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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTCCGTTTTAATAACAGCAGTATTTACTGAGGCAATAAAAAATGCAGTAGGTCGACCTCGACCAGACTTCTTCTGGCGATGTTTTCCAGATGGAAAGGATgtatgttttcctttaattttaggttttcaattcatatttatcaattatgttggttcttaatagtgggcataattaattattagtggcttcttgttag

Basic information

species Glycine max
transcript GLYMA18G53100.1
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA18G53100.1 (Glycine max), 5'ss of exon 4
lower sequence: LOC_Os01g04660.2 (Oryza sativa), 5'ss of exon 5
CTCCGTTTTAATAACAGCAGTATTTACTGAGGCAATAAAAAATGCAGTAGGTCGACCTCGACCAGACTTCTTCTGGCGATGTTTTCCAGATGGAAAGGATgtatgttttcctttaattttaggttttcaattcatatttatcaatt-atgttggttcttaatagtgggcataattaattattagtggct-tcttgttag-----------
||| ||  | ||||| |||||  | |||   |   |||| |||||||||||  ||||| | ||||||||||| ||||| |||||||| ||||||||| | |||   ||| | | || | |   |   ||| |  | | || || || |||||| || ||| | ||     |    | | |  ||   || |  || ||            
CTCGGTGCTGATAACTGCAGTTGTAACTACTGTGGTAAAGAATGCAGTAGGAAGACCTAGGCCAGACTTCTTTTGGCGGTGTTTTCCTGATGGAAAGCAGgtagagttttcctcaaatgtttatgcacaaatagt-tctaccattttatgttgcttgttatttgtcaattttgaaactgacaaggcactgttctggtaattttatctcag

upper sequence: GLYMA18G53100.1 (Glycine max), 5'ss of exon 4
lower sequence: GRMZM2G174343_T07 (Zea mays), 5'ss of exon 2
CTCCGTTTTAATAACAGCAGTATTTACTGAGGCAATAAAAAATGCAGTAGGTCGACCTCGACCAGACTTCTTCTGGCGATGTTTTCCAGATGGAAAGGATgtatgttttccttta-attttaggttttcaattcatatttatcaattatgttggttcttaat---agtgggcataattaattattagtggcttcttgttag
| | ||  | ||||| ||||| ||||| || |  ||||| | |||||||||  ||||  | |||||||||||||||||||| ||||| ||||||||| | ||||  || | | || |  || |  | |  ||   | ||    |   ||| |  ||| || |   | |   || | |   |   | ||   ||      ||
CGCTGTGCTGATAACTGCAGTTTTTACCGATGTGATAAAGACTGCAGTAGGGAGACCGAGGCCAGACTTCTTCTGGCGATGCTTTCCTGATGGAAAGCAGgtatacttccttgtatacatttgcgtgtagataattcttccctagagatgctttttcatagtttaaatcaacacagtgcttctatggtatatttggtgcag

upper sequence: GLYMA18G53100.1 (Glycine max), 5'ss of exon 4
lower sequence: AT3G02600.5 (Arabidopsis thaliana), 5'ss of exon 4
CTCCGTTTTAATAACAGCAGTATTTACTGAGGCAATAAAAAATGCAGTAGGTCGACCTCGACCAGACTTCTTCTGGCGATGTTTTCCAGATGGAAAGGATgtatgttttcctttaattttaggttttcaattcatatttatcaattatgttggttcttaatagtgggcataattaattattagtggcttcttgttag
||| ||| |  | ||||||||| |||| || |||||||| |||||||| |||||||| || || |||||||||||||| |||||||||||||| || | ||||  | || |  | | |||   |  | |  || | ||||    || |  ||  |||| |   | |   |   | || |                  
CTCTGTTCTGGTGACAGCAGTACTTACCGATGCAATAAAGAATGCAGTTGGTCGACCACGTCCTGACTTCTTCTGGCGTTGTTTTCCAGATGGCAAAGCTgtacatgtttcaatgagttt--ttacttatctcgt-tttaaatcttgttctgcctcttgaatctcgattttgcttatcag-----------------

upper sequence: GLYMA18G53100.1 (Glycine max), 5'ss of exon 4
lower sequence: Vv14s0006g02480.t01 (Vitis vinifera), 5'ss of exon 3
CTCCGTTTTAATAACAGCAGTATTTACTGAGGCAATAAAAAATGCAGTAGGTCGACCTCGACCAGACTTCTTCTGGCGATGTTTTCCAGATGGAAAGGATgtatgttttcctttaattttaggttttcaattcatatttatcaattatgttggttcttaatagtgggcat---aattaat-tattagt--ggcttcttgttag-----
||| ||| |  ||||||  ||  ||||||| ||||||||||||||||| ||||||||||||||||||||||| ||||| |||||||| ||||| ||||||||||| ||  |   |||   || | ||  ||      || | |||      |  | ||  | | |   ||   | ||    | ||| |  ||   |||  |       
CTCTGTTCTGGTAACAGTGGTTATTACTGATGCAATAAAAAATGCAGTTGGTCGACCTCGACCAGACTTCTTTTGGCGTTGTTTTCCTGATGGGAAGGATgtatgcttctcacaaatgcaagttctttcatagtagcttgttaatggaacagtattttttttgggacaatttcacttggcatgttaattagggaacttaatgtgtcag

upper sequence: GLYMA18G53100.1 (Glycine max), 5'ss of exon 4
lower sequence: EFJ15968 (Selaginella moellendorffii), 5'ss of exon 3
CTCCGTTTTAATAACAGCAGTATTTACTGAGGCAATAAAAAATGCAGTAGGTCGACCTCGACCAGACTTCTTCTGGCGATGTTTTCCAGATGGAAAGGATgtatgttttcctttaattttaggttttcaattcatatttatcaattatgttggttcttaatagtgggcataattaattattagtggcttcttgttag
|||  |     |  | |  ||  | ||  | || || ||     | || ||||| ||||| || || |||||||||||||| ||||||||||||   || ||||||     |||  |||    |     |  | | | |     || | | | |||                                         
CTCACTCGCTCTTGCTGGTGTTGTGACAAATGCGATCAAGGTGTCTGTTGGTCGGCCTCGGCCGGATTTCTTCTGGCGATGCTTTCCAGATGGAGTCGAGgtatgtagcagtttcttttccaat----gacacctttgtgattgttttctcgattcag---------------------------------------

upper sequence: GLYMA18G53100.1 (Glycine max), 5'ss of exon 4
lower sequence: EFJ33338 (Selaginella moellendorffii), 5'ss of exon 3
CTCCGTTTTAATAACAGCAGTATTTACTGAGGCAATAAAAAATGCAGTAGGTCGACCTCGACCAGACTTCTTCTGGCGATGTTTTCCAGATGGAAAGGATgtatgttttcctttaattttaggttttcaattcatatttatcaattatgttggttcttaatagtgggcataattaattattagtggcttcttgttag
|||  |    ||  | |  ||  | ||  | || || ||     | || ||||| |||||||| || |||||||||||||| ||||| ||||||   || ||||||     |||  |||    |     |  | | | |     || | | | |||                                         
CTCACTCGCTATTGCTGGTGTTGTGACAAATGCGATCAAGGTGTCTGTTGGTCGGCCTCGACCGGATTTCTTCTGGCGATGCTTTCCGGATGGAGTCGAGgtatgtagcagtttcttttccaat----gacacctttgtgattgttttctcgattcag---------------------------------------

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|51338216|gb|CO982082.1|CO982082
EST:     GTCGANNNCGACCAGACNNCNTCTGGCGATGTTTTCCAGATGGAAAGGAT                         GTTTATGATAAATGGGGAGATGTCATTTGTCATGGTGACCAAAAGGTCATA
genomic: GTCGACCTCGACCAGACTTCTTCTGGCGATGTTTTCCAGATGGAAAGGATgtatgttttc ... ttcttgttagGTTTATGATAAATGGGGAGATGTCATTTGTCATGGTGACCAAAAGGTCATA
EST: gi|18040504|gb|BM308798.1|BM308798
EST:     GTCGACCTCGACCAGACTTCTTCTGGCGATGTTTTCCAGATGGAAAGGAT                         GTTTATGATAAATGGGGAGATGTCATTTGTCATGGTGACCAAA-GGTCATA
genomic: GTCGACCTCGACCAGACTTCTTCTGGCGATGTTTTCCAGATGGAAAGGATgtatgttttc ... ttcttgttagGTTTATGATAAATGGGGAGATGTCATTTGTCATGGTGACCAAAAGGTCATA
EST: gi|192294776|gb|FG986625.1|FG986625
EST:     GTCGACCTCGACCAGACTTCTTCTGGCGATGTTTTCCAGATGGAAAGGAT                         GTTTATGATAAATGGGGAGATGTCATTTGTCATGGTGACCAAAAG-TCATA
genomic: GTCGACCTCGACCAGACTTCTTCTGGCGATGTTTTCCAGATGGAAAGGATgtatgttttc ... ttcttgttagGTTTATGATAAATGGGGAGATGTCATTTGTCATGGTGACCAAAAGGTCATA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTCCGTTTTAATAACAGCAGTATTTACTGAGGCAATAAAAAATGCAGTAGGTCGACCTCGACCAGACTTCTTCTGGCGATGTTTTCCAGATGGAAAGGATgtatgttttcctttaattttaggttttcaattcatatttatcaattatgttggttcttaatagtgggcataattaattattagtggcttcttgttag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA