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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...attttattttgttttaatgatcttttatagcacttgagtttttagttttactgaccactctcggctttcttattttgtcaattttttgaatttcgtgtagTGAGGGGGGATTTTTCAATGCCATTATGAGCTTTCCACCCAACTACCCAAATAGTCCGCCATCAGTGAAATTTACCTCAGAGTTATGGCATCCCAATG

Basic information

species Glycine max
transcript GLYMA15G04470.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA15G04470.2 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G085600_T03 (Zea mays), 3'ss of exon 2
attttattttgttttaatgatctt---ttatagcacttgagtttttagttttactgaccactctcggctttcttattttgtcaattttttgaatttcgtgtagTGAGGGGGGATTTTTCAATGCCATTATGAGCTTTCCACCCAACTACCCAAATAGTCCGCCATCAGTGAAATTTACCTCAGAGTTATGGCATCCCAATG
   | || |  || || | |||||     || ||| |   |   | |  |  |  |  |  | |     |||| |      || |  |    |     || ||||| || || |  |||||||| || |||||||| ||||  || |||||||| || ||||||||||| | ||||||||| ||  | |||||||| ||||
---tgatgtccttgtatttatcttgaagcattgcattcatgcagtcatgtaaatagtactttatttatcttctgaccaacacactaataaccaaactttgcagTGATGGAGGGTACTTCAATGCAATAATGAGCTTCCCACAAAATTACCCAAACAGCCCGCCATCAGTCAGATTTACCTCTGAAATGTGGCATCCAAATG

upper sequence: GLYMA15G04470.2 (Glycine max), 3'ss of exon 2
lower sequence: Vv06s0004g04430.t01 (Vitis vinifera), 3'ss of exon 2
attttattttgttttaatgatcttttatagcacttgagtttttagttttactgaccactctcggctttcttattttgtcaattttttgaatttcg--tgtagTGAGGGGGGATTTTTCAATGCCATTATGAGCTTTCCACCCAACTACCCAAATAGTCCGCCATCAGTGAAATTTACCTCAGAGTTATGGCATCCCAATG
|    |||  | |  |||||   | | |     ||    ||   |  | |   |    |     |    || | |||   |||   |||| |  |  || ||||| |||||||||||||||||||| ||||||||||||||||| || || || ||||| ||| ||||||| ||||| |||||  | |||||||||||||
acacaattaggct--aatgacactattttttgttttcaattaaggcataaagcatggattgtttcccaattgtgttgattattcactgaaatatgactgcagTGATGGGGGATTTTTCAATGCCATCATGAGCTTTCCACCCAATTATCCGAACAGTCCTCCAACAGTGAAGTTTACTTCAGAAGTGTGGCATCCCAATG
















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|151408087|gb|EV277895.1|EV277895
EST:     AACATTTTTGAATGGAGTGTAACTATAATTGGACCTCCCGATACTCTTTA                         TGAGGGGGGATTTTTCAATGCCATTATGAGCTTTCCACCCAACTACCCAAA
genomic: AACATTTTTGAATGGAGTGTAACTATAATTGGACCTCCCGATACTCTTTAgtaagctgtg ... tttcgtgtagTGAGGGGGGATTTTTCAATGCCATTATGAGCTTTCCACCCAACTACCCAAA
EST: gi|192330036|gb|FK020852.1|FK020852
EST:     TGTAACTATAATTGGACCTCCCGATACTCTTTA                         TGAGGGGGGATTTTTCAATGCCATTATGAGCTTTCCACCCAACTACCCAAA
genomic: TGTAACTATAATTGGACCTCCCGATACTCTTTAgtaagctgtg ... tttcgtgtagTGAGGGGGGATTTTTCAATGCCATTATGAGCTTTCCACCCAACTACCCAAA
EST: gi|16996926|gb|BM086298.1|BM086298
EST:     AACATTTTTGAATGGAGTGTAACTATAATTGGACCTCCCGATACTCTTTA                         TGAGGGGGGATTTTTCAATGCCATTATGAGCTTTCCACCCAACTACCCAAA
genomic: AACATTTTTGAATGGAGTGTAACTATAATTGGACCTCCCGATACTCTTTAgtaagctgtg ... tttcgtgtagTGAGGGGGGATTTTTCAATGCCATTATGAGCTTTCCACCCAACTACCCAAA
EST: gi|192331436|gb|FK019909.1|FK019909
EST:     AACATTTTTGAATGGAGTGTAACTATAATTGGACCTCCCGATACTCTTTA                         TGAGGGGGGATTTTTCAATGCCATTATGAGCTTTCCACCCAACTACCCAAA
genomic: AACATTTTTGAATGGAGTGTAACTATAATTGGACCTCCCGATACTCTTTAgtaagctgtg ... tttcgtgtagTGAGGGGGGATTTTTCAATGCCATTATGAGCTTTCCACCCAACTACCCAAA
EST: gi|5688311|gb|AI941326.1|AI941326
EST:     AACATTTTTGAATGGAGTGTAACTATAATTGGACCTCCCGATACTCTTTA                         TGAGGGGGGATTTTTCAATGCCATTATGAGCTTTCCACCCAACTACCCAAA
genomic: AACATTTTTGAATGGAGTGTAACTATAATTGGACCTCCCGATACTCTTTAgtaagctgtg ... tttcgtgtagTGAGGGGGGATTTTTCAATGCCATTATGAGCTTTCCACCCAACTACCCAAA
EST: gi|192330035|gb|FK020851.1|FK020851
EST:     AACATTTTTGAATGGAGTGTAACTATAATTGGACCTCCCGATACTCTTTA                         TGAGGGGGGATTTTTCAATGCCATTATGAGCTTTCCACCCAACTACCCAAA
genomic: AACATTTTTGAATGGAGTGTAACTATAATTGGACCTCCCGATACTCTTTAgtaagctgtg ... tttcgtgtagTGAGGGGGGATTTTTCAATGCCATTATGAGCTTTCCACCCAACTACCCAAA
EST: gi|18732524|gb|BM527091.1|BM527091
EST:     AACATTTTTGAATGGAGTGTAACTATAATTGGACCTCCCGATACTCTTTA                         TGAGGGGGGATTTTTCAATGCCATTATGAGCTTTCCACCCAACTACCCAAA
genomic: AACATTTTTGAATGGAGTGTAACTATAATTGGACCTCCCGATACTCTTTAgtaagctgtg ... tttcgtgtagTGAGGGGGGATTTTTCAATGCCATTATGAGCTTTCCACCCAACTACCCAAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttactgaccactctcggctttcttattttgtcaattttttgaatttcgtgtagTGAGGGGGGATTTTTCAATGCCATTATGAGCTTTCCACCCAACTACCCAAATAGTCCGCCATCAGTGAAATTTACCTCAGAGTTATGGCATCCCAATG
   tactgac  putative branch site (score: 1)
                    tttcttattttgtcaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
attttattttgttttaatgatcttttatagcacttgagtttttagttttactgaccactctcggctttcttattttgtcaattttttgaatttcgtgtagTGAGGGGGGATTTTTCAATGCCATTATGAGCTTTCCACCCAACTACCCAAATAGTCCGCCATCAGTGAAATTTACCTCAGAGTTATGGCATCCCAATG

- - - - - - - - - - - - - - - cacttga
- - - - - - - - - - - - - - - - - - - - - - - - - -tgaccac