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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAACAGGCATGGAGATTTCTTCTCTGCCCTGATGAAGGCACAGCCACAATTTCTAAATGACTGGAAGGCAAAGTTGTGGTCTCGATTCTTCTGTCTATCGgtaacttttcccttttgcttaccattatgcattcctttaagattcttagatgaaacctcaatacctagtgccagttgttgctagcttaaggttgtgagaa...

Basic information

species Glycine max
transcript GLYMA19G30350.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA19G30350.1 (Glycine max), 5'ss of exon 3
lower sequence: GRMZM2G043109_T01 (Zea mays), 5'ss of exon 3
GAACAGGCATGGAGATTTCTTCTCTGCCCTGATGAAGGCACAGCCACAATTTCTAAATGACTGGAAGGCAAAGTTGTGGTCTCGATTCTTCTGTCTATCGgtaacttttcccttttgcttaccattatgcattcctttaagattcttagatgaaacctcaatacctagtgccagttgttgc-tagcttaaggttgtgagaa
|||||||||||| || ||||||||||||||| ||||||| ||||| || || || |||||||||||||| ||| | ||||| || |||||||| || ||||||| |||||    |    |     |||| ||     |    |   |  |       |     || | |||   | | ||  |  ||| |  ||   ||  
GAACAGGCATGGTGACTTCTTCTCTGCCCTGCTGAAGGCTCAGCCGCAGTTCCTCAATGACTGGAAGGCCAAGCTCTGGTCACGGTTCTTCTGCCTCTCGgtaatttttcgagctattcttttgctatgtatgtagatcgattaactccaaaggttgttgtgccccattgctgatagctgtgttacttgacctttgcag--

upper sequence: GLYMA19G30350.1 (Glycine max), 5'ss of exon 3
lower sequence: GRMZM2G081462_T02 (Zea mays), 5'ss of exon 3
GAACAGGCATGGAGATTTCTTCTCTGCCCTGATGAAGGCACAGCCACAATTTCTAAATGACTGGAAGGCAAAGTTGTGGTCTCGATTCTTCTGTCTATCGgtaacttttccct-tttgcttaccattatgcattcctttaagattcttagatgaaacctcaatacctagtgccagttgttgctagcttaaggttgtgagaa-
||||||||| || || ||||||||||||||| | ||||| ||||| || || || |||||||||||||| ||| | ||||| || |||||||| || ||||||| ||    || ||  | |   | ||| |||   ||  || | |  || |     | |     ||  |  ||| ||| | ||   || |    |  | | 
GAACAGGCACGGCGACTTCTTCTCTGCCCTGCTCAAGGCTCAGCCGCAGTTCCTCAATGACTGGAAGGCCAAGCTCTGGTCACGGTTCTTCTGCCTCTCGgtaatttcgagctattctcctgttaatatacatcagtt--agctccaaaggttgctgcgcccc-tctcctaacagctgt-gttactatatgaccttttgcag

upper sequence: GLYMA19G30350.1 (Glycine max), 5'ss of exon 3
lower sequence: AT3G56940.2 (Arabidopsis thaliana), 5'ss of exon 4
GAACAGGCATGGAGATTTCTTCTCTGCCCTGATGAAGGCACAGCCACAATTTCTAAATGACTGGAAGGCAAAGTTGTGGTCTCGATTCTTCTGTCTATCGgtaacttttcccttttgcttaccattatgcattcctttaagattcttagatgaaacctcaatacctagtgccagttgttgctagcttaaggttgtgagaa
|||| | ||||| ||||||||||||||  ||||||| || ||||| || || || ||||||||| | || ||| | |||||||| |||||||| || |||||||        ||   || | |  | |  | | ||  | |  ||||  |      |  ||   | |||   ||   | |||   |||  |         
GAACCGTCATGGTGATTTCTTCTCTGCTTTGATGAAAGCTCAGCCTCAGTTCCTCAATGACTGGCAAGCCAAGCTCTGGTCTCGCTTCTTCTGCCTCTCGgtaa--------ttaaactaaactctctttagttctcaatgtgtcttgcacattggcctaa---ccagtaagaggattggct---ttacag---------

upper sequence: GLYMA19G30350.1 (Glycine max), 5'ss of exon 3
lower sequence: Vv08s0040g00390.t01 (Vitis vinifera), 5'ss of exon 3
GAACAGGCATGGAGATTTCTTCTCTGCCCTGATGAAGGCACAGCCACAATTTCTAAATGACTGGAAGGCAAAGTTGTGGTCTCGATTCTTCTGTCTATCGgtaacttttcccttttgcttaccattatgcattccttta--agattcttagatgaaacctcaatacctagtgccagt-tgttgctagcttaaggttgt-gagaa--------------------------------------------------
|||||||||||| ||||||||||||||  ||||||||||||| || || || || ||||| |||||||||||||||||| ||||||||||||| |||||||||| | |    |  |   |  |   || || |  | ||  |||||   | ||   | || |||   |    | ||| ||||   | |||  | || | |||||                                                  
GAACAGGCATGGTGATTTCTTCTCTGCATTGATGAAGGCACAACCCCAGTTCCTCAATGATTGGAAGGCAAAGTTGTGGGCTCGATTCTTCTGCCTATCGgtaattatagtataataagtttctacattcaattgtatactagattgc-aaatattatcttaattttttaccctagtgtgtttaaatctttggcttctcgagaacctctgggattcctctggtcctcttatgacttcccaaatttgtcttgcag

upper sequence: GLYMA19G30350.1 (Glycine max), 5'ss of exon 3
lower sequence: PP1S97_248V6.1 (Physcomitrella patens), 5'ss of exon 2
GAACAGGCATGGAGATTTCTTCTCTGCCCTGATGAAGGCACAGCCACAATTTCTAAATGACTGGAAGGCAAAGTTGTGGTCTCGATTCTTCTGTCTATCGgtaacttttccctt--ttgcttaccattatgcattcctttaagattcttagatgaaacctcaatacctagtgccagtt--gttgctagct-taaggttgtgagaa
|||| | || || ||||||||||| || || |||||||||||||| || || ||||| ||||||||||| ||  | ||| |||| |||||||| || || |||| |||  |||   || ||| ||    || |||||| || |  |  |||||   | ||   |  | |      ||   | |  || || || ||   | |   
GAACCGTCACGGTGATTTCTTCTCGGCTCTCATGAAGGCACAGCCTCAGTTCCTAAACGACTGGAAGGCCAAACTTTGGGCTCGTTTCTTCTGCCTTTCTgtaagtttcacctccatttcttgcctgagtg-attcctgtatg--ttgtagatagtaactatctgacgatcttaggtctgggttttatctgtatggcacttaa--

upper sequence: GLYMA19G30350.1 (Glycine max), 5'ss of exon 3
lower sequence: PP1S239_18V6.2 (Physcomitrella patens), 5'ss of exon 2
GAACAGGCATGGAGATTTCTTCTCTGCCCTGATGAAGGCACAGCCACAATTTCTAAATGACTGGAAGGCAAAGTTGTGGTCTCGATTCTTCTGTCTATCGgtaacttttcccttttgcttaccattatgcattcctttaagattcttagatgaaacctcaatacctagtgc-cagttgttgctagcttaaggttgtgagaa
|||| | || || |||||||||||||| || |||||||||||||| || ||| | |||||||||||||| ||| | ||| |||| |||||||| || || |||| | || | || |   | |  ||      |    |  |   |   |||   |||   | ||   | ||    ||||   |   | ||   ||      
GAACCGTCACGGTGATTTCTTCTCTGCACTCATGAAGGCACAGCCCCAGTTTTTGAATGACTGGAAGGCCAAGCTCTGGGCTCGTTTCTTCTGCCTCTCTgtaagtatttcgttctttctgcttttccagtgtttgatgtgtcaccacgatcggaccctgacacaatgggcattcttgtcaatctttaaacactgcagtg-

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|151404600|gb|EV274414.1|EV274414
EST:     TTCTAAATGACTGGAAGGCAAAGTTGTGGTCTCGATTCTTCTGTCTATCG                         GTTTATGTTACAATGTATCTCAATGATTGCCAACGTACAGCTTTCTATGAA
genomic: TTCTAAATGACTGGAAGGCAAAGTTGTGGTCTCGATTCTTCTGTCTATCGgtaacttttc ... ttgtttgcagGTTTATGTTACAATGTATCTCAATGATTGCCAACGTACAGCTTTCTATGAA
EST: gi|209715892|gb|BW650905.1|BW650905
EST:     TTCTAAATGACTGGAAGGCAAAGTTGTGGTCTCGATTCTTCTGTCTATCG                         GTTTATGTTACAATGTATCTCAATGATTGCCAACGTACAGCTTTCTATGAA
genomic: TTCTAAATGACTGGAAGGCAAAGTTGTGGTCTCGATTCTTCTGTCTATCGgtaacttttc ... ttgtttgcagGTTTATGTTACAATGTATCTCAATGATTGCCAACGTACAGCTTTCTATGAA
EST: gi|151401411|gb|EV271225.1|EV271225
EST:     TTCTAAATGACTGGAAGGCAAAGTTGTGGTCTCGATTCTTCTGTCTATCG                         GTTTATGTTACAATGTATCTCAATGATTGCCAACGTACAGCTTTCTATGAA
genomic: TTCTAAATGACTGGAAGGCAAAGTTGTGGTCTCGATTCTTCTGTCTATCGgtaacttttc ... ttgtttgcagGTTTATGTTACAATGTATCTCAATGATTGCCAACGTACAGCTTTCTATGAA
EST: gi|209722212|gb|BW675058.1|BW675058
EST:     CTCGATTCTTCTGTCTATCG                         GTTTATGTTACAATGTATCTCAATGATTGCCAACGTACAGCTTCCTATGAA
genomic: CTCGATTCTTCTGTCTATCGgtaacttttc ... ttgtttgcagGTTTATGTTACAATGTATCTCAATGATTGCCAACGTACAGCTTTCTATGAA
EST: gi|20811475|gb|BQ295953.1|BQ295953
EST:     TTCTAAATGACTGGAAGGCAAAGTTGTGGTCTCGATTCTTCTGTCTATCG                         GTTTATGTTACAATGTATCTCAATGATTGCCAACGTACAGCTTTCTATGAA
genomic: TTCTAAATGACTGGAAGGCAAAGTTGTGGTCTCGATTCTTCTGTCTATCGgtaacttttc ... ttgtttgcagGTTTATGTTACAATGTATCTCAATGATTGCCAACGTACAGCTTTCTATGAA
EST: gi|151400167|gb|EV269981.1|EV269981
EST:     TTCTAAATGACTGGAAGGCAAAGTTGTGGTCTCGATTCTTCTGTCTATCG                         GTTTATGTTACAATGTATCTCAATGATTGCCAACGTACAGCTTTCTATGAA
genomic: TTCTAAATGACTGGAAGGCAAAGTTGTGGTCTCGATTCTTCTGTCTATCGgtaacttttc ... ttgtttgcagGTTTATGTTACAATGTATCTCAATGATTGCCAACGTACAGCTTTCTATGAA
EST: gi|192307925|gb|FG998942.1|FG998942
EST:     TTCTAAATGACTGGAAGGCAAAGTTGTGGTCTCGATTCTTCTGTCTATCG                         GTTTATGTTACAATGTATCTCAATGATTGCCAACGTACAGCTTTCTATGAA
genomic: TTCTAAATGACTGGAAGGCAAAGTTGTGGTCTCGATTCTTCTGTCTATCGgtaacttttc ... ttgtttgcagGTTTATGTTACAATGTATCTCAATGATTGCCAACGTACAGCTTTCTATGAA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAACAGGCATGGAGATTTCTTCTCTGCCCTGATGAAGGCACAGCCACAATTTCTAAATGACTGGAAGGCAAAGTTGTGGTCTCGATTCTTCTGTCTATCGgtaacttttcccttttgcttaccattatgcattcctttaagattcttagatgaaacctcaatacctagtgccagttgttgctagcttaaggttgtgagaa

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAAG