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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAAGAATTTCAGTTGGCATTGTTCAAGACGAACAAGAAAGAGAGCTTATTTGCAGATAGGgtacatagaacattaacttcttgtttttctttttccaactgttttttacatttccaccctgaggaaaaagaaacaacaatataaaaatattggcttaaat...

Basic information

species Glycine max
transcript GLYMA17G00830.1
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA17G00830.1 (Glycine max), 5'ss of exon 4
lower sequence: LOC_Os03g42840.1 (Oryza sativa), 5'ss of exon 3
GAAGAATTTCAGTTGGCATTGTTCAAGACGAACAAGAAAGAGAGCTTATTTGCAGATAGGgtacatagaacattaacttcttgtttttctttttccaactgttttttacatttccaccctgaggaaaaagaaacaacaatataaaaatattggcttaaat--
|| || |||||||||||  |||||||||| |||||||| ||||| |||||||| ||  | |||     |||| |||  |    |   |    |   || | |  | ||  | || ||  |   |||    || |||  ||  ||  |  |||| |    |  
GAGGAGTTTCAGTTGGCGCTGTTCAAGACCAACAAGAAGGAGAGTTTATTTGCTGACCGTgtaagaccaacaataatataacttgcctaccatggaaaatatcctgtaactgtctacattt--gaagtgaaatcaattatgaaattagtttggttatgctct

upper sequence: GLYMA17G00830.1 (Glycine max), 5'ss of exon 4
lower sequence: AT5G55990.1 (Arabidopsis thaliana), 5'ss of exon 5
GAAGAATTTCAGTTGGCATTGTTCAAGACGAACAAGAAAGAGAGCTTATTTGCAGATAGGgtacatagaacattaacttc-ttgtttttctttttccaactgttttttacatttccaccctgaggaaaaagaaacaacaatataaaaatattggcttaaat
||||| ||||||||||| ||||| ||||| || || |||||||| || ||||||||| ||||| ||    | ||     | || |   | || ||  | |  |||||  ||    ||   | || | |||     ||  || |    || |||  |  |  
GAAGAGTTTCAGTTGGCTTTGTTTAAGACAAATAAAAAAGAGAGTTTGTTTGCAGATCGGgta-atgtttctttcttcacattataagtgttcttaaacccatttttgtcaagatcaagtttagaagaaatgctgaaatatgt---gattttgtttctag-

upper sequence: GLYMA17G00830.1 (Glycine max), 5'ss of exon 4
lower sequence: AT4G26570.1 (Arabidopsis thaliana), 5'ss of exon 5
GAAGAATTTCAGTTGGCATTGTTCAAGACGAACAAGAAAGAGAGCTTATTTGCAGATAGGgtacatagaacattaacttcttgtttttctttttccaactgttttttacatttccaccctgaggaaaaagaaacaacaatataaaaatattggcttaaat
|||||||||||||| || ||||||||||| || || ||||||||||| ||||||||  |||||  |            ||||  |||| |  |   ||   ||| |||    |   ||  ||         ||  | ||  | | | ||        |  
GAAGAATTTCAGTTAGCCTTGTTCAAGACAAATAAAAAAGAGAGCTTGTTTGCAGACCGGgtatgt------------tctt-cttttttaatcaaaagactttgttatccatttgccaagatcctttttgaaagataacttgacagtaccaatcacag-

upper sequence: GLYMA17G00830.1 (Glycine max), 5'ss of exon 4
lower sequence: AT4G26570.2 (Arabidopsis thaliana), 5'ss of exon 5
GAAGAATTTCAGTTGGCATTGTTCAAGACGAACAAGAAAGAGAGCTTATTTGCAGATAGGgtacatagaacattaacttcttgtttttctttttccaactgttttttacatttccaccctgaggaaaaagaaacaacaatataaaaatattggcttaaat
|||||||||||||| || ||||||||||| || || ||||||||||| ||||||||  |||||  |    | ||   ||  |        |||   | |  |||   |   | |       | || ||    |||                         
GAAGAATTTCAGTTAGCCTTGTTCAAGACAAATAAAAAAGAGAGCTTGTTTGCAGACCGGgtatgttcttcttt--tttaatcaaaagactttgttatccatttgccaagatcctttttgaaagataacttgacag------------------------

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|15812919|gb|BI785194.1|BI785194
EST:     AGTTGGCATTGTTCAAGACGAACAAGAAAGAGAGCTTATTTGCAGATAGG                         GTGTTTGACTTGTTTGATACAAAGCACAACGGGATACTTGATTTTGAAGAG
genomic: AGTTGGCATTGTTCAAGACGAACAAGAAAGAGAGCTTATTTGCAGATAGGgtacatagaa ... ctgtttgtagGTGTTTGACTTGTTTGATACAAAGCACAACGGGATACTTGATTTTGAAGAG
EST: gi|9820145|gb|BE555655.1|BE555655
EST:     AGTTGGCATTGTTCAAGACGAACAAGAAAGAGAGCTTATTTGCAGATAGG                         GTGTTTGACTTGTTTGATACAAAGCACAATGGGATACTTGATTTTGAAGAG
genomic: AGTTGGCATTGTTCAAGACGAACAAGAAAGAGAGCTTATTTGCAGATAGGgtacatagaa ... ctgtttgtagGTGTTTGACTTGTTTGATACAAAGCACAACGGGATACTTGATTTTGAAGAG
EST: gi|19054016|gb|BM732683.1|BM732683
EST:     AGTTGGCATTGTTCAAGACGAACAAGAAAGAGAGCTTATTTGCAGATAGG                         GTGTTTGACTTGTTTGATACAAAGCACAACGGGATACTTGATTTTGAAGAG
genomic: AGTTGGCATTGTTCAAGACGAACAAGAAAGAGAGCTTATTTGCAGATAGGgtacatagaa ... ctgtttgtagGTGTTTGACTTGTTTGATACAAAGCACAACGGGATACTTGATTTTGAAGAG
EST: gi|151412447|gb|EV282259.1|EV282259
EST:     AGTTGGCATTGTTCAAGACGAACAAGAAAGAGAGCTTATTTGCAGATAGG                         GTGTTTGACTTGTTTGATACAAAGCACAACGGGATACTTGATTTTGAAGAG
genomic: AGTTGGCATTGTTCAAGACGAACAAGAAAGAGAGCTTATTTGCAGATAGGgtacatagaa ... ctgtttgtagGTGTTTGACTTGTTTGATACAAAGCACAACGGGATACTTGATTTTGAAGAG

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
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---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAAGAATTTCAGTTGGCATTGTTCAAGACGAACAAGAAAGAGAGCTTATTTGCAGATAGGgtacatagaacattaacttcttgtttttctttttccaactgttttttacatttccaccctgaggaaaaagaaacaacaatataaaaatattggcttaaat

- - - - - - - - - - - - - - - -  AAGAAA
- - - - - - - - - - - - - - - - - -  AAGAGA
- - - - - - - - - - - - - - - - - - - - AGAGCT
- - - - - - - - - - - - - - - - - - - -  GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - -  GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ccaccct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ggaaaaag