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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCATATAACTCGTGGTGAGTATGATGAAGAGACGAAATATCCGGAGACCAAAACACTAACCATTGGCCAATTTAAGCTGGGACTATGCCATGGCCATCAGgtctgattttgactctgatattatttgccctgtttttttttcttaaatggacctaagaaaattgggagcgtggatgaatcataacgaaattacctttgat...

Basic information

species Glycine max
transcript GLYMA14G05340.2
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA14G05340.2 (Glycine max), 5'ss of exon 3
lower sequence: GRMZM2G068489_T02 (Zea mays), 5'ss of exon 1
GCATATAACTCGTGGTGAGTATGATGAAGAGACGAAATATCCGGAGACCAAAACACTAACCATTGGCCAATTTAAGCTGGGACTATGCCATGGCCATCAGgtctgattttgactctgatattatttgccctgtttttttttcttaaatggac-ctaagaaaattgggagcgtggatgaatcataacgaaattacctttgat
 ||||| ||  | |||||  ||||||| ||  |   ||| || ||||| || ||||| || ||||| || |||||||| || || ||||||||||||||||| || ||||||||| || | | | |     | |      | |||  |  |  |  |    | |   |   |   |  |      |    | ||     | 
CCATATTACCAGAGGTGAACATGATGAGGATGCTCGATACCCAGAGACTAAGACACTTACAATTGGTCAGTTTAAGCTTGGGCTGTGCCATGGCCATCAGgtttgtttttgactcagaaaatgtataggaggctaggagctattagtttcatgcccatggtaataataatatttttacaggtgctccttgtcacacaaaa-

upper sequence: GLYMA14G05340.2 (Glycine max), 5'ss of exon 3
lower sequence: Vv17s0000g05880.t01 (Vitis vinifera), 5'ss of exon 2
GCATATAACTCGTGGTGAGTATGATGAAGAGACGAAATATCCGGAGACCAAAACACTAACCATTGGCCAATTTAAGCTGGGACTATGCCATGGCCATCAGgtctgattttgactctgatattatttgccctgtttttttttcttaaatggacctaagaaaattgggagcgtggatgaatcataacgaaattacctttgat---------
|||||| || || ||||| |||||||| |||||    || || |||||||||||||| |||||||| ||||| ||||| |||||||||||||| ||||||||   ||||| | ||      |||| ||    | |||| ||  | | |  |  |  |   ||            | || |||  ||| |||      |||         
GCATATTACCCGAGGTGAATATGATGAGGAGACACGTTACCCAGAGACCAAAACACTTACCATTGGTCAATTCAAGCTTGGACTATGCCATGGTCATCAGgttcaattttcattcc----ctattggc---atcttttcttgatgattacaaatccgtgcatgtttcttacaagtaaaacat--cgagattctacaggatatagatgga
















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|10238098|gb|BE806986.1|BE806986
EST:     AAACACTAACCATTGGCCAATTTAAGCTGGGACTATGCCATGGCCATCAG                         GTTATTCCATGGGGAGACCTAGACTCGCTGGCAATGCTACAGAGGCAGCTT
genomic: AAACACTAACCATTGGCCAATTTAAGCTGGGACTATGCCATGGCCATCAGgtctgatttt ... ggttgtgaagGTTATTCCATGGGGAGACCTAGACTCGCTGGCAATGCTACAGAGGCAGCTT
EST: gi|193706244|gb|FK645784.1|FK645784
EST:     AAACACTAACCATTGGCCAATTTAAGCTGGGACTATGCCATGGCCATCAG                         GTTATTCCATGGGGAGACCTAGACTCGCTGGCAATGCTACAGAGGCAGCTT
genomic: AAACACTAACCATTGGCCAATTTAAGCTGGGACTATGCCATGGCCATCAGgtctgatttt ... ggttgtgaagGTTATTCCATGGGGAGACCTAGACTCGCTGGCAATGCTACAGAGGCAGCTT
EST: gi|193596969|gb|FK549159.1|FK549159
EST:     GCTGGGACTATGCCATGGCCATCAG                         GTTATTCCATGGGGAGACCTAGACTCGCTAGCAATGCTACAGAGGCAGCTT
genomic: GCTGGGACTATGCCATGGCCATCAGgtctgatttt ... ggttgtgaagGTTATTCCATGGGGAGACCTAGACTCGCTGGCAATGCTACAGAGGCAGCTT
EST: gi|208120523|gb|GD918876.1|GD918876
EST:     AAACACTAACCATTGGCCAACTTAAGCTGGGACTATGCCATGGCCATCAG                         GTTATTCCATGGGGAGACCTAGACTCGCTGGCAATGCTACAGAGGCAGCTT
genomic: AAACACTAACCATTGGCCAATTTAAGCTGGGACTATGCCATGGCCATCAGgtctgatttt ... ggttgtgaagGTTATTCCATGGGGAGACCTAGACTCGCTGGCAATGCTACAGAGGCAGCTT
EST: gi|209726980|gb|BW680299.1|BW680299
EST:     AAACACTAACCATTGGCCAATTTAAGCTGGGACTATGCCATGGCCATCAG                         GTTATTCCATGGGGAGACCTAGACTCGCTGGCAATGCTACAGAGGCAGCTT
genomic: AAACACTAACCATTGGCCAATTTAAGCTGGGACTATGCCATGGCCATCAGgtctgatttt ... ggttgtgaagGTTATTCCATGGGGAGACCTAGACTCGCTGGCAATGCTACAGAGGCAGCTT
EST: gi|193381454|gb|FK347507.1|FK347507
EST:     GCTGGGACTATGCCATGGCCATCAG                         GTTATTCCATGGGGAGACCTAGACTCGCTGGCAATGCTACAGAGGCAGCTT
genomic: GCTGGGACTATGCCATGGCCATCAGgtctgatttt ... ggttgtgaagGTTATTCCATGGGGAGACCTAGACTCGCTGGCAATGCTACAGAGGCAGCTT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCATATAACTCGTGGTGAGTATGATGAAGAGACGAAATATCCGGAGACCAAAACACTAACCATTGGCCAATTTAAGCTGGGACTATGCCATGGCCATCAGgtctgattttgactctgatattatttgccctgtttttttttcttaaatggacctaagaaaattgggagcgtggatgaatcataacgaaattacctttgat

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