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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ccaataaataccatggacttttctataatagaccgtgcctagaatctatgtatatgtttattaattgttttgatttggttttctcctgaaaatgttgtagGTTCTTGCCGTGAAGAAGATAGATTCATCTGTCCTTCCCAATGATATGTCTGATGATTTTGTAGAACTGGTTTCAAACATATCCCAATTGCATCATCCCA

Basic information

species Glycine max
transcript GLYMA07G05230.1
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA07G05230.1 (Glycine max), 3'ss of exon 11
lower sequence: Vv09s0002g00150.t01 (Vitis vinifera), 3'ss of exon 11
--ccaata--aataccatggacttttctataatagaccgtgcctagaatctatgtatatgtttattaattgttttgatttggttttctcctgaaaatgttgtagGTTCTTGCCGTGAAGAAGATAGATTCATCTGTCCTTCCCAATGATATGTCTGATGATTTTGTAGAACTGGTTTCAAACATATCCCAATTGCATCATCCCA
  | || |   ||  || | | ||   |  |||  |  |  | |  |   | | ||| |||||| ||      || |     |||     ||  ||||||||||||| |||| || ||||| |||||||||||||  || ||| || |  | ||||| |||||   |||  | || || || || ||||| |||||||| || |
accgaacattgatgtcaagcaattga-tggaattaaaagaccatttaggttgtttatttgtttaatatcatccttaa---aatttctctttgccaatgttgtagGTTGTTGCTGTCAAGAAAATAGATTCATCTGCTCTCCCCGATCAATTTTCTGAAGATTTCACAGAGATAGTATCTAATATCTCCCAGTTGCATCACCCAA
















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|7686042|gb|AW756690.1|AW756690
EST:     GTGAGGGGTCTTTTGGACGTGTATACCGTGCTCAATTTGATGAGGGAAAG                         GTTCTTGCCGTGAAGAAGATAGATTCATCTGTCCTTCCCAATGATATGTCT
genomic: GTGAGGGGTCTTTTGGACGTGTATACCGTGCTCAATTTGATGAGGGAAAGgtattcctta ... aatgttgtagGTTCTTGCCGTGAAGAAGATAGATTCATCTGTCCTTCCCAATGATATGTCT
EST: gi|7685767|gb|AW756415.1|AW756415
EST:     GTGAGGGGTCTTTTGGACGTGTATACCGTGCTCAATTTGATGAGGGAAAG                         GTTCTTGCCGTGAAGAAGATAGATTCATCTGTCCTTCCCAATGATATGTCT
genomic: GTGAGGGGTCTTTTGGACGTGTATACCGTGCTCAATTTGATGAGGGAAAGgtattcctta ... aatgttgtagGTTCTTGCCGTGAAGAAGATAGATTCATCTGTCCTTCCCAATGATATGTCT
EST: gi|208313277|gb|GE110933.1|GE110933
EST:     GTGAGGGGTCTTTTGGACGTGTATACCGTGCTCAATTTGATGAGGGAAAG                         GTTCTTGCCGTGAAGAAGATAGATTCATCTGTCCTTCCCAATGATATGTCT
genomic: GTGAGGGGTCTTTTGGACGTGTATACCGTGCTCAATTTGATGAGGGAAAGgtattcctta ... aatgttgtagGTTCTTGCCGTGAAGAAGATAGATTCATCTGTCCTTCCCAATGATATGTCT
EST: gi|10709647|gb|BF009371.1|BF009371
EST:     CTCAATTTGATGAGGGAAAG                         GTTCTTGCCGTGAAGAAGATAGATTCATCTGTCCTTCCCAATGATATGTCT
genomic: CTCAATTTGATGAGGGAAAGgtattcctta ... aatgttgtagGTTCTTGCCGTGAAGAAGATAGATTCATCTGTCCTTCCCAATGATATGTCT
EST: gi|22540779|gb|BU090630.1|BU090630
EST:     GTGAGGGGTCTTTTGGACGTGTATACCGTGCTCAATTTGATGAGGGAAAG                         GTTCTTGCCGTGAAGAAGATAGATTCATCTGTCCTTCCCAATGATATGTCT
genomic: GTGAGGGGTCTTTTGGACGTGTATACCGTGCTCAATTTGATGAGGGAAAGgtattcctta ... aatgttgtagGTTCTTGCCGTGAAGAAGATAGATTCATCTGTCCTTCCCAATGATATGTCT
EST: gi|23734067|gb|BU765250.1|BU765250
EST:     GTGAGGGGTCTTTTGGACGTGTATACCGTGCTCAATTTGATGAGGGAAAG                         GTTCTTGCCGTGAAGAAGATAGATTCATCTGTCCTTCCCAATGATATGTCT
genomic: GTGAGGGGTCTTTTGGACGTGTATACCGTGCTCAATTTGATGAGGGAAAGgtattcctta ... aatgttgtagGTTCTTGCCGTGAAGAAGATAGATTCATCTGTCCTTCCCAATGATATGTCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctatgtatatgtttattaattgttttgatttggttttctcctgaaaatgttgtagGTTCTTGCCGTGAAGAAGATAGATTCATCTGTCCTTCCCAATGATATGTCTGATGATTTTGTAGAACTGGTTTCAAACATATCCCAATTGCATCATCCCA
     tatatgtttattaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ccaataaataccatggacttttctataatagaccgtgcctagaatctatgtatatgtttattaattgttttgatttggttttctcctgaaaatgttgtagGTTCTTGCCGTGAAGAAGATAGATTCATCTGTCCTTCCCAATGATATGTCTGATGATTTTGTAGAACTGGTTTCAAACATATCCCAATTGCATCATCCCA

ccaataaa
- - - - - -catggac
- - - - - - - - - - - - - - - - ccgtgcc
- - - - - - - - - - - - - - - - - - - - - - -ctatgta
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgttttg