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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTGCAACATTGGCGAGGGAGGTATTGCACTTGCTGAGGCTGTACATGGTTCGGCACCTGATATTGCTGGAAAGgtaagctgtgaaagtactcattttaccttatattatccggcctaaaccttcttgtgccctgttgtcatggaatgtgaattttttcaagagattgtttcat...

Basic information

species Glycine max
transcript GLYMA13G20790.1
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA13G20790.1 (Glycine max), 5'ss of exon 6
lower sequence: AT3G09810.1 (Arabidopsis thaliana), 5'ss of exon 6
CTGCAACATTGGCGAGGGAGGTATTGCACTTGCTGAGGCTGTACATGGTTCGGCACCTGATATTGCTGGAAAGgtaagctgtgaaagtactcattttaccttatattatccggcctaaaccttcttgtgccctg--ttgtcatggaat-gtgaattttttcaagagatt--gtttcat---
    || ||||| ||||  |||||||| |||||||| ||||| || || || ||||||||||||||||||| ||| ||   | |         | |||  |  ||| |||   |  ||  | | |  |||   |  ||||  |  | | || || || ||  ||  | |  | || |    
TATGAATATTGGGGAGGATGGTATTGCCCTTGCTGAAGCTGTTCACGGCTCTGCACCTGATATTGCTGGAATGgttagtcatcat--------tcttagatgttatcatcgttctaaattcgtttgatgcatagagttgttgttaacttgttaaattattagagtaaataggatttagaca

upper sequence: GLYMA13G20790.1 (Glycine max), 5'ss of exon 6
lower sequence: Vv08s0040g01700.t01 (Vitis vinifera), 5'ss of exon 6
CTGCAACATTGGCGAGGGAGGTATTGCACTTGCTGAGGCTGTACATGGTTCGGCACCTGATATTGCTGGAAAGgtaagctgtgaaagtactcattttaccttatattatccggcctaaaccttcttgtgccctgttgtcatggaatgtgaattttttcaagagattgtttcat--
|||||| ||||| |||||||||||||| |||||||| || || |||||||| ||||| ||||||||||||||||| ||     ||||      | | |  || |  | ||  |   |  | | | | ||   || |        |||    | | ||||  |  ||  |||||  
CTGCAATATTGGAGAGGGAGGTATTGCTCTTGCTGAAGCCGTTCATGGTTCTGCACCAGATATTGCTGGAAAGgttagtcactaaagctactgtatgatttt-tggtctcgtgttcactcatgcct-tgtgttgctacatatccatgcatctatgttcattaacttcattcatgc
















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|209702313|gb|BW667501.1|BW667501
EST:     TTGCACTTGCTGAGGCTGTACATGGTTCGGCACCTGATATTGCTGGAAAG                         AATTTGGCAAATCCAACTGCTTTACTGCTAAGTGGTGTTACAATGTTGCGC
genomic: TTGCACTTGCTGAGGCTGTACATGGTTCGGCACCTGATATTGCTGGAAAGgtaagctgtg ... gtatatgtagAATTTGGCAAATCCAACTGCTTTACTGCTAAGTGGTGTTACAATGTTGCGC
EST: gi|22928996|gb|BU546135.1|BU546135
EST:     TTGCACTTGCTGAGGCTGTACATNNNTCGGCACCTGATATTGCTGGAAAG                         AATTTGGCAAATCCAACTGCTTTACTGCTAAGTGGTGTTACAATGTTGCGC
genomic: TTGCACTTGCTGAGGCTGTACATGGTTCGGCACCTGATATTGCTGGAAAGgtaagctgtg ... gtatatgtagAATTTGGCAAATCCAACTGCTTTACTGCTAAGTGGTGTTACAATGTTGCGC
EST: gi|151406995|gb|EV276810.1|EV276810
EST:     CTGCACTTGCTGAGGCTGTACATGGTTCGGCACCTGATATTGCTGGAAAG                         AATTTGGCAAATCCAACTGCTTTACTGCTAAGTGGTGTTACAATGTTGCGC
genomic: TTGCACTTGCTGAGGCTGTACATGGTTCGGCACCTGATATTGCTGGAAAGgtaagctgtg ... gtatatgtagAATTTGGCAAATCCAACTGCTTTACTGCTAAGTGGTGTTACAATGTTGCGC
EST: gi|21677612|gb|BQ629963.1|BQ629963
EST:     TTGCACTTGCTGAGGCTGTACATGGTTCGGCACCTGATATTGCTGGAAAG                         AATTTGGCAAATCCAACTGCTTTACTGCTAAGTGGTGTTACAATGTTGCGC
genomic: TTGCACTTGCTGAGGCTGTACATGGTTCGGCACCTGATATTGCTGGAAAGgtaagctgtg ... gtatatgtagAATTTGGCAAATCCAACTGCTTTACTGCTAAGTGGTGTTACAATGTTGCGC
EST: gi|254321137|gb|GR827586.1|GR827586
EST:     TTGCACTTGCTGAGGCTGTACATGGTTCGGCACCTGATATTGCTGGAAAG                         AATTTGGCAAATCCAACTGCTTTACTGCTAAGTGGTGTTACAATGTTGCGC
genomic: TTGCACTTGCTGAGGCTGTACATGGTTCGGCACCTGATATTGCTGGAAAGgtaagctgtg ... gtatatgtagAATTTGGCAAATCCAACTGCTTTACTGCTAAGTGGTGTTACAATGTTGCGC
EST: gi|22930892|gb|BU548031.1|BU548031
EST:     TTGCACTTGCTGAGGCTGTACATGGTTCGGCACCTGATATTGCTGGAAAG                         AATTTGGCAAATCCAACTGCTTTACTGCTAAGTGGTGTTACAATGTTGCGC
genomic: TTGCACTTGCTGAGGCTGTACATGGTTCGGCACCTGATATTGCTGGAAAGgtaagctgtg ... gtatatgtagAATTTGGCAAATCCAACTGCTTTACTGCTAAGTGGTGTTACAATGTTGCGC
EST: gi|213612273|gb|DB976850.1|DB976850
EST:     GCACTTG-TGAAGGCTGTACATGTTTCTGTTA-CTGATATTGCTGGAAAG                         AATTTGGCAAATCCAACTGCTTTACTGCTAAGTGGTGTTACAATGTTGCGC
genomic: GCACTTGCTG-AGGCTGTACATGGTTC-GGCACCTGATATTGCTGGAAAGgtaagctgtg ... gtatatgtagAATTTGGCAAATCCAACTGCTTTACTGCTAAGTGGTGTTACAATGTTGCGC
EST: gi|7924579|gb|AW830605.1|AW830605
EST:     TTGCACTTGCTGAGGCTGTACATGGTTCGGCACCTGATATTGCTGGAAAG                         AATTTGGCAAATCCAACTGCTTTACTGCTAAGTGGGGTTACAATGGTGCGC
genomic: TTGCACTTGCTGAGGCTGTACATGGTTCGGCACCTGATATTGCTGGAAAGgtaagctgtg ... gtatatgtagAATTTGGCAAATCCAACTGCTTTACTGCTAAGTGGTGTTACAATGTTGCGC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTGCAACATTGGCGAGGGAGGTATTGCACTTGCTGAGGCTGTACATGGTTCGGCACCTGATATTGCTGGAAAGgtaagctgtgaaagtactcattttaccttatattatccggcctaaaccttcttgtgccctgttgtcatggaatgtgaattttttcaagagattgtttcat

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA