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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttgtgcgctgtgctctcgctgatatatgtttctcttgtccgtgtaaattattatatatagaagcacccaatttttaactaaattggctaatcaacttcttttgttttgttttcatctagTTCCTGCCAGTGGTGGAAGGAACCGGGATAGGATCCCTGGAGAGGGAGCAAACTGAAAAAATATTGAACAAGATCATCTCCAAGAATTCTCATAACATAC

Basic information

species Glycine max
transcript GLYMA13G23700.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA13G23700.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv15s0048g02730.t01 (Vitis vinifera), 3'ss of exon 6
gttgtgcgctgtgctctcgctgatatatgtttctcttgtccgtgtaaattattatatatagaagcacccaatttttaactaaattggctaatcaacttcttttgttttgttttcatctagTTCCTGCCAGTGGTGGAAGGAACCGGGATAGGATCCCTGGAGAGGGAGCAAACTGAAAAAATATTGAACAAGATCATCTCCAAGAATTCTCATAACATAC
| || | | | || | | || |||| || | || || | | || | ||| | || | | || ||||| || ||||||||||| || |||||||| || || || ||||| || |||| | |||||||||||||||| ||||||||| | |||||||||||||| ||| | ||||
------------------gtctgtacacataaccctattaca-gtgaattcttcagttctt---ttcctaactataaaatctgatgg--agctgacataatccatt--gtttttatttagTTCCTGCCGGTAGTGGAAGGGACAGGAATTGGATCACTAGAGAAGCAGCAAACTGAAAAAATTTTGAACAAGCTAATCTCCAAGAATTCCCATGAGATAC

upper sequence: GLYMA13G23700.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv15s0046g01120.t01 (Vitis vinifera), 3'ss of exon 6
gttgtgcgctgtgctctcgctgatatatgtttctcttgtccgtgtaaattattatatatagaagcacccaatttttaactaaattggctaatcaacttcttttgttttgttttcatctagTTCCTGCCAGTGGTGGAAGGAACCGGGATAGGATCCCTGGAGAGGGAGCAAACTGAAAAAATATTGAACAAGATCATCTCCAAGAATTCTCATAACATAC
| | | | |||| || || |||| || | | || | | | | ||| | | || | | ||||||| | |||||||||||||| ||||||||||| || || ||||| | |||| | |||||||||||||| | ||||| | | | |||||||||||||| ||| | ||||
------------------gtctgtgcacataactct-gttaccgtgaattcttcagttctttttcttcctaaatcttaaggaatcactgacttcacctttccc-ccttgtttttgtttagTTCCTGCCAGTAGTGGAAGGAACAGGAATTGGATCACAAGAGAAGCAGCAAACTGAAAAAGTTTTGAATAGGCTAATCTCCAAGAATTCCCATGAGATAC
















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|207679622|gb|GD663572.1|GD663572
EST:     AGAAATTGGCAGGTGAAAAGCCTCAGAAACATGAAGGAAAATATCGGAAG                         TTCCTGCCAGTGGTGGAAGGAACCGGGATAGGATCCCTGGAGAGGGAGCAA
genomic: AGAAATTGGCAGGTGAAAAGCCTCAGAAACATGAAGGAAAATATCGGAAGgttgtgcgct ... tttcatctagTTCCTGCCAGTGGTGGAAGGAACCGGGATAGGATCCCTGGAGAGGGAGCAA
EST: gi|254320386|gb|GR826403.1|GR826403
EST:     AGAAATTGGCAGGTGAAAAGCCTCAGAAACATGAAGGAAAATATCGGAAG                         TTCCTGCCAGTGGTGGAAGGAACCGGGATAGGATCCCTGGAGAGGGAGCAA
genomic: AGAAATTGGCAGGTGAAAAGCCTCAGAAACATGAAGGAAAATATCGGAAGgttgtgcgct ... tttcatctagTTCCTGCCAGTGGTGGAAGGAACCGGGATAGGATCCCTGGAGAGGGAGCAA
EST: gi|193675378|gb|FK616466.1|FK616466
EST:     AGAAATTGGCAGGTGAAAAGCCTCAGAAACATGAAGGAAAATATCGGAAG                         TTCCTGCCAGTGGTGGAAGGAACCGGGATAGGATCCCTGGAGAGGGAGCAA
genomic: AGAAATTGGCAGGTGAAAAGCCTCAGAAACATGAAGGAAAATATCGGAAGgttgtgcgct ... tttcatctagTTCCTGCCAGTGGTGGAAGGAACCGGGATAGGATCCCTGGAGAGGGAGCAA
EST: gi|207826496|gb|GD798193.1|GD798193
EST:     AGAAATTGGCAGGTGAAAAGCCTCAGAAACATGAAGGAAAATATCGGAAG                         TTCCTGCCAGTGGTGGAAGGAACCGGGATAGGATCCCTGGAGAGGGAGCAA
genomic: AGAAATTGGCAGGTGAAAAGCCTCAGAAACATGAAGGAAAATATCGGAAGgttgtgcgct ... tttcatctagTTCCTGCCAGTGGTGGAAGGAACCGGGATAGGATCCCTGGAGAGGGAGCAA
EST: gi|208039255|gb|GD832341.1|GD832341
EST:     AGAAATTGGCAGGTGAAAAGCCTCAGAAACATGAAGGAAAATATCGGAAG                         TTCCTGCCAGTGGTGGAAGGAACCGGGATAGGATCCCTGGAGAGGGAGCAA
genomic: AGAAATTGGCAGGTGAAAAGCCTCAGAAACATGAAGGAAAATATCGGAAGgttgtgcgct ... tttcatctagTTCCTGCCAGTGGTGGAAGGAACCGGGATAGGATCCCTGGAGAGGGAGCAA
EST: gi|193581998|gb|FK536909.1|FK536909
EST:     AGAAATTGGCAGGTGAAAAGCCTCAGAAACATGAAGGAAAATATCGGAAG                         TTCCTGCCAGTGGTGGAAGGAACCGGGATAGGATCCCTGGAGAGGGAGCAA
genomic: AGAAATTGGCAGGTGAAAAGCCTCAGAAACATGAAGGAAAATATCGGAAGgttgtgcgct ... tttcatctagTTCCTGCCAGTGGTGGAAGGAACCGGGATAGGATCCCTGGAGAGGGAGCAA
EST: gi|15204065|gb|BI426833.1|BI426833
EST:     AGAAATTGGCAGGTGAAAAGCCTCAGAAACATGAAGGAAAATATCGGAAG                         TTCCTGCCAGTGGTGGAAGGAACCGGGATAGGATCCCTGGAGAGGGAGCAA
genomic: AGAAATTGGCAGGTGAAAAGCCTCAGAAACATGAAGGAAAATATCGGAAGgttgtgcgct ... tttcatctagTTCCTGCCAGTGGTGGAAGGAACCGGGATAGGATCCCTGGAGAGGGAGCAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acccaatttttaactaaattggctaatcaacttcttttgttttgttttcatctagTTCCTGCCAGTGGTGGAAGGAACCGGGATAGGATCCCTGGAGAGGGAGCAAACTGAAAAAATATTGAACAAGATCATCTCCAAGAATTCTCATAACATAC
                              cttcttttgttttgtt  CT-rich tract
 atttttaactaaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttgtgcgctgtgctctcgctgatatatgtttctcttgtccgtgtaaattattatatatagaagcacccaatttttaactaaattggctaatcaacttcttttgttttgttttcatctagTTCCTGCCAGTGGTGGAAGGAACCGGGATAGGATCCCTGGAGAGGGAGCAAACTGAAAAAATATTGAACAAGATCATCTCCAAGAATTCTCATAACATAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA