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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tattatgatttagaaagtaactttcacattgtctgatttttctgcttatttacttttgctacgaaagctgatgtgaaaagtgcattatttttgtgggcagGAAGGAGATTCTGTTGTAGCACATTTCGAATATCACAAGCACCCAATCACATCCATTGAGTGGAGTCCACATGAAGCCTCTTCATTGGCAGTTTCTTCAT

Basic information

species Glycine max
transcript GLYMA08G11020.1
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA08G11020.1 (Glycine max), 3'ss of exon 10
lower sequence: Vv11s0016g02270.t01 (Vitis vinifera), 3'ss of exon 9
-tattatgatttagaaagtaactttcacattgtctgatttttctgcttatttacttttgctacgaaagctgatgtgaaaagtgcattat----ttttgtgggcagGAAGGAGATTCTGTTGTAGCACATTTCGAATATCACAAGCACCCAATCACATCCATTGAGTGGAGTCCACATGAAGCCTCTTCATTGGCAGTTTCTTCAT
 || ||  | |  ||   | | ||  |    |||| ||| |   | | | | |   ||  |   |  | ||||||||    ||  ||||    |||| ||||||||| ||||||||||| ||||||||||| |||||||| || ||||| || ||||||||||| ||||| ||||||||||||||  ||||||||||||||||||
ttactaacagt-ggaggatgagttggag---gtctcattatggggatgaatcaggcttcttttcattgatgatgtgattc-tgttttatgctcttttttgggcagGATGGAGATTCTGTGGTAGCACATTTTGAATATCATAAACACCCCATTACATCCATTGAATGGAGCCCACATGAAGCCTCCACATTGGCAGTTTCTTCAT
















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|11273936|gb|BF324324.1|BF324324
EST:     CGGGGAGTGATGATGGGACTATATCTATTCGTGATCTCAGACTGCTCAAG                         GAAGGAGATTCTGTTGTAGCACATTTCGAATATCACAAGCACCCAATCACA
genomic: CGGGGAGTGATGATGGGACTATTTCTATTCGTGATCTCAGACTGCTCAAGgtataggtag ... ttgtgggcagGAAGGAGATTCTGTTGTAGCACATTTCGAATATCACAAGCACCCAATCACA
EST: gi|23729869|gb|BU763041.1|BU763041
EST:     CGGGGAGTGATGATGGGACTATTTCTATTCGTGATCTCAGACTGCTCAAG                         GAAGGAGATTCTGTTGTAGCACATTTCGAATATCACAAGCACCCAATCACA
genomic: CGGGGAGTGATGATGGGACTATTTCTATTCGTGATCTCAGACTGCTCAAGgtataggtag ... ttgtgggcagGAAGGAGATTCTGTTGTAGCACATTTCGAATATCACAAGCACCCAATCACA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttatttacttttgctacgaaagctgatgtgaaaagtgcattatttttgtgggcagGAAGGAGATTCTGTTGTAGCACATTTCGAATATCACAAGCACCCAATCACATCCATTGAGTGGAGTCCACATGAAGCCTCTTCATTGGCAGTTTCTTCAT
                    agctgat  putative branch site (score: 4)
                                       ttattttt  putative PPT
                                      attatttttgt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tattatgatttagaaagtaactttcacattgtctgatttttctgcttatttacttttgctacgaaagctgatgtgaaaagtgcattatttttgtgggcagGAAGGAGATTCTGTTGTAGCACATTTCGAATATCACAAGCACCCAATCACATCCATTGAGTGGAGTCCACATGAAGCCTCTTCATTGGCAGTTTCTTCAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC
- - - - - - - - - - ctttcac
- - - - - - - - - - - - - - ttgtctg
- - - - - - - - - - - - - - - - - - - -ttctgct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gctgatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgcatta