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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ggattgcacagtgatcgaacatttaaattttttatttttctagtgtgtatgttcggtatattaaatggattttttaatgttgtcatgcacttaatatcagATTGCAGATGTCTGGTCATGTGGAGTAACCTTGTTTGTGATGCTAGTGGGATCATATCCTTTTGAAGATCCTAATGATCCAAAGGATTTCCGGAAGACAA

Basic information

species Glycine max
transcript GLYMA01G39020.2
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA01G39020.2 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os03g41460.1 (Oryza sativa), 3'ss of exon 4
----------------------------------------------------------ggattgcacagtg----atcgaacatttaaattttttatttttctagtg--tgtatgttc-----ggtatattaaatggattttttaatgttgtcatgcacttaatatcagATTGCAGATGTCTGGTCATGTGGAGTAACCTTGTTTGTGATGCTAGTGGGATCATATCCTTTTGAAGATCCTAATGATCCAAAGGATTTCCGGAAGACAA
                                                          |  | | | | ||    |||  |||| ||   ||||      |  ||    ||||  |||     |    || |    ||||  | | |       ||    | |    ||||||| ||||| ||||| |||||||||||| | |  || ||||| || ||  ||||||||||||| |||||  |||| || ||| ||||| |||||||||
gtactcatatatttgaatttacatgcttgcgtcctgaatatggtgtcatggtgtctcagtctggtatattgatacatcatacatgtaccattttctccacttaagcaattgtactttcttcgcgaggcatcagtgcgattgctgactaaatatttgtttctcaacaaagATTGCTGATGTGTGGTCGTGTGGAGTAACCCTCTACGTAATGCTGGTTGGTGCATATCCTTTTGAGGATCCAGATGAGCCTAAGAATTTCAGGAAGACAA

upper sequence: GLYMA01G39020.2 (Glycine max), 3'ss of exon 6
lower sequence: Vv07s0197g00080.t01 (Vitis vinifera), 3'ss of exon 6
-ggattgcacagtgatcgaacattta--aattttttatttttctagtgtgta--tgttcggtatattaaatggattttttaatgttgtcatgcacttaatatcagATTGCAGATGTCTGGTCATGTGGAGTAACCTTGTTTGTGATGCTAGTGGGATCATATCCTTTTGAAGATCCTAATGATCCAAAGGATTTCCGGAAGACAA
 |  ||  |   || | ||   | |   |       | | ||  | | | ||  | |||     || ||||   |  ||| |  ||  ||       ||| |||||||||||| || ||||||||||| ||||| || | ||| ||||| || ||  ||||||||||||| |||||| |||| || ||||| ||||| || ||||
agttttttattctgcttgagtgtcttccagacacacagtgtttcattatctaattattcaaagaatcaaatttctggtttgacttttacaaa-----aatttcagATTGCAGACGTGTGGTCATGTGGGGTAACATTATATGTTATGCTTGTTGGTGCATATCCTTTTGAGGATCCTGATGAACCCAAGGACTTCCGAAAAACAA
















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|58015703|gb|CX702445.1|CX702445
EST:     CAGCATATATTGCTCCAGAAGTATTGCTGAAGCAAGAGTATGATGGCAAG                         ATTGCAGATGTCTGGTCATGTGGAGTAACCTTGTTTGTGATGCTAGTGGGA
genomic: CAGCATATATTGCTCCAGAAGTATTGCTGAAGCAAGAGTATGATGGCAAGgtagagtact ... ttaatatcagATTGCAGATGTCTGGTCATGTGGAGTAACCTTGTTTGTGATGCTAGTGGGA
EST: gi|7693434|gb|AW761526.1|AW761526
EST:     CAGCATATATTGCTCCAGAAGTATTGCTGAAGCAAGAGTATGATGGCAAG                         ATTGCAGATGTCTGGTCATGTGGAGTAACCTTGTTTGTGATGCTAGTGGGA
genomic: CAGCATATATTGCTCCAGAAGTATTGCTGAAGCAAGAGTATGATGGCAAGgtagagtact ... ttaatatcagATTGCAGATGTCTGGTCATGTGGAGTAACCTTGTTTGTGATGCTAGTGGGA
EST: gi|21888347|gb|BQ741560.1|BQ741560
EST:     CAGCATATATTGCTCCAGAAGTATTGCTGAAGCAAGAGTATGATGGCAAG                         ATTGCAGATGTCTGGTCATGTGGAGTAACCTTGTTTGTGATGCTAGTGGGA
genomic: CAGCATATATTGCTCCAGAAGTATTGCTGAAGCAAGAGTATGATGGCAAGgtagagtact ... ttaatatcagATTGCAGATGTCTGGTCATGTGGAGTAACCTTGTTTGTGATGCTAGTGGGA
EST: gi|27424851|gb|CA936371.1|CA936371
EST:     CAGCATATATTGCTCCAGAAGTATTGCTGAAGCAAGAGTATGATGGCAAG                         ATTGCAGATGTCTGGTCATGTGGAGTAACCTTGTTTGTGATGCTAGTGGGA
genomic: CAGCATATATTGCTCCAGAAGTATTGCTGAAGCAAGAGTATGATGGCAAGgtagagtact ... ttaatatcagATTGCAGATGTCTGGTCATGTGGAGTAACCTTGTTTGTGATGCTAGTGGGA
EST: gi|11413312|gb|BF425323.1|BF425323
EST:     CAGCATATATTGCTCCAGAAGTATTGCTGAAGCAAGAGTATGATGGCAAG                         ATTGCAGATGTCTGGTCATGTGGAGTAACCTTGTTTGTGATGCTAGTGGGA
genomic: CAGCATATATTGCTCCAGAAGTATTGCTGAAGCAAGAGTATGATGGCAAGgtagagtact ... ttaatatcagATTGCAGATGTCTGGTCATGTGGAGTAACCTTGTTTGTGATGCTAGTGGGA
EST: gi|58015395|gb|CX702137.1|CX702137
EST:     CAGCATATATTGCTCCAGAAGTATTGCTGAAGCAAGAGTATGATGGCAAG                         ATTGCAGATGTCTGGTCATGTGGAGTAACCTTGTTTGTGATGCTAGTGGGA
genomic: CAGCATATATTGCTCCAGAAGTATTGCTGAAGCAAGAGTATGATGGCAAGgtagagtact ... ttaatatcagATTGCAGATGTCTGGTCATGTGGAGTAACCTTGTTTGTGATGCTAGTGGGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtatgttcggtatattaaatggattttttaatgttgtcatgcacttaatatcagATTGCAGATGTCTGGTCATGTGGAGTAACCTTGTTTGTGATGCTAGTGGGATCATATCCTTTTGAAGATCCTAATGATCCAAAGGATTTCCGGAAGACAA
           tatattaaatggattt  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
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---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ggattgcacagtgatcgaacatttaaattttttatttttctagtgtgtatgttcggtatattaaatggattttttaatgttgtcatgcacttaatatcagATTGCAGATGTCTGGTCATGTGGAGTAACCTTGTTTGTGATGCTAGTGGGATCATATCCTTTTGAAGATCCTAATGATCCAAAGGATTTCCGGAAGACAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA