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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATCGTAAGAAGCAGCATTCAGACAGAAATGTTTTGCAGTGCTTTGTTTTTGGGCCTAGGAAGGCTGGAAAATCTGCATTATTGAATTCTTTTATTGGAAGgtatttttataatttattttgtgttaccttgaagcttcttggtaatataacttccaacaccatataccttattgttgttgaatcaataatgcag

Basic information

species Glycine max
transcript GLYMA20G37730.2
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA20G37730.1 (Glycine max), 5'ss of exon 9
lower sequence: Vv14s0128g00400.t01 (Vitis vinifera), 5'ss of exon 11
ATCGTAAGAAGCAGCATTCAGACAGAAATGTTTTGCAGTGCTTTGTTTTTGGGCCTAGGAAGGCTGGAAAATCTGCATTATTGAATTCTTTTATTGGAAGgtat-ttttataatttattttgtgttaccttgaagcttctt-ggtaatataacttccaa--caccata-taccttattgttgttgaatcaataatgcag----------------------------
||||||| |||||||| ||||||||||||||||| ||||||||||||||||| ||||   ||||||||||||||| |||||| ||| ||||| | || ||||   | || |  |  || |   |||||  |||    ||||  ||    | |  ||     || | |  ||| | |||  ||| || |  ||  |   |                            
ATCGTAAAAAGCAGCAATCAGACAGAAATGTTTTCCAGTGCTTTGTTTTTGGACCTAAAGAGGCTGGAAAATCTGGATTATTAAATGCTTTTCTGGGGAGgtgcatcttctggtccatatca-gttactctgatttatctttagttgagttatatctggttcatcttggtacttcatttatgt-gagttgattgttatgctataatattccacctgttaaaatgcag

upper sequence: GLYMA20G37730.1 (Glycine max), 5'ss of exon 9
lower sequence: PP1S255_41V6.1 (Physcomitrella patens), 5'ss of exon 10
ATCGTAAGAAGCAGCATTCAGACAGAAATGTTTTGCAGTGCTTTGTTTTTGGGCCTAGGAAGGCTGGAAAATCTGCATTATTGAATTCTTTTATTGGAAGgtat----ttttataatttattttgtgttaccttgaagcttc--ttggtaatataacttccaacaccatataccttattgttgttgaatcaataatgcag------------------------------------------------------------------------------------------------------
|||  || ||||| |  | | |  ||   ||  | ||||||||||||||||| ||||||||  |||||||||||||  | ||| || | || ||||| |||| |    | || |  | ||||||| | |   | | ||||||  ||  || | ||||||       |  ||   ||  |    |   |   | |  |                                                                                                         
ATCAGAAAAAGCAACGATTACAACGAGGGGTCATTCAGTGCTTTGTTTTTGGTCCTAGGAAATCTGGAAAATCTGCTATTTTGGATGCCTTGATTGGCAGgtgtgtcttcttgtgttgtattttgcgat-tgtcgtagcttcagttaatagt-taacttgagttttcgcattattttctcgcatgagagagaaatggtcacctttgtccaggaggtcattatttgtattgtgttcgttcgatttttggcctgacatgctgaattggggactgcgtcttcctgtattttctacaattctccag
















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|208046511|gb|GD849095.1|GD849095
EST:     GGGCCTAGGAAGGCTGGAAAATCTGCATTATTGAATTCTTTTATTGGAAG                         GCCATATTCTGAAAGTTACAATCCAACCACTGAAGATCGTTATG
genomic: GGGCCTAGGAAGGCTGGAAAATCTGCATTATTGAATTCTTTTATTGGAAGgtatttttat ... aataatgcagGCCATATTCTGAAAGTTACAATCCAACCACTGAAGATCGTTATG
EST: gi|208201934|gb|GD997025.1|GD997025
EST:     GGGCCTAGGAAGGCTGGAAAATCTGCATTATTGAATTCTTTTATTGGAAG                         GCCATATTCTGAAAGTTACAATCCAACCACTGAAGATCGTTATGCTGTAAA
genomic: GGGCCTAGGAAGGCTGGAAAATCTGCATTATTGAATTCTTTTATTGGAAGgtatttttat ... aataatgcagGCCATATTCTGAAAGTTACAATCCAACCACTGAAGATCGTTATGCTGTAAA
EST: gi|12773933|gb|BG238860.1|BG238860
EST:     GGGCCTAGGAAGGCTGGAAAATCTGCATTATTGAATTCTTTTATTGGAAG                         GCCATATTCTGAAAGTTACAATCCAACCACTGAAGATCGTTATGCTGTAAA
genomic: GGGCCTAGGAAGGCTGGAAAATCTGCATTATTGAATTCTTTTATTGGAAGgtatttttat ... aataatgcagGCCATATTCTGAAAGTTACAATCCAACCACTGAAGATCGTTATGCTGTAAA
EST: gi|254344505|gb|GR851202.1|GR851202
EST:     GGGCCTAGGAAGGCTGGAAAATCTGCATTATTGAATTCTTTTATTGGAAG                         GCCATATTCTGAAAGTTACAATCCAACCACTGAAGATCGTTATGCTGTAAA
genomic: GGGCCTAGGAAGGCTGGAAAATCTGCATTATTGAATTCTTTTATTGGAAGgtatttttat ... aataatgcagGCCATATTCTGAAAGTTACAATCCAACCACTGAAGATCGTTATGCTGTAAA
EST: gi|298168984|gb|HO020288.1|HO020288
EST:     GGGCCTAGGAAGGCTGGAAAATCTGCATTATTGAATTCTTTTATTGGAAG                         GCCATATTCTGAAAGTTACAATCCAACCACTGAAGATCGTTATGCTGTAAA
genomic: GGGCCTAGGAAGGCTGGAAAATCTGCATTATTGAATTCTTTTATTGGAAGgtatttttat ... aataatgcagGCCATATTCTGAAAGTTACAATCCAACCACTGAAGATCGTTATGCTGTAAA
EST: gi|207696263|gb|GD677772.1|GD677772
EST:     GGGCCTAGGAAGGCTGGAAAATCTGCATTATTGAAT-CTTT-ATTGGAAG                         GCCATATTCTGAAAGTTACAATCCAACCA
genomic: GGGCCTAGGAAGGCTGGAAAATCTGCATTATTGAATTCTTTTATTGGAAGgtatttttat ... aataatgcagGCCATATTCTGAAAGTTACAATCCAACCA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATCGTAAGAAGCAGCATTCAGACAGAAATGTTTTGCAGTGCTTTGTTTTTGGGCCTAGGAAGGCTGGAAAATCTGCATTATTGAATTCTTTTATTGGAAGgtatttttataatttattttgtgttaccttgaagcttcttggtaatataacttccaacaccatataccttattgttgttgaatcaataatgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG