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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtaacttagaagattgtagggctgtttatccatcctttgcagttatatggatgaaaaagttgcttaggcatatttccatttatcctttttttccattcagGCCTTTTCTTGTCAATGAATTGGAACAGCAACACCTTCTTCATGATCGAAGGAAAGTATATGAG

Basic information

species Vitis vinifera
transcript Vv14s0066g02540.t01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv14s0066g02540.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA18G49000.1 (Glycine max), 3'ss of exon 4
---------gtaacttagaagattgtagggctgtttatccatcctttgcagttatatggatgaaaaagttgcttaggcatatttccatttatcctttttttccattcagGCCTTTTCTTGTCAATGAATTGGAACAGCAACACCTTCTTCATGATCGAAGGAAAGTATATGAG
          |   |||     || |     |   |||   |   || ||||||| ||| ||| || |||  ||   |  | |||  |  |   |         | |||||| ||||| || |||||| |||| |  ||||||||||||||||||||||| ||||| ||||||
ttttttcaattgtgttatgttgttattttatttaatatagttttctttcagttat-tgggtgagaatgtttattgatctaaattctgtgcactgtg-------gtccaGGCCCTTTCTAGTAAATGAACTGGAGCCACAACACCTTCTTCATGATCGAAGAAAAGTGTATGAG

upper sequence: Vv14s0066g02540.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA19G02260.1 (Glycine max), 3'ss of exon 2
---gtaacttagaagattgtagggctgtttatccatcctttgcagttatatggatgaaaaagttgcttaggcatatttccatttatcctttttttccattcagGCCTTTTCTTGTCAATGAATTGGAACAGCAACACCTTCTTCATGATCGAAGGAAAGTATATGAG
    |||   |     ||||     |  || |   |    |     | | ||||||| || |||     | |  |     | | || |  | |    || ||| |||||||| || |||||| |||| |  ||| |||||||||||||| |||||||||||||||||
actctaatacattcctttgttatttttgttgtatttttactttgaatgtttggatgagaaggtttacaggtctaaaaattactcatacactgtg---atgcagACCTTTTCTAGTAAATGAACTGGAGCCCCAATACCTTCTTCATGATAGAAGGAAAGTATATGAG

upper sequence: Vv14s0066g02540.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA09G37610.1 (Glycine max), 3'ss of exon 2
-----gtaacttagaagattgtagggctgtttatc---catcctttgcagttatatggatgaaaaagttgcttaggcatatttccatttatcctttttttccattcagGCCTTTTCTTGTCAATGAATTGGAACAGCAACACCTTCTTCATGATCGAAGGAAAGTATATGAG
      | | ||   | |||||     | |||||      |   ||  |||||| ||||||| || |||  ||   |  | |||  |  |   |        || ||| || ||||| || |||||| |||| |  ||||||||||||||||||||||| |||||||| |||
ctgtttttaattgttacattgttattttatttattatagttttcttttagttat-tggatgagaatgtttattgatctaaattctgtgcactgtg-------atccagACCCTTTCTAGTAAATGAACTGGAGCCTCAACACCTTCTTCATGATCGAAGAAAAGTATACGAG

upper sequence: Vv14s0066g02540.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: EFJ07403 (Selaginella moellendorffii), 3'ss of exon 4
gtaacttagaagattgtagggctgtttatccatcctttgcagttatatggatgaaaaagttgcttaggcatatttccatttatcctttttttccattcagGCCTTTTCTTGTCAATGAATTGGAACAGCAACACCTTCTTCATGATCGAAGGAAAGTATATGAG
               ||  |  |  || ||  |  | |    || | |   |     | ||  ||   || |||  ||   |   |  || ||  ||||||||||||||||| |||||||||||||  || || ||| | |||||  |  | ||||| |||  |
---------------gtgagtatcgttttcttttttcttttcttttttctct-----actttttt---cagATTGTCAA--AAGGTGCTTATCATTTCAGGCCTTTTCTTGTTAATGAATTGGAACCCCAGCATCTTTTGCATGACAGGCGCAAAGTTTATTCG

upper sequence: Vv14s0066g02540.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: EFJ19878 (Selaginella moellendorffii), 3'ss of exon 4
gtaacttagaagattgtagggctgtttatccatcctttgcagttatatggatgaaaaagttgcttaggcatatttccatttatcctttttttccattcagGCCTTTTCTTGTCAATGAATTGGAACAGCAACACCTTCTTCATGATCGAAGGAAAGTATATGAG
               ||  |  |  || ||  |  | |    || | |   |     | ||  |    || |||  ||   |   |  || ||  ||||||||||||||||| |||||||||||||  || || ||| | |||||  |  | ||||| |||  |
---------------gtgagtatcgttttcttttttcttttcttttttctct-----actttttc---cagATTGTCAAAAA--GTGCTTATCATTTCAGGCCTTTTCTTGTTAATGAATTGGAACCCCAGCATCTTTTGCATGACAGGCGCAAAGTTTATTCG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatggatgaaaaagttgcttaggcatatttccatttatcctttttttccattcagGCCTTTTCTTGTCAATGAATTGGAACAGCAACACCTTCTTCATGATCGAAGGAAAGTATATGAG
                         tatttccatttatcct  CT-rich tract
                                atttatccttttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaacttagaagattgtagggctgtttatccatcctttgcagttatatggatgaaaaagttgcttaggcatatttccatttatcctttttttccattcagGCCTTTTCTTGTCAATGAATTGGAACAGCAACACCTTCTTCATGATCGAAGGAAAGTATATGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - gggctgt
- - - - - - - - - - - - - - -ccatcct
- - - - - - - - - - - - - - - - - - -tgcagtt
- - - - - - - - - - - - - - - - - - - - - - - - - -tgaaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgcttag