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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...attaatctgattgtttatgcatgccctttgtcctagattgtttgtcttatttcatgtcttttgtcatcatttatgcattcttacattacatttccatcagGAAACAAGGAAATCTATTTTCAGCAATATGGGCGATGGAATATAGATAAAATTTGGAGAGATGATGTGTTACCTTGTCGGGTTTATCTTCGACACTG

Basic information

species Glycine max
transcript GLYMA15G16320.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA15G16320.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv05s0077g01810.t01 (Vitis vinifera), 3'ss of exon 6
attaatctgattg-tttatgcatgccctttgtcctagattgtttgtcttatttcatgtcttttgtcatcatttatgcattcttacattacatttccat-cagGAAACAAGGAAATCTATTTTCAGCAATATGGGCGATGGAATATAGATAAAATTTGGAGAGATGATGTGTTACCTTGTCGGGTTTATCTTCGACACTG
  || |     ||  |    |||     ||||    |  |  || |   ||||| |  |   |||  |  | | |||    || |     | || ||| |||| | |||||| || | |||| |||||||||||||||  || ||  | || |||||| |||||||||| || ||||| || ||||||||||| |||||
tgtactgcagctgactcgatcattggacttgttaaggggtcatt-ttgaatttctttccacatgttcttctct-tgctaatttgctagctactttcatacagGGAGCAAGGAGATGTTTTTTGAGCAATATGGGCGATATAACATCCACAAGATTTGGCGAGATGATGTCTTCCCTTGCCGTGTTTATCTTCGGCACTG

upper sequence: GLYMA15G16320.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv05s0077g01800.t01 (Vitis vinifera), 3'ss of exon 6
attaatctgattgtttatgcatgccctttgtcctagattgtttgtcttatttcatgtcttttgtcatcattt-atgcattcttacattacatttccatcagGAAACAAGGAAATCTATTTTCAGCAATATGGGCGATGGAATATAGATAAAATTTGGAGAGATGATGTGTTACCTTGTCGGGTTTATCTTCGACACTG
 ||  | |  |  ||  |   | | |||| |||    ||| |  |  |  || |  | |          | | ||  ||| ||    |||  ||    ||||||  ||||| || ||||||||||||||||| ||    || ||  |||| |||||| |||||||||| |||||||| || |||||||||||||||||
tttttttttttaattcctttgtactctttttccgcctttgctgcttgtcattgaaatgtaggaatgcattctcatatatttttttgctactattatg-cagGAAGTAAGGAGATATATTTTCAGCAATATGGCCGCCATAACATCCATAAGATTTGGCGAGATGATGTTTTACCTTGCCGTGTTTATCTTCGACACTG
















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|209708043|gb|BW657085.1|BW657085
EST:     CCTTTGTGCTCGTTATAGTGATGAGGAATTTTTCGACAATAGATGTAAAG                         GAAACAAGGAAATCTATTTTCAGCAATATGGGCGATGGAATATAAATAAAA
genomic: CCTTTGTGCTCGTTATAGTGATGAGGAATTTTTCGACAATAGATGTAAAGgtaagtctcg ... tttccatcagGAAACAAGGAAATCTATTTTCAGCAATATGGGCGATGGAATATAGATAAAA
EST: gi|31307340|gb|CD392543.1|CD392543
EST:     CCTTTGTGCTCGTNATAGTGACGAGGAATTTTTCGACAATAGATGTAAAG                         GAAACAAGGAAATCTATTTTCAGCAATATGGGCGATGGAATATAGATAAAA
genomic: CCTTTGTGCTCGTTATAGTGATGAGGAATTTTTCGACAATAGATGTAAAGgtaagtctcg ... tttccatcagGAAACAAGGAAATCTATTTTCAGCAATATGGGCGATGGAATATAGATAAAA
EST: gi|14991401|gb|BI317074.1|BI317074
EST:     CCTTTGTGCTCGTTATAGTGATGAGGAATTTTTCGACAATAGATGTAAAG                         GAAACAAGGAAATCTATTTTCAGCAATATGGGCGATGGAATATAGATAAAA
genomic: CCTTTGTGCTCGTTATAGTGATGAGGAATTTTTCGACAATAGATGTAAAGgtaagtctcg ... tttccatcagGAAACAAGGAAATCTATTTTCAGCAATATGGGCGATGGAATATAGATAAAA
EST: gi|9819601|gb|BE555114.1|BE555114
EST:     CCTTTGTGCTCGTTATAGTGATGAGGAATTTTTCGACAATAGATGTAAAG                         GAAACAAGGAAATCTATTTTCAGCAATATGGGCGATGGAATATAGATAAAA
genomic: CCTTTGTGCTCGTTATAGTGATGAGGAATTTTTCGACAATAGATGTAAAGgtaagtctcg ... tttccatcagGAAACAAGGAAATCTATTTTCAGCAATATGGGCGATGGAATATAGATAAAA
EST: gi|31475024|gb|CD417052.1|CD417052
EST:     CCTTTGTGCTCGTTATAGTGACGAGGAATTTTTCGACAATAGATGTAAAG                         GAAACAAGGAAATCTATTTTCAGCAATATGGGCGATGGAATATAGATAAAA
genomic: CCTTTGTGCTCGTTATAGTGATGAGGAATTTTTCGACAATAGATGTAAAGgtaagtctcg ... tttccatcagGAAACAAGGAAATCTATTTTCAGCAATATGGGCGATGGAATATAGATAAAA
EST: gi|20207814|gb|BQ133903.1|BQ133903
EST:     CCTTTGTGCTCGTTATAGTGATGAGGAATTTTTCGACAATAGATGTAAAG                         GAAACAAGGAAATCTATTTTCAGCAATATGGGCGATGGAATATAGATAAAA
genomic: CCTTTGTGCTCGTTATAGTGATGAGGAATTTTTCGACAATAGATGTAAAGgtaagtctcg ... tttccatcagGAAACAAGGAAATCTATTTTCAGCAATATGGGCGATGGAATATAGATAAAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttatttcatgtcttttgtcatcatttatgcattcttacattacatttccatcagGAAACAAGGAAATCTATTTTCAGCAATATGGGCGATGGAATATAGATAAAATTTGGAGAGATGATGTGTTACCTTGTCGGGTTTATCTTCGACACTG
                                ttcttac  putative branch site (score: 2)
                                             tttccatc  putative PPT
                    atcatttat  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
attaatctgattgtttatgcatgccctttgtcctagattgtttgtcttatttcatgtcttttgtcatcatttatgcattcttacattacatttccatcagGAAACAAGGAAATCTATTTTCAGCAATATGGGCGATGGAATATAGATAAAATTTGGAGAGATGATGTGTTACCTTGTCGGGTTTATCTTCGACACTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATG
- - - ctgattg
- - - - - - - - - -catgccc
- - - - - - - - - - - - - - - - - - -ttgtttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgtcatc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gcattct