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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacagtctgttgctcatcttttttttatgcttttattagtggatctataattacatgttaataaagattattttcttgtgattcagGAACCCCTGCTCTCACATCTAGGGGATTTGTTGAGGAAGATTTTGAAAAAGTAGCTGAATACTTTGATGCGGCTGTCAAGTTAGCCTTGCAGATTAAGGA

Basic information

species Glycine max
transcript GLYMA14G36280.1
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA14G36280.1 (Glycine max), 3'ss of exon 13
lower sequence: Vv18s0001g07960.t01 (Vitis vinifera), 3'ss of exon 13
gtacagtctgttgctcatcttttttttatgcttttattagtggatctataattac---atgttaataaagattattttcttgtgat------tcagGAACCCCTGCTCTCACATCTAGGGGATTTGTTGAGGAAGATTTTGAAAAAGTAGCTGAATACTTTGATGCGGCTGTCAAGTTAGCCTTGCAGATTAAGGA
    ||| |  | ||| | | ||| |  ||| | || |  | | |  ||||||||   |  || || |||     | |||| || |      ||||||||||| ||||| ||||||||||||||||||||||| |||||||  |||||||| || |  |||||||| ||||||||||| || ||| |||| || | 
--gtagtgtactcctcctttgtttctcttgcctctactgattgctagataattacttcactttgatgaagtcatctctcttctgttggcacctcagGAACCCCAGCTCTTACATCTAGGGGATTTGTTGAGGAGGATTTTGTGAAAGTAGCCGAGTTATTTGATGCTGCTGTCAAGTTGGCTTTGAAGATCAAAGC
















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|6915301|gb|AW396831.1|AW396831
EST:     TACCGTTCCAGGGGATGTGTCTGCTATGGTTCCTGGAGGCATTCGAATGG                         GAACCCCTGCTCTCACATCTATGGGATTTGTTGAGGAAGATTTTGAAAAAG
genomic: TACCGTTCCAGGGGATGTGTCTGCTATGGTTCCTGGAGGCATTCGAATGGgtacagtctg ... tgtgattcagGAACCCCTGCTCTCACATCTAGGGGATTTGTTGAGGAAGATTTTGAAAAAG
EST: gi|7796703|gb|AW782097.1|AW782097
EST:     TACCGTTCCANGGGATGTGTCTGCTATGGTTCCTGGAGGCATTCGAATGG                         GAACCCCTGCTCTCACATCTAGGGGATCTGTTGAGGAAGATNNTGAAAAAG
genomic: TACCGTTCCAGGGGATGTGTCTGCTATGGTTCCTGGAGGCATTCGAATGGgtacagtctg ... tgtgattcagGAACCCCTGCTCTCACATCTAGGGGATTTGTTGAGGAAGATTTTGAAAAAG
EST: gi|151398597|gb|EV268468.1|EV268468
EST:     TACCGTTCCAGGGGATGTGTCTGCTATGGTTCCTGGAGGCATTCGAATGG                         GAACCCCTGCTCTCACATCTAGGGGATTTGTTGAGGAAGATTTTGAAAAAG
genomic: TACCGTTCCAGGGGATGTGTCTGCTATGGTTCCTGGAGGCATTCGAATGGgtacagtctg ... tgtgattcagGAACCCCTGCTCTCACATCTAGGGGATTTGTTGAGGAAGATTTTGAAAAAG
EST: gi|151409184|gb|EV278992.1|EV278992
EST:     TACCGTTCCAGGGGATGTGTCTGCTATGGTTCCTGGAGGCATTCGAATGG                         GAACCCCTGCTCTCACATCTAGGGGATTTGTTGAGGAAGATTTTGAAAAAG
genomic: TACCGTTCCAGGGGATGTGTCTGCTATGGTTCCTGGAGGCATTCGAATGGgtacagtctg ... tgtgattcagGAACCCCTGCTCTCACATCTAGGGGATTTGTTGAGGAAGATTTTGAAAAAG
EST: gi|22931163|gb|BU548302.1|BU548302
EST:     TACCGTTCCAGGGGATGTGTCTGCTATGGTTCNNNGAGGCATTCGAATGG                         GAACCCCTGCTCTCACATCTAGGGGATTTGTTGAGGAAGATTTTGAAAAAG
genomic: TACCGTTCCAGGGGATGTGTCTGCTATGGTTCCTGGAGGCATTCGAATGGgtacagtctg ... tgtgattcagGAACCCCTGCTCTCACATCTAGGGGATTTGTTGAGGAAGATTTTGAAAAAG
EST: gi|209724641|gb|BW651426.1|BW651426
EST:     TACCGTTCCAGGGGATGTGTCTGCTATGGTTCCTGGAGGCATTCGAATGG                         GAACCCCTGCTCTCACATCTAGGGGATTTGTTGAGGAAGATTTTGAAAAAG
genomic: TACCGTTCCAGGGGATGTGTCTGCTATGGTTCCTGGAGGCATTCGAATGGgtacagtctg ... tgtgattcagGAACCCCTGCTCTCACATCTAGGGGATTTGTTGAGGAAGATTTTGAAAAAG
EST: gi|192315079|gb|FK010449.1|FK010449
EST:     TACCGTTCCAGGGGATGTGCCTGCTATGGTTCCTGGAGGCATTCGAATGG                         GAACCCCTGCTCTCACATCTAGGGGATTTGTTGAGGAAGATTTTGAAAAAG
genomic: TACCGTTCCAGGGGATGTGTCTGCTATGGTTCCTGGAGGCATTCGAATGGgtacagtctg ... tgtgattcagGAACCCCTGCTCTCACATCTAGGGGATTTGTTGAGGAAGATTTTGAAAAAG
EST: gi|13240115|gb|BG359424.1|BG359424
EST:     TACCGTTCCAAGGGATGTGTCTGCTATGGTTCCTGGAGGCATTCGAATGG                         GAACCCCTGCTCTCACATCTAGGGGATTTGTTGAGGAAGATTTT
genomic: TACCGTTCCAGGGGATGTGTCTGCTATGGTTCCTGGAGGCATTCGAATGGgtacagtctg ... tgtgattcagGAACCCCTGCTCTCACATCTAGGGGATTTGTTGAGGAAGATTTT
EST: gi|192298247|gb|FG992067.1|FG992067
EST:     TACCGTTCCAGGGGATGTGTCTGCTATGGTTCCTGGAGGCATTCGAATGG                         GAACCCCTGCTCTCACATCTAGGGGATTTGTTGAGGAAGATTTTGAAAAAG
genomic: TACCGTTCCAGGGGATGTGTCTGCTATGGTTCCTGGAGGCATTCGAATGGgtacagtctg ... tgtgattcagGAACCCCTGCTCTCACATCTAGGGGATTTGTTGAGGAAGATTTTGAAAAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttattagtggatctataattacatgttaataaagattattttcttgtgattcagGAACCCCTGCTCTCACATCTAGGGGATTTGTTGAGGAAGATTTTGAAAAAGTAGCTGAATACTTTGATGCGGCTGTCAAGTTAGCCTTGCAGATTAAGGA
                        tgttaat  putative branch site (score: 3)
                                    ttattttctt  putative PPT
           atctataattacatgt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacagtctgttgctcatcttttttttatgcttttattagtggatctataattacatgttaataaagattattttcttgtgattcagGAACCCCTGCTCTCACATCTAGGGGATTTGTTGAGGAAGATTTTGAAAAAGTAGCTGAATACTTTGATGCGGCTGTCAAGTTAGCCTTGCAGATTAAGGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGAT