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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctcttgtttccttgggctttgaatttagtttgtaaccatttgtctcttcagttatgtaatgtttagaagatcccaacaatttttttattggaattttcagGATTATACAGAAATGTCCAAAGCGTATAGGCCTTCACATGCAGATGCTACTTATGACTTCAAGTATGGTGTGAGGTCGGTGCAG

Basic information

species Vitis vinifera
transcript Vv13s0019g04190.t01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv13s0019g04190.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: LOC_Os03g14990.1 (Oryza sativa), 3'ss of exon 4
-----------------------------------------------------------------------------ctcttgtttccttgggctttgaattta-gtttgtaaccatttgtctcttcagttat-----gtaatgtttagaagatcccaacaatttttttattggaattttcagGATTATACAGAAATGTCCAAAGCGTATAGGCCTTCACATGCAGATGCTACTTATGACTTCAAGTATGGTGTGAGGTCGGTGCAG
                                                                              ||| |   |            ||| |    |  ||    || | | ||  |  |      ||||  | |  ||| |   || ||   |   |||        |||||||| |  |||||| | || || || || ||||||||||||||||| |||||||||||||| || ||||| ||  | ||||||
gtaagtacctaagttttttcgcattaatgtattgaaatactacctccgtcccaaaatataacaacttttggctacgaatctggacacacaattgcccagattcatagctaaaaatgcttatattttgggacagagggagtaacatattaaagctggaaataaccat---attcattcccacagGATTACAGTGAAATGGCTAAGGCCTACAGACCTTCACATGCAGATGCAACTTATGACTTCAAATACGGTGTTAGAGCAGTGCAG

upper sequence: Vv13s0019g04190.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM2G164562_T01 (Zea mays), 3'ss of exon 4
----ctcttgtttccttgggctttgaatttagtttgtaac--catttgtctcttcagttatg-taatgtt--tagaagatcccaaca-atttttttattggaattttcagGATTATACAGAAATGTCCAAAGCGTATAGGCCTTCACATGCAGATGCTACTTATGACTTCAAGTATGGTGTGAGGTCGGTGCAG
     | |    | || |   | |  ||||  |    ||    | |||    || ||    |  | |||   ||| | ||        ||     || | |  | | |||||||| |  |||||||| || ||||| || || || ||||||||||| || ||||||||||||||||| || ||  | ||||||
gtaagtatctaattctggatatatatattttctcatgaatggaagttgaacatttagaagggacagtgtcagtagtatattttgtttcataaacatactcgcttctacagGATTACAGTGAAATGTCTAAGGCGTACAGACCATCCCATGCAGATGCAACCTATGACTTCAAGTATGGAGTTAGAGCTGTGCAG

upper sequence: Vv13s0019g04190.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM2G036861_T01 (Zea mays), 3'ss of exon 4
--ctcttgtttccttgggctttgaatttagtttgtaaccatttgtctc-----ttcagttatgtaatg-tttagaagatcccaacaatttttttattggaatttt------cagGATTATACAGAAATGTCCAAAGCGTATAGGCCTTCACATGCAGATGCTACTTATGACTTCAAGTATGGTGTGAGGTCGGTGCAG
     | || |   |  |   || | ||  ||| |   ||  | |        || ||    | || | ||| |   ||    | |  ||||| ||    || ||      |||||| |    |||||  |||| | |||  | ||||| |||||||| || ||||||||||||||||| ||||| ||  | || |||
gtgagtagtatatatacgtactgtactttttttatggacaactctactgaacatttagaagagcaaggattttgttaataaatatatgtttttcataaccatgttggtccacagGATCACCGTGAAATAGCCAATGTGTACCGACCTTCTCATGCAGACGCAACTTATGACTTCAAGTACGGTGTTAGAGCTGTACAG

upper sequence: Vv13s0019g04190.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA10G35560.1 (Glycine max), 3'ss of exon 4
ctcttgtttccttgggctttgaatttagtttgtaac---catttgtctcttcagttatgtaatgtttagaagatcccaacaatttttttattggaattttcagGATTATACAGAAATGTCCAAAGCGTATAGGCCTTCACATGCAGATGCTACTTATGACTTCAAGTATGGTGTGAGGTCGGTGCAG
   |   |  ||   |||  ||  || |||| | ||   ||    |    | | ||  |  ||| | | || ||    |   |  | |        ||||||||| ||||| || ||| |   ||| ||||||||||| |||||||||||||| |||||| | ||||||||||| || || || |||
--gtgagtatctaatgctaggagctt-gtttatgacaagcaacaattatcttaatttagggatgctgataaaat----attgtactctgggaaactttttcagGACTATACTGAGATGGCAGTAGCTTATAGGCCTTCCCATGCAGATGCTACCTATGACATGAAGTATGGTGTCAGATCCGTTCAG

upper sequence: Vv13s0019g04190.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA20G31980.1 (Glycine max), 3'ss of exon 4
ctcttgtttccttgggctttgaatttagtttgtaac---catttgtctcttcagttatgtaatgtttagaagatcccaacaatttttttattggaattttcagGATTATACAGAAATGTCCAAAGCGTATAGGCCTTCACATGCAGATGCTACTTATGACTTCAAGTATGGTGTGAGGTCGGTGCAG
    ||  |   ||    | ||  || |||| | ||   ||    |    | | ||  |  ||| | | || ||    |   |  | |        ||||||||| ||||  || ||| |   ||| |||||||| || |||||||||||||| |||||| | ||||||||||| || || || |||
---gtgagtatctgatactagagctt-gtttatgacaagcaaccattatcttaatttagggatgctgataaaat----attgtactctgggaaactttttcagGACTATAGCGAGATGGCAGTAGCTTATAGGCCCTCCCATGCAGATGCTACCTATGACATGAAGTATGGTGTCAGATCAGTTCAG

upper sequence: Vv13s0019g04190.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: EFJ22409 (Selaginella moellendorffii), 3'ss of exon 3
ctcttgtttccttgggctttgaatttagtttgtaaccatttgtctcttcagttatgtaatgtttagaagatcccaacaatttttttattggaattttcagGATTATACAGAAATGTCCAAAGCGTATAGGCCTTCACATGCAGATGCTACTTATGACTTCAAGTATGGTGTGAGGTCGGTGCAG
                                        |   | |||  | ||| ||     |   || |  ||       | | ||    | | ||||||||  |||| ||| |   ||| ||| |||| || ||||||||||||||||| ||||||||||||||  |  |  | || |||
---------------------------------------gtaagttttcgttaatggaagaaacactggaacttaatgtgcggtgtttt----tctgcagGATTACTCAGAGATGGCTCTAGCTTATCGGCCATCTCATGCAGATGCTACTTACGACTTCAAGTATGGAATTCGAGCTGTCCAG

upper sequence: Vv13s0019g04190.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: EFJ25489 (Selaginella moellendorffii), 3'ss of exon 4
ctcttgtttccttgggctttgaatttagtttgtaaccatttgtctcttcagttatgtaatgtttagaagatcccaacaatttttttattggaattttcagGATTATACAGAAATGTCCAAAGCGTATAGGCCTTCACATGCAGATGCTACTTATGACTTCAAGTATGGTGTGAGGTCGGTGCAG
                                        |   | |||  | ||| ||     |   || |  ||       | | ||    | | ||||||||  |||| ||| |   ||| ||| |||| || ||||||||||||||||| ||||||||||||||  |  |  | || |||
---------------------------------------gtaagttttcgttaatggaagaaacactggagcttaatgtgcggtgtttt----tctgcagGATTACTCAGAGATGGCTCTAGCTTATCGGCCATCTCATGCAGATGCTACTTACGACTTCAAGTATGGAATTCGAGCTGTCCAG

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|352790897|gb|FQ477345.1|FQ477345
EST:     CTGGATCACCAATAATGGTAAATGTACCTAATACTGATCAGAGAGGAAAT                         GATTATACATAAATGTC-ATAACCGTATAGGCCTTCACATGCAGATGCTAC
genomic: CTGGATCACCAATAATGGTAAATGTACCTAATACTGATCAGAGAGGAAATgtgagtatcc ... gaattttcagGATTATACAGAAATGTCCA-AAGCGTATAGGCCTTCACATGCAGATGCTAC
EST: gi|71880899|gb|DT029954.1|DT029954
EST:     CTGGATCACCAATAATGGTAAATGTACCTAATACTGATCAGAGAGGAAAT                         GATTATACAGAAATGTCAAAAGCGTATAGGCCTTCACATGCAGATGCTACT
genomic: CTGGATCACCAATAATGGTAAATGTACCTAATACTGATCAGAGAGGAAATgtgagtatcc ... gaattttcagGATTATACAGAAATGTCCAAAGCGTATAGGCCTTCACATGCAGATGCTACT
EST: gi|71877721|gb|DT026776.1|DT026776
EST:     CTGGATCACCAATAATGGTAAATGTACCTAATACTGATCAGAGAGGAAAT                         GATTATACAGAAATGTCAAAAGCGTATAGGCCTTCACATGCAGATGCTACT
genomic: CTGGATCACCAATAATGGTAAATGTACCTAATACTGATCAGAGAGGAAATgtgagtatcc ... gaattttcagGATTATACAGAAATGTCCAAAGCGTATAGGCCTTCACATGCAGATGCTACT
EST: gi|71863219|gb|DT012274.1|DT012274
EST:     CTGGATCACCAATAATGGTAAATGTACCTAATACTGATCAGAGAGGAAAT                         GATTATACAGAAATGTCAAAAGCGTATAGGCCTTCACATGCAGATGCTACT
genomic: CTGGATCACCAATAATGGTAAATGTACCTAATACTGATCAGAGAGGAAATgtgagtatcc ... gaattttcagGATTATACAGAAATGTCCAAAGCGTATAGGCCTTCACATGCAGATGCTACT
EST: gi|352778035|gb|FQ467088.1|FQ467088
EST:     CTGGATCACCAATAATGGTAAATGTACCTAATACTGATCAGAGAGGAAAT                         GATTATACAGAAATGTCCAAAGCGTATAGGCCTTCACATGCAGATGCTACT
genomic: CTGGATCACCAATAATGGTAAATGTACCTAATACTGATCAGAGAGGAAATgtgagtatcc ... gaattttcagGATTATACAGAAATGTCCAAAGCGTATAGGCCTTCACATGCAGATGCTACT
EST: gi|71855293|gb|DT004348.1|DT004348
EST:     CTGGATCACCAATAATGGTAAATGTACCTAATACTGATCAGAGAGGAAAT                         GATTATACAGAAATGTCAAAAGCGTATAGGCCTTCACATGCAGATGCTACT
genomic: CTGGATCACCAATAATGGTAAATGTACCTAATACTGATCAGAGAGGAAATgtgagtatcc ... gaattttcagGATTATACAGAAATGTCCAAAGCGTATAGGCCTTCACATGCAGATGCTACT
EST: gi|71861705|gb|DT010760.1|DT010760
EST:     CTGGATCACCAATAATGGTAAATGTACCTAATACTGATCAGAGAGGAAAT                         GATTATACAGAAATGTCAAAAGCGTATAGGCCTTCACATGCAGATGCTACT
genomic: CTGGATCACCAATAATGGTAAATGTACCTAATACTGATCAGAGAGGAAATgtgagtatcc ... gaattttcagGATTATACAGAAATGTCCAAAGCGTATAGGCCTTCACATGCAGATGCTACT
EST: gi|71879200|gb|DT028255.1|DT028255
EST:     CTGGATCACCAATAATGGTAAATGTACCTAATACTGATCAGAGAGGAAAT                         GATTATACAGAAATGTCAAAAGCGTATAGGCCTTCACATGCAGATGCTACT
genomic: CTGGATCACCAATAATGGTAAATGTACCTAATACTGATCAGAGAGGAAATgtgagtatcc ... gaattttcagGATTATACAGAAATGTCCAAAGCGTATAGGCCTTCACATGCAGATGCTACT
EST: gi|71880874|gb|DT029929.1|DT029929
EST:     CTGGATCACCAATAATGGTAAATGTACCTAATACTGATCAGAGAGGAAAT                         GATTATACAGAAATGTCAAAAGCGTATAGGCCTTCACATGCAGATGCTACT
genomic: CTGGATCACCAATAATGGTAAATGTACCTAATACTGATCAGAGAGGAAATgtgagtatcc ... gaattttcagGATTATACAGAAATGTCCAAAGCGTATAGGCCTTCACATGCAGATGCTACT
EST: gi|352776661|gb|FQ465459.1|FQ465459
EST:     CTGGATCACCAATAATGGTAAATGTACCTAATACTGATCAGAGAGGAAAT                         GATTATACAGAAATGTCCAAAGCGTATAGGCCTTCACATGCAGATGCTACT
genomic: CTGGATCACCAATAATGGTAAATGTACCTAATACTGATCAGAGAGGAAATgtgagtatcc ... gaattttcagGATTATACAGAAATGTCCAAAGCGTATAGGCCTTCACATGCAGATGCTACT
EST: gi|352777956|gb|FQ467009.1|FQ467009
EST:     CTGGATCACCAATAATGGTAAATGTACCTAATACTGATCAGAGAGGAAAT                         GATTATACAGAAATGTCCAAAGCGTATAGGCCTTCACATGCAGATGCTACT
genomic: CTGGATCACCAATAATGGTAAATGTACCTAATACTGATCAGAGAGGAAATgtgagtatcc ... gaattttcagGATTATACAGAAATGTCCAAAGCGTATAGGCCTTCACATGCAGATGCTACT
EST: gi|351024445|gb|FQ426254.1|FQ426254
EST:     CTGGATCACCAATAATGGTAAATGTACCTAATACTGATCAGAGAGGAAAT                         GATTATACAGAAATGTCAAAAGCGTATAGGCCTTCACATGCAGATGCTACT
genomic: CTGGATCACCAATAATGGTAAATGTACCTAATACTGATCAGAGAGGAAATgtgagtatcc ... gaattttcagGATTATACAGAAATGTCCAAAGCGTATAGGCCTTCACATGCAGATGCTACT
EST: gi|352778092|gb|FQ467145.1|FQ467145
EST:     CTGGATCACCAATAATGGTAAATGTACCTAATACTGATCAGAGAGGAAAT                         GATTATACAGAAATGTCCAAAGCGTATAGGCCTTCACATGCAGATGCTACT
genomic: CTGGATCACCAATAATGGTAAATGTACCTAATACTGATCAGAGAGGAAATgtgagtatcc ... gaattttcagGATTATACAGAAATGTCCAAAGCGTATAGGCCTTCACATGCAGATGCTACT
EST: gi|352763986|gb|FQ467556.1|FQ467556
EST:     CTGGATCACCAATAATGGTAAATGTACCTAATACTGATCAGAGAGGAAAT                         GATTATACAGAAATGTCCAAAGCGTATAGGCCTTCACATGCAGATGCTACT
genomic: CTGGATCACCAATAATGGTAAATGTACCTAATACTGATCAGAGAGGAAATgtgagtatcc ... gaattttcagGATTATACAGAAATGTCCAAAGCGTATAGGCCTTCACATGCAGATGCTACT
EST: gi|352768213|gb|FQ467352.1|FQ467352
EST:     CTGGATCACCAATAATGGTAAATGTACCTAATACTGATCAAAGAGGAAAT                         GATTATACAGAAATGTCCAAAACGTATAGGCCTTCACATGCAGATGCTACT
genomic: CTGGATCACCAATAATGGTAAATGTACCTAATACTGATCAGAGAGGAAATgtgagtatcc ... gaattttcagGATTATACAGAAATGTCCAAAGCGTATAGGCCTTCACATGCAGATGCTACT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttcagttatgtaatgtttagaagatcccaacaatttttttattggaattttcagGATTATACAGAAATGTCCAAAGCGTATAGGCCTTCACATGCAGATGCTACTTATGACTTCAAGTATGGTGTGAGGTCGGTGCAG
                                                ttttc  CT-rich tract
                             aacaatttttttattg  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ctcttgtttccttgggctttgaatttagtttgtaaccatttgtctcttcagttatgtaatgtttagaagatcccaacaatttttttattggaattttcagGATTATACAGAAATGTCCAAAGCGTATAGGCCTTCACATGCAGATGCTACTTATGACTTCAAGTATGGTGTGAGGTCGGTGCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG
- - - -ttccttg
- - - - - - - - - - - - - - - -gtaacca
- - - - - - - - - - - - - - - - - - - - - -ctcttca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ccaacaa