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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GATCGTGGTATAGCGTTGCACAAAATGATTAGGCTTATTACCATGGGTCTTGGTGGTGAAGGGTATTTAAATTTTATGGGGAATGAATTTGGCCATCCTGgtaatcatatttgacttttgtcatgtcattacttagagattcaataatgatatgaccagttgttagattttatgttatcaagttaagtttagcattgctcattcattgttgctctcttcag

Basic information

species Glycine max
transcript GLYMA03G35020.1
intron # 17
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA03G35020.1 (Glycine max), 5'ss of exon 17
lower sequence: LOC_Os02g32660.1 (Oryza sativa), 5'ss of exon 17
GATCGTGGTATAGCGTTGCACAAAATGATTAGGCTTATTACCATGGGTCTTGGTGGTGAAGGGTATTTAAATTTTATGGGGAATGAATTTGGCCATCCTGgtaa--------------------tcatatttgacttttgtcatgtcattacttagagattcaataatgatatgaccagttgt-tag-attttatgttatcaagttaagtttagcattgctcattcattgttgctctcttcag
|||||||| ||||| ||||| ||||||||||| ||||| || |||||  | || || ||||| ||| | || |||||||| ||||| || || ||||||||| |                     ||| ||||  | || |  | | || |  |    |||  || |  ||    |  ||    ||| ||||| ||  |   | ||   || |       | ||  |   ||  | | | |||
GATCGTGGAATAGCATTGCATAAAATGATTAGACTTATCACAATGGGGTTAGGAGGAGAAGGCTATCTTAACTTTATGGGAAATGAGTTCGGACATCCTGgtgagatttaataacaatcacacaccatgtttgtttcttattttat-atcaacttctcatttgatgacaatggttcttgtcacctagtattttctgggaaacaattggcttaaaggccattgatctaccttttattt-tgcag

upper sequence: GLYMA03G35020.1 (Glycine max), 5'ss of exon 17
lower sequence: GRMZM2G073054_T02 (Zea mays), 5'ss of exon 17
GATCGTGGTATAGCGTTGCACAAAATGATTAGGCTTATTACCATGGGTCTTGGTGGTGAAGGGTATTTAAATTTTATGGGGAATGAATTTGGCCATCCTGgtaatcatatttgacttt-tgtcatgt--cattacttagagattcaa-taatgatatgaccagttgttagattttatgttatcaagttaagtt-tagcattgctcattcattgttgctctcttcag-----
|||||||| ||||| || || ||||||||||||||| | || |||||| | || |||||||| ||| ||||||| ||||| ||||| ||||| ||||||||| |   |  |  | ||| |  |||||  ||| |   | || | | | | || || |     ||  ||  ||   |||    | | || |    | |      | ||   | ||| |  | | |       
GATCGTGGGATAGCATTACATAAAATGATTAGGCTTGTCACAATGGGTTTAGGAGGTGAAGGCTATCTAAATTTCATGGGAAATGAGTTTGGGCATCCTGgttagtcttctcaattttattgcatgttgcataatgcatagttacgagttataatgtttttggtccttgcatggcatgcagcctaattcatcagtggaggaagttatgactagtttcattttacgtggcag

upper sequence: GLYMA03G35020.1 (Glycine max), 5'ss of exon 17
lower sequence: AT5G03650.1 (Arabidopsis thaliana), 5'ss of exon 17
GATCGTGGTATAGCGTTGCACAAAATGATTAGGCTTATTACCATGGGTCTTGGTGGTGAAGGGTATTTAAATTTTATGGGGAATGAATTTGGCCATCCTGgta----atcatatttgacttttgtcatgtcattacttagagattcaataatgatatgaccagttgttagattttatgttatcaagttaagtttagcattgctcattcattgttgctctcttcag
||| | || ||||| ||||||||||||||||||||||| || |||||  | || |||||||| || |||||||||||||| || ||||| || ||||| ||||    |||   ||   ||| | |||| |  || ||  |  |   |||  |||  ||  || ||  |  || |  |  |   |  || ||                                  
GATAGAGGAATAGCTTTGCACAAAATGATTAGGCTTATAACTATGGGATTAGGCGGTGAAGGTTACTTAAATTTTATGGGAAACGAATTCGGACATCCAGgtactaaatcgatttaagcttgtttcatttactttctgtgcaaa--aattttga-gtgtacaatttcttcatctactcctgcaatattcag----------------------------------

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|13562782|gb|BG551002.1|BG551002
EST:     TGGTGGTGAAGGGTATTTAAATTTTATGGGGAATGAATTTGGCCATCCTG                         AGTGGATTGATTTTCCAAGGGGTGATCAACATCTTCCT
genomic: TGGTGGTGAAGGGTATTTAAATTTTATGGGGAATGAATTTGGCCATCCTGgtaatcatat ... ctctcttcagAGTGGATTGATTTTCCAAGGGGTGATCAACATCTTCCT
EST: gi|22522391|gb|BU081202.1|BU081202
EST:     TGGTGGTGAAGGGTATTTAAATTTTATGGGGAATGAATTTGGCCATCCTG                         AGTGGATTGATTTTCCAAGGGGTGATCAACATCTTCCTACTGGCGTAATAG
genomic: TGGTGGTGAAGGGTATTTAAATTTTATGGGGAATGAATTTGGCCATCCTGgtaatcatat ... ctctcttcagAGTGGATTGATTTTCCAAGGGGTGATCAACATCTTCCTACTGGCGTAATAG
EST: gi|151398683|gb|EV268554.1|EV268554
EST:     TGGTGGTGAAGGGTATTTAAATTTTATGGGGAATGAATTTGGCCATCCTG                         AGTGGATTGATTTTCCAAGGGGTGATCAACATCTTCCTACTGGCGTAATAG
genomic: TGGTGGTGAAGGGTATTTAAATTTTATGGGGAATGAATTTGGCCATCCTGgtaatcatat ... ctctcttcagAGTGGATTGATTTTCCAAGGGGTGATCAACATCTTCCTACTGGCGTAATAG
EST: gi|15662274|gb|BI699645.1|BI699645
EST:     TGGTGGTGAAGGGTATTTAAATTTTATGGGGAATGAATTTGGCCATCCTG                         AGTGGATTGATTTTCCAAGGGGTGATCAACATCTTCCTACTGGCGTAATAG
genomic: TGGTGGTGAAGGGTATTTAAATTTTATGGGGAATGAATTTGGCCATCCTGgtaatcatat ... ctctcttcagAGTGGATTGATTTTCCAAGGGGTGATCAACATCTTCCTACTGGCGTAATAG
EST: gi|20448926|gb|BQ253050.1|BQ253050
EST:     TGGTGGTGAAGGGTATTTAAATTTTATGGGGAATGAATTTGGCCATCCTG                         AGTGGATTGATTTTCCAAGGGGTGATCAACATCTTCCT
genomic: TGGTGGTGAAGGGTATTTAAATTTTATGGGGAATGAATTTGGCCATCCTGgtaatcatat ... ctctcttcagAGTGGATTGATTTTCCAAGGGGTGATCAACATCTTCCT
EST: gi|18040842|gb|BM309136.1|BM309136
EST:     TGGTGGTGAAGGGTATTTAAATTTTATGGGGAATGAATTTGGCCATCCTG                         AGTGGATTGATTTTCCAAGGGGTGATCAACATCTTCCTACTGGCGTAATAG
genomic: TGGTGGTGAAGGGTATTTAAATTTTATGGGGAATGAATTTGGCCATCCTGgtaatcatat ... ctctcttcagAGTGGATTGATTTTCCAAGGGGTGATCAACATCTTCCTACTGGCGTAATAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GATCGTGGTATAGCGTTGCACAAAATGATTAGGCTTATTACCATGGGTCTTGGTGGTGAAGGGTATTTAAATTTTATGGGGAATGAATTTGGCCATCCTGgtaatcatatttgacttttgtcatgtcattacttagagattcaataatgatatgaccagttgttagattttatgttatcaagttaagtttagcattgctcattcattgttgctctcttcag

- - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG