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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATCGTATAGCTGCCGGATTACCTTGTGGAAGTGAAGGGTTTCTATTAATGTATGCTCGGTGGAAAAAGCTTGAAAGGGACTTGTATAATGAACGCAAGGAgtaagcatttacatttattgtgtttaatcttgttttgttttattgtatttccttctacatattaaaaaacgaaatgttacttcaaataccattgacacat...

Basic information

species Glycine max
transcript GLYMA09G37610.1
intron # 20
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA09G37610.1 (Glycine max), 5'ss of exon 20
lower sequence: AT5G15070.2 (Arabidopsis thaliana), 5'ss of exon 23
ATCGTATAGCTGCCGGATTACCTTGTGGAAGTGAAGGGTTTCTATTAATGTATGCTCGGTGGAAAAAGCTTGAAAGGGACTTGTATAATGAACGCAAGGAgtaagcatttacatttattgtgtttaatcttgttttgttttattgtatttccttctacatattaaaaaacgaaatgttacttcaaataccattgacacat
 ||| || |||||||||||||||||||| ||||||||||| || || |||| ||| ||||||| ||| || ||||||||  | || || ||| | |  ||||||| |  |     |||  | | | ||  | | ||    | ||  |  |    ||     ||  |  |   ||||                        
GTCGGATTGCTGCCGGATTACCTTGTGGTAGTGAAGGGTTCCTTTTGATGTTTGCCCGGTGGAGAAAACTCGAAAGGGATCTCTACAACGAAAGAAGAGAgtaagtaaatggccatatgctctcttattctctgtttgagttttagaaatggcactgatcgttgga--attgaatgcag---------------------

upper sequence: GLYMA09G37610.1 (Glycine max), 5'ss of exon 20
lower sequence: Vv14s0066g02540.t01 (Vitis vinifera), 5'ss of exon 22
ATCGTATAGCTGCCGGATTACCTTGTGGAAGTGAAGGGTTTCTATTAATGTATGCTCGGTGGAAAAAGCTTGAAAGGGACTTGTATAATGAACGCAAGGAgtaagcatttacatttattgtgtttaatcttgttttgttttattgtatttccttctacatattaaaaaacgaaatgttacttcaaataccattgacacat-
| ||||| ||||| |||||||| ||||| ||||| || || || || |||| |||||| |||| ||| ||||| || ||||| || ||||||||||| |||||||||| || | || || |   |      || | ||| |||       |    | |  |        |   |  ||  | |   || |   |  | |  
ACCGTATTGCTGCTGGATTACCATGTGGTAGTGAGGGATTCCTTTTGATGTTTGCTCGCTGGAGAAAACTTGAGAGAGACTTATACAATGAACGCAAAGAgtaagcatctataatt-ttttacatgtatcagtatggttgtatgaggagccaagattctcaactgtttgctttaattttttccccttatctgaggtataat
















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|120531780|gb|EH259913.1|EH259913
EST:     TATGCTCGGTGGAAAAAGCTTGAAAGGGACTTGTATAATGAACGCAAGGA                         GCGTTTTGACATCACCCAAATTCCTGATGTCTATGATTCATGCAA
genomic: TATGCTCGGTGGAAAAAGCTTGAAAGGGACTTGTATAATGAACGCAAGGAgtaagcattt ... actttcacagGCGTTTTGACATCACCCAAATTCCTGATGTCTATGATTCATGCAA
EST: gi|10237535|gb|BE806423.1|BE806423
EST:     AAAGCTTGAAAGGGACTTGTATAATGAACGCAAGGA                         GCGTTTTGACATCACTCAAATTCCTGATGTCTATGATTCATGCAA
genomic: AAAGCTTGAAAGGGACTTGTATAATGAACGCAAGGAgtaagcattt ... actttcacagGCGTTTTGACATCACCCAAATTCCTGATGTCTATGATTCATGCAA
EST: gi|19348846|gb|BM893378.1|BM893378
EST:     TTGAAAGGGACTTGTATAATGAACGCAAGGA                         GCGTTTTGACATCACCCAAATTCCTGATGTCTATGATTCATGCAA
genomic: TTGAAAGGGACTTGTATAATGAACGCAAGGAgtaagcattt ... actttcacagGCGTTTTGACATCACCCAAATTCCTGATGTCTATGATTCATGCAA
EST: gi|15203141|gb|BI425909.1|BI425909
EST:     TATGCTCGGTGGAAAAAGCTTGAAAGGGACTTGTATAATGAACGCAAGGA                         GCGTTTTGACATCACTCAAATTCCTGATGTCTATGATTCATGCAA
genomic: TATGCTCGGTGGAAAAAGCTTGAAAGGGACTTGTATAATGAACGCAAGGAgtaagcattt ... actttcacagGCGTTTTGACATCACCCAAATTCCTGATGTCTATGATTCATGCAA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATCGTATAGCTGCCGGATTACCTTGTGGAAGTGAAGGGTTTCTATTAATGTATGCTCGGTGGAAAAAGCTTGAAAGGGACTTGTATAATGAACGCAAGGAgtaagcatttacatttattgtgtttaatcttgttttgttttattgtatttccttctacatattaaaaaacgaaatgttacttcaaataccattgacacat

- - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaacgaaa