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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tcaggcctcaacttcaaatactggaaggccaagtttactgttttgtgcatgtagatagtagtgttgtcttcttatctgatgtagaattaatcctttgcagAATGAGGATAGAACCCTCTGGAAGCTTGGAACCTTACCCCCAGGACTAATCACCTTTTATAATCTGACCTATCCGTTAGATCGAGGCTGGCATGTTTTGG

Basic information

species Glycine max
transcript GLYMA05G09200.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA05G09200.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv03s0038g03750.t01 (Vitis vinifera), 3'ss of exon 5
tcaggcctcaacttcaaatactggaaggccaagtttactgttttg-tgcatgtagatagtagtgttgtcttcttatctgat--gtagaattaatcctttgcagAATGAGGATAGAACCCTCTGGAAGCTTGGAACCTTACCCCCAGGACTAATCACCTTTTATAATCTGACCTATCCGTTAGATCGAGGCTGGCATGTTTTGG
   |        | ||   ||   |||   | |  | || ||    | ||| || |   |    |  || || |     |   ||  || |  |  |||||||||||| |||||||| |||||||| |||||| | || || || ||||| ||||| || || || ||||| ||||| || |||||  |||||||||| ||||
---gatgatttttccagtcacccaaagaaaatgcctcctattccaatacatctaaaatttttcttcatcatcattcacaactcgtctaaatcctgttttgcagAATGAAGATAGAACTCTCTGGAAACTTGGATCGTTGCCACCGGGACTGATCACTTTCTACAACCTGACATATCCATTGGATCGTAGCTGGCATGTGTTGG

upper sequence: GLYMA05G09200.1 (Glycine max), 3'ss of exon 4
lower sequence: EFJ28191 (Selaginella moellendorffii), 3'ss of exon 3
tcaggcctcaacttcaaatactggaaggccaagtttactgttttgtgcatgtagatagtagtgttgtcttcttatctgatgtagaattaatcctttgcagAATGAGGATAGAACCCTCTGGAAGCTTGGAACCTTACCCCCAGGACTAATCACCTTTTATAATCTGACCTATCCGTTAGATCGAGGCTGGCATGTTTTGG
                                            ||    ||     | |  ||  |      || ||   ||   |   ||  ||||||||  ||||||| || ||||||||||| |||||||| || || ||||| |||||||| || || || || || ||| | ||   |  |||||| ||  |||
--------------------------------------------gtaagcgttttctggaaagtc-taaaacgatgtggc-taagctctttctcttgcagAACAAGGATAGGACACTCTGGAAGCTGGGAACCTTGCCTCCGGGACTCATCACCTTCTACAACCTCACGTACCCGCTCGACAAATCCTGGCACGTCCTGG

upper sequence: GLYMA05G09200.1 (Glycine max), 3'ss of exon 4
lower sequence: EFJ29683 (Selaginella moellendorffii), 3'ss of exon 3
tcaggcctcaacttcaaatactggaaggccaagtttactgttttgtgcatgtagatagtagtgttgtcttcttatctgatgtagaattaatcctttgcagAATGAGGATAGAACCCTCTGGAAGCTTGGAACCTTACCCCCAGGACTAATCACCTTTTATAATCTGACCTATCCGTTAGATCGAGGCTGGCATGTTTTGG
                                            ||    ||   | | |  ||  |      || ||   ||   |   ||  ||||||||  ||||||| || ||||||||||| |||||||| || || ||||| |||||||| || || || || || ||| | ||   |  |||||| ||  |||
--------------------------------------------gtaagcgttttttggaaagtc-taaaacgatgtggc-taagctctttctcttgcagAACAAGGATAGGACACTCTGGAAGCTGGGAACCTTGCCTCCGGGACTCATCACCTTCTACAACCTCACGTACCCGCTCGACAAATCCTGGCACGTCCTGG

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|208108290|gb|GD902074.1|GD902074
EST:     AGTGGAAGAAACGAAACATCACTGGTATCTATCATCGGTGGCAAGATATG                         AATGAGGATAGAACCCTCTGGAA
genomic: AGTGGAAGAAACGAAACATCACTGGTATCTATCATCGGTGGCAAGATATGgtaaatttca ... tcctttgcagAATGAGGATAGAACCCTCTGGAA
EST: gi|208233739|gb|GE030934.1|GE030934
EST:     AGTGGAAGAAACGAAACATCACTGGTATCTATCATCGGTGGCAAGATATG                         AATGAGGATAGAACCCTCTGGAAGCTTGGAACCTTACCCCCAGGACTAATC
genomic: AGTGGAAGAAACGAAACATCACTGGTATCTATCATCGGTGGCAAGATATGgtaaatttca ... tcctttgcagAATGAGGATAGAACCCTCTGGAAGCTTGGAACCTTACCCCCAGGACTAATC
EST: gi|208276429|gb|GE079049.1|GE079049
EST:     AGTGGAAGAAACGAAACATCACTGGTATCTATCATCGGTGGCAAGATATG                         AATGAGGATAGAACCCTCTGGAAGCTTGGAACCTTACCCC-AGGACTAATC
genomic: AGTGGAAGAAACGAAACATCACTGGTATCTATCATCGGTGGCAAGATATGgtaaatttca ... tcctttgcagAATGAGGATAGAACCCTCTGGAAGCTTGGAACCTTACCCCCAGGACTAATC
EST: gi|208235806|gb|GE033772.1|GE033772
EST:     AGTGGAAGAAACGAAACATCACTGGTATCTATCATCGGTGGCAAGATATG                         AATGAGGATAGAACCCTCTGGAAGCTTGGAACCTTACCCCCAGGACTAATC
genomic: AGTGGAAGAAACGAAACATCACTGGTATCTATCATCGGTGGCAAGATATGgtaaatttca ... tcctttgcagAATGAGGATAGAACCCTCTGGAAGCTTGGAACCTTACCCCCAGGACTAATC
EST: gi|7286252|gb|AW598739.1|AW598739
EST:     CATCACTGGTATCTATCATCGGTGGCCAGATATG                         AATGAGGATACAACCCTCTGGAAGCTTGGAACCTTACCCCCAGGACTAATC
genomic: CATCACTGGTATCTATCATCGGTGGCAAGATATGgtaaatttca ... tcctttgcagAATGAGGATAGAACCCTCTGGAAGCTTGGAACCTTACCCCCAGGACTAATC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgcatgtagatagtagtgttgtcttcttatctgatgtagaattaatcctttgcagAATGAGGATAGAACCCTCTGGAAGCTTGGAACCTTACCCCCAGGACTAATCACCTTTTATAATCTGACCTATCCGTTAGATCGAGGCTGGCATGTTTTGG
                                       aattaat  putative branch site (score: 3)
                                             tcctttgc  CT-rich tract
                                    tagaattaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tcaggcctcaacttcaaatactggaaggccaagtttactgttttgtgcatgtagatagtagtgttgtcttcttatctgatgtagaattaatcctttgcagAATGAGGATAGAACCCTCTGGAAGCTTGGAACCTTACCCCCAGGACTAATCACCTTTTATAATCTGACCTATCCGTTAGATCGAGGCTGGCATGTTTTGG

- - -cctcaac
- - - - - - - - - - -tggaagg
- - - - - - - - - - - - - - - - - - - tgttttg
- - - - - - - - - - - - - - - - - - - - - - - gcatgta