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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgtgtggtcattttgcactggaatatggggcattttcatgctttgccatgttgcaagagttaatagtataatatcagaattctaatgctaacctctacagGCCACAATCTTGAAACCTGCTGTAATGATTGGTACAGAGGATCGGATTTTGAATCCATGGGCTCATTTTGCTAAAAAGTATGGCTTTCTTCCGTTGTTTG

Basic information

species Glycine max
transcript GLYMA13G18950.1
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA13G18950.1 (Glycine max), 3'ss of exon 7
lower sequence: LOC_Os02g57180.2 (Oryza sativa), 3'ss of exon 5
-----------tgtgtggtcattttgcactggaatatggggcattttcatgctttg-------ccatgttgca--agagttaatagt--ataatatcagaattctaat-gctaacctctacagGCCACAATCTTGAAACCTGCTGTAATGATTGGTACAGAGGATCGGATTTTGAATCCATGGGCTCATTTTGCTAAAAAGTATGGCTTTCTTCCGTTGTTTG
             |  ||  ||  || |||    | |    ||||  |     ||         |||||  ||     |||   |||   |   | || |||| |  | ||     || |||||| |||||  |||  |||||    |||||||| ||||| |||||||||||||||  |||||| || ||||| ||||| |  || || || ||  |  |||
gtgatcatctacattaggcaatactgaactcctgtttcta-cattaccgaaagttagaagcaaacatgtcccatttatgttggcagttactttaaccaaaattttgtttgcatggatcaacagGCTACAATTATGAGGCCTGCAACTATGATTGGCACAGAAGATCGGATTTTGAATAGATGGGCACAGTTTGCCAAAAATTGGGGTTTCCTCCCTCTTGTTG

upper sequence: GLYMA13G18950.1 (Glycine max), 3'ss of exon 7
lower sequence: Vv07s0005g04440.t01 (Vitis vinifera), 3'ss of exon 7
tgtgtggtcattttgcactg-gaatatggggcattttcatgctttgccatgttgcaagagttaatagtat-aatatcagaattc-taatgctaacctctac----agGCCACAATCTTGAAACCTGCTGTAATGATTGGTACAGAGGATCGGATTTTGAATCCATGGGCTCATTTTGCTAAAAAGTATGGCTTTCTTCCGTTGTTTG
       |    ||| |  | | | |  |   || || |   ||||  || |    |   | ||||   | || ||| |||||| |||||    | || ||    ||||||||||  ||| ||| |||||||||||||||||||||||||||||| |||| |  ||||| || ||||| ||||| ||||||||| | ||  | | ||
-----attttgcttggatggtgcacaaagaatatctttacaatttg--atttcctgatgctgaatatcttgaaaatcggaattcctaatgtatgcttccactttcagGCCACAATTATGAGACCGGCTGTAATGATTGGTACAGAGGATCGGATTCTGAACCGGTGGGCACAATTTGCAAAAAAATATGGCTTTTTGCCTCTCTATG
















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|151398563|gb|EV268434.1|EV268434
EST:     TCAGAACTAAATCAGCTGCTGAGGAAATGATTTTAAGGGA-CTACCTGAG                         GCCACAGTCTTGAAA
genomic: TCAGAACTAAATCAGCTGCTGAGGAAATGATTTTAAGGGAACTACCTGAGgtacatttaa ... acctctacagGCCACAATCTTGAAA
EST: gi|151403355|gb|EV273165.1|EV273165
EST:     CAGAACTAAATCAGCTGCTGAGGAAATGATTTTAAAGGGAACTACCTGAG                         GCCACAATCTTGAAACCTGCTGTAATGATTGGTACAGAGGATCGGATTTTG
genomic: CAGAACTAAATCAGCTGCTGAGGAAATGATTTTAA-GGGAACTACCTGAGgtacatttaa ... acctctacagGCCACAATCTTGAAACCTGCTGTAATGATTGGTACAGAGGATCGGATTTTG
EST: gi|254347887|gb|GR854136.1|GR854136
EST:     TCAGAACTAAATCAGCTGCTGAGGAAATGATTTTAAGG-AACTACCTGAG                         GCCACAATCTTGAAACCTGCTGTAATGATTGGTACAGAGGATCGGATTTTG
genomic: TCAGAACTAAATCAGCTGCTGAGGAAATGATTTTAAGGGAACTACCTGAGgtacatttaa ... acctctacagGCCACAATCTTGAAACCTGCTGTAATGATTGGTACAGAGGATCGGATTTTG
EST: gi|151397287|gb|EV267160.1|EV267160
EST:     TCAGAACTAAATCAGCTGCTGAGGAAATGATTTTAAGGGAACTACCTGAG                         GCCACAATCTTGAAACCTGCTGTAATGATTGGTACAGAGGATCGGATTTTG
genomic: TCAGAACTAAATCAGCTGCTGAGGAAATGATTTTAAGGGAACTACCTGAGgtacatttaa ... acctctacagGCCACAATCTTGAAACCTGCTGTAATGATTGGTACAGAGGATCGGATTTTG
EST: gi|48575725|gb|CO036542.1|CO036542
EST:     TCAGAACTAAATCAGCTGCTGAGGAAATGATTTTAAGGGAACTACCTGAG                         GCCACAATCTTGAAACCTGCTGTAATGATTGGTAC
genomic: TCAGAACTAAATCAGCTGCTGAGGAAATGATTTTAAGGGAACTACCTGAGgtacatttaa ... acctctacagGCCACAATCTTGAAACCTGCTGTAATGATTGGTAC
EST: gi|192312568|gb|FK005026.1|FK005026
EST:     CCAGAACTAAATCAGCTGCTGAGGAAATGATTTTAAGGGAACTACCTGAG                         -CCACAATCTTGAA-CCTGCTGTAATGAT-GGTACAGAG-ATCGGATTT-G
genomic: TCAGAACTAAATCAGCTGCTGAGGAAATGATTTTAAGGGAACTACCTGAGgtacatttaa ... acctctacagGCCACAATCTTGAAACCTGCTGTAATGATTGGTACAGAGGATCGGATTTTG
EST: gi|192300056|gb|FG991860.1|FG991860
EST:     TCAGAACTAAATCAGCTGCTGAGGAAATGATTTTAAGGGAACTACCTGAG                         GCCACAATCTTGAAACCTGCTGTAATGATTGGTACAGAGGATCGGATTTTG
genomic: TCAGAACTAAATCAGCTGCTGAGGAAATGATTTTAAGGGAACTACCTGAGgtacatttaa ... acctctacagGCCACAATCTTGAAACCTGCTGTAATGATTGGTACAGAGGATCGGATTTTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccatgttgcaagagttaatagtataatatcagaattctaatgctaacctctacagGCCACAATCTTGAAACCTGCTGTAATGATTGGTACAGAGGATCGGATTTTGAATCCATGGGCTCATTTTGCTAAAAAGTATGGCTTTCTTCCGTTGTTTG
                                        tgctaac  putative branch site (score: 1)
                                              cctctac  CT-rich tract
              ttaatagtataatatc  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgtgtggtcattttgcactggaatatggggcattttcatgctttgccatgttgcaagagttaatagtataatatcagaattctaatgctaacctctacagGCCACAATCTTGAAACCTGCTGTAATGATTGGTACAGAGGATCGGATTTTGAATCCATGGGCTCATTTTGCTAAAAAGTATGGCTTTCTTCCGTTGTTTG

tgtgtgg
- - - - - - -tgcactg
- - - - - - - - - - - - - - ggcattt
- - - - - - - - - - - - - - - - - - - - - - - - - -tgcaaga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctaatgc