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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCTCCTTAAGCTCATCAATGCCAAGAACACCATGGAAATTGGTGTCTACACTGGATATTCACTTCTTGCCACCGCTCTCGCTCTTCCTGAAGATGGAAAGgtattaaaagcagagcttagcacccccaaagaataaagctttatttttctctctataaaatcaaaattttctgacaaccattttctatgcaattatagtc...

Basic information

species Glycine max
transcript GLYMA02G11530.2
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA02G11530.2 (Glycine max), 5'ss of exon 3
lower sequence: AT4G34050.1 (Arabidopsis thaliana), 5'ss of exon 2
GCTCCTTAAGCTCATCAATGCCAAGAACACCATGGAAATTGGTGTCTACACTGGATATTCACTTCTTGCCACCGCTCTCGCTCTTCCTGAAGATGGAAAGgtattaaaagcagagcttagcacccccaaagaataaagctttatttttctctctataaaatcaaaattttctgacaaccattttctatgcaattatagtc
|||  | |||||| | || ||||||||||| ||||| || || || |||||||| || || ||||| ||||||||||| ||||| |||||||| || || |||    || |    |||    | ||       |   |     ||| ||   ||    |||  ||| ||||    | || |||| |   ||         
GCTTATCAAGCTCGTTAACGCCAAGAACACAATGGAGATCGGAGTTTACACTGGCTACTCTCTTCTCGCCACCGCTCTTGCTCTCCCTGAAGACGGCAAAgtaaatcaatct---cttcatcctcctctgttttttggtgggttttgtcgaacttgggaattgaaagtttc----atcctttttatcatcag--------

upper sequence: GLYMA02G11530.2 (Glycine max), 5'ss of exon 3
lower sequence: Vv03s0063g00140.t01 (Vitis vinifera), 5'ss of exon 3
GCTCCTTAAGCTCATCAATGCCAAGAACACCATGGAAATTGGTGTCTACACTGGATATTCACTTCTTGCCACCGCTCTCGCTCTTCCTGAAGATGGAAAGgtattaaaagcagagcttagcacccccaaagaataaagctttatttttctctctataaaatcaaaatttt-ctgacaaccatt--ttctatgcaattatagtc
||| || ||||||||||||||||||||||||||||| || || ||||||||||| || || ||||| ||||| || || ||||| || || || |||||||  |    |   |  | |||     | | | | |||    | ||         |||||||  |   | |  |||| ||  |||  ||||      ||  ||  
GCTTCTCAAGCTCATCAATGCCAAGAACACCATGGAGATAGGCGTCTACACTGGCTACTCTCTTCTGGCCACAGCCCTTGCTCTCCCCGATGACGGAAAGg--tcgggaaatggtcataga---tcaacacagtaa----tcatccaagcacgtataaaaaaatgttatggctgaaaaaaattggttcttgattgttgcag--
















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|13481062|gb|BG510405.1|BG510405
EST:     CTGGATATTCACTTCTTGCCACCGCTCTCGCTCTTCCTGAAGATGGAAAG                         ATCTTGGCCATGGATATTAACAGGGAGAATTATGAATTGGGTTTGCCAGTA
genomic: CTGGATATTCACTTCTTGCCACCGCTCTCGCTCTTCCTGAAGATGGAAAGgtattaaaag ... cttggtgcagATCTTGGCCATGGATATTAACAGGGAGAATTATGAATTGGGTTTGCCAGTA
EST: gi|15201563|gb|BI424930.1|BI424930
EST:     CTGGATATTCACTTCTTGCCACCGCTCTCGCTCTTCCTGAAGATGGAAAG                         ATCTTGGCCATGGATATTAACAGGGAGAATTATGAATTGGGTTTGCCAGTA
genomic: CTGGATATTCACTTCTTGCCACCGCTCTCGCTCTTCCTGAAGATGGAAAGgtattaaaag ... cttggtgcagATCTTGGCCATGGATATTAACAGGGAGAATTATGAATTGGGTTTGCCAGTA
EST: gi|19935964|gb|BQ080661.1|BQ080661
EST:     CTGGATATTCACTTCTTGCCACCGCTCTCGCTCTTCCTGAAGATGGAAAG                         ATCTTGGCCATGGATATTAACAGGGAGAATTATGAATTGGGTTTGC
genomic: CTGGATATTCACTTCTTGCCACCGCTCTCGCTCTTCCTGAAGATGGAAAGgtattaaaag ... cttggtgcagATCTTGGCCATGGATATTAACAGGGAGAATTATGAATTGGGTTTGC
EST: gi|26047747|gb|CA784441.1|CA784441
EST:     CTGGATATTCACTTCTTGCCACCGCTCTCGCTCTTCCTGAAGATGGAAAG                         ATCTTGGCCATGGATATTAACAGGGAGAATTATGAATTGGGTTTGCCAGTA
genomic: CTGGATATTCACTTCTTGCCACCGCTCTCGCTCTTCCTGAAGATGGAAAGgtattaaaag ... cttggtgcagATCTTGGCCATGGATATTAACAGGGAGAATTATGAATTGGGTTTGCCAGTA
EST: gi|17402133|gb|BM178915.1|BM178915
EST:     CTGGATATTCACTTCTTGCCACCGCTCTCGCTCTTCCTGAAGATGGAAAG                         ATCTTGGCCATGGATATTAACAGGGAGAATTATGAATTGGGTTTGCCAGTA
genomic: CTGGATATTCACTTCTTGCCACCGCTCTCGCTCTTCCTGAAGATGGAAAGgtattaaaag ... cttggtgcagATCTTGGCCATGGATATTAACAGGGAGAATTATGAATTGGGTTTGCCAGTA
EST: gi|17401035|gb|BM177817.1|BM177817
EST:     CTGGATATTCACTTCTTGCCACCGCTCTCGCTCTTCCTGAAGATGGAAAG                         ATCTTGGCCATGGATATTAACAGGGAGAATTATGAATTGGGTTTGCCAGTA
genomic: CTGGATATTCACTTCTTGCCACCGCTCTCGCTCTTCCTGAAGATGGAAAGgtattaaaag ... cttggtgcagATCTTGGCCATGGATATTAACAGGGAGAATTATGAATTGGGTTTGCCAGTA
EST: gi|23733582|gb|BU764995.1|BU764995
EST:     CTGGATATTCACTTCTTGCCACCGCTCTCGCTCTTCCTGAAGATGGAAAG                         ATCTTGGCCATGGATATTAACAGGGAGAATTATGAATT
genomic: CTGGATATTCACTTCTTGCCACCGCTCTCGCTCTTCCTGAAGATGGAAAGgtattaaaag ... cttggtgcagATCTTGGCCATGGATATTAACAGGGAGAATTATGAATT
EST: gi|16346918|gb|BI972513.1|BI972513
EST:     CTGGATATTCACTTCTTGCCACCGCTCTCGCTCTTCCTGAAGATGGAAAG                         ATCTTGGCCATGGATATTAACAGGGAGAATTATGAATTGGGTTTGCCAGTA
genomic: CTGGATATTCACTTCTTGCCACCGCTCTCGCTCTTCCTGAAGATGGAAAGgtattaaaag ... cttggtgcagATCTTGGCCATGGATATTAACAGGGAGAATTATGAATTGGGTTTGCCAGTA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCTCCTTAAGCTCATCAATGCCAAGAACACCATGGAAATTGGTGTCTACACTGGATATTCACTTCTTGCCACCGCTCTCGCTCTTCCTGAAGATGGAAAGgtattaaaagcagagcttagcacccccaaagaataaagctttatttttctctctataaaatcaaaattttctgacaaccattttctatgcaattatagtc

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - caccccc