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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cagggtgaaacttactctgcctcgtatcagcgtgtgagtttttatcttttctcctcctcctatatttacataccatatgtctgtgacctttttttaacagAGGGCAGGGAAAAATATTTTGAACAATACGGAGAATATAAGATCCATAAGATTTGGCGGGATGATGTTTTCCCATGCCGTGTTTATCTTCGTCACTG

Basic information

species Glycine max
transcript GLYMA07G37370.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA07G37370.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv05s0077g01810.t01 (Vitis vinifera), 3'ss of exon 6
cagggtgaaacttactctgcc-tcgtatcagcgtgtgagtttttatcttttctcctcctcctatatttacataccatatgtctgtgaccttttttta-acagAGGGCAGGGAAAAATATTTTGAACAATACGGAGAATATAAGATCCATAAGATTTGGCGGGATGATGTTTTCCCATGCCGTGTTTATCTTCGTCACTG
     || | || ||||   | | | |   |     | ||  || |   ||    ||| |  || ||    |        | ||  | ||  ||| | |||| | ||| ||| |  | |||||| ||||| ||   |||||| ||||| ||||||||||| |||||||| ||||| ||||||||||||||||| |||||
tgtactgcagctgactcgatcattggacttgttaaggggtcattttgaatttctttccac--atgttcttctcttgctaatttgctagctactttcatacagGGAGCAAGGAGATGTTTTTTGAGCAATATGGGCGATATAACATCCACAAGATTTGGCGAGATGATGTCTTCCCTTGCCGTGTTTATCTTCGGCACTG

upper sequence: GLYMA07G37370.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv05s0077g01800.t01 (Vitis vinifera), 3'ss of exon 6
cagggtgaaacttactctgcctcgta-tcagcgtgtgagtttttatcttttctcctcctcctatatttacatac-catatgtctgtgaccttttttta-acagAGGGCAGGGAAAAATATTTTGAACAATACGGAGAATATAAGATCCATAAGATTTGGCGGGATGATGTTTTCCCATGCCGTGTTTATCTTCGTCACTG
     |     ||    | | | ||| ||    |  |  |||    ||| ||         ||    | ||| | ||||| | | |   ||  | |||  |||   | | ||| | ||||||| | ||||| ||     |||| ||||||||||||||||| ||||||||||| || ||||||||||||||||| |||||
---tttttttttttaattcctttgtactctttttccgcctttgctgcttgtcattgaaatgtaggaatgcattctcatatatttttttgctactattatgcagGAAGTAAGGAGATATATTTTCAGCAATATGGCCGCCATAACATCCATAAGATTTGGCGAGATGATGTTTTACCTTGCCGTGTTTATCTTCGACACTG
















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|254333784|gb|GR848702.1|GR848702
EST:     TCTCTGTGCTTCTTACACTGATGAGGAATTCTTTAAATTTAGATGCAGTG                         AGGGCAGGGAAAAATATTTTGAACAATACGGAGAATATAAGATCCATAAGA
genomic: TCTCTGTGCTTCTTACACTGATGAGGAATTCTTTAAATTTAGATGCAGTGgtaatgttac ... tttttaacagAGGGCAGGGAAAAATATTTTGAACAATACGGAGAATATAAGATCCATAAGA
EST: gi|7691086|gb|AW759220.1|AW759220
EST:     TCTCTGTGCTTCTTACACTGATGAGGAATTCTTTAAATTTAGATGCAGTG                         AGGGCAGGGAAAAATATTTTGAACAATACGGAGAATATAAGATCCATAAGA
genomic: TCTCTGTGCTTCTTACACTGATGAGGAATTCTTTAAATTTAGATGCAGTGgtaatgttac ... tttttaacagAGGGCAGGGAAAAATATTTTGAACAATACGGAGAATATAAGATCCATAAGA
EST: gi|209728568|gb|BW663568.1|BW663568
EST:     TCTCTGTGCTTCTTACACTGATGAGGAATTCTTTAAATTTAGATGCAGTG                         AGGGCAGGGAAAAATATTTTGAACAATACGGAGAATATAAGATCCATAAGA
genomic: TCTCTGTGCTTCTTACACTGATGAGGAATTCTTTAAATTTAGATGCAGTGgtaatgttac ... tttttaacagAGGGCAGGGAAAAATATTTTGAACAATACGGAGAATATAAGATCCATAAGA
EST: gi|254333783|gb|GR848701.1|GR848701
EST:     TCTCTGTGCTTCTTACACTGATGAGGAATTCTTTAAATTTAGATGCAGTG                         AGGGCAGGGAAAAATATTTTGAACAATACGGAGAATATAAGATCCATAAGA
genomic: TCTCTGTGCTTCTTACACTGATGAGGAATTCTTTAAATTTAGATGCAGTGgtaatgttac ... tttttaacagAGGGCAGGGAAAAATATTTTGAACAATACGGAGAATATAAGATCCATAAGA
EST: gi|22541783|gb|BU091626.1|BU091626
EST:     TCTCTGTGCTTCTTACACTGATGAGGAATTCTTTAAATTTAGATGCAGTG                         AGGGCATGGAACAATATTTTGAACAATACGGAGAATATAAGATCCATAAG
genomic: TCTCTGTGCTTCTTACACTGATGAGGAATTCTTTAAATTTAGATGCAGTGgtaatgttac ... tttttaacagAGGGCAGGGAAAAATATTTTGAACAATACGGAGAATATAAGATCCATAAG
EST: gi|10231639|gb|BE800527.1|BE800527
EST:     TCTCTGTGCTTCTTACACTGATGAGGAATTCTTTAAATGTAGATGCAGTG                         AGGGCAGGGAAAAATATTTTGAACA
genomic: TCTCTGTGCTTCTTACACTGATGAGGAATTCTTTAAATTTAGATGCAGTGgtaatgttac ... tttttaacagAGGGCAGGGAAAAATATTTTGAACA
EST: gi|21888794|gb|BQ742007.1|BQ742007
EST:     TCTCTGTGCTTCTTACACTGATGAGGAATTCTTTAAATTTAGATGCAGTG                         AGGGCAGGGAAAAATATTTTGAACAATACGGAGAA
genomic: TCTCTGTGCTTCTTACACTGATGAGGAATTCTTTAAATTTAGATGCAGTGgtaatgttac ... tttttaacagAGGGCAGGGAAAAATATTTTGAACAATACGGAGAA
EST: gi|6482218|gb|AW201489.1|AW201489
EST:     TCTCTGTGCTTCTTACACTGATGAGGAATTCTTTAAATTTAGATGCAGTG                         AGGGCAGGGAAAAATATTTTGAACAATACCGAGAATATAAGATCCATAAGA
genomic: TCTCTGTGCTTCTTACACTGATGAGGAATTCTTTAAATTTAGATGCAGTGgtaatgttac ... tttttaacagAGGGCAGGGAAAAATATTTTGAACAATACGGAGAATATAAGATCCATAAGA
EST: gi|192300324|gb|FG988801.1|FG988801
EST:     TCTCTGTGCTTCTTACACTGATGAGGAATTCTTTAAATTTAGATGCAGTG                         AGGGCAGGGAAAAATATTTTGAACAATACGGAGAATATAAGATCCATAAGA
genomic: TCTCTGTGCTTCTTACACTGATGAGGAATTCTTTAAATTTAGATGCAGTGgtaatgttac ... tttttaacagAGGGCAGGGAAAAATATTTTGAACAATACGGAGAATATAAGATCCATAAGA
EST: gi|192323856|gb|FK015637.1|FK015637
EST:     TCTCTGTGCTTCTTACACTGATGAGGAATTCTTTAAATTTAGATGCAGTG                         AGGGCAGGGAAAAATATTTTGAACAATACGGAGAATATAAGATCCATAAGA
genomic: TCTCTGTGCTTCTTACACTGATGAGGAATTCTTTAAATTTAGATGCAGTGgtaatgttac ... tttttaacagAGGGCAGGGAAAAATATTTTGAACAATACGGAGAATATAAGATCCATAAGA
EST: gi|4298808|gb|AI442814.1|AI442814
EST:     CTCTGTGCTTCTTACACTGATGAGNG-ATTCTTTAAATTTAGATGCAGTG                         AGGGCAGGGAAAAATATTTTGAACAATACGGAGAATAT-AGATCCATAAGA
genomic: CTCTGTGCTTCTTACACTGATGAG-GAATTCTTTAAATTTAGATGCAGTGgtaatgttac ... tttttaacagAGGGCAGGGAAAAATATTTTGAACAATACGGAGAATATAAGATCCATAAGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttttctcctcctcctatatttacataccatatgtctgtgacctttttttaacagAGGGCAGGGAAAAATATTTTGAACAATACGGAGAATATAAGATCCATAAGATTTGGCGGGATGATGTTTTCCCATGCCGTGTTTATCTTCGTCACTG
                                         ccttttttt  CT-rich tract
               tatatttacata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cagggtgaaacttactctgcctcgtatcagcgtgtgagtttttatcttttctcctcctcctatatttacataccatatgtctgtgacctttttttaacagAGGGCAGGGAAAAATATTTTGAACAATACGGAGAATATAAGATCCATAAGATTTGGCGGGATGATGTTTTCCCATGCCGTGTTTATCTTCGTCACTG

- gggtgaa
- - - - - - - ctctgcc
- - - - - - - - - - - - - - -gcgtgtg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gtctgtg