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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atatgagccctgtatcgtttccatacttactattctttttctgatcttagactttgagggatgcaattagtaaattgaccgagcttttttgtttttgtagGAAATTAAGTTTGAACCAAATGTCATGTGTGAACCTATTGACAAGAAAGTAACATTTCGAACAAGCCAG

Basic information

species Glycine max
transcript GLYMA20G11330.1
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA20G11330.1 (Glycine max), 3'ss of exon 11
lower sequence: LOC_Os12g30540.1 (Oryza sativa), 3'ss of exon 19
----atatgagccctgtatcgtttccat-acttactattctttttctgat-cttagactttgagggatgcaattagtaaattgaccgagcttttttgtttttgtagGAAATTAAGTTTGAACCAAATGTCATGTGTGAACCTATTGACAAGAAAGTAACATTTCGAACAAGCCAG
     | |      | || | || |  | ||||   | |  | |  |||| |||   |  |||   |  |  | ||  | ||| |     |||| || |   | |||||||||||||||| |||||||| ||||| ||||  |||||||||||| |||| || ||  | || |||
tattgtgttgttaatatagcattactctgacttgaaagtgatgtagtgatgcttttcccatgattaacactctgagctatttggc---atttttatgct---gcagGAAATTAAGTTTGAGCCAAATGTGATGTGCGAACACATTGACAAGAAACTAACTTTCCGTTCCAGTCAG

upper sequence: GLYMA20G11330.1 (Glycine max), 3'ss of exon 11
lower sequence: GRMZM2G303655_T01 (Zea mays), 3'ss of exon 9
atatgagccctgtatcgtttccatacttactattctttttctgatctta--gactttgagggatgcaattagtaaattgaccgagcttttttgtttttgtagGAAATTAAGTTTGAACCAAATGTCATGTGTGAACCTATTGACAAGAAAGTAACATTTCGAACAAGCCAG
  || |    | ||  ||    | |  |  |   |||       || |   ||  ||      |  |||      ||        | || || || | | |||||||||||||||| |||||||| ||||| |||| ||||||||||||| | || || ||  | || |||
-aataattaatttaatgtagtaaaatgttgtgcacttaacgatgtcgtgatgatcttcccaagttgaatattctgatgcttttgacattcttattct-gcagGAAATTAAGTTTGAGCCAAATGTGATGTGCGAACATATTGACAAGAAACTTACTTTCCGCTCTAGTCAG

upper sequence: GLYMA20G11330.1 (Glycine max), 3'ss of exon 11
lower sequence: GRMZM2G014805_T01 (Zea mays), 3'ss of exon 19
----atatgagccctgtatcgt-ttccatacttactattctttttctgatcttagactttgagggatgcaattagtaaattgaccgagcttttttgtttttgtagGAAATTAAGTTTGAACCAAATGTCATGTGTGAACCTATTGACAAGAAAGTAACATTTCGAACAAGCCAG
     | | |     |||   | ||    ||||| || |  | |  ||||  |   ||||    | || |  |  |||       ||  || || ||| ||  |||||||||||||||| |||||||| ||||| |||| ||||||||||||| | || || ||  | || |||
gtcattgttaatgtagtacaatgttatgcacttaataatgatgtcgtgatgat---ctttccaagttgaatattctaatgcttttgaaattctt-gttctt-cagGAAATTAAGTTTGAGCCAAATGTGATGTGCGAACATATTGACAAGAAACTTACTTTCCGTTCTAGTCAG

upper sequence: GLYMA20G11330.1 (Glycine max), 3'ss of exon 11
lower sequence: Vv06s0009g00960.t01 (Vitis vinifera), 3'ss of exon 19
----atatgagccctgtatcgtttccatacttactattctttttctgatcttagactttgagggatgcaattagtaaattgaccgagcttttttgtttttgtagGAAATTAAGTTTGAACCAAATGTCATGTGTGAACCTATTGACAAGAAAGTAACATTTCGAACAAGCCAG
    ||| |  ||  || |       |||        | |    || |  ||| | || | |        ||| |   || | |   |||| |  | ||   ||||||| |||||||| || | ||||||||||||||| ||||| |||||| | ||||| ||| | ||||||
ttgaata-ggaccaagtgttaaccttatataagactgtgtagaact-acattataattagtgaaggcatcttattttcttaatcatcctttgtgatgttc--agGAAATCAAGTTTGATCCTAGTGTCATGTGTGAACCCATTGATAAGAAATTCACATTCCGAGCTAGCCAG

upper sequence: GLYMA20G11330.1 (Glycine max), 3'ss of exon 11
lower sequence: EFJ14291 (Selaginella moellendorffii), 3'ss of exon 16
atatgagccctgtatcgtttccatacttactattctttttctgatcttagactttgagggatgcaattagt--aaattgaccgagctttt--ttgtttttg-tagGAAATTAAGTTTGAACCAAATGTCATGTGTGAACCTATTGACAAGAAAGTAACATTTCGAACAAGCCAG
                                                      |     |||   ||| |  | |||||      |  |  ||||||| |  |||||||||| ||||| || ||||| ||||| ||||| |||||||||||| | || ||||||   || |||
-----------------------------------------------------gtagataatgtttttattctatattgatttgcttcatcattgttttcgacagGAAATTAAATTTGACCCGAATGTGATGTGCGAACCAATTGACAAGAAACTTACGTTTCGAGACAGTCAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttagactttgagggatgcaattagtaaattgaccgagcttttttgtttttgtagGAAATTAAGTTTGAACCAAATGTCATGTGTGAACCTATTGACAAGAAAGTAACATTTCGAACAAGCCAG
                           aattgac  putative branch site (score: 3)
                                      cttttttgtttttgt  putative PPT
                                       ttttttgtttttgta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atatgagccctgtatcgtttccatacttactattctttttctgatcttagactttgagggatgcaattagtaaattgaccgagcttttttgtttttgtagGAAATTAAGTTTGAACCAAATGTCATGTGTGAACCTATTGACAAGAAAGTAACATTTCGAACAAGCCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - -ccctgta
- - - - - - - - - - ccatact
- - - - - - - - - - - - - - - - - - - - - - - - -gactttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - ggatgca