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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTCTGTGAAGAAGATTATTGAAATTAATCCGTATATGCTTGGGACAATGGCTGGAGGTGCTGCTGATTGTCAGTTTTGGCACAGGAATCTTGGGATCAAGgtaatctatgcaaccttgaaccttgtatattgcatggttgcttttgtctgttctgttatctttaggtcagtctcctgcaaaatttctgccctagtttccc...

Basic information

species Glycine max
transcript GLYMA06G17960.1
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA06G17960.1 (Glycine max), 5'ss of exon 4
lower sequence: LOC_Os06g06030.1 (Oryza sativa), 5'ss of exon 3
GTCTGTGAAGAAGATTATTGAAATTAATCCGTATATGCTTGGGACAATGGCTGGAGGTGCTGCTGATTGTCAGTTTTGGCACAGGAATCTTGGGATCAAGgtaatctatgcaaccttgaaccttgtatattgcatggttgcttttgtctgt---tctgttatctttaggtcagtctcctgcaaaatttctgccctagtttccc
  |||||| ||| ||||||||||| |||||||| |||||||| |||||||| |||||||||||||||||||| |||||||| |||||  | || |||||||| |  | | |||| |         |  ||| |||  ||||      ||     |  |||||  ||   ||||                              
AACTGTGAGGAAAATTATTGAAATAAATCCGTACATGCTTGGAACAATGGCAGGAGGTGCTGCTGATTGTCAATTTTGGCATAGGAACTTGGGCATCAAGgttagattt-caacttgattgtacttgcatttcatcattgcagagaactaaaagtaggttatgcttt--tcag------------------------------

upper sequence: GLYMA06G17960.1 (Glycine max), 5'ss of exon 4
lower sequence: GRMZM2G102596_T02 (Zea mays), 5'ss of exon 3
GTCTGTGAAGAAGATTATTGAAATTAATCCGTATATGCTTGGGACAATGGCTGGAGGTGCTGCTGATTGTCAGTTTTGGCACAGGAATCTTGGGATCAAGgt--aatctatgcaaccttgaaccttgtatattgcatggttgcttttgtctgttctgttatctttaggtcagtctcctgcaaaatttctgccctagtttccc
  | |||| ||| ||||||||||| ||||| || ||||| ||||||||||||||||||||||||||||| || |||||||| ||||| || || | ||||||   |  |  ||  ||||  |     ||| |   ||| ||||   |   ||    ||     | |  |  ||    | ||                     
AACCGTGAGGAAAATTATTGAAATAAATCCTTACATGCTGGGGACAATGGCTGGAGGTGCTGCTGATTGCCAATTTTGGCATAGGAACCTAGGAACCAAGgtcagaagtcggcttcctttcaataattatctcttatg-ttgcccct--ttgcagggtggggctaacataggttcttttcag--------------------

upper sequence: GLYMA06G17960.1 (Glycine max), 5'ss of exon 4
lower sequence: AT1G13060.1 (Arabidopsis thaliana), 5'ss of exon 4
GTCTGTGAAGAAGATTATTGAAATTAATCCGTATATGCTTGGGACAATGGCTGGAGGTGCTGCTGATTGTCAGTTTTGGCACAGGAATCTTGGGATCAAGgtaatctat--gcaaccttgaaccttgtatattgcatggttgcttttgtctgttctgttatctttaggtcagtctcctgcaaaatttctgc--cctagtttccc
 ||||||||||||||||||||||| ||||| |||||||| || |||||||||||||| ||||||||||| || || |||||||| |||||||| || ||||||    |   | || |||       || | |    || |  |||   ||| ||   | ||||||   || ||      |   | |  |||  ||| |||    
ATCTGTGAAGAAGATTATTGAAATCAATCCTTATATGCTCGGTACAATGGCTGGAGGAGCTGCTGATTGCCAATTCTGGCACAGAAATCTTGGAATTAAGgtacctaactagaaatctttttggccgtgtctgaactgataacttggatct-ttgattaatctttctctctgtggttatcgggaatcttgctgccttgtta---

upper sequence: GLYMA06G17960.1 (Glycine max), 5'ss of exon 4
lower sequence: AT3G26340.1 (Arabidopsis thaliana), 5'ss of exon 4
GTCTGTGAAGAAGATTATTGAAATTAATCCGTATATGCTTGGGACAATGGCTGGAGGTGCTGCTGATTGTCAGTTTTGGCACAGGAATCTTGGGATCAAGgtaatcta-tgcaaccttg----aaccttgtatattgcatggttgcttttgtctgttctgttatctttaggtcagtctcctgcaaaatttctgccctagtttccc
 ||||||||||||||||||||||||||||| ||||||||||| ||||||||||| ||||||||||||||||| || |||||||| ||||| || || ||||||  |||  |  |  ||     | | || |  |||| ||| |||  | | || ||| | ||  | ||      |    | |   | ||  | || |   ||   
ATCTGTGAAGAAGATTATTGAAATTAATCCTTATATGCTTGGTACAATGGCTGGTGGTGCTGCTGATTGTCAATTCTGGCACAGAAATCTGGGAATTAAGgtaccctaacgttagtttttgttagctttctgaattg-atgattgggtctatcagttatctt--ccttgctgtggcaatccggttacttcttaccttcccttt--

upper sequence: GLYMA06G17960.1 (Glycine max), 5'ss of exon 4
lower sequence: Vv01s0010g02900.t01 (Vitis vinifera), 5'ss of exon 4
GTCTGTGAAGAAGATTATTGAAATTAATCCGTATATGCTTGGGACAATGGCTGGAGGTGCTGCTGATTGTCAGTTTTGGCACAGGAATCTTGGGATCAAGgtaatctatgcaaccttgaaccttgtatattgcatggttgcttttgtctgt--tctgttatctttaggtcagtctcctgcaaaatttctgcc-ctagtttccc
 ||||||||||| ||||||||||||||||| || |||||||| |||||||||||||| ||||||||||| |||||||||||||| ||| | || || |||||||| |||      |||     | ||  |||||   ||  |   | ||||  |||   ||  ||| |  |   |     |  | |  | |  ||| | |   
ATCTGTGAAGAAAATTATTGAAATTAATCCCTACATGCTTGGCACAATGGCTGGAGGAGCTGCTGATTGCCAGTTTTGGCACAGAAATTTGGGCATTAAGgtaatgtatttt-tgttgttttctctaatttgcactctttttcaggcctgtgatctacaataattatggaatgatttgatagtactggttctgctactgta--

upper sequence: GLYMA06G17960.1 (Glycine max), 5'ss of exon 4
lower sequence: PP1S2_300V6.1 (Physcomitrella patens), 5'ss of exon 3
GTCTGTGAAGAAGATTATTGAAATTAATCCGTATATGCTTGGGACAATGGCTGGAGGTGCTGCTGATTGTCAGTTTTGGCACAGGAATCTTGGGATCAAGgtaa-tctatgcaaccttgaaccttgtatattgcatggttgcttttgtctgttctgttatctttaggtcagtctcc-tgcaaaatttctgccctagtttccc--
 || |||||||| ||| | ||||| || || ||  || | || |||||||||||||||||||| |||||||||||||||||  | ||||| || |     |||  || | | |   |||   ||| ||  ||   ||  ||   | |     |  | | |   || ||   | | | |||||     || |     |  |    
ATCGGTGAAGAAAATTTTGGAAATCAACCCTTACTTGTTGGGCACAATGGCTGGAGGTGCTGCAGATTGTCAGTTTTGGCAACGAAATCTAGGCACACGAgtatctcaacgtacttttgttgcttcta-gttctctgaatg---tagaacagtaggctgtgagtatgtggatgttcatgcaagtcaactactgggatcacagta

upper sequence: GLYMA06G17960.1 (Glycine max), 5'ss of exon 4
lower sequence: PP1S39_347V6.1 (Physcomitrella patens), 5'ss of exon 3
GTCTGTGAAGAAGATTATTGAAATTAATCCGTATATGCTTGGGACAATGGCTGGAGGTGCTGCTGATTGTCAGTTTTGGCACAGGAATCTTGGGATCAAGgtaatctatgcaaccttgaac-cttgtatattgcatggttgcttttgtctgttctgttatctttaggtcagtctcctg--caaaatttctgccctagtttccc
 || |||||||| ||| | || || || || ||  || | || || ||||| |||||||| ||||||||||||||||||||  |||||||||| |    |||| |  |  | || || |   |||   |  | |||  |||     ||  |   ||   | |  |  |   | |  ||  ||  |||   ||    | |    
ATCGGTGAAGAAAATTCTGGAGATCAACCCCTACTTGTTGGGCACTATGGCGGGAGGTGCCGCTGATTGTCAGTTTTGGCAACGGAATCTTGGCACTCGGgtacttcaacctactttcattgctttggttcttcatttttgggacggtacgcagtgaattgtggatcttgattttttgtgcaggattctcgcatgtgcta---

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|57574193|gb|CX547168.1|CX547168
EST:     CTGGAGGTGCTGCTGATTGTCAGTTTTGGCACAGGAATCTTGGGATCAAG                         TGTCGTTTGCACGAGTTGGCAAATAAAAGGAGAATTTCAGTGACAGGAGCC
genomic: CTGGAGGTGCTGCTGATTGTCAGTTTTGGCACAGGAATCTTGGGATCAAGgtaatctatg ... ttatttgtagTGTCGTTTGCACGAGTTGGCAAATAAAAGGAGAATTTCAGTGACAGGAGCC
EST: gi|192326892|gb|FK015134.1|FK015134
EST:     CTGGAGGTGCTGCTGATTGTCAGTTTTGGCACAGGAATCTTGGGAACAAG                         TGTCGTTTGCACGAGTTGGCAAATAAAAGGAGAATTTCAGTGACAGGAGCC
genomic: CTGGAGGTGCTGCTGATTGTCAGTTTTGGCACAGGAATCTTGGGATCAAGgtaatctatg ... ttatttgtagTGTCGTTTGCACGAGTTGGCAAATAAAAGGAGAATTTCAGTGACAGGAGCC
EST: gi|192317518|gb|FK008970.1|FK008970
EST:     CTGGAGGTGCTGCTGATTGTCAGTTTTGGCACAGGAATCTTGGGATCAAG                         TGTCGTTTGCACGAGTTGGCAAATAAAAGGAGAATTTCAGTGACAGGAGCC
genomic: CTGGAGGTGCTGCTGATTGTCAGTTTTGGCACAGGAATCTTGGGATCAAGgtaatctatg ... ttatttgtagTGTCGTTTGCACGAGTTGGCAAATAAAAGGAGAATTTCAGTGACAGGAGCC
EST: gi|193530927|gb|FK487504.1|FK487504
EST:     CTGGAGGTGCTGCTGATTGTCAGTTTTGGCACAGGAATCTTGGGATCAAG                         TGTCGTTTGCACGA
genomic: CTGGAGGTGCTGCTGATTGTCAGTTTTGGCACAGGAATCTTGGGATCAAGgtaatctatg ... ttatttgtagTGTCGTTTGCACGA
EST: gi|209696468|gb|BW664017.1|BW664017
EST:     CTGGAGGTGCTGCTGATTGTCAGTTTTGGCACAGGAATCTTGGGATCAAG                         TGTCGTTTGCACGAGTTGGCAAATAAAAGGAGAATTTCAGTGACAGGAGCC
genomic: CTGGAGGTGCTGCTGATTGTCAGTTTTGGCACAGGAATCTTGGGATCAAGgtaatctatg ... ttatttgtagTGTCGTTTGCACGAGTTGGCAAATAAAAGGAGAATTTCAGTGACAGGAGCC
EST: gi|151396982|gb|EV266855.1|EV266855
EST:     CTGGAGGTGCTGCTGATTGTCAGTTTTGGCACAGGAATCTTGGGATCAAG                         TGTCGTTTGCACGAGTTGGCAAATAAAAGGAGAATTTCAGTGACAGGAGCC
genomic: CTGGAGGTGCTGCTGATTGTCAGTTTTGGCACAGGAATCTTGGGATCAAGgtaatctatg ... ttatttgtagTGTCGTTTGCACGAGTTGGCAAATAAAAGGAGAATTTCAGTGACAGGAGCC
EST: gi|6724865|gb|AW309264.1|AW309264
EST:     CAGTTTTGGCACAGGAATCTGGGGATCAAG                         GGTCGTTTGCACGAGTTGGC-AATAAAAGGAGAATTTCAGTGACAGGAGCC
genomic: CAGTTTTGGCACAGGAATCTTGGGATCAAGgtaatctatg ... ttatttgtagTGTCGTTTGCACGAGTTGGCAAATAAAAGGAGAATTTCAGTGACAGGAGCC
EST: gi|207769493|gb|GD742101.1|GD742101
EST:     CTGGAGGTGCTGCTGATTGTCAGTTTTGGCACAGGAATCTTGGGATCAAG                         TGTCGTTTGCACGAGTTGGCAAATAAAAGGAGAATTTCAGTGACAGGAGCC
genomic: CTGGAGGTGCTGCTGATTGTCAGTTTTGGCACAGGAATCTTGGGATCAAGgtaatctatg ... ttatttgtagTGTCGTTTGCACGAGTTGGCAAATAAAAGGAGAATTTCAGTGACAGGAGCC
EST: gi|6502012|gb|AW203385.1|AW203385
EST:     CTGGAGGTGCTGCTGATTGTCAGTTTTGGCACAGGAATCTTGGGATCAAG                         TGTCGTTTGCACGAGTTGGCAAATAAAAGGAGAATT
genomic: CTGGAGGTGCTGCTGATTGTCAGTTTTGGCACAGGAATCTTGGGATCAAGgtaatctatg ... ttatttgtagTGTCGTTTGCACGAGTTGGCAAATAAAAGGAGAATT
EST: gi|209722634|gb|BW682710.1|BW682710
EST:     CTGGAGGTGCTGCTGATTGTCAGTTTTGGCACAGGAATCTTGGGATCAAG                         TGTCGTTTGCACGAGTTGGCAAATAAAAGGAGAATTTCAGTGACAGGAGCC
genomic: CTGGAGGTGCTGCTGATTGTCAGTTTTGGCACAGGAATCTTGGGATCAAGgtaatctatg ... ttatttgtagTGTCGTTTGCACGAGTTGGCAAATAAAAGGAGAATTTCAGTGACAGGAGCC
EST: gi|57574361|gb|CX547336.1|CX547336
EST:     CTGGAGGTGCTGCTGATTGTCAGTTTTGGCACAGGAATCTTGGGATCAAG                         TGTCGTTTGCACGAGTTGGCAAATAAAAGGAGAATTTCAGTGACAGGAGCC
genomic: CTGGAGGTGCTGCTGATTGTCAGTTTTGGCACAGGAATCTTGGGATCAAGgtaatctatg ... ttatttgtagTGTCGTTTGCACGAGTTGGCAAATAAAAGGAGAATTTCAGTGACAGGAGCC
EST: gi|9440180|gb|BE440690.1|BE440690
EST:     CTGGAGGTGCTGCTGATTGTCAGTTTTGGCACAGGAATCTTGGGATCAAG                         TGTCGTTTGCACGAGTTGGCAAATAAAAGGAGAATTTCAGTGACAGGAGCC
genomic: CTGGAGGTGCTGCTGATTGTCAGTTTTGGCACAGGAATCTTGGGATCAAGgtaatctatg ... ttatttgtagTGTCGTTTGCACGAGTTGGCAAATAAAAGGAGAATTTCAGTGACAGGAGCC
EST: gi|17023638|gb|BM094672.1|BM094672
EST:     CTGGAGGTGCTGCTGATTGTCAGTTTTGGCACAGGAATCTTGGGATCAAG                         TGTCGTTTGCACGAGTTGGCAAATAAAAGGAGAATTTCAGTGACAGGAGCC
genomic: CTGGAGGTGCTGCTGATTGTCAGTTTTGGCACAGGAATCTTGGGATCAAGgtaatctatg ... ttatttgtagTGTCGTTTGCACGAGTTGGCAAATAAAAGGAGAATTTCAGTGACAGGAGCC
EST: gi|120532998|gb|EH261131.1|EH261131
EST:     CTGGAGGTGCTGCTGATTGTCAGTTTTGGCACAGGAATCTTGGGATCAAG                         TGTCGTTTGCACGAGTTGGCAAATAAAAGGAGAATTTCAGTGACAGGAGCC
genomic: CTGGAGGTGCTGCTGATTGTCAGTTTTGGCACAGGAATCTTGGGATCAAGgtaatctatg ... ttatttgtagTGTCGTTTGCACGAGTTGGCAAATAAAAGGAGAATTTCAGTGACAGGAGCC
EST: gi|298182845|gb|HO031580.1|HO031580
EST:     CTGGAGGTGCTGCTGATTGTCAGTTTTGGCACAGGAATCTTGGGATCAAG                         TGTCGTTTGCACGAGTTGGCAAATAAAAGGAGAATTTCAGTGACAGGAGCC
genomic: CTGGAGGTGCTGCTGATTGTCAGTTTTGGCACAGGAATCTTGGGATCAAGgtaatctatg ... ttatttgtagTGTCGTTTGCACGAGTTGGCAAATAAAAGGAGAATTTCAGTGACAGGAGCC
EST: gi|21639185|gb|BM140231.1|BM140231
EST:     CTGGAGGTGCTGCTGATTGTCAGTTTTGGCACAGGAATCTTGGGATCAAG                         TGTCGTTTGCACGAGTTGGCAAATAAAAGGGGAATTTCAGTGACAGGAGCC
genomic: CTGGAGGTGCTGCTGATTGTCAGTTTTGGCACAGGAATCTTGGGATCAAGgtaatctatg ... ttatttgtagTGTCGTTTGCACGAGTTGGCAAATAAAAGGAGAATTTCAGTGACAGGAGCC
EST: gi|254332573|gb|GR846511.1|GR846511
EST:     CTGGAGGTGCTGCTGATTGTCAGTTTTGGCACAGGAATCTTGGGATCAAG                         TGTCGTTTGCACGAGTTGGCAAATAAAAGGAGAATTTCAGTGACAGGAGCC
genomic: CTGGAGGTGCTGCTGATTGTCAGTTTTGGCACAGGAATCTTGGGATCAAGgtaatctatg ... ttatttgtagTGTCGTTTGCACGAGTTGGCAAATAAAAGGAGAATTTCAGTGACAGGAGCC
EST: gi|120533057|gb|EH261190.1|EH261190
EST:     CTGGAGGTGCTGCTGATTGTCAGTTTTGGCACAGGAATCTTGGGATCAAG                         TGTCGTTTGCACGAGTTGGCAAATAAAAGGAGAATTTCAGTGACAGGAGCC
genomic: CTGGAGGTGCTGCTGATTGTCAGTTTTGGCACAGGAATCTTGGGATCAAGgtaatctatg ... ttatttgtagTGTCGTTTGCACGAGTTGGCAAATAAAAGGAGAATTTCAGTGACAGGAGCC
EST: gi|151402945|gb|EV272758.1|EV272758
EST:     CTGGAGGTGCTGCTGATTGTCAGTTTTGGCACAGGAATCTTGGGATCAAG                         TGTCGTTTGCACGAGTTGGCAAATAAAAGGAGAATTTCAGTGACAGGAGCC
genomic: CTGGAGGTGCTGCTGATTGTCAGTTTTGGCACAGGAATCTTGGGATCAAGgtaatctatg ... ttatttgtagTGTCGTTTGCACGAGTTGGCAAATAAAAGGAGAATTTCAGTGACAGGAGCC
EST: gi|298181007|gb|HO022446.1|HO022446
EST:     CTGGAGGTGCTGCTGATTGTCAGTTTTGGCACAGGAATCTTGGGATCAAG                         TGTCGTTTGCACGAGTTGGCAAATAAAAGGAGAATTTCAGTGACAGGAGCC
genomic: CTGGAGGTGCTGCTGATTGTCAGTTTTGGCACAGGAATCTTGGGATCAAGgtaatctatg ... ttatttgtagTGTCGTTTGCACGAGTTGGCAAATAAAAGGAGAATTTCAGTGACAGGAGCC
EST: gi|4314044|gb|AI461163.1|AI461163
EST:     CTGGAAGTGCTGCTGATTGTCAGTTTTGGCACAGGAATCTTGGGATCAAG                         TGTCGTTTGCACGAGTTGGCAAATAAAAGGAGAATTTCAGTGACAGGAGCC
genomic: CTGGAGGTGCTGCTGATTGTCAGTTTTGGCACAGGAATCTTGGGATCAAGgtaatctatg ... ttatttgtagTGTCGTTTGCACGAGTTGGCAAATAAAAGGAGAATTTCAGTGACAGGAGCC
EST: gi|213599779|gb|DB968429.1|DB968429
EST:     CTGGAGGTGCTGCTGATTGTCAGTTTTGGCACAGGAATCTTGGGATCAAG                         TGTCGTTTGCACGAGTTGGCAAATAAAAGGAGAATTTCAGTGACAGGAGCC
genomic: CTGGAGGTGCTGCTGATTGTCAGTTTTGGCACAGGAATCTTGGGATCAAGgtaatctatg ... ttatttgtagTGTCGTTTGCACGAGTTGGCAAATAAAAGGAGAATTTCAGTGACAGGAGCC
EST: gi|19345836|gb|BM890716.1|BM890716
EST:     CTGGAGGTGCTGCTGATTGTCAGTTTTGGCACAGGAATCTTGGGATCAAG                         TGTCGTTTGCACGAGTTGGCAAATAAAAGGAGAATTTCAGTGACAGGAGCC
genomic: CTGGAGGTGCTGCTGATTGTCAGTTTTGGCACAGGAATCTTGGGATCAAGgtaatctatg ... ttatttgtagTGTCGTTTGCACGAGTTGGCAAATAAAAGGAGAATTTCAGTGACAGGAGCC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTCTGTGAAGAAGATTATTGAAATTAATCCGTATATGCTTGGGACAATGGCTGGAGGTGCTGCTGATTGTCAGTTTTGGCACAGGAATCTTGGGATCAAGgtaatctatgcaaccttgaaccttgtatattgcatggttgcttttgtctgttctgttatctttaggtcagtctcctgcaaaatttctgccctagtttccc

- - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGAT