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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CACCAGAAGCAAATGCTTCAACAGAGAGCATTTATAATGCTGCATTGGCTCTAGGCATTGCAAATCAACTTACTAACATACTCAGAGATGTTGGAGAGGAgtaagtttctttgaacacttcaatgtcatgcaattaaaccaaaaaaagtaaagaaatgacatttgaaatcatgccactcaagggtatctcaccccataac...

Basic information

species Glycine max
transcript GLYMA02G45270.1
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA02G45270.1 (Glycine max), 5'ss of exon 4
lower sequence: Vv12s0028g00960.t01 (Vitis vinifera), 5'ss of exon 4
CACCAGAAGCAAATGCTTCAACAGAGAGCATTTATAATGCTGCATTGGCTCTAGGCATTGCAAATCAACTTACTAACATACTCAGAGATGTTGGAGAGGAgtaagtttctttgaacacttcaatgtcatgcaattaaaccaaaaaaagtaaagaaatgacatttgaaatcatgcc-actcaagggtatctcaccccataac-----
|||||||  |||| || |||||||||||  |||| ||||||||||| || || || || || ||||| || |||||||||||||||||||| || ||||||||||||||||   |  |   ||| ||     | | ||| |  || |  ||   |||    | | |  |  |     ||| | | ||  |||  |  |||      
CACCAGATTCAAAGGCCTCAACAGAGAGTGTTTACAATGCTGCATTAGCCCTTGGGATAGCCAATCAGCTCACTAACATACTCAGAGATGTCGGGGAGGAgtaagtttcttatgatgcagaaatctc----cactgaactaggaagaaaaattcaattctttgtcatgttttctttgctccaagataa-tcattc-gtaattgggg
















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|208324971|gb|GE124869.1|GE124869
EST:     CTAGGCATTGCAAATCAACTTACTAACATACTCAGAGATGTTGGAGAGGA                         TGCTAGAAGAGGAAGAGTATATCTCCCACAAGATGAATTGGCACTAGCTGG
genomic: CTAGGCATTGCAAATCAACTTACTAACATACTCAGAGATGTTGGAGAGGAgtaagtttct ... atcattatagTGCTAGAAGAGGAAGAGTATATCTCCCACAAGATGAATTGGCACTAGCTGG
EST: gi|193570413|gb|FK524924.1|FK524924
EST:     CAAATCAACTTACTAACATACTCAGAGATGTTGGAGAGGA                         TGCTAGAAGAGGAAGAGTATATCTCCCAACAAGATGAATTGGCACTAGCTG
genomic: CAAATCAACTTACTAACATACTCAGAGATGTTGGAGAGGAgtaagtttct ... atcattatagTGCTAGAAGAGGAAGAGTATATCTCCC-ACAAGATGAATTGGCACTAGCTG
EST: gi|193353707|gb|FK320301.1|FK320301
EST:     CTAGGCATTGCAAATCAACTTACTAACATACTCAGAGATGTTGGAGAGGA                         TGCTAGAAGAGGAAGAGTATATCTCCCACAAGATGAAATGGCACTAGCTGG
genomic: CTAGGCATTGCAAATCAACTTACTAACATACTCAGAGATGTTGGAGAGGAgtaagtttct ... atcattatagTGCTAGAAGAGGAAGAGTATATCTCCCACAAGATGAATTGGCACTAGCTGG

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
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---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CACCAGAAGCAAATGCTTCAACAGAGAGCATTTATAATGCTGCATTGGCTCTAGGCATTGCAAATCAACTTACTAACATACTCAGAGATGTTGGAGAGGAgtaagtttctttgaacacttcaatgtcatgcaattaaaccaaaaaaagtaaagaaatgacatttgaaatcatgccactcaagggtatctcaccccataac

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaaaaaag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - taaagaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctcaccc