213602215|gb|DB958475.1|DB958475
EST:     GAACTGTGTCTGGAGTTGCTGGGCCATTGGTCATTCTTGATAAAGTTAAG                         GGACCTAAGTTTCAAGAGATTGTTAATATTCGCTTGGGAGATGGAACTACT
genomic: GAACTGTGTCTGGAGTTGCTGGGCCATTGGTCATTCTTGATAAAGTTAAGgtaatgactg ... actccatcagGGACCTAAGTTTCAAGAGATTGTTAATATTCGCTTGGGAGATGGAACTACT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atgaccaactattttttgtgttgtgaccgagttttatgctgatcaactccatcagGGACCTAAGTTTCAAGAGATTGTTAATATTCGCTTGGGAGATGGAACTACTCGGCGTGGACAAGTGCTAGAAGTTGATGGTGAAAAGGCTGTTGTTCAG
                                    tgctgat  putative branch site (score: 3)
                                              ctccatc  putative PPT
      aactatttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaatgactgtagtgtgatactcctctgtatgctatgcttattctaaaattttcaacttttctcaatgaagatgaccaactattttttgtgttgtgaccgagttttatgctgatcaactccatcagGGACCTAAGTTTCAAGAGATTGTTAATATTCGCTTGGGAGATGGAACTACTCGGCGTGGACAAGTGCTAGAAGTTGATGGTGAAAAGGCTGTTGTTCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGTT