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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTTGCAAAAACCCCGTCGACGGCTTCTCTGCCGGTTTGGTCGATGAAACCAACATTTTCGAATGGAGTGTCACCATAATTGGACCGCCCGATACTCTTTAgtaagccccttttgattaatatatcatgcttttgcttttgccactctgacggaattttttttctgtgattctcgattcaaagtttggatttttgggtttt...

Basic information

species Glycine max
transcript GLYMA12G06960.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA12G06960.1 (Glycine max), 5'ss of exon 2
lower sequence: Vv06s0004g04430.t01 (Vitis vinifera), 5'ss of exon 2
TTTGCAAAAACCCCGTCGACGGCTTCTCTGCCGGTTTGGTCGATGAAACCAACATTTTCGAATGGAGTGTCACCATAATTGGACCGCCCGATACTCTTTAgtaagc--cccttttgattaatatatcatgctt-ttgcttttgccactctgacggaattttttttctgtgattc-tcgattcaaagtttggatttttgggtttt
|||| ||||||||||| || |||||||| |||||||||||||| || | ||| || || ||||||||||||||||| |||||||| ||||||||||| ||||| |    ||  |   ||  | |    ||  | |||  |       | ||    |  ||||  |||| ||    | |  |||| |||  ||||   | |  | 
TTTGTAAAAACCCCGTTGATGGCTTCTCCGCCGGTTTGGTCGACGAGAGCAATATCTTTGAATGGAGTGTCACCATTATTGGACCTCCCGATACTCTGTAgtacgtgttccaatctctttttttgctttgaatgttgtgtactttgttatgttttaggttttactctgggaaggattggatcaaggttgagatt---gtgcct-
















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|298170658|gb|HO019282.1|HO019282
EST:     AACATTTTCGAATGGAGTGTCACCATAATTGGACCGCCCGATACTCTTTA                         CGAGGGGGGATTTTTCAATGCTATTATGAGTTTCCCATCCAATTACCCAAA
genomic: AACATTTTCGAATGGAGTGTCACCATAATTGGACCGCCCGATACTCTTTAgtaagcccct ... tttctcatagCGAGGGGGGATTTTTCAATGCTATTATGAGTTTCCCATCCAATTACCCAAA
EST: gi|27425977|gb|CA937497.1|CA937497
EST:     AACATTTTCGAATGGAGTGTCACCATAATTGGACCGCCCGATACTCTTTA                         CGAGGGGGGATTTTTCAATGCTATTATGAGTTTCCCATCCAATTACCCAAA
genomic: AACATTTTCGAATGGAGTGTCACCATAATTGGACCGCCCGATACTCTTTAgtaagcccct ... tttctcatagCGAGGGGGGATTTTTCAATGCTATTATGAGTTTCCCATCCAATTACCCAAA
EST: gi|209702411|gb|BW656387.1|BW656387
EST:     AACATTTTCGAATGGAGTGTCACCATAATTGGACCGCCCGATACTCTTTA                         CGAGGGGGGATTTTTCAATGCTATTATGAGTTTCCCATCCAATTACCCAAA
genomic: AACATTTTCGAATGGAGTGTCACCATAATTGGACCGCCCGATACTCTTTAgtaagcccct ... tttctcatagCGAGGGGGGATTTTTCAATGCTATTATGAGTTTCCCATCCAATTACCCAAA
EST: gi|17022209|gb|BM093243.1|BM093243
EST:     AACATTTTCGAATGGAGTGTCACCATAATTGGACCGCCCGATACTCTTTA                         CGAGGGGGGATTTTTCAATGCTATTATGAGTTTCCCATCCAATTACCCAAA
genomic: AACATTTTCGAATGGAGTGTCACCATAATTGGACCGCCCGATACTCTTTAgtaagcccct ... tttctcatagCGAGGGGGGATTTTTCAATGCTATTATGAGTTTCCCATCCAATTACCCAAA
EST: gi|15337487|gb|BI498143.1|BI498143
EST:     AACATTTTCGAATGGAGTGTCACCATAATTGGACCGCCCGATACTCTTTA                         CGAGGGGGGATTTTTCAATGCTATTATGAGTTTCCCATCCAATTACCCAAA
genomic: AACATTTTCGAATGGAGTGTCACCATAATTGGACCGCCCGATACTCTTTAgtaagcccct ... tttctcatagCGAGGGGGGATTTTTCAATGCTATTATGAGTTTCCCATCCAATTACCCAAA
EST: gi|27426740|gb|CA938260.1|CA938260
EST:     AACATTTTCGAATGGAGTGTCACCATAATTGGACCGCCCGATACTCTTTA                         CGAGGGGGGATTTTTCAATGCTATTATGAGTTTCCCATCCAATTACCCAAA
genomic: AACATTTTCGAATGGAGTGTCACCATAATTGGACCGCCCGATACTCTTTAgtaagcccct ... tttctcatagCGAGGGGGGATTTTTCAATGCTATTATGAGTTTCCCATCCAATTACCCAAA
EST: gi|151400067|gb|EV269881.1|EV269881
EST:     AACATTTTCGAATGGAGTGTCACCATAATTGGACCGCCCGATACTCTTTA                         CGAGGGGGGATTTTTCAATGCTATTATGAGTTTCCCATCCAATTACCCAAA
genomic: AACATTTTCGAATGGAGTGTCACCATAATTGGACCGCCCGATACTCTTTAgtaagcccct ... tttctcatagCGAGGGGGGATTTTTCAATGCTATTATGAGTTTCCCATCCAATTACCCAAA
EST: gi|13252164|gb|BG363067.1|BG363067
EST:     AACATTTTCGAATGGAGTGTCACCATAATTGGACCGCCCGATACTCTTTA                         CGAGGGGGGATTTTTCAATGCTATTATGAGTTTCCCATCCAATTACCCAAA
genomic: AACATTTTCGAATGGAGTGTCACCATAATTGGACCGCCCGATACTCTTTAgtaagcccct ... tttctcatagCGAGGGGGGATTTTTCAATGCTATTATGAGTTTCCCATCCAATTACCCAAA
EST: gi|33389826|gb|CA853033.1|CA853033
EST:     AACATTTTCGAATGGAGTGTCACCATAATTGGACCGCCCGATACTCTTTA                         CGAGGGGGGATTTTTCAATGCTATTATGAGTTTCCCATCCAATTACCCAAA
genomic: AACATTTTCGAATGGAGTGTCACCATAATTGGACCGCCCGATACTCTTTAgtaagcccct ... tttctcatagCGAGGGGGGATTTTTCAATGCTATTATGAGTTTCCCATCCAATTACCCAAA
EST: gi|298173257|gb|HO020241.1|HO020241
EST:     AACATTTTCGAATGGAGTGTCACCATAATTGGACCGCCCGATACTCTTTA                         CGAGGGGGGATTTTTCAATGCTATTATGAGTTTCCCATCCAATTACCCAAA
genomic: AACATTTTCGAATGGAGTGTCACCATAATTGGACCGCCCGATACTCTTTAgtaagcccct ... tttctcatagCGAGGGGGGATTTTTCAATGCTATTATGAGTTTCCCATCCAATTACCCAAA
EST: gi|151397271|gb|EV267144.1|EV267144
EST:     AACATTTTCGAATGGAGTGTCACCATAATTGGACCGCCCGATACTCTTTA                         CGAGGGGGGATTTTTCAATGCTATTATGAGTTTCCCATCCAATTACCCAAA
genomic: AACATTTTCGAATGGAGTGTCACCATAATTGGACCGCCCGATACTCTTTAgtaagcccct ... tttctcatagCGAGGGGGGATTTTTCAATGCTATTATGAGTTTCCCATCCAATTACCCAAA
EST: gi|33387309|gb|CA850516.1|CA850516
EST:     AACATTTTCGAATGGAGTGTCACCATAATTGGACCGCCCGATACTCTTTA                         CGAGGGGGGATTTTTCAATGCTATTATGAGTTTCCCATCCAATTACCCAAA
genomic: AACATTTTCGAATGGAGTGTCACCATAATTGGACCGCCCGATACTCTTTAgtaagcccct ... tttctcatagCGAGGGGGGATTTTTCAATGCTATTATGAGTTTCCCATCCAATTACCCAAA
EST: gi|14259958|gb|BG882866.1|BG882866
EST:     AACATTTTCGAATGGAGTGTCACCATAATTGGACCGCCCGATACTCTTTA                         CGAGGGGGGATTTTTCAATGCTATTATGAGTTTCCCATCCAATTACCCAAA
genomic: AACATTTTCGAATGGAGTGTCACCATAATTGGACCGCCCGATACTCTTTAgtaagcccct ... tttctcatagCGAGGGGGGATTTTTCAATGCTATTATGAGTTTCCCATCCAATTACCCAAA
EST: gi|19268884|gb|BM885140.1|BM885140
EST:     AACATTTTCGAATGGAGTGTCACCATAATTGGACCGCCCGATACTCTTTA                         CGAGGGGGGATTTTTCAATGCTATTATGAGTTTCCCATCCAATTACCCAAA
genomic: AACATTTTCGAATGGAGTGTCACCATAATTGGACCGCCCGATACTCTTTAgtaagcccct ... tttctcatagCGAGGGGGGATTTTTCAATGCTATTATGAGTTTCCCATCCAATTACCCAAA
EST: gi|208062016|gb|GD856804.1|GD856804
EST:     AACATTTTCGAATGGAGTGTCACCATAATTGGACCGCCCGATACTCTTTA                         CGAGGGGGGATTTTT
genomic: AACATTTTCGAATGGAGTGTCACCATAATTGGACCGCCCGATACTCTTTAgtaagcccct ... tttctcatagCGAGGGGGGATTTTT
EST: gi|20498658|gb|BQ273588.1|BQ273588
EST:     AACATTTTCGAATGGAGTGTCACCATAATTGGACCGCCCGATACTCTTTA                         CGAGGGGGGATTTTTCAATGCTATTATGAGTTTCCCATCCAATTACCCAAA
genomic: AACATTTTCGAATGGAGTGTCACCATAATTGGACCGCCCGATACTCTTTAgtaagcccct ... tttctcatagCGAGGGGGGATTTTTCAATGCTATTATGAGTTTCCCATCCAATTACCCAAA
EST: gi|298182923|gb|HO028136.1|HO028136
EST:     AACATTTTCGAATGGAGTGTCACCATAATTGGACCGCCCGATACTCTTTA                         CGAGGGGGGATTTTTCAATGCTATTATGAGTTTCCCATCCAATTACCCAAA
genomic: AACATTTTCGAATGGAGTGTCACCATAATTGGACCGCCCGATACTCTTTAgtaagcccct ... tttctcatagCGAGGGGGGATTTTTCAATGCTATTATGAGTTTCCCATCCAATTACCCAAA
EST: gi|20498754|gb|BQ273684.1|BQ273684
EST:     AACATTTTCGAATGGAGTGTCACCATAATTGGACCGCCCGATACTCTTTA                         CGAGGGGGGATTTTTCAATGCTATTATGAGTTTCCCATCCAATTACCCAAA
genomic: AACATTTTCGAATGGAGTGTCACCATAATTGGACCGCCCGATACTCTTTAgtaagcccct ... tttctcatagCGAGGGGGGATTTTTCAATGCTATTATGAGTTTCCCATCCAATTACCCAAA
EST: gi|209704114|gb|BW673714.1|BW673714
EST:     AACATTTTCGAATGGAGTGTCACCATAATTGGACCGCCCGATACTCTTTA                         CGAGGGGGGATTTTTCAATGCTATTATGAGTTTCCCATCCAATTACCCAAA
genomic: AACATTTTCGAATGGAGTGTCACCATAATTGGACCGCCCGATACTCTTTAgtaagcccct ... tttctcatagCGAGGGGGGATTTTTCAATGCTATTATGAGTTTCCCATCCAATTACCCAAA
EST: gi|209702412|gb|BW656388.1|BW656388
EST:     AACATTTTCGAATGGAGTGTCACCATAATTGGACCGCCCGATACTCTTTA                         CGAGGGGGGATTTTTCAATGCTATTATGAGTTTCCCATCCAATTACCCAAA
genomic: AACATTTTCGAATGGAGTGTCACCATAATTGGACCGCCCGATACTCTTTAgtaagcccct ... tttctcatagCGAGGGGGGATTTTTCAATGCTATTATGAGTTTCCCATCCAATTACCCAAA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTTGCAAAAACCCCGTCGACGGCTTCTCTGCCGGTTTGGTCGATGAAACCAACATTTTCGAATGGAGTGTCACCATAATTGGACCGCCCGATACTCTTTAgtaagccccttttgattaatatatcatgcttttgcttttgccactctgacggaattttttttctgtgattctcgattcaaagtttggatttttgggtttt

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