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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tttagaagcaattaagtgcacttgttgagtatgtcttttacttgatgatacaagagttcaaaagctaatgaagattttaacttgtgatttggtgaaacagGAGGCTGCAGCATTGGCTGCAACACAAGTTGCTTTTGTGCTGCAATCAGGACAACGAAGGGGTCTGCAGTTCACAGTTGCACCAGCACATGTAGTAGCTC

Basic information

species Vitis vinifera
transcript Vv01s0026g02470.t01
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv01s0026g02470.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GLYMA01G05800.1 (Glycine max), 3'ss of exon 7
--tttagaagcaattaagtgcacttgttgagtatgtcttttacttgatgatacaagagttcaaaagctaatgaagattttaactt-gtgatttggtgaaacagGAGGCTGCAGCATTGGCTGCAACACAAGTTGCTTTTGTGCTGCAATCAGGACAACGAAGGGGTCTGCAGTTCACAGTTGCACCAGCACATGTAGTAGCTC
  |||        ||    | | |       ||| |  |||    | ||  |    ||||     | | ||  |  |   |  || ||  | ||||||||||||||||||||||| | || ||||| |||||||||||||| || ||||| || || || || ||| | |||||  || | ||||||| ||       |   |
agtttgtccatcgttttcagaattacaatgctatatggttt-taggctggaatctaagtttgt--gttcatatatctcacatttttgtattatggtgaaacagGAGGCTGCAGCACTAGCGGCAACCCAAGTTGCTTTTGTTCTACAATCTGGTCAGCGTAGAGGTTTACAGTTTGCAATAGCACCAGGACCACCCACACTAC

upper sequence: Vv01s0026g02470.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GLYMA02G11960.1 (Glycine max), 3'ss of exon 7
-----------------------------------------tttagaagcaattaagtgcacttgttgagtatgtcttttacttga---tgatacaagagttcaaaagctaatga--agattttaa---cttgtgatttggtgaaacagGAGGCTGCAGCATTGGCTGCAACACAAGTTGCTTTTGTGCTGCAATCAGGACAACGAAGGGGTCTGCAGTTCACAGTTGCACCAGCACATGTAGTAGCTC
                                          ||||      |    |   |    | |  ||   || |  ||     | |  |   | |  ||||| |  |||  | || | |     ||||| | ||||||||||||||||||||||| | || ||||| ||||||||||| || || ||||| || || || || ||| | |||||  || | ||||||| |         |  |
gtcagtcttcattatagttattaatatttgttttggttttgcttagtcagtgtatcattttcggaataaaaatactttatggtttctttttaggctgcaatctaaaagtttgtgatcatatctcacatttttgtgttatggtgaaacagGAGGCTGCAGCACTAGCAGCAACCCAAGTTGCTTTCGTTCTACAATCTGGGCAGCGTAGAGGTTTACAGTTTGCAATAGCACCAGGATCACCCACTGTAC

upper sequence: Vv01s0026g02470.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GLYMA20G04870.1 (Glycine max), 3'ss of exon 6
------tttagaagcaattaagtgcacttgttga-gtatgtcttttacttgatgatacaagagttcaaaagctaatgaagattttaacttgtgatttggtgaaacagGAGGCTGCAGCATTGGCTGCAACACAAGTTGCTTTTGTGCTGCAATCAGGACAACGAAGGGGTCTGCAGTTCACAGTTGCACCAGCACATGTAGTAGCTC
      |||  || || | |     |       | |||  |   || || | |  |     | |   ||  || |||  | ||| |     || | ||| |||||||||||| |||||| | || ||||| ||||||||||| || || ||||| || || || ||||||||||||||  || | ||||||| ||    |  |    
atctattttgcaaacattcatccaaatgcacacacgtagatggattgctagttattttctaactagtaactctcatg--gttttca-----tgttatggcgaaacagGAGGCGGCAGCACTAGCGGCAACCCAAGTTGCTTTCGTTCTACAATCCGGGCAGCGTAGGGGTCTGCAGTTTGCAATAGCACCAGGACCACCAACAATGA

upper sequence: Vv01s0026g02470.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GLYMA07G35750.1 (Glycine max), 3'ss of exon 6
tttagaagcaattaagtgcacttgttgagtatgtcttttacttgatgatacaagagttcaaaagctaatgaagattttaac-----ttgtgatttggtgaaacagGAGGCTGCAGCATTGGCTGCAACACAAGTTGCTTTTGTGCTGCAATCAGGACAACGAAGGGGTCTGCAGTTCACAGTTGCACCAGCACATGTAGTAGCTC
   | || |||||  ||| ||  ||| |         | ||  |  |||  |  | |    | | |   | | ||| | |      |  || |  |||||||||||| || |||||| | || ||||| |||||||||||||| || ||| | || || || ||||||||||||||  || | | ||||| ||    |  |    
---aaaatcaatttggtgaac--gttcaaccaaatactcacaagtagatggattactatttatgttccaggaaattctcatggttttcatgttacggtgaaacagGAAGCGGCAGCACTAGCGGCAACCCAAGTTGCTTTTGTTCTACAAACCGGGCAGCGTAGGGGTCTGCAGTTTGCAATAGGACCAGGACCACCAACAATGA

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|30327724|gb|CD010986.1|CD010986
EST:     ACATTATGGCCTGGGCCATTAGTATCTTGCAGCGTCGAAGACAGAGGCAG                         GAGGCTGCAGCATTGGCTGCAACACAAGTTGCTTTTGTGCTGCAATCAGGA
genomic: ACATTATGGCCTGGGCCATTAGTATCTTGCAGCGTCGAAGACAGAGGCAGgttagtgtct ... ggtgaaacagGAGGCTGCAGCATTGGCTGCAACACAAGTTGCTTTTGTGCTGCAATCAGGA
EST: gi|110689841|gb|EE066416.1|EE066416
EST:     ACATTATGGCCTGGGCCATTAGTATCTTGCAGCGTCGAAGACAGAGGCAG                         GAGGCTGCAGCATTGGCTGCAACACAAGTTGCTTTTGTGCTGCAATCAGGA
genomic: ACATTATGGCCTGGGCCATTAGTATCTTGCAGCGTCGAAGACAGAGGCAGgttagtgtct ... ggtgaaacagGAGGCTGCAGCATTGGCTGCAACACAAGTTGCTTTTGTGCTGCAATCAGGA
EST: gi|110713173|gb|EE088860.1|EE088860
EST:     ACATTATGGCCTGNGCCATTAGTATCTTGCAGCGTCNAAAAC-GAAGCAN                         GANGCTGCAGCATTGGCTGCAA-ACAAGTTGCTTTTGTGCTGCAA
genomic: ACATTATGGCCTGGGCCATTAGTATCTTGCAGCGTCGAAGACAGAGGCAGgttagtgtct ... ggtgaaacagGAGGCTGCAGCATTGGCTGCAACACAAGTTGCTTTTGTGCTGCAA
EST: gi|32248365|gb|CD714184.1|CD714184
EST:     ACATTATGGCCTGGGCCATTAGTATCTTGCAGCGTCGAAGACAGAGGCAG                         GAGGCTGCAGCATTGGCTGCAACACAAGTTGCTTTTGTGCTGCAATCAGGA
genomic: ACATTATGGCCTGGGCCATTAGTATCTTGCAGCGTCGAAGACAGAGGCAGgttagtgtct ... ggtgaaacagGAGGCTGCAGCATTGGCTGCAACACAAGTTGCTTTTGTGCTGCAATCAGGA
EST: gi|32249399|gb|CD715218.1|CD715218
EST:     ACATTATGGCCTGGGCCATTAGTATCTTGCAGCGTCGAAGACAGAGGCAG                         GAGGCTGCAGCATTGGCTGCAACACAAGTTGCTTTTGTGCTGCAATCAGGA
genomic: ACATTATGGCCTGGGCCATTAGTATCTTGCAGCGTCGAAGACAGAGGCAGgttagtgtct ... ggtgaaacagGAGGCTGCAGCATTGGCTGCAACACAAGTTGCTTTTGTGCTGCAATCAGGA
EST: gi|110695828|gb|EE074293.1|EE074293
EST:     ACATTATGGCCTGGGCCATTAGTATCTTGCAGCGTCGAAGACAGAGGCAG                         GAGGCTGCAGCATTGGCTGCAACACAAGTTGCTTTTGTGCTGCAATCAGGA
genomic: ACATTATGGCCTGGGCCATTAGTATCTTGCAGCGTCGAAGACAGAGGCAGgttagtgtct ... ggtgaaacagGAGGCTGCAGCATTGGCTGCAACACAAGTTGCTTTTGTGCTGCAATCAGGA
EST: gi|30327239|gb|CD010501.1|CD010501
EST:     ACATTATGGCCTGGGCCATTAGTATCTTGCAGCGTCGAAGACAGAGGCAG                         GAGGCTGCAGCATTGGCTGCAACACAAGTTGCTTTTGTGCTGCAATCAGGA
genomic: ACATTATGGCCTGGGCCATTAGTATCTTGCAGCGTCGAAGACAGAGGCAGgttagtgtct ... ggtgaaacagGAGGCTGCAGCATTGGCTGCAACACAAGTTGCTTTTGTGCTGCAATCAGGA
EST: gi|110715491|gb|EE093604.1|EE093604
EST:     ACATTATGGCCTGGGCCATTAGTATCTTGCAGCGTCGAAGACAGAGGCAG                         GAGGCTGCAGCATTGGCTGCAACACAAGTTGCTTTTGTGCTGCAATCAGGA
genomic: ACATTATGGCCTGGGCCATTAGTATCTTGCAGCGTCGAAGACAGAGGCAGgttagtgtct ... ggtgaaacagGAGGCTGCAGCATTGGCTGCAACACAAGTTGCTTTTGTGCTGCAATCAGGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgatacaagagttcaaaagctaatgaagattttaacttgtgatttggtgaaacagGAGGCTGCAGCATTGGCTGCAACACAAGTTGCTTTTGTGCTGCAATCAGGACAACGAAGGGGTCTGCAGTTCACAGTTGCACCAGCACATGTAGTAGCTC
                             ttttaac  putative branch site (score: 2)
                    taatgaagattttaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tttagaagcaattaagtgcacttgttgagtatgtcttttacttgatgatacaagagttcaaaagctaatgaagattttaacttgtgatttggtgaaacagGAGGCTGCAGCATTGGCTGCAACACAAGTTGCTTTTGTGCTGCAATCAGGACAACGAAGGGGTCTGCAGTTCACAGTTGCACCAGCACATGTAGTAGCTC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGCAG
- - gaagcaa
- - - - - - - - -gcacttg
- - - - - - - - - - - - - - gtatgtc
- - - - - - - - - - - - - - - - - - - - - - - gatacaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - caaaagc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aatgaaga