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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaatatatgttgcttcggtacttttattttattttttaatataatttttcttaatatggtttatgatataaattttttgtctttttatgttaattattccatggaaattttcttatatgttttagactctgtaatgtaagGTAACTGTTGGAGCTTCTTTTTTGTCACAAACAATAGCTCTGCAAGACTCTACAACAGTCAAGTTTGAAATATGGGATACTGCTGGTCAAGAGAG

Basic information

species Glycine max
transcript GLYMA20G32320.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA20G32320.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os10g30520.1 (Oryza sativa), 3'ss of exon 3
gtaaatatatgttgcttcggtacttttattttattttttaatataatttttcttaatatggtttatgatataaattttttgtctttttatgttaattattccatggaaattttcttatatgttttagactctgtaatgtaagGTAACTGTTGGAGCTTCTTTTTTGTCACAAACAATAGCTCTGCAAGACTCTACAACAGTCAAGTTTGAAATATGGGATACTGCTGGTCAAGAGAG
                  |  ||    | || ||| |||  || |  ||| ||  | |  |   |    ||    || |   | | | || |   |||||| ||           | | |||||||   |   | |  | |||| |||||||| || || ||||||||||||||| | ||  || | || || |||||||| ||||||||||||||||||||||||||||| |||||
----------------gtgaaacagacacttgattattttttacaggtttcctgtacagaggacacaccatttgattctc--cctataatatggcttattctat---------tctgtttgtttta--ttaaatgaatttagGTGACTGTTGGTGCATCATTTTTGTCACAAACATTGGCGTTGGAGGATTCCACAACAGTAAAGTTTGAAATATGGGATACTGCTGGTCAGGAGAG

upper sequence: GLYMA20G32320.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os03g05740.1 (Oryza sativa), 3'ss of exon 3
gtaaatatatgttgcttcggtactttta-ttttattttttaatataatttttcttaatatggtttatgatataaattttttgtctttttatgtt-aattattccatggaaattttcttatatgttttagactctgtaatgtaagGTAACTGTTGGAGCTTCTTTTTTGTCACAAACAATAGCTCTGCAAGACTCTACAACAGTCAAGTTTGAAATATGGGATACTGCTGGTCAAGAGAG
     |   |  || || |   || ||| ||| | ||  |||| | ||| |||    ||        |||  |   || ||   ||   | |||  ||| ||  |     |||| || | ||              ||| | |||||||||| || || || ||||| ||||||||| | ||| || | ||||| |||| ||| || ||||||||||||||||| ||||| ||||||||
----gtgattactgttttgagtctcttagtttcagttgataatgttattcttcacctta--------gatgcatgattcttactttcagaagttcgattgttttaaacttatttcctcaaat--------------aatttcagGTAACTGTCGGTGCATCATTTTTATCACAAACATTGGCTTTGGAGGACTCAACAATAGTGAAATTTGAAATATGGGATACCGCTGGACAAGAGAG

upper sequence: GLYMA20G32320.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G362088_T02 (Zea mays), 3'ss of exon 4
gtaaatatatgttgcttcggtacttttattttattttttaatataatttttcttaatatggtttatgatataaattttttgtctttttatgttaattattccatggaaattttcttatatgttttagactctgtaatgtaagGTAACTGTTGGAGCTTCTTTTTTGTCACAAACAATAGCTCTGCAAGACTCTACAACAGTCAAGTTTGAAATATGGGATACTGCTGGTCAAGAGAG
                                 |  |||| | |   |||  | |    |    ||||   ||| |||    ||||   |   |    ||||||      |  |  |  | | ||        |  |   ||||||||||||| || |||||||| ||||||||| | ||  || | || || |||| ||| ||||||||||| |||||||||||||| ||||||||
--------------------------------gtgatttactgt---tttgatcagatcgacccatgaatgaaacttta---ctttcggttgcagcatttccat------tccccaacttatcttc--tcaaatggttacagGTAACTGTTGGCGCATCTTTTTTATCACAAACATTGGCATTGGAGGATTCAACAATAGTGAAGTTTGAAATTTGGGATACTGCTGGGCAAGAGAG

upper sequence: GLYMA20G32320.1 (Glycine max), 3'ss of exon 3
lower sequence: AT3G54840.2 (Arabidopsis thaliana), 3'ss of exon 3
----gtaaatatatgttgcttcggtacttttattttattttttaatataatttttcttaatatggt-ttatgatataaat---tttttgtctttttatgttaattattccatggaaattttcttatatgttttagactctgtaatgtaagGTAACTGTTGGAGCTTCTTTTTTGTCACAAACAATAGCTCTGCAAGACTCTACAACAGTCAAGTTTGAAATATGGGATACTGCTGGTCAAGAGAG
    |||||    ||||   |   |   ||||||  |   | | | |    ||||   || |   |  | |||| | | |   | || | || ||   ||  | |  ||       |  | || |    |  ||| || ||||   | |||||||||||||||| || || ||||| ||||| |||||  ||||||||||||| ||||| |||||||||||||||||||| || || || |||||
gtaagtaaagccttgttatctaattgtctttattg-accatctgacac--ctttttagaacaccatgctctgatgtgagtgaatattagactattagagtatacttatctgccactagat-ctcaagactactag-ctatgta---tcagGTAACTGTTGGAGCCTCGTTCTTGTCCCAAACTATAGCATTGCAAGACTCTACCACAGTGAAGTTTGAAATATGGGATACAGCAGGACAGGAGAG

upper sequence: GLYMA20G32320.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv13s0019g04680.t01 (Vitis vinifera), 3'ss of exon 3
-------------gtaaatatatgttgcttcg---gtacttttattttattttttaatata----atttttcttaatatggttt-atgata-taaatttt-----ttgtctttttatgttaa-----------ttattccatgg-aaattttcttatatgttttagactctgtaatgtaagGTAACTGTTGGAGCTTCTTTTTTGTCACAAACAATAGCTCTGCAAGACTCTACAACAGTCAAGTTTGAAATATGGGATACTGCTGGTCAAGAGAG
              ||  ||||| ||   |       | |||| ||||   ||||| ||||    ||| |  | ||  | ||||  ||  | |  || ||        || | | |||  ||           ||||| ||||  | |||| |||| ||   ||   ||   |||  | |||| ||||| |||||||| || |||||||||||||| ||  ||||||| ||||| ||||| ||||||||||||||||| |||||||||||||||||
gtaagaaatatacatagctatatattatgtgatgcacattttttttttcccttttattatattaaattctgttcaaccttgttttgtgccaatggatgttagcatcaatcctctcatgcaaaatacatggatgttatttcatgatagatttacttagattggttgatcttaataacttcagGTGACTGTAGGAGCTTCATTCTTGTCACAAACAATTGCCTTGCAAGATTCTACGACAGTTAAGTTTGAAATATGGGACACTGCTGGTCAAGAGAG

upper sequence: GLYMA20G32320.1 (Glycine max), 3'ss of exon 3
lower sequence: EFJ26700 (Selaginella moellendorffii), 3'ss of exon 3
gtaaatatatgttgcttcggtacttttattttattttttaatataatttttcttaatatggtttatgatataaattttttgtctttttatgttaattattccatggaaattttcttatatgttttagactctgtaatgtaagGTAACTGTTGGAGCTTCTTTTTTGTCACAAACAATAGCTCTGCAAGACTCTACAACAGTCAAGTTTGAAATATGGGATACTGCTGGTCAAGAGAG-----
                                                                                          |  | |  | |  |  |  | ||    |||  ||| ||    ||  |  | ||| |||||||| |||||||||||||| ||||| |||||||| |||||||| |  ||||| |||||||| |||||||| || || || ||||||||     
------------------------------------------------------------------------------------------gcaagtagtgcttttaatgtgtt----tattattttgatatggtgctaca-gGTTACTGTTGGTGCTTCTTTTTTGTCGCAAACTATAGCTCTCCAAGACTCGAGCACAGTTAAGTTTGAGATATGGGACACCGCAGGACAAGAGAGATATG

upper sequence: GLYMA20G32320.1 (Glycine max), 3'ss of exon 3
lower sequence: EFJ26987 (Selaginella moellendorffii), 3'ss of exon 3
gtaaatatatgttgcttcggtacttttattttattttttaatataatttttcttaatatggtttatgatataaattttttgtctttttatgttaattattccatggaaattttcttatatgttttagactctgtaatgtaagGTAACTGTTGGAGCTTCTTTTTTGTCACAAACAATAGCTCTGCAAGACTCTACAACAGTCAAGTTTGAAATATGGGATACTGCTGGTCAAGAGAG-----
                                                                                          || | |  | |  |  |  | ||    |||  ||| ||    ||  |  | ||| |||||||| |||||||||||||| ||||| |||||||| |||||||| |  ||||| |||||||| |||||||| || || || ||||||||     
------------------------------------------------------------------------------------------gtaagtagtgcttttaatgtgtt----tattattttgatatggtgctaca-gGTTACTGTTGGTGCTTCTTTTTTGTCGCAAACTATAGCTCTCCAAGACTCGAGCACAGTTAAGTTTGAGATATGGGACACCGCAGGACAAGAGAGATATG

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|208162464|gb|GD963167.1|GD963167
EST:     GCTGTATTGTTCTACGATTTGTTCGTGGTCAGTTTGATCCAACATCTAAG                         GTAACTGTTGGAGCTTCTTTTTTGTCACAAACAATAGCTCTGCAAGACT
genomic: GCTGTATTGTTCTACGATTTGTTCGTGGTCAGTTTGATCCAACATCTAAGgtaaatatat ... gtaatgtaagGTAACTGTTGGAGCTTCTTTTTTGTCACAAACAATAGCTCTGCAAGACT
EST: gi|298188274|gb|HO034967.1|HO034967
EST:     GCTGTATTGTTCTACGATTTGTTCGTGGTCAGTTTGATCCAACATCTAAG                         GTAACTGTTGGAGCTTCTTTTTTGTCACAAACAATAGCTCTGCAAGACTCT
genomic: GCTGTATTGTTCTACGATTTGTTCGTGGTCAGTTTGATCCAACATCTAAGgtaaatatat ... gtaatgtaagGTAACTGTTGGAGCTTCTTTTTTGTCACAAACAATAGCTCTGCAAGACTCT
EST: gi|151401597|gb|EV271411.1|EV271411
EST:     GCTGTATTGTTCTACGATTTGTTCGTGGTCAGTTTGATCCAACATCTAAG                         GTAACTGTTGGAGCTTCTTTTTTGTCACAAACAATAGCTCTGCAAGACTCT
genomic: GCTGTATTGTTCTACGATTTGTTCGTGGTCAGTTTGATCCAACATCTAAGgtaaatatat ... gtaatgtaagGTAACTGTTGGAGCTTCTTTTTTGTCACAAACAATAGCTCTGCAAGACTCT
EST: gi|14009240|gb|BG725844.1|BG725844
EST:     GCTGTATTGTTCTACGATTTGTTCGTGGTCAGTTTGATCCAACATCTAAG                         GTAACTGTTGGAGCTTCTTTTTTGTCACAAACAATAGCTCTGCAAGACTCT
genomic: GCTGTATTGTTCTACGATTTGTTCGTGGTCAGTTTGATCCAACATCTAAGgtaaatatat ... gtaatgtaagGTAACTGTTGGAGCTTCTTTTTTGTCACAAACAATAGCTCTGCAAGACTCT
EST: gi|21887641|gb|BQ740854.1|BQ740854
EST:     GCTGTATTGTTCTACGATTTGTTCGTGGTCAGTTTGATCCAACATCTAAG                         GTAACTGTTGGAGCTTCTTTTTTGTCACAAACAATAGCTCTGCAAGACTCT
genomic: GCTGTATTGTTCTACGATTTGTTCGTGGTCAGTTTGATCCAACATCTAAGgtaaatatat ... gtaatgtaagGTAACTGTTGGAGCTTCTTTTTTGTCACAAACAATAGCTCTGCAAGACTCT
EST: gi|120530730|gb|EH258863.1|EH258863
EST:     GCTGTATTGTTCTACGATTTGTTCGTGGTCAGTTTGATCCAACATCTAAG                         GTAACTGTTGGAGCTTCTTTTTTGTCACAAACAATAGCTCTGCAAGACTCT
genomic: GCTGTATTGTTCTACGATTTGTTCGTGGTCAGTTTGATCCAACATCTAAGgtaaatatat ... gtaatgtaagGTAACTGTTGGAGCTTCTTTTTTGTCACAAACAATAGCTCTGCAAGACTCT
EST: gi|33388034|gb|CA851241.1|CA851241
EST:     GCTGTATTGTTCTACGATTTGTTCGTGGTCAGTTTGATCCAACATCTAAG                         GTAACTGTTGGAGCTTCTTTTTTGTCACAAACAATAGCTCTGCAAGACTCT
genomic: GCTGTATTGTTCTACGATTTGTTCGTGGTCAGTTTGATCCAACATCTAAGgtaaatatat ... gtaatgtaagGTAACTGTTGGAGCTTCTTTTTTGTCACAAACAATAGCTCTGCAAGACTCT
EST: gi|120530900|gb|EH259033.1|EH259033
EST:     GCTGTATTGTTCTACGATTTGTTCGTGGTCAGTTTGATCCAACATCTAAG                         GTAACTGTTGGAGCTTCTTTTTTGTCACAAACAATAGCTCTGCAAGACTCT
genomic: GCTGTATTGTTCTACGATTTGTTCGTGGTCAGTTTGATCCAACATCTAAGgtaaatatat ... gtaatgtaagGTAACTGTTGGAGCTTCTTTTTTGTCACAAACAATAGCTCTGCAAGACTCT
EST: gi|213603351|gb|DB966610.1|DB966610
EST:     GCTGTATTGTTCTACGATTTGTTCGTGGTCAGTTTGATCCAACATCTAAG                         GTAACTGTTGGAGCTTCTTTTTTGTCACAAACAATAGCTCTGCAAGACTCT
genomic: GCTGTATTGTTCTACGATTTGTTCGTGGTCAGTTTGATCCAACATCTAAGgtaaatatat ... gtaatgtaagGTAACTGTTGGAGCTTCTTTTTTGTCACAAACAATAGCTCTGCAAGACTCT
EST: gi|14126037|gb|BG790475.1|BG790475
EST:     GCTGTATTGTTCTACGATTTGTTCGTGGTCAGTTTGATCCAACATCTAAG                         GTAACTGTTGGAGCTTCTTTTTTGTCACAAACAATAGCTCTGCAAGACTCT
genomic: GCTGTATTGTTCTACGATTTGTTCGTGGTCAGTTTGATCCAACATCTAAGgtaaatatat ... gtaatgtaagGTAACTGTTGGAGCTTCTTTTTTGTCACAAACAATAGCTCTGCAAGACTCT
EST: gi|11687687|gb|BF595363.1|BF595363
EST:     GCTGTATTGTTCTACGATTTGTTCGTGGTCAGTTTGATCCAACATCTAAG                         GTAACTGTTGGAGCTTCTTTTTTGTCACAAACAATAGCTCTGCAAGACTCT
genomic: GCTGTATTGTTCTACGATTTGTTCGTGGTCAGTTTGATCCAACATCTAAGgtaaatatat ... gtaatgtaagGTAACTGTTGGAGCTTCTTTTTTGTCACAAACAATAGCTCTGCAAGACTCT
EST: gi|58017129|gb|CX703871.1|CX703871
EST:     GCTGTATTGTTCTACGATTTGTTCGTGGTCAGTTTGATCCAACATCTAAG                         GTAACTGTTGGAGCTTCTTTTTTGTCACAAACAATAGCTCTGCAAGACTCT
genomic: GCTGTATTGTTCTACGATTTGTTCGTGGTCAGTTTGATCCAACATCTAAGgtaaatatat ... gtaatgtaagGTAACTGTTGGAGCTTCTTTTTTGTCACAAACAATAGCTCTGCAAGACTCT
EST: gi|151409251|gb|EV279059.1|EV279059
EST:     GCTGTATTGTTCTACGATTTGTTCGTGGTCAGTTTGATCCAACATCTAAG                         GTAACTGTTGGAGCTTCTTTTTTGTCACAAACAATAGCTCTGCAAGACTCT
genomic: GCTGTATTGTTCTACGATTTGTTCGTGGTCAGTTTGATCCAACATCTAAGgtaaatatat ... gtaatgtaagGTAACTGTTGGAGCTTCTTTTTTGTCACAAACAATAGCTCTGCAAGACTCT
EST: gi|192303625|gb|FG998635.1|FG998635
EST:     GCTGTATTGTTCTACGATTTGTTCGTGGTCAGTTTGATCCAACATCTAAG                         GTAACTGTTGGAGCTTCTTTTTTGTCACAAACAATAGCTCTGCAAGACTCT
genomic: GCTGTATTGTTCTACGATTTGTTCGTGGTCAGTTTGATCCAACATCTAAGgtaaatatat ... gtaatgtaagGTAACTGTTGGAGCTTCTTTTTTGTCACAAACAATAGCTCTGCAAGACTCT
EST: gi|151399728|gb|EV269599.1|EV269599
EST:     GCTGTATTGTTCTACGATTTGTTCGTGGTCAGTTTGATCCAACATCTAAG                         GTAACTGTTGGAGCTTCTTTTTTGTCACAAACAATAGCTCTGCAAGACTCT
genomic: GCTGTATTGTTCTACGATTTGTTCGTGGTCAGTTTGATCCAACATCTAAGgtaaatatat ... gtaatgtaagGTAACTGTTGGAGCTTCTTTTTTGTCACAAACAATAGCTCTGCAAGACTCT
EST: gi|13478097|gb|BG507714.1|BG507714
EST:     GCTGTATTGTTCTACGATTTGTTCGTGGTCAGTTTGATCCAACATCTAAG                         GTAACTGTTGGAGCTTCTTTTTTGTCACAAACAATAGCTCTGCAAGACTCT
genomic: GCTGTATTGTTCTACGATTTGTTCGTGGTCAGTTTGATCCAACATCTAAGgtaaatatat ... gtaatgtaagGTAACTGTTGGAGCTTCTTTTTTGTCACAAACAATAGCTCTGCAAGACTCT
EST: gi|19053755|gb|BM732422.1|BM732422
EST:     GCTGTATTGTTCTACGATTTGTTCGTGGTCAGTTTGATCCAACATCTAAG                         GTAACTGTTGGAGCTTCTTTTTTGTCACAAACAATAGCTCTGCAAGACTCT
genomic: GCTGTATTGTTCTACGATTTGTTCGTGGTCAGTTTGATCCAACATCTAAGgtaaatatat ... gtaatgtaagGTAACTGTTGGAGCTTCTTTTTTGTCACAAACAATAGCTCTGCAAGACTCT
EST: gi|6912828|gb|AW394312.1|AW394312
EST:     GCTGTATTGTTCTACGATTTGTTCGTGGTCAGTTTGATCCAACATCTAAG                         GTAACTGTTGGAGCTTCTTTTTTGTCACAAACAATAGCTCTGCAAGACTCT
genomic: GCTGTATTGTTCTACGATTTGTTCGTGGTCAGTTTGATCCAACATCTAAGgtaaatatat ... gtaatgtaagGTAACTGTTGGAGCTTCTTTTTTGTCACAAACAATAGCTCTGCAAGACTCT
EST: gi|6665996|gb|AW277455.1|AW277455
EST:     GCTGTATTGTTCTACGATTTGTTCGTGGTCAGTTTGATCCAACATCTAAG                         GTAACTGTTGGAGCTTCTTTTTTGTCACAAACAATAGCTCTGCAAGACTCT
genomic: GCTGTATTGTTCTACGATTTGTTCGTGGTCAGTTTGATCCAACATCTAAGgtaaatatat ... gtaatgtaagGTAACTGTTGGAGCTTCTTTTTTGTCACAAACAATAGCTCTGCAAGACTCT
EST: gi|6455577|gb|AW186260.1|AW186260
EST:     GCTGTATTGTTCTACGATTTGTTCGTGGTCAGTTTGATCCAACATCTAAG                         GTAACTGTTGGAGCTTCTTTTTTGTCACAAACAATAGCTCTGCAAGACTCT
genomic: GCTGTATTGTTCTACGATTTGTTCGTGGTCAGTTTGATCCAACATCTAAGgtaaatatat ... gtaatgtaagGTAACTGTTGGAGCTTCTTTTTTGTCACAAACAATAGCTCTGCAAGACTCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatgttaattattccatggaaattttcttatatgttttagactctgtaatgtaagGTAACTGTTGGAGCTTCTTTTTTGTCACAAACAATAGCTCTGCAAGACTCTACAACAGTCAAGTTTGAAATATGGGATACTGCTGGTCAAGAGAG
  tgttaat  putative branch site (score: 3)
                   aaattttcttatatgt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaatatatgttgcttcggtacttttattttattttttaatataatttttcttaatatggtttatgatataaattttttgtctttttatgttaattattccatggaaattttcttatatgttttagactctgtaatgtaagGTAACTGTTGGAGCTTCTTTTTTGTCACAAACAATAGCTCTGCAAGACTCTACAACAGTCAAGTTTGAAATATGGGATACTGCTGGTCAAGAGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA