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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...attttaacatagctgtcatttgtgtagttttgattaaattatcaaagtttattctgttagatttgattgatttctctatcttattgattattctgtccagATTCTTGAAATGGACACTTACAGATACCATGGACACTCTATGTCTGATCATGGCAGCACATACCGTACACGTGATGAAATTTCTGGTGTGAGACAG

Basic information

species Glycine max
transcript GLYMA01G04470.2
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA01G04470.2 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os06g13720.1 (Oryza sativa), 3'ss of exon 3
------attttaacatagctgtcatttgtgtagttttgattaaattatcaaagtttattctgttagatttgattgatttctctatcttattgattattctgtccagATTCTTGAAATGGACACTTACAGATACCATGGACACTCTATGTCTGATCATGGCAGCACATACCGTACACGTGATGAAATTTCTGGTGTGAGACAG
      ||| |   |||| |    |     || |    | || |  |   ||   |  |||   ||||     | | || ||||| |  |      |  |||  |||||||||| |||||||| ||||||||||| |||||||||||||| ||||  || ||||| ||||| ||  | ||||||||| | ||  | ||||||
gctcatattgttcgatagattcagtgccgctaatc---agtagaaaacacaatcctgctcttggagatgcatgtaacttttctatatcctct-cggtgttgt--agATTCTTGAGATGGACACCTACAGATACCACGGACACTCTATGTCAGATCCAGGGAGCACTTACCGCACCAGAGATGAAATTGCAGGCATAAGACAG

upper sequence: GLYMA01G04470.2 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os02g50620.1 (Oryza sativa), 3'ss of exon 3
-attttaacatagctgtcatttgt-gtagttttgattaaattatcaaagtttattctgttagatttgattgatttctctatcttattgattattctgtccagATTCTTGAAATGGACACTTACAGATACCATGGACACTCTATGTCTGATCATGGCAGCACATACCGTACACGTGATGAAATTTCTGGTGTGAGACAG
   ||   | |    |   ||||| | | ||     | ||| |  || ||||    | |   |  |||| | |     | | |      |  || | |  || ||||||||||||| || ||||| |||||||| || |||||||| ||||  || ||||| ||||||||  | ||||| || || ||||| ||||||
tggttgtgcctgctagcagtttgtagcaattcacccttaatga--aatgtttcagttttagtaagtgatggttactaatgtttccccactctttgtatttagGTTCTTGAAATGGATACCTACAGGTACCATGGCCATTCTATGTCAGATCCCGGAAGCACTTACCGTACCAGGGATGAGATCTCAGGTGTAAGACAG

upper sequence: GLYMA01G04470.2 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G361693_T01 (Zea mays), 3'ss of exon 3
attttaacatagctgtcatttgtgtagttttgattaaattatcaaagtttattc--tgttagatttga---ttgatttctcta-tcttattgattattctgtccagATTCTTGAAATGGACACTTACAGATACCATGGACACTCTATGTCTGATCATGGCAGCACATACCGTACACGTGATGAAATTTCTGGTGTGAGACAG
      |   |    |  |   || |  |  |   |   |  || | ||  |||  |  |||   |||    || || ||  |  | ||  | |   | | || || | ||||| ||||| || |||||||||||||| ||||||||||| ||||  || ||||| ||||| ||  | ||||| ||||| ||||| || |||
------aggcaagccttctccctgcaaatgcggagaggctcgcataattatttcatttctagtgctgaagaatggttactaaaaccctaaggttctatatatctagGTCCTTGAGATGGATACCTACAGATACCATGGCCACTCTATGTCAGATCCAGGAAGCACTTACCGCACCAGGGATGAGATTTCAGGTGTCAGGCAG

upper sequence: GLYMA01G04470.2 (Glycine max), 3'ss of exon 1
lower sequence: AT1G24180.1 (Arabidopsis thaliana), 3'ss of exon 3
attttaacatagctgtcatttgtgtagttttgattaaattatcaaagtttattctgttagatttgattgatttctctatcttattg--attattctgtccagATTCTTGAAATGGACACTTACAGATACCATGGACACTCTATGTCTGATCATGGCAGCACATACCGTACACGTGATGAAATTTCTGGTGTGAGACAG
 || | |  |   |  |||     |    || ||   ||| | | | |  ||||| |      |||||     |   ||   ||||  |||||| ||  ||||| ||||| |||||||||||||||||||| || |||||||||||||| |  || ||||| |||||||| ||||||||||| ||||| |||||||||
-ttgtgaattcaatcacatagcgttgacatttatcgtatttttataatccattctctacctagtgattatgaccaacataccattgccattatt-tgcgcagATCCTTGAGATGGACACTTACAGATACCACGGTCACTCTATGTCTGACCCAGGAAGCACTTACCGTACTCGTGATGAAATCTCTGGCGTGAGACAG

upper sequence: GLYMA01G04470.2 (Glycine max), 3'ss of exon 1
lower sequence: AT1G59900.1 (Arabidopsis thaliana), 3'ss of exon 3
attttaacatagctgtcatttgtgtagttttgattaaattatcaaagtttattctgttagatttgattgatttct------ctatcttattgattattctgtccagATTCTTGAAATGGACACTTACAGATACCATGGACACTCTATGTCTGATCATGGCAGCACATACCGTACACGTGATGAAATTTCTGGTGTGAGACAG
      | |||  |   |  | ||   ||   ||| | ||  |   ||||||||| |   ||   || |||| |        ||    || | || |||| | ||||||||||| |||||||| ||||| ||||| || ||||| |||||||||| ||| |||||||||||||| || ||||| || ||||||||||| |||
-----catataagtagtagctttg-gtttccaatttattttcctgtgtttattctttcctatcatatggattacagaagcattaatacatcgtttcttctatacagATTCTTGAGATGGACACATACAGGTACCACGGTCACTCCATGTCTGATCCTGGGAGCACATACCGTACCCGAGATGAGATATCTGGTGTGAGGCAG

upper sequence: GLYMA01G04470.2 (Glycine max), 3'ss of exon 1
lower sequence: Vv01s0026g00990.t01 (Vitis vinifera), 3'ss of exon 3
attttaacatagctgtcatttgtgtagttttgattaaattatcaaagtttattctgttagatt---tgattgatttctctatcttattgattattctgtccagATTCTTGAAATGGACACTTACAGATACCATGGACACTCTATGTCTGATCATGGCAGCACATACCGTACACGTGATGAAATTTCTGGTGTGAGACAG
  |||||  | | ||  | |  | |   | |  |   ||| |||   |||  | ||| |||||   | |||| ||| | | |||| |  ||  |  ||| ||||||||||||||||||||||| || |||||||| ||||| |||||||||| ||| ||||| ||||||||||||||||| ||||||||||||||||||
-ctttaatgttgttgctagtaatttctctcttttggcattgtcatcattt--tatgtgagattgactaattgctttatttttcttctaaatgctggtgttcagATTCTTGAAATGGACACTTATAGGTACCATGGTCACTCCATGTCTGATCCTGGGAGCACCTACCGTACACGTGATGAGATTTCTGGTGTGAGACAG

upper sequence: GLYMA01G04470.2 (Glycine max), 3'ss of exon 1
lower sequence: Vv09s0018g01940.t01 (Vitis vinifera), 3'ss of exon 3
attttaacatagctgtcatttgtgtagt-tttgattaaat-tatcaaagtttattctg--ttagatt---tgattgatttctctatcttattgattattctgtccagATTCTTGAAATGGACACTTACAGATACCATGGACACTCTATGTCTGATCATGGCAGCACATACCGTACACGTGATGAAATTTCTGGTGTGAGACAG
       |    |||  |||  |  | | |||| || |   | ||     | ||| |   | |||||   | |||||||| ||| |||| |  ||  || ||| ||||||||||||||||||||||| || |||||||| ||||| |||||||||| ||| || ||||||||||| |||||||| ||||||||||||||||||
-------cccgcctgcaattctttcattctttgcttgagcatgtctgtcatcattttacatgagattgactaattgatttatctttcttctaaatgcttgtgttcagATTCTTGAAATGGACACTTATAGGTACCATGGTCACTCCATGTCTGATCCTGGGAGTACATACCGTACGCGTGATGAGATTTCTGGTGTGAGACAG

upper sequence: GLYMA01G04470.2 (Glycine max), 3'ss of exon 1
lower sequence: PP1S201_84V6.1 (Physcomitrella patens), 3'ss of exon 3
-------------------------------------------------------------attttaacatagctgtcatttgt-gtagttttgattaaattat--caaagtttattctgttagatttgattgatttctctatcttattgattattctgtccagATTCTTGAAATGGACACTTACAGATACCATGGACACTCTATGTCTGATCATGGCAGCACATACCGTACACGTGATGAAATTTCTGGTGTGAGACAG
                                                               ||||    |  ||   | ||| | || |||   | | ||||  |  |    |     ||    |||  |  ||| |||   ||||   || |    |  || || | || ||||| || |||||||| ||||| |||||||||||||| |  |||||||| ||||| || |||||||| || ||||||||  |||||
gtaagtgatgctgttgttttcctaaccagcacatggatactttaccttcttctaatcatggggtttactccatttgctgtgtgttgcagctttacgtcagttatgtcgtaaccgagatgcttttgcttgggttctttttctgaattatattttctggcatggagGTTTTGGAGATGGATACGTACAGATATCATGGTCACTCTATGTCTGACCCAGGCAGCACCTACCGAACCCGTGATGAGATCTCTGGTGTACGACAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agtttattctgttagatttgattgatttctctatcttattgattattctgtccagATTCTTGAAATGGACACTTACAGATACCATGGACACTCTATGTCTGATCATGGCAGCACATACCGTACACGTGATGAAATTTCTGGTGTGAGACAG
                                    tattgat  putative branch site (score: 3)
                                             ttctgtcc  putative PPT
                               tatcttattgattatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
attttaacatagctgtcatttgtgtagttttgattaaattatcaaagtttattctgttagatttgattgatttctctatcttattgattattctgtccagATTCTTGAAATGGACACTTACAGATACCATGGACACTCTATGTCTGATCATGGCAGCACATACCGTACACGTGATGAAATTTCTGGTGTGAGACAG

- - - - - -gctgtca
- - - - - - - - - tttgtgt
- - - - - - - - - - - - - - - - - - - - - - - - - -ttctgtt