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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgaatcctgtaaagatattaacaacgtgcagttttctgatggtttaaaattttcactttatcaactataattgaagttttaatgagcataattgcaacagTTGTCAGGTGATATAAATGAGGAAGTGGATAGTCATAACCGGATGCTGGATCGTATG

Basic information

species Glycine max
transcript GLYMA10G04020.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA10G04020.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv07s0005g02990.t01 (Vitis vinifera), 3'ss of exon 3
---tgaatcctgta-aagatattaacaacgtgcagttttctgatggtttaaaattttcactttatcaactataattgaagttttaatgagcataattgcaacagTTGTCAGGTGATATAAATGAGGAAGTGGATAGTCATAACCGGATGCTGGATCGTATG
   | |   ||| |  |    ||||     ||  ||    | ||| | | || |  || |     | | | | | | |  ||||  |     | |||  |||||||| ||||||||||| ||||||| || || ||||||||||| |||||||||||  ||
ctttaagatctgaatgaagctttaaagttttgaggtgcattaatgatatcaa-taatcgcccaggcgaatgttaat-acattttgctc--tgtcattttaacagTTGACAGGTGATATACATGAGGAGGTTGAGAGTCATAACCGCATGCTGGATCGAGTG
















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|208043026|gb|GD841886.1|GD841886
EST:     ATGAACAAGCATTGGATGGATTGCAAGATAGAGTCAATCTGCTTAAAAGA                         TTGTCAGGTGATATAAATGAGGAAGTGGATAGTCATAACCGGATGCTGGAT
genomic: ATGAACAAGCATTGGATGGATTGCAAGATAGAGTCAATCTGCTTAAAAGAgtaaacattt ... attgcaacagTTGTCAGGTGATATAAATGAGGAAGTGGATAGTCATAACCGGATGCTGGAT
EST: gi|193430346|gb|FK393292.1|FK393292
EST:     TCAATCTGCTTAAAAGA                         TTGTCAGGTGATATAAATGAGGAAGTGGATAGTCATAACCGGATGCTGGAT
genomic: TCAATCTGCTTAAAAGAgtaaacattt ... attgcaacagTTGTCAGGTGATATAAATGAGGAAGTGGATAGTCATAACCGGATGCTGGAT
EST: gi|192323181|gb|FK018952.1|FK018952
EST:     ATGAACAAGCATTGGATGGATTGCAAGATAGAGTCAATCTGCTTAAAAGA                         TTGTCAGGTGATATAAATGAGGAAGTGGATAGTCATAACCGGATGCTGGAT
genomic: ATGAACAAGCATTGGATGGATTGCAAGATAGAGTCAATCTGCTTAAAAGAgtaaacattt ... attgcaacagTTGTCAGGTGATATAAATGAGGAAGTGGATAGTCATAACCGGATGCTGGAT
EST: gi|192298747|gb|FG988613.1|FG988613
EST:     ATGAACAAGCATTGGATGGATTGCAAGATAGAGTCAATCTGCTTAAAAGA                         TTGTCAGGTGATATAAATGAGGAAGTGGATAGTCATAACCGGATGCTGGAT
genomic: ATGAACAAGCATTGGATGGATTGCAAGATAGAGTCAATCTGCTTAAAAGAgtaaacattt ... attgcaacagTTGTCAGGTGATATAAATGAGGAAGTGGATAGTCATAACCGGATGCTGGAT
EST: gi|31306277|gb|CD391480.1|CD391480
EST:     ATGAACAAGCATTGGATGGATTGCAAGATAGAGTCAATCTGCTTAAAAGA                         TTGTCAGGTGATATAAATGAGGAAGTGGATAGTCATAACCGGATGCTGGAT
genomic: ATGAACAAGCATTGGATGGATTGCAAGATAGAGTCAATCTGCTTAAAAGAgtaaacattt ... attgcaacagTTGTCAGGTGATATAAATGAGGAAGTGGATAGTCATAACCGGATGCTGGAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaaattttcactttatcaactataattgaagttttaatgagcataattgcaacagTTGTCAGGTGATATAAATGAGGAAGTGGATAGTCATAACCGGATGCTGGATCGTATG
                               ttttaat  putative branch site (score: 3)
           tttatcaactataatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgaatcctgtaaagatattaacaacgtgcagttttctgatggtttaaaattttcactttatcaactataattgaagttttaatgagcataattgcaacagTTGTCAGGTGATATAAATGAGGAAGTGGATAGTCATAACCGGATGCTGGATCGTATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - tcctgta
- - - - - - - - - - - - - tgcagtt
- - - - - - - - - - - - - - - - - tctgatg