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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CATGTCTATGTCAGGTTGCACAAAGGCCAGACCATCGATGACATGAGTGAGGGTTTACTGGAAGACTGTGCTCAGCTTGTCAAAGCAAATTCAATTCAAGgtaaaagcctgactgattatattcctttggcttattagttttaattgatttaaaagccaattttatatatcattgcaaagctggtaaatagtatgtcacg...

Basic information

species Glycine max
transcript GLYMA04G08530.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA04G08530.3 (Glycine max), 5'ss of exon 3
lower sequence: GRMZM2G157332_T05 (Zea mays), 5'ss of exon 2
CATGTCTATGTCAGGTTGCACAAAGGCCAGACCATCGATGACATGAGTGAGGGTTTACTGGAAGACTGTGCTCAGCTTGTCAAAGCAAATTCAATTCAAGgt-----aaaagcctgactgattatattcctttggcttattagttttaattgatttaaaagccaattttatatatcattgcaaagctggtaaatagtatgtcacg----------------
||||| ||||| || ||| | ||||| ||  | || |||||||||||||||||||| |||||||||||||| |||||||||||||| ||||| |||||||||     |||   |  |  ||  |||||   |       || |  || |||  ||        ||| |   |||  |     |  | || | ||   |||                     
CATGTGTATGTGAGATTGAATAAAGGTCAATCAATGGATGACATGAGTGAGGGTTTGCTGGAAGACTGTGCGCAGCTTGTCAAAGCTAATTCCATTCAAGgttggacaaactacaaagagacaatattatatcacaaattttggcttcattttttcttgcaagaatgtggaatacaagctgtagtccggcacatgtgatgatttcttcatttttggtgcag

upper sequence: GLYMA04G08530.3 (Glycine max), 5'ss of exon 3
lower sequence: AT5G11500.2 (Arabidopsis thaliana), 5'ss of exon 2
CATGTCTATGTCAGGTTGCACAAAGGCCAGACCATCGATGACATGAGTGAGGGTTTACTGGAAGACTGTGCTCAGCTTGTCAAAGCAAATTCAATTCAAGgtaaaagcctgactgattatattcctttggcttattagtttta-----attgatttaaaag--ccaattttatatatcattgcaaagctggtaaatagtatgtcacg------------------------------------
||||| ||  | ||| | || | |||||| |   | |||||||| ||||| ||| | ||||| ||||||||||||||||| ||||| || || |||||||||||    ||   |   ||  |  | |   ||||  | ||  |     |||  | | | ||  ||| |||  | | |    | |  ||   || |  || | |   |                                    
CATGTTTACTTGAGGCTTCATAGAGGCCAAAGTTTTGATGACATTAGTGAAGGTGTGCTGGAGGACTGTGCTCAGCTTGTGAAAGCTAACTCCATTCAAGgtaa---tctttttttctacctgtcgtgaacttaacatttgcataaccattagtcttagagtaccagtttgttttttagaaggagggcacatata-ggttttttctgttttcttaccgactggtgtctgggattatgtgccag

upper sequence: GLYMA04G08530.3 (Glycine max), 5'ss of exon 3
lower sequence: Vv04s0008g03810.t01 (Vitis vinifera), 5'ss of exon 2
CATGTCTATGTCAGGTTGCACAAAGGCCAGACCATCGATGACATGAGTGAGGGTTTACTGGAAGACTGTGCTCAGCTTGTCAAAGCAAATTCAATTCAAGgtaaaagcctgactgattatattcctttggcttattagttttaattgatttaaaagccaattttatatatcattgcaaagctggtaaatagtatgtcacg
||||| ||||| || |||||||| || ||||| || ||||| || ||||| ||||||||||| || ||||||||||||||||||||||| || || ||||| ||||      | || | | ||  | |   || ||| |     ||| ||| |        | ||| ||   |       || | || || | |  | | 
CATGTTTATGTAAGATTGCACAAGGGTCAGACAATTGATGATATAAGTGAAGGTTTACTGGAGGATTGTGCTCAGCTTGTCAAAGCAAACTCCATCCAAGgcaaaatatgctcagactctttttttatttatttttattacattttgttttcacgtatttgtctatttaatctatgtggtctagcaagtattctacctca

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|151406482|gb|EV276297.1|EV276297
EST:     GGGTTTACTGGAAGACTGTGCTCAGCTTGTCAAAGCAAATTCAATTCAAG                         GAAATAAAGTGAACAATGTCGATGTTGTTTACACACCCTGGTCTAATTTAA
genomic: GGGTTTACTGGAAGACTGTGCTCAGCTTGTCAAAGCAAATTCAATTCAAGgtaaaagcct ... ttcatggcagGAAATAAAGTGAACAATGTCGATGTTGTTTACACACCCTGGTCTAATTTAA
EST: gi|192327626|gb|FK020659.1|FK020659
EST:     GGGTTTACTGGAAGACTGTGCTCAGCTTGTCAAAGCAAATTCAATTCAAG                         GAAATAAAGTGAACAATGTCGATGTTGTTTACACACCCTGGTCTAATTTAA
genomic: GGGTTTACTGGAAGACTGTGCTCAGCTTGTCAAAGCAAATTCAATTCAAGgtaaaagcct ... ttcatggcagGAAATAAAGTGAACAATGTCGATGTTGTTTACACACCCTGGTCTAATTTAA
EST: gi|213597525|gb|DB964430.1|DB964430
EST:     GGGTTTACTGGAAGACTGTGCTCAGCTTGTCAAAGCAAATTCAATTCAAG                         GAAATAAAGTGAACAATGTCGATGTTGTTTACACACCCTGGTCTAATTTAA
genomic: GGGTTTACTGGAAGACTGTGCTCAGCTTGTCAAAGCAAATTCAATTCAAGgtaaaagcct ... ttcatggcagGAAATAAAGTGAACAATGTCGATGTTGTTTACACACCCTGGTCTAATTTAA
EST: gi|298178450|gb|HO024185.1|HO024185
EST:     GGGTTTACTGGAAGACTGTGCTCAGCTTGTCAAAGCAAATTCAATTCAAG                         GAAATAAAGTGAACAATGTCGATGTTGTTTACACACCCTGGTCTAATTTAA
genomic: GGGTTTACTGGAAGACTGTGCTCAGCTTGTCAAAGCAAATTCAATTCAAGgtaaaagcct ... ttcatggcagGAAATAAAGTGAACAATGTCGATGTTGTTTACACACCCTGGTCTAATTTAA
EST: gi|298170636|gb|HO019260.1|HO019260
EST:     GGGTTTACTGGAAGACTGTGCTCAGCTTGTCAAAGCAAATTCAATTCAAG                         GAAATAAAGTGAACAATGTCGATGTTGTTTACACACCCTGGTCTAATTTAA
genomic: GGGTTTACTGGAAGACTGTGCTCAGCTTGTCAAAGCAAATTCAATTCAAGgtaaaagcct ... ttcatggcagGAAATAAAGTGAACAATGTCGATGTTGTTTACACACCCTGGTCTAATTTAA
EST: gi|151394888|gb|EV264759.1|EV264759
EST:     GGGTTTACTGGAAGACTGTGCTCAGCTTGTCAAAGCAAATTCAATTCAAG                         GAAATAAAGTGAACAATGTCGATGTTGTTTACACACCCTGGTCTAATTTAA
genomic: GGGTTTACTGGAAGACTGTGCTCAGCTTGTCAAAGCAAATTCAATTCAAGgtaaaagcct ... ttcatggcagGAAATAAAGTGAACAATGTCGATGTTGTTTACACACCCTGGTCTAATTTAA
EST: gi|192331951|gb|FK026735.1|FK026735
EST:     AAAGCAAATTCAATTCAAG                         GAAATAAAGTGAACAATGTCGATGTTGTTTACACACCCTGGTCTAATTTAA
genomic: AAAGCAAATTCAATTCAAGgtaaaagcct ... ttcatggcagGAAATAAAGTGAACAATGTCGATGTTGTTTACACACCCTGGTCTAATTTAA
EST: gi|298178024|gb|HO023873.1|HO023873
EST:     GGGTTTACTGGAAGACTGTGCTCAGCTTGTCAAAGCAAATTCAATTCAAG                         GAAATAAAGTGAACAATGTCGATGTTGTTTACACACCCTGGTCTAA
genomic: GGGTTTACTGGAAGACTGTGCTCAGCTTGTCAAAGCAAATTCAATTCAAGgtaaaagcct ... ttcatggcagGAAATAAAGTGAACAATGTCGATGTTGTTTACACACCCTGGTCTAA
EST: gi|14011293|gb|BG726224.1|BG726224
EST:     GGGTTTACTGGAAGACTGTGCTCAGCTTGTCAAAGCAAATTCAATTCAAG                         GAAATAAAGTGAACAATGTCGATGTTGTTTACACACCCTGGTCTAATTTAA
genomic: GGGTTTACTGGAAGACTGTGCTCAGCTTGTCAAAGCAAATTCAATTCAAGgtaaaagcct ... ttcatggcagGAAATAAAGTGAACAATGTCGATGTTGTTTACACACCCTGGTCTAATTTAA
EST: gi|192327625|gb|FK020658.1|FK020658
EST:     GGGTTTACTGGAAGACTGTGCTCAGCTTGTCAAAGCAAATTCAATTCAAG                         GAAATAAAGTGAACAATGTCGATGTTGTTTACACACCCTGGTCTAATTTAA
genomic: GGGTTTACTGGAAGACTGTGCTCAGCTTGTCAAAGCAAATTCAATTCAAGgtaaaagcct ... ttcatggcagGAAATAAAGTGAACAATGTCGATGTTGTTTACACACCCTGGTCTAATTTAA
EST: gi|298185114|gb|HO030327.1|HO030327
EST:     GGGTTTACTGGAAGACTGTGCTCAGCTTGTCAAAGCAAATTCAATTCAAG                         GAAATAAAGTGAACAATGTCGATGTTGTTTACACACCCTGGTCTAATTTAA
genomic: GGGTTTACTGGAAGACTGTGCTCAGCTTGTCAAAGCAAATTCAATTCAAGgtaaaagcct ... ttcatggcagGAAATAAAGTGAACAATGTCGATGTTGTTTACACACCCTGGTCTAATTTAA
EST: gi|17518633|gb|BM187675.1|BM187675
EST:     GGGTTTACTGGAAGACTGTGCTCAGCTTGTCAAAGCAAATTCAATTCAAG                         GAAATAAAGTGAACAATGTCGATGTTGTTTACACACCCTGGTCTAATTTAA
genomic: GGGTTTACTGGAAGACTGTGCTCAGCTTGTCAAAGCAAATTCAATTCAAGgtaaaagcct ... ttcatggcagGAAATAAAGTGAACAATGTCGATGTTGTTTACACACCCTGGTCTAATTTAA
EST: gi|208250509|gb|GE046930.1|GE046930
EST:     ACTGTGCTCAGCTTGTCAAAGCAAATTCAATTCAAG                         GAAATAAAGTGAACAATGTCGATGTTGTTTACACACCCTGGTCTAATTTAA
genomic: ACTGTGCTCAGCTTGTCAAAGCAAATTCAATTCAAGgtaaaagcct ... ttcatggcagGAAATAAAGTGAACAATGTCGATGTTGTTTACACACCCTGGTCTAATTTAA
EST: gi|298182837|gb|HO031572.1|HO031572
EST:     GGGTTTACAGGAAGACTGTGCTCAGCTTGTCAAAGCAGATTCAATTCGAG                         GAAATAAAGTGAACAATGTCGATGTTGTTTACACACCCTGGTCTAATTTAA
genomic: GGGTTTACTGGAAGACTGTGCTCAGCTTGTCAAAGCAAATTCAATTCAAGgtaaaagcct ... ttcatggcagGAAATAAAGTGAACAATGTCGATGTTGTTTACACACCCTGGTCTAATTTAA
EST: gi|192303639|gb|FG994533.1|FG994533
EST:     GGGTTTACTGGAAGACTGTGCTCAGCTTGTCAAAGCAAATTCAATTCAAG                         GAAATAAAGTGAACAATGTCGATGTTGTTTACACACCCTGGTCTAATTTAA
genomic: GGGTTTACTGGAAGACTGTGCTCAGCTTGTCAAAGCAAATTCAATTCAAGgtaaaagcct ... ttcatggcagGAAATAAAGTGAACAATGTCGATGTTGTTTACACACCCTGGTCTAATTTAA
EST: gi|151412807|gb|EV282619.1|EV282619
EST:     GGGTTTACTGGAAGACTGTGCTCAGCTTGTCAAAGCAAATTCAATTCAAG                         GAAATAAAGTGAACAATGTCGATGTTGTTTACACACCCTGGTCTAATTTAA
genomic: GGGTTTACTGGAAGACTGTGCTCAGCTTGTCAAAGCAAATTCAATTCAAGgtaaaagcct ... ttcatggcagGAAATAAAGTGAACAATGTCGATGTTGTTTACACACCCTGGTCTAATTTAA
EST: gi|208048593|gb|GD847524.1|GD847524
EST:     ACTGTGCTCAGCTTGTCAAAGCAAATTCAATTCAAG                         GAAATAAAGTGAACAATGTCGATGTTGTTTACACACCCTGGTCTAATTTAA
genomic: ACTGTGCTCAGCTTGTCAAAGCAAATTCAATTCAAGgtaaaagcct ... ttcatggcagGAAATAAAGTGAACAATGTCGATGTTGTTTACACACCCTGGTCTAATTTAA
EST: gi|192299132|gb|FG992878.1|FG992878
EST:     GGGTTTACTGGAAGACTGTGCTCAGCTTGTCAAAGCAAATTCAATTCAAG                         GAAATAAAGTGAACAATGTCGATGTTGTTTACACACCCTGGTCTAATTTAA
genomic: GGGTTTACTGGAAGACTGTGCTCAGCTTGTCAAAGCAAATTCAATTCAAGgtaaaagcct ... ttcatggcagGAAATAAAGTGAACAATGTCGATGTTGTTTACACACCCTGGTCTAATTTAA
EST: gi|298191108|gb|HO038587.1|HO038587
EST:     GGGTTTACTGGAAGACTGTGCTCAGCTTGTCAAAGCAAATTCAATTCAAG                         GAAATAAAGTGAACAATGTCGATGTTGTTTACACACCCTGGTCTAATTTAA
genomic: GGGTTTACTGGAAGACTGTGCTCAGCTTGTCAAAGCAAATTCAATTCAAGgtaaaagcct ... ttcatggcagGAAATAAAGTGAACAATGTCGATGTTGTTTACACACCCTGGTCTAATTTAA
EST: gi|8282557|gb|BE020118.1|BE020118
EST:     GGGTTTACTGGAAGACTGTGCTCAGCTTGTCAAAGCAAATTCAATTCAAG                         GAAATAAAGTGAACAATGTCGATGTTGTTTACACACCCTGGTCTAATTTAA
genomic: GGGTTTACTGGAAGACTGTGCTCAGCTTGTCAAAGCAAATTCAATTCAAGgtaaaagcct ... ttcatggcagGAAATAAAGTGAACAATGTCGATGTTGTTTACACACCCTGGTCTAATTTAA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CATGTCTATGTCAGGTTGCACAAAGGCCAGACCATCGATGACATGAGTGAGGGTTTACTGGAAGACTGTGCTCAGCTTGTCAAAGCAAATTCAATTCAAGgtaaaagcctgactgattatattcctttggcttattagttttaattgatttaaaagccaattttatatatcattgcaaagctggtaaatagtatgtcacg

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA