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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...attaagctgtactcttaatataggaggatgcttactgcttagaattcatgaagctttgttgattaaatttgataacttgaattttctgtcatgcctccagGTTCTTGGTGAGGCAAATCAGCGAGATATAGTAGAGTTTTGCAAGCAAGAAGGTTTGGTTCTTTTAGCTGATGAG

Basic information

species Glycine max
transcript GLYMA07G05130.1
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA07G05130.1 (Glycine max), 3'ss of exon 9
lower sequence: AT1G72330.3 (Arabidopsis thaliana), 3'ss of exon 9
attaagctgtactcttaatataggaggatgcttactgcttagaattcatgaagctttgttgattaaatttgataacttgaattttctgtcatgcctccagGTTCTTGGTGAGGCAAATCAGCGAGATATAGTAGAGTTTTGCAAGCAAGAAGGTTTGGTTCTTTTAGCTGATGAG-------------------------
                  || |    |||  | |   ||   |    |  ||  | |        | | |  |||  |    ||  | |  ||  |  |||||||||  || | ||| ||||| || || ||  | || ||||||||||| |||||||||||||||||||||||                          
-----------------gtacaaacagattttcaagact---agcctaacaaaatgtaac-----attcttctaatcttgcgttcttattctggtt--agGTTCTTGCGGAAGAAAACCAGCGTGACATTGTTAATTTCTGCAAGCAAGAGGGTTTGGTTCTTTTAGCTGATGAAGTCTACCAAGAAAATGTTTACGTCC
















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|21677454|gb|BQ629805.1|BQ629805
EST:     TCAATGTTAGGGCTTTAGTTGTTATAAATCCTGGCAATCCAACGGGGCAG                         GTTCTTGGTGAGGCAAATCAGCGAGATATAGTAGAGTTTTGCAAGCAAGAA
genomic: TCAATGTTAGGGCTTTAGTTGTTATAAATCCTGGCAATCCAACGGGGCAGgtgagcggca ... atgcctccagGTTCTTGGTGAGGCAAATCAGCGAGATATAGTAGAGTTTTGCAAGCAAGAA
EST: gi|14999909|gb|BI320723.1|BI320723
EST:     TCAATGTTAGGGCTTTAGTTGTTATAAATCCTGGCAATCCAACGGGGCAG                         GTTCTTGGTGAGGCAAATCAGCGAGATATAGTAGAGTTTTGCAAGCAAGAA
genomic: TCAATGTTAGGGCTTTAGTTGTTATAAATCCTGGCAATCCAACGGGGCAGgtgagcggca ... atgcctccagGTTCTTGGTGAGGCAAATCAGCGAGATATAGTAGAGTTTTGCAAGCAAGAA
EST: gi|21888381|gb|BQ741594.1|BQ741594
EST:     TCAATGTTAGGGCTTTAGTTGTTATAAATCCTGGCAATCCAACGGGGCAG                         GTTCTTGGTGAGGCAAATCAGCGAGATATAGTAGAGTTTTGCAAGCAAGAA
genomic: TCAATGTTAGGGCTTTAGTTGTTATAAATCCTGGCAATCCAACGGGGCAGgtgagcggca ... atgcctccagGTTCTTGGTGAGGCAAATCAGCGAGATATAGTAGAGTTTTGCAAGCAAGAA
EST: gi|208039408|gb|GD836778.1|GD836778
EST:     TAGGGCTTTAGTTGTTATAAATCCTGGCAATCCAACGGGGCAG                         GTTCTTGGTGAGGCAAATCAGCGAGATATAGTAGAGTTTTGCAAGCAAGAA
genomic: TAGGGCTTTAGTTGTTATAAATCCTGGCAATCCAACGGGGCAGgtgagcggca ... atgcctccagGTTCTTGGTGAGGCAAATCAGCGAGATATAGTAGAGTTTTGCAAGCAAGAA
EST: gi|17021823|gb|BM092857.1|BM092857
EST:     TGGCAATCCAACGGGGCAG                         GTTCTTGGTGAGGCAAATCAGCGAGATATAGTAGAGTTTTGCAAGCAAGAA
genomic: TGGCAATCCAACGGGGCAGgtgagcggca ... atgcctccagGTTCTTGGTGAGGCAAATCAGCGAGATATAGTAGAGTTTTGCAAGCAAGAA
EST: gi|254337075|gb|GR844965.1|GR844965
EST:     GGCAATCCAACGGGGCAG                         GTTCTTGGTGAGGCAAATCAGCGAGATATAGTAGAGTTTTGCAAGCAAGAA
genomic: GGCAATCCAACGGGGCAGgtgagcggca ... atgcctccagGTTCTTGGTGAGGCAAATCAGCGAGATATAGTAGAGTTTTGCAAGCAAGAA
EST: gi|9258266|gb|BE346413.1|BE346413
EST:     TCAATGTTAGGGCTTTAGTTGTTATAAATCCTGGCAATCCAACGGGGCAG                         GTTCTTGGTGAGGCAAATCAGCGAGATATAGTAGAGTTTTGCAAGCACGAA
genomic: TCAATGTTAGGGCTTTAGTTGTTATAAATCCTGGCAATCCAACGGGGCAGgtgagcggca ... atgcctccagGTTCTTGGTGAGGCAAATCAGCGAGATATAGTAGAGTTTTGCAAGCAAGAA
EST: gi|58024010|gb|CX710751.1|CX710751
EST:     CCAACGGGGCAG                         GTTCTGGGTGAGGCAAATCAGCGAGATATAGTAGAG-TTTGCAAGCAAGAA
genomic: CCAACGGGGCAGgtgagcggca ... atgcctccagGTTCTTGGTGAGGCAAATCAGCGAGATATAGTAGAGTTTTGCAAGCAAGAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcatgaagctttgttgattaaatttgataacttgaattttctgtcatgcctccagGTTCTTGGTGAGGCAAATCAGCGAGATATAGTAGAGTTTTGCAAGCAAGAAGGTTTGGTTCTTTTAGCTGATGAG
                        tgataac  putative branch site (score: 2)
                                              tgcctcc  putative PPT
             ttgattaaatttgata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
attaagctgtactcttaatataggaggatgcttactgcttagaattcatgaagctttgttgattaaatttgataacttgaattttctgtcatgcctccagGTTCTTGGTGAGGCAAATCAGCGAGATATAGTAGAGTTTTGCAAGCAAGAAGGTTTGGTTCTTTTAGCTGATGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
- - agctgta
- - - - - - - - - - - - -ggatgct
- - - - - - - - - - - - - - - - tactgct
- - - - - - - - - - - - - - - - - - - - - - ttcatga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - tgttgat