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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aaaagttcatattggagttgtatttagaactgctatcgctgggacacttgtttactttcatttctggacacgtatctgaaaaggattgatgatgatacagGAAGATGAGAAATTGAAGCTATCAGAGGTTACTGGACTAGACCAGAAGCAGATTAACAACTGGTTCATAAACCAGAGGAAGCGGCATTGGAAACCATCAG

Basic information

species Vitis vinifera
transcript Vv14s0060g01180.t01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv14s0060g01180.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: LOC_Os05g03884.1 (Oryza sativa), 3'ss of exon 4
aaaagttcatattggagttgtatttagaactgctatcgctgggacacttgtttactttcatt--tctggacacgtatctgaaaaggattgatgatgatacagGAAGATGAGAAATTGAAGCTATCAGAGGTTACTGGACTAGACCAGAAGCAGATTAACAACTGGTTCATAAACCAGAGGAAGCGGCATTGGAAACCATCAG
            |   || |     |   ||  |         | |     | ||   || |   ||||     | |||   ||   |||||  |   ||||||||| || ||  ||| |||  | | | | ||||| || |||| ||||||||| |||||||||||||| |||||||||||| |||| ||||| ||||| |
-----------gtaatgtcgcgaaaacgccttttcgacacacaaaagcctctaacccacactgacctgggactctgtcttccaa---ttgatcttt-cacagGAAGAGGATAAGGTGAGGCTGGCCGCGATGACTGGCCTCGACCCGAAGCAGATCAACAACTGGTTCATCAACCAGAGGAAGAGGCACTGGAAGCCATCGG

upper sequence: Vv14s0060g01180.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: LOC_Os01g19694.1 (Oryza sativa), 3'ss of exon 4
aaaagttcatattggagttgtatttagaactg-ctatcgctgggacacttgtttactttcatttctggacacgt-atctgaaaaggattgatgatgat--acagGAAGATGAGAAATTGAAGCTATCAGAGGTTACTGGACTAGACCAGAAGCAGATTAACAACTGGTTCATAAACCAGAGGAAGCGGCATTGGAAACCATCAG
     |   |     | ||| ||       |  || |  |||  |   |    ||| || || |  | | |  |  |||||    |  || || ||||  ||||||||| || ||  ||| |||  ||| |   || || || ||||  |||||||| ||||| |||||||| |||||||||||| |||| ||||| ||||| |
-cgcttgtctgccccacttgcatcccttcttttctgtaactgaaattttgtggtacatt-atgttagtatatattgtctgacgttg--tggtgctgattgacagGAAGAAGATAAGCTGAGGCTTGCAGCGAGGACAGGTCTTGACCCAAAGCAGATCAACAATTGGTTCATCAACCAGAGGAAGAGGCACTGGAAGCCATCGG

upper sequence: Vv14s0060g01180.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM2G087741_T01 (Zea mays), 3'ss of exon 4
aaaagttcatattggagttgtatttagaactgctatcgctgggacacttgtttactttcatttctggacacgtatctgaaaaggattgatgatgatacagGAAGATGAGAAATTGAAGCTATCAGAGGTTACTGGACTAGACCAGAAGCAGATTAACAACTGGTTCATAAACCAGAGGAAGCGGCATTGGAAACCATCAG
  | ||      |||   | | |||  | |    |           |  ||  ||| | |    ||       ||||||    |  || || |||  ||||| || || ||  ||| |||  |||   | || || || |||| ||||||||| |||||||||||||| |||||||||||| |||||||||| ||||| |
gtatgtaggcgctggccattttttttcaccaaacaatctgaacctgcaggtgcactgtgaccagtgactgataatctgatgctg--tgctgctga--cagGAGGAAGACAAGGTGAGGCTCGCAGCAATGACCGGTCTCGACCCGAAGCAGATCAACAACTGGTTCATCAACCAGAGGAAGAGGCATTGGAAGCCATCTG

upper sequence: Vv14s0060g01180.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM5G832409_T01 (Zea mays), 3'ss of exon 4
----------aaaagttcatattggagttgtatttagaactgctatcgctg-ggacacttgtttactttcatttctggacacgtatctgaaaaggattgatgatgatacagGAAGATGAGAAATTGAAGCTATCAGAGGTTACTGGACTAGACCAGAAGCAGATTAACAACTGGTTCATAAACCAGAGGAAGCGGCATTGGAAACCATCAG
           | ||  || |   | | |||   | || ||    |||||  | ||      |    |   |    ||     |      |     |   |  |    ||||| || || ||  ||| |||  | |   | ||||| || |||| ||||||||| |||||||||||||| |||||| |||||||||||||||| || || |
gtaacatgctcacagcacacacctgtgctgtgact-gatctttcctcgctttgaacgaacaatcgaatctgtgatcggcattttgctcagactaagtatcttgttcggcagGAGGAGGATAAGGTGAGGCTGGCGGCCATGACTGGGCTGGACCCGAAGCAGATCAACAACTGGTTCATCAACCAGCGGAAGCGGCATTGGAAGCCGTCGG

upper sequence: Vv14s0060g01180.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM2G094241_T01 (Zea mays), 3'ss of exon 4
aaaagttcatattggagttgtatttagaactgctatcgctgggacacttgtttactttcatttctggacacgtatctgaaaaggatt-gatgatgatacagGAAGATGAGAAATTGAAGCTATCAGAGGTTACTGGACTAGACCAGAAGCAGATTAACAACTGGTTCATAAACCAGAGGAAGCGGCATTGGAAACCATCAG
      | |   || |    |  |   ||   |    || |   || | | |  ||   ||     | ||  | | |||  || ||| |  |  | | ||||| || || ||  ||| |||  | | ||  ||||| || |||| ||||||||| |||||||||||||| |||||| |||||||||| ||||| || || |
-----gtaaccatgcatgcatcctggcaaacac-gcagcagcagca-tcgctcgctggaat-----ggcagatctgtgaccagcattagccggcggtgcagGAGGAGGACAAGGTGAGGCTGGCGGCGGCGACTGGGCTGGACCCGAAGCAGATCAACAACTGGTTCATCAACCAGCGGAAGCGGCACTGGAAGCCGTCCG

upper sequence: Vv14s0060g01180.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA03G39040.1 (Glycine max), 3'ss of exon 4
aaaagttcatattg-gagttgtatttagaactgctatcgctgggacacttgtttactttcattt-ctggacacgtat--ctgaaaaggattgatgatgatacagGAAGATGAGAAATTGAAGCTATCAGAGGTTACTGGACTAGACCAGAAGCAGATTAACAACTGGTTCATAAACCAGAGGAAGCGGCATTGGAAACCATCAG
    ||   |||    | ||| | |    |    |     |    ||   |     |      |  | ||   | ||  ||  |||   ||    |||||||||||||| |||||| ||||| | |||||  |||||||||| || || |||||||| || || |||||||| || ||||| || || |||||||||||| | |
----gtgggtataacaaattgcactctataacatttctatttaagcaaaagaccgatccagcctatttgatgtgaatgccttgaaactgttatcaatgatacagGAAGAGGAGAAAGTGAAGTTGTCAGAAATTACTGGACTGGATCAAAAGCAGATCAATAATTGGTTCATCAATCAGAGAAAACGTCATTGGAAACCAACTG

upper sequence: Vv14s0060g01180.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA19G41610.1 (Glycine max), 3'ss of exon 4
aaaagttcatattggagttgtatttagaactgctatcgctgggac--acttgtttactttcatttctggacacgtatctgaaaaggattgat---gatgatacagGAAGATGAGAAATTGAAGCTATCAGAGGTTACTGGACTAGACCAGAAGCAGATTAACAACTGGTTCATAAACCAGAGGAAGCGGCATTGGAAACCATCAG
  || |   ||||    |   |  | | ||| ||||  |   |||    |  || || ||  | | |   ||     |  |      ||| |    ||||||||||| || |||||| ||||| |||||||  ||||||| || || || |||||||| || || |||||||| || ||||| || ||||||||||||||  | |
-taattagttattc---tcacaaattgcact-ctataacaaagactaggtaattaacatttctctttaagcaaaagacccagcctatttgttatcaatgatacagGAGGAGGAGAAAGTGAAGTTATCAGAAATTACTGGTCTGGATCAAAAGCAGATCAATAATTGGTTCATCAATCAGAGAAAACGGCATTGGAAACCTACCG

upper sequence: Vv14s0060g01180.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA10G28820.1 (Glycine max), 3'ss of exon 4
----aaaagttcatattggagttgt--atttagaactgctatcgctgggacacttgtttactttcatttctggacacgtatctgaaaaggattgatgatgatacagGAAGATGAGAAATTGAAGCTATCAGAGGTTACTGGACTAGACCAGAAGCAGATTAACAACTGGTTCATAAACCAGAGGAAGCGGCATTGGAAACCATCAG
     |    |  |     | |  |  ||  || || | |  |  |   ||| || ||  ||     || |  | | |  |   || |    |  || |     |||| || |||||| || ||||||||||  | |||||||| || || |||||||| || || |||||||| || || || || |||||||||||||||||||
ccatgagcacttgtggccaattaattaatcaagcacagtttccatttaaacatttatt-gctaaatcttatataaatgccttgcaacaaatcttttgtt-----agGAGGAGGAGAAAGTGCAGCTATCAGAAATGACTGGACTTGATCAAAAGCAGATCAATAATTGGTTCATCAATCAAAGAAAACGGCATTGGAAACCATCAG

upper sequence: Vv14s0060g01180.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA20G22980.1 (Glycine max), 3'ss of exon 1
----aaaagttcatattggagttgt--atttagaactgctatcgctgggacacttgtttactttcatttctggacacgtatctgaaaaggattgatgatgatacagGAAGATGAGAAATTGAAGCTATCAGAGGTTACTGGACTAGACCAGAAGCAGATTAACAACTGGTTCATAAACCAGAGGAAGCGGCATTGGAAACCATCAG
     |    |  |     | |  |  ||  || || | |  |  |   | |    ||  |    | |  |  | |  |  ||  |||    | || ||     |||| || |||||| || ||||||||||  | || ||||| || || |||||||| || || |||||||| || || ||||| ||||||||||||||| |||
ccctgagccctggtggccaattaatcaatcaagcacagtttccatttaaatagacattgcca---aatcttatataaatgccttgaaa---ctaatcatttgttagGAGGAAGAGAAAGTGCAGCTATCAGAAATGACCGGACTTGATCAAAAGCAGATCAATAATTGGTTCATCAATCAAAGGAAACGGCATTGGAAACCAACAG

upper sequence: Vv14s0060g01180.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: EFJ23803 (Selaginella moellendorffii), 3'ss of exon 4
-----------------------------------aaaagttcatattggagttgtatttagaactgctatcgctgggacacttgtttactttcatttctggacacgtatctgaaaag---gattgatgatgat--acagGAAGATGAGAAATTGAAGCTATCAGAGGTTACTGGACTAGACCAGAAGCAGATTAACAACTGGTTCATAAACCAGAGGAAGCGGCATTGGAAACCATCAG
                                        |   | | |   | |    | |   ||| || |||  |   ||| |||   | | ||||    |   | |||   |     | ||  |  || |  ||||||  |  | || | ||| ||  |  |    || || || ||||  |||||||| ||||||||||| ||||||||| | |||||||| ||||| ||    |
gtgagtacctttgtgttctttcttgttggcattctgtgtctctttctcgttatggctagtgggcgtgccatggctttgttccttctttgtgtccttttcatcgcttttttctttgacatttgcttcgttgtgctggacagGAGAACCAAAAGTCGAATCTCGCGCAATCCACCGGGCTGGACCCAAAGCAGATCAACAACTGGTTTATAAACCAGCGAAAGCGGCACTGGAATCCGCAGG

upper sequence: Vv14s0060g01180.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: EFJ21443 (Selaginella moellendorffii), 3'ss of exon 5
-----------------------------------aaaagttcatattggagttgtatttagaactgctatcgctgggacacttgtttactttcatttctggacacgtatctgaaaag---gattgatgatgat--acagGAAGATGAGAAATTGAAGCTATCAGAGGTTACTGGACTAGACCAGAAGCAGATTAACAACTGGTTCATAAACCAGAGGAAGCGGCATTGGAAACCATCAG
                                        |   | | |   | |    | |   ||| || |||  |   ||| |||   | | ||||    |   | |||   |     | ||     || |  ||||||  |  | || | ||| ||  |  |    || || || ||||  |||||||| ||||||||||| ||||||||| | |||||||| ||||| |||   |
gtgagtacctttgtgttctttcttgttggcattccgtgtctctttctcgttatggctagtgggcgtgccatggctttgttccttctttgtgtccttttcattgcttttttctttgacatttgcttcgctgtgctggacagGAGAACCAAAAGTCGAATCTCGCGCAATCCACCGGCCTGGACCCAAAGCAGATCAACAACTGGTTTATAAACCAGCGAAAGCGGCACTGGAATCCACAGG

upper sequence: Vv14s0060g01180.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: EFJ07541 (Selaginella moellendorffii), 3'ss of exon 5
aaaagttcatattggagttgtatttagaactgctatcgctgggacact-tgtttactttcatttctggacacgtatctgaaaaggattgatgatgatacagGAAGATGAGAAATTGAAGCTATCAGAGGTTACTGGACTAGACCAGAAGCAGATTAACAACTGGTTCATAAACCAGAGGAAGCGGCATTGGAAACCATCAG
                                         | |   | || |   |||||||   | |    |||    |   | |||     | | |||||| | ||||||   || ||  ||   | ||||||||| ||||||||||| |||||||||||||| || |||||||| ||||| |||||||| || ||||
-----------------------------------------gtatgttgtgatagttttcatt---gaatttatattcttagttgtttggctg-gtttcagGAACAGGAGAAAGCTAACCTCGCAACTGATACTGGACTCGACCAGAAGCAAATTAACAACTGGTTTATCAACCAGAGAAAGCGTCATTGGAATCCTTCAG

upper sequence: Vv14s0060g01180.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: EFJ10744 (Selaginella moellendorffii), 3'ss of exon 5
aaaagttcatattggagttgtatttagaactgctatcgctgggacact-tgtttactttcatttctggacacgtatctgaaaaggattgatgatgatacagGAAGATGAGAAATTGAAGCTATCAGAGGTTACTGGACTAGACCAGAAGCAGATTAACAACTGGTTCATAAACCAGAGGAAGCGGCATTGGAAACCATCAG
                                         | |   | || |   |||||||   | |    |||    |   | |||     | | |||||| | ||||||   || ||  ||   | ||||||||| ||||||||||| |||||||| ||||| || |||||||| ||||| |||||||| || ||||
-----------------------------------------gtatgttgtgatagttttcatt---gaatttatattcttagttgtttggctg-gtttcagGAACAGGAGAAAGCTAACCTCGCAACTGATACTGGACTCGACCAGAAGCAAATTAACAATTGGTTTATCAACCAGAGAAAGCGTCATTGGAATCCTTCAG

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|110373234|gb|EC937453.1|EC937453
EST:     CAATGTTGCTGGAATGGTGGAATACCCATTATAGATGGCCATATCCCACG                         GAAGATGAGAAATTGAAGCTATCAGAGGTTACTGGACTAGACCAGAAGCAG
genomic: CAATGTTGCTGGAATGGTGGAATACCCATTATAGATGGCCATATCCCACGgtaattaatt ... gatgatacagGAAGATGAGAAATTGAAGCTATCAGAGGTTACTGGACTAGACCAGAAGCAG
EST: gi|110390997|gb|EC955948.1|EC955948
EST:     CAATGTTGCTGGAATGGTGGAATACCCATTATAGATGGCCATATCCCACG                         GAAGATGAGAAATTGAAGCTATCAGAGGTTACTGGACTAGACCAGAAGCAG
genomic: CAATGTTGCTGGAATGGTGGAATACCCATTATAGATGGCCATATCCCACGgtaattaatt ... gatgatacagGAAGATGAGAAATTGAAGCTATCAGAGGTTACTGGACTAGACCAGAAGCAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acttgtttactttcatttctggacacgtatctgaaaaggattgatgatgatacagGAAGATGAGAAATTGAAGCTATCAGAGGTTACTGGACTAGACCAGAAGCAGATTAACAACTGGTTCATAAACCAGAGGAAGCGGCATTGGAAACCATCAG
                                      gattgat  putative branch site (score: 4)
     tttacttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aaaagttcatattggagttgtatttagaactgctatcgctgggacacttgtttactttcatttctggacacgtatctgaaaaggattgatgatgatacagGAAGATGAGAAATTGAAGCTATCAGAGGTTACTGGACTAGACCAGAAGCAGATTAACAACTGGTTCATAAACCAGAGGAAGCGGCATTGGAAACCATCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA
- - - - - - - - - - - - - - -ctgctat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaaagga