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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagccttcttttatttaccttctgtcctcaatgcattaaatacaacgtttttcagcctaaactttatgcaaaataccttgtcagGTTTGTTAAGGACTACAATCAACAAATTGAAGCAAGAGAGATGCATCACTCCCAAGCTCATTTTTATTCGAGGAGGGCATGATGATGCCTCAATTTTTGA

Basic information

species Glycine max
transcript GLYMA12G09540.1
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA12G09540.1 (Glycine max), 3'ss of exon 13
lower sequence: Vv06s0080g00510.t01 (Vitis vinifera), 3'ss of exon 13
gtaagccttcttttatttaccttctgtcctcaatgcattaaatacaacgttt----ttcagcctaaactttatg----caaaataccttgt----cagGTTTGTTAAGGACTACAATCAACAAATTGAAGCAAGAGAGATGCATCACTCCCAAGCTCATTTTTATTCGAGGAGGGCATGATGATGCCTCAATTTTTGA
|||||     ||| |||    | ||| |||| ||  |   |||| |   ||      |  | |  || || ||     | ||||  ||| |    ||||||| ||  | |||||||||||||||||||||||||||||| | |||||||| |||||  | ||||| || |||||||| ||||||||  ||   |||||
gtaagttgattttaattg--ttgctg-cctccatagaaccaatatagttttcaaaactgggacagaatttgattttgtctaaatgtcttctactacagGTTTATTGCGCACTACAATCAACAAATTGAAGCAAGAGAGAAGTATCACTCCAAAGCTTCTATTTATCCGGGGAGGGCAGGATGATGCTACAGCATTTGA
















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|209714787|gb|BW657342.1|BW657342
EST:     TTATTCTTCGACTGCAGACCCGACACTTCCTTTTCCTCCACCCCATGATT                         GTTTGTTAAGGACTACAATCAACAAATTGAAGCAAGAGAGATGCATCACTC
genomic: TTATTCTTCGACTGCAGACCCGACACTTCCTTTTCCTCCACCCCATGATTgtaagccttc ... accttgtcagGTTTGTTAAGGACTACAATCAACAAATTGAAGCAAGAGAGATGCATCACTC
EST: gi|22525871|gb|BU084682.1|BU084682
EST:     TTATTCTTCGACTGCAGACCCGACACTTCCTTTTCCTCCACCCCATGATT                         GTTTGTTAAGGACTACAATCAACAAATTGAAGCAAGAGAGATGCATCACTC
genomic: TTATTCTTCGACTGCAGACCCGACACTTCCTTTTCCTCCACCCCATGATTgtaagccttc ... accttgtcagGTTTGTTAAGGACTACAATCAACAAATTGAAGCAAGAGAGATGCATCACTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aatgcattaaatacaacgtttttcagcctaaactttatgcaaaataccttgtcagGTTTGTTAAGGACTACAATCAACAAATTGAAGCAAGAGAGATGCATCACTCCCAAGCTCATTTTTATTCGAGGAGGGCATGATGATGCCTCAATTTTTGA
                         gcctaaa  putative branch site (score: 3)
                                              ccttgtc  putative PPT
     attaaatacaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagccttcttttatttaccttctgtcctcaatgcattaaatacaacgtttttcagcctaaactttatgcaaaataccttgtcagGTTTGTTAAGGACTACAATCAACAAATTGAAGCAAGAGAGATGCATCACTCCCAAGCTCATTTTTATTCGAGGAGGGCATGATGATGCCTCAATTTTTGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG