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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGAAATGCTTTATGGGTATACGCCATTCCGGGGGAAAACAAGACAAAAAACATTTGCAAATATTCTTCACAAGGACCTTAAATTTCCCAAAAGTAAACCGgtgagtgttatccttcctaacttatcatacatttgttgcttacaggttgctttgctacagcttaattttcaattttgatctgagttatgaaattcacctt...

Basic information

species Glycine max
transcript GLYMA13G40550.1
intron # 20
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA13G40550.1 (Glycine max), 5'ss of exon 20
lower sequence: GRMZM2G001457_T01 (Zea mays), 5'ss of exon 2
TGAAATGCTTTATGGGTATACGCCATTCCGGGGGAAAACAAGACAAAAAACATTTGCAAATATTCTTCACAAGGACCTTAAATTTCCCAAAAGTAAACCGgtgagtgttatccttcctaacttatcatacatttgttgcttacaggttgctttgctacagcttaattttcaattttgatctgagttatgaaattcacctt
||| ||| | ||||| ||||| || ||| | ||||||||||||||||  |||||||| |||||||| ||||||||  | | ||||||    || | || ||| |   | |       ||   ||  |       |||| |  ||  |   | |  |  |   ||  | | |||| |                        
TGAGATGTTATATGGTTATACACCGTTCAGAGGGAAAACAAGACAAAGGACATTTGCTAATATTCTGCACAAGGATATCAGATTTCCTGCGAGCATACAGgtaataataaaaacatttattctagtaggtgagcgttg-tggcaaatgtttgtaatgta---tatatgttaattgtag----------------------

upper sequence: GLYMA13G40550.1 (Glycine max), 5'ss of exon 20
lower sequence: Vv06s0004g03700.t01 (Vitis vinifera), 5'ss of exon 21
TGAAATGCTTTATGGGTATACGCCATTCCGGGGGAAAACAAGACAAAAAACATTTGCAAATATTCTTCACAAGGACCTTAAATTTCCCAAAAGTAAACCGgtgagtgttatccttcctaacttatcatacatttgttgcttacaggttgcttt-gctacagcttaattttcaattttgatctgagttatgaaattcacctt-----
||||||||||||||| ||||| |||||  |||| || ||||| ||||| |||||||| || ||||||||||| || |||||||||||   ||||| | |||||||   | | || | ||  || ||||   ||| |   ||  |  |  |||    ||   | ||    |||| |    |     || |    |||| |||     
TGAAATGCTTTATGGATATACACCATTTAGGGGAAAGACAAGGCAAAAGACATTTGCCAACATTCTTCACAAAGATCTTAAATTTCCATCAAGTATATCGgtgaga--tcttctacatatgttgtcatttttttttcctttttatttcacttccagtaattcatatgaatcaaatgcccttgacattct----ttcatcttaaaat
















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|208243984|gb|GE037941.1|GE037941
EST:     CCCAAAAGTAAACCG                         GTAAGTCTCCAGGGAAAGCAGCTAATTTACTGGTTGTTGCAGAGAGATCCA
genomic: CCCAAAAGTAAACCGgtgagtgtta ... attgatgcagGTAAGTCTCCAGGGAAAGCAGCTAATTTACTGGTTGTTGCAGAGAGATCCT
EST: gi|19270595|gb|BM886851.1|BM886851
EST:     CATTTGCAAATATTCTTCACAAGGACCTTAAATTTCCCAAAAGTAAACCG                         GTAAGTCTCCAGGGAAAGCAGCTAATTTACTGGTTGTTGCAGAGAGATCCT
genomic: CATTTGCAAATATTCTTCACAAGGACCTTAAATTTCCCAAAAGTAAACCGgtgagtgtta ... attgatgcagGTAAGTCTCCAGGGAAAGCAGCTAATTTACTGGTTGTTGCAGAGAGATCCT
EST: gi|208228595|gb|GE023665.1|GE023665
EST:     CATTTGCAAATATTCTTCACAAGGATCTTAAATTTCCCAAAAGTAAACCG                         GTAAGTCTCCAGGGAAAGCAGCTAATTTACTGGTTGTTGCAGAGAGAT
genomic: CATTTGCAAATATTCTTCACAAGGACCTTAAATTTCCCAAAAGTAAACCGgtgagtgtta ... attgatgcagGTAAGTCTCCAGGGAAAGCAGCTAATTTACTGGTTGTTGCAGAGAGAT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGAAATGCTTTATGGGTATACGCCATTCCGGGGGAAAACAAGACAAAAAACATTTGCAAATATTCTTCACAAGGACCTTAAATTTCCCAAAAGTAAACCGgtgagtgttatccttcctaacttatcatacatttgttgcttacaggttgctttgctacagcttaattttcaattttgatctgagttatgaaattcacctt

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ccttcct