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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aggtttcaagatacatatatgtagttaatttttcttcacattcatgtatttccttccaattactaaattctgtgtctaccaattactttattcatggcagGAAATAAAGTGAACAATGTCGATGTTGTTTACACACCCTGGTCTAATTTAAAGAAAACTGCTTCAATGGATGTTGGCCAAGTTGGTTTTCACAACTCAAA

Basic information

species Glycine max
transcript GLYMA04G08530.3
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA04G08530.3 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os05g13440.1 (Oryza sativa), 3'ss of exon 3
aggtttcaaga--tacat-atatgtagttaat-ttttcttcacattcatgtatttccttccaattactaaattctgtgtctacca-attactttattcatggcagGAAATAAAGTGAACAATGTCGATGTTGTTTACACACCCTGGTCTAATTTAAAGAAAACTGCTTCAATGGATGTTGGCCAAGTTGGTTTTCACAACTCAAA
  |||   | |  ||||| |||  |   ||||   |  |||| |    |   ||| ||| |  |   |   |||| ||||   || |||   |||||  |  |||| |||||    || ||  | ||||| ||||| ||||| |||| |||| ||||||| ||| | || |||||||| || |||||||||||||||||||| ||
--gttgggaaaattacatgataattctgtaatacctggttcaaaccttttgttttgctttccctagtttggttctttgtcagacacatttaattattttta-cagGTAATAAGACTAATAACATTGATGTGGTTTATACACCATGGTATAATCTAAAGAAGACTCCATCCATGGATGTGGGTCAAGTTGGTTTTCACAACTCTAA

upper sequence: GLYMA04G08530.3 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G157332_T05 (Zea mays), 3'ss of exon 2
---------------------aggtttcaagatacatatatgtagttaatttttcttcacattcatgtatttccttccaattactaaattctgtgtctaccaattactttattcatgg--cagGAAATAAAGTGAACAATGTCGATGTTGTTTACACACCCTGGTCTAATTTAAAGAAAACTGCTTCAATGGATGTTGGCCAAGTTGGTTTTCACAACTCAAA
                        | | |    ||| || |    || ||||||  |  ||   ||||      | | |  |             | |    ||| ||| |||  |||  |||| |||||||| || ||  | ||||| ||||| || || ||||  ||||| ||||| ||  ||||||||||||| ||||||||||||||||||||| | ||
gttggacaaactacaaagagacaatattatatcacaaattttggcttcattttttcttgcaagaatgtggaa--tacaagctgtagtccggcacatgtgatgatttcttcatttttggtgcagGTAATAAAGTCAATAACATTGATGTAGTTTATACTCCATGGTACAATTTGAAGAAGACCCCTTCAATGGATGTAGGCCAAGTTGGTTTTCACAACCCTAA

upper sequence: GLYMA04G08530.3 (Glycine max), 3'ss of exon 3
lower sequence: AT5G11500.2 (Arabidopsis thaliana), 3'ss of exon 2
-----------------------aggtttcaagatacatatatgtagttaatttttcttcacattcatgtatttcc---------ttccaattactaaattctgtgtc--taccaattacttt-----att-catggcagGAAATAAAGTGAACAATGTCGATGTTGTTTACACACCCTGGTCTAATTTAAAGAAAACTGCTTCAATGGATGTTGGCCAAGTTGGTTTTCACAACTCAAA
                        |   | || ||    |||     ||| | ||     ||     ||| |||             |  ||   |   |||||| |   |||| | |  | |     |||   || |||| || || |||||||| || |||||||| ||||| || ||||| || || ||||||||||| || ||||||||||| ||||||||||| ||||| |||||
gtaatctttttttctacctgtcgtgaacttaacatttgcata-accattagtcttagagtaccagtttgttttttagaaggagggcacatataggttttttctgttttcttaccgactggtgtctgggattatgtgccagGCAACAAGGTGAACAACGTTGATGTTGTGTACACTCCGTGGTCCAACTTGAAGAAAACTGCCTCCATGGATGTTGGTCAAGTTGGTTTCCACAATTCAAA

upper sequence: GLYMA04G08530.3 (Glycine max), 3'ss of exon 3
lower sequence: Vv04s0008g03810.t01 (Vitis vinifera), 3'ss of exon 2
-aggtttcaagatacatatatgtagttaatttttcttcacattcatgtatttccttccaattactaaattctgtgtctaccaattactttattcatggcagGAAATAAAGTGAACAATGTCGATGTTGTTTACACACCCTGGTCTAATTTAAAGAAAACTGCTTCAATGGATGTTGGCCAAGTTGGTTTTCACAACTCAAA
     | ||||   |  |  | |   |  |  || |    |   ||     | | ||||| || | | || | ||  |  || |   |   | ||||||||| || || ||||||||||| || || || ||||| || |||   ||| | |||||||||||||| |||||||||||||||||||||||| |||| |||||
tttcatccaagggtcccacttttttctgctaattttgagtaag-ataatgattcatccaaatagttacttatttggatgacattatttgcttacatggcagGCAACAAGGTGAACAATGTTGACGTCGTATACACTCCATGGCACAATCTGAAGAAAACTGCTTCTATGGATGTTGGCCAAGTTGGTTTTTACAATTCAAA

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|192327626|gb|FK020659.1|FK020659
EST:     GGGTTTACTGGAAGACTGTGCTCAGCTTGTCAAAGCAAATTCAATTCAAG                         GAAATAAAGTGAACAATGTCGATGTTGTTTACACACCCTGGTCTAATTTAA
genomic: GGGTTTACTGGAAGACTGTGCTCAGCTTGTCAAAGCAAATTCAATTCAAGgtaaaagcct ... ttcatggcagGAAATAAAGTGAACAATGTCGATGTTGTTTACACACCCTGGTCTAATTTAA
EST: gi|192331951|gb|FK026735.1|FK026735
EST:     AAAGCAAATTCAATTCAAG                         GAAATAAAGTGAACAATGTCGATGTTGTTTACACACCCTGGTCTAATTTAA
genomic: AAAGCAAATTCAATTCAAGgtaaaagcct ... ttcatggcagGAAATAAAGTGAACAATGTCGATGTTGTTTACACACCCTGGTCTAATTTAA
EST: gi|208250509|gb|GE046930.1|GE046930
EST:     ACTGTGCTCAGCTTGTCAAAGCAAATTCAATTCAAG                         GAAATAAAGTGAACAATGTCGATGTTGTTTACACACCCTGGTCTAATTTAA
genomic: ACTGTGCTCAGCTTGTCAAAGCAAATTCAATTCAAGgtaaaagcct ... ttcatggcagGAAATAAAGTGAACAATGTCGATGTTGTTTACACACCCTGGTCTAATTTAA
EST: gi|18713863|gb|BM522747.1|BM522747
EST:     GGGTTTACTGGAAGACTGTGCTCAGCTTGTCAAAGCAAATTCAATTCAAG                         GAAATAAAGTGAACAATGTCGATGTTGTTTACACACCCTGGTCTAATTTAA
genomic: GGGTTTACTGGAAGACTGTGCTCAGCTTGTCAAAGCAAATTCAATTCAAGgtaaaagcct ... ttcatggcagGAAATAAAGTGAACAATGTCGATGTTGTTTACACACCCTGGTCTAATTTAA
EST: gi|208048593|gb|GD847524.1|GD847524
EST:     ACTGTGCTCAGCTTGTCAAAGCAAATTCAATTCAAG                         GAAATAAAGTGAACAATGTCGATGTTGTTTACACACCCTGGTCTAATTTAA
genomic: ACTGTGCTCAGCTTGTCAAAGCAAATTCAATTCAAGgtaaaagcct ... ttcatggcagGAAATAAAGTGAACAATGTCGATGTTGTTTACACACCCTGGTCTAATTTAA
EST: gi|23725673|gb|BU760799.1|BU760799
EST:     GGGTTTACTGGAAGACTGTGCTCAGCTTGTCAAAGCAAATTCAATTCAAG                         GAAATAAAGTGAACAATGTCGATGTTGTTTACACACCCTGGTCTAATTTAA
genomic: GGGTTTACTGGAAGACTGTGCTCAGCTTGTCAAAGCAAATTCAATTCAAGgtaaaagcct ... ttcatggcagGAAATAAAGTGAACAATGTCGATGTTGTTTACACACCCTGGTCTAATTTAA
EST: gi|192315597|gb|FK007425.1|FK007425
EST:     GGGTTTACTGGAAGACTGTGCTCAGCTTGTCAAAGCAAATTCAATTCAAG                         GAAATAAAGTGAACAATGTCGATGTTGTTTACACACCCTGGTCTAATTTAA
genomic: GGGTTTACTGGAAGACTGTGCTCAGCTTGTCAAAGCAAATTCAATTCAAGgtaaaagcct ... ttcatggcagGAAATAAAGTGAACAATGTCGATGTTGTTTACACACCCTGGTCTAATTTAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtatttccttccaattactaaattctgtgtctaccaattactttattcatggcagGAAATAAAGTGAACAATGTCGATGTTGTTTACACACCCTGGTCTAATTTAAAGAAAACTGCTTCAATGGATGTTGGCCAAGTTGGTTTTCACAACTCAAA
               tactaaa  putative branch site (score: 1)
                                        ctttattc  putative PPT
                                   aattactttattcat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aggtttcaagatacatatatgtagttaatttttcttcacattcatgtatttccttccaattactaaattctgtgtctaccaattactttattcatggcagGAAATAAAGTGAACAATGTCGATGTTGTTTACACACCCTGGTCTAATTTAAAGAAAACTGCTTCAATGGATGTTGGCCAAGTTGGTTTTCACAACTCAAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA