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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...acagggtgtcattataactaattttccttttctctgcttttcatttttaaatactattgctctttaacatagaacatgaactcttaataatgttttgcagGTTAATACACATCTCACACCCCGACCAATTTTACTTACTAGGCATGGAGAGAGTCGGGATAATGTTAGAGGTAGAATTGGGGGTGACACTGCATTAAG

Basic information

species Vitis vinifera
transcript Vv06s0004g06920.t01
intron # 15
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv06s0004g06920.t01 (Vitis vinifera), 3'ss of exon 15
lower sequence: GLYMA14G37520.1 (Glycine max), 3'ss of exon 26
acagggtgtcattataactaattttccttttctctgctttt--catttttaaatactattgctctttaacatagaacatgaactcttaataatgttttgcagGTTAATACACATCTCACACCCCGACCAATTTTACTTACTAGGCATGGAGAGAGTCGGGATAATGTTAGAGGTAGAATTGGGGGTGACACTGCATTAAG
   |    | | || |  | ||||    ||    ||| ||    |  |  || | | | |    | |||  | | |   |   | ||  || | | |||||||||||||||||||| ||||| || ||||| ||||||||  |||||||||| |||| | ||||||| ||||| |||||||| || ||| ||||||||||
ttggaagattaata-atgtgatttgttattatcttgcattcagtaaatgcaactgcaaatcacttgtaagcttgtatgagtgat-ttgttattatcttgcagGTTAATACACATCTTACACCACGCCCAATATTACTTACCCGGCATGGAGAAAGTCAGTATAATGTGAGAGGCAGAATTGGTGGAGACTCTGCATTAAG

upper sequence: Vv06s0004g06920.t01 (Vitis vinifera), 3'ss of exon 15
lower sequence: GLYMA02G39390.1 (Glycine max), 3'ss of exon 15
acagggtgtcattataactaattttccttttctctgcttttcatttt--taaatactattgctctttaacatagaac----atgaactcttaataatgttttgcagGTTAATACACATCTCACACCCCGACCAATTTTACTTACTAGGCATGGAGAGAGTCGGGATAATGTTAGAGGTAGAATTGGGGGTGACACTGCATTAAG
      ||| || ||   |  | ||       |     | | | ||   ||||| | | |||   | |      | |    |||     ||  || | | |||||||||||||||||||| ||||| || ||||| ||||||||  |||||||||| |||| | ||||||| ||||| |||||||| || ||| ||||||||||
------tgtgataatcgtttttgttggaagattaataatgtgaattcagtaaatgcaactgcaaatcacttgtaagcttctatggtgatttgttattatcttgcagGTTAATACACATCTTACACCACGCCCAATATTACTTACCCGGCATGGAGAAAGTCAGTATAATGTGAGAGGCAGAATTGGAGGAGACTCTGCATTAAG

upper sequence: Vv06s0004g06920.t01 (Vitis vinifera), 3'ss of exon 15
lower sequence: GLYMA18G06770.1 (Glycine max), 3'ss of exon 17
------------acagggtgtcattata-actaattttccttttctctgcttttcattt--ttaaatactattgctct-ttaacatagaa-----catgaactcttaataatgttttgcagGTTAATACACATCTCACACCCCGACCAATTTTACTTACTAGGCATGGAGAGAGTCGGGATAATGTTAGAGGTAGAATTGGGGGTGACACTGCATTAAG-
              ||| |||  ||| | || ||    | |     |||    | |  |  |||| || | || || | || ||  | |       ||||||    | | ||||| ||||||| ||||||||||| || || || ||||||||||||||| | ||||| || |||| ||||||||| ||||| |||||||| || || |||||| |||| 
gtaagtatttttgaaggatgtagttaaataccaaaacccatggatgctggaactaagctaattaactagtttttctatattgacccatacatttctatgaacctaaatttatgttctgcagGTAAATACACATCTTACCCCACGCCCAATTTTACTTACTCGACATGGGGAAAGTCAGGATAATGTGAGAGGCAGAATTGGAGGGGATACTGCAATAAGG

upper sequence: Vv06s0004g06920.t01 (Vitis vinifera), 3'ss of exon 15
lower sequence: GLYMA11G27870.1 (Glycine max), 3'ss of exon 16
-acagggtgtcattataactaattttccttttctctgcttttcatttttaaatactattgctctttaacatagaac-atgaactcttaataatgttttgcagGTTAATACACATCTCACACCCCGACCAATTTTACTTACTAGGCATGGAGAGAGTCGGGATAATGTTAGAGGTAGAATTGGGGGTGACACTGCATTAAG
 |      | | || || |   | |  ||| |   |   |   |  ||||  | |||||    ||| | | |   | ||||||    | | ||||  ||||||| ||||||||||| ||||| || ||||||||||||||  | ||||| || |||| ||||||||| ||||| |||||||| || || |||||| ||||
tatgcataggctttgtaccacttgtaacttatgaataaatagaaacttta--ttctatttggttttcatacatttctatgaacctaaatttatgtgatgcagGTAAATACACATCTTACACCACGCCCAATTTTACTTACCCGACATGGGGAAAGTCAGGATAATGTGAGAGGCAGAATTGGAGGGGATACTGCAATAAG

upper sequence: Vv06s0004g06920.t01 (Vitis vinifera), 3'ss of exon 15
lower sequence: GLYMA11G27410.1 (Glycine max), 3'ss of exon 21
-acagggtgtcattataactaattttccttttctctgcttttcatttttaaatactattgctctttaacatagaac-atgaactcttaataatgttttgcagGTTAATACACATCTCACACCCCGACCAATTTTACTTACTAGGCATGGAGAGAGTCGGGATAATGTTAGAGGTAGA---ATTGGGGGTGACACTGCATTAAG
 |      | | |  || |   | |  ||| |   |       |  ||||  | ||||| |  ||| | | |   | ||||||    | | ||||  ||||||| ||||||||||| ||||| || ||||||||||||||  | ||||| || |||| ||||||||||||||| |||   ||||| || || |||||| ||| 
tatgcataggcttcgtatcacttgtaacttatgaataaacagaaacttta--ttctatttcgttttcatacatttctatgaacctaaatttatgtgatgcagGTAAATACACATCTTACACCACGCCCAATTTTACTTACCCGACATGGGGAAAGTCAGGATAATGTTAGAGGCAGAAGAATTGGAGGGGATACTGCAATAA-

upper sequence: Vv06s0004g06920.t01 (Vitis vinifera), 3'ss of exon 15
lower sequence: AT1G07110.1 (Arabidopsis thaliana), 3'ss of exon 15
acagggtgtcattataactaattttccttttctctgcttttcatttttaaatactattgctctttaacatagaacatgaactcttaa-----taatgtt-ttgcagGTTAATACACATCTCACACCCCGACCAATTTTACTTACTAGGCATGGAGAGAGTCGGGATAATGTTAGAGGTAGAATTGGGGGTGACACTGCATTAAG
     || |      |||  | |   | ||  ||  ||  | || |  |||||   | |     | |   | | |||    | ||||     | || || ||  |||| ||||| |||||||| || ||||||||  |||| ||| |||||||||| ||   ||||||||||||||| |||||||| || || |  | | ||||
-----gtctatcgccaacagactcaacattcatcgtctaattatataaaaataacctagagtgctcatg-acatcatcgttttttaaagcgctgattttcttctagGTGAATACGCATCTCACCCCACGACCAATACTACTCACTCGGCATGGAGAAAGCATGGATAATGTTAGAGGCAGAATTGGAGGAGATAGCGTAATAAG

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|30322291|gb|CD005553.1|CD005553
EST:     GTCAACAATATCAGTGGCTATCTTCCTGGGCGGATTGTGTTTTTCTTG                         GTTAATACACACCTCACACCCCGACCAATTTTACTTACTAGGCATGGAGAG
genomic: GTCAACAATATCAGTGGCTATCTTCCTGGGCGGATTGTGTTTTTCTTGgtatgttgcc ... tgttttgcagGTTAATACACATCTCACACCCCGACCAATTTTACTTACTAGGCATGGAGAG
EST: gi|30321972|gb|CD005234.1|CD005234
EST:     GTCAACAATATCAGTGGCTATCTTCCTGGGCGGATTGTGTTTTTCTTG                         GTTAATACACACCTCACACCCCGACCAATTTTACTTACTAGGCATGGAGAG
genomic: GTCAACAATATCAGTGGCTATCTTCCTGGGCGGATTGTGTTTTTCTTGgtatgttgcc ... tgttttgcagGTTAATACACATCTCACACCCCGACCAATTTTACTTACTAGGCATGGAGAG
EST: gi|27580319|gb|CB003014.1|CB003014
EST:     GTCAACAATATCAGTGGCTATCTTCCTGGGCGGATTGTGTTTTTCTTG                         GTTAATACACACCTCACACCCCGACCAATTTTACTTACTAGGCATGGAGAG
genomic: GTCAACAATATCAGTGGCTATCTTCCTGGGCGGATTGTGTTTTTCTTGgtatgttgcc ... tgttttgcagGTTAATACACATCTCACACCCCGACCAATTTTACTTACTAGGCATGGAGAG
EST: gi|27581545|gb|CB004240.1|CB004240
EST:     GTCAACAATATCAGTGGCTATCTTCCTGGGCGGATTGTGTTTTTCTTG                         GTTAATACACACCTCACACCCCGACCAATTTTACTTACTAGGCATGGAGAG
genomic: GTCAACAATATCAGTGGCTATCTTCCTGGGCGGATTGTGTTTTTCTTGgtatgttgcc ... tgttttgcagGTTAATACACATCTCACACCCCGACCAATTTTACTTACTAGGCATGGAGAG
EST: gi|27580309|gb|CB003004.1|CB003004
EST:     GTCAACAATATCAGTGGCTATCTTCCTGGGCGGATTGTGTTTTTCTTG                         GTTAATACACACCTCACACCCCGACCAATTTTACTTACTAGGCATGGAGAG
genomic: GTCAACAATATCAGTGGCTATCTTCCTGGGCGGATTGTGTTTTTCTTGgtatgttgcc ... tgttttgcagGTTAATACACATCTCACACCCCGACCAATTTTACTTACTAGGCATGGAGAG
EST: gi|32250239|gb|CD716058.1|CD716058
EST:     GTCAACAATATCAGTGGCTATCTTCCTGGGCGGATTGTGTTTTTCTTG                         GTTAATACACACCTCACACCCCGACCAATTTTACTTACTAGGCATGGAGAG
genomic: GTCAACAATATCAGTGGCTATCTTCCTGGGCGGATTGTGTTTTTCTTGgtatgttgcc ... tgttttgcagGTTAATACACATCTCACACCCCGACCAATTTTACTTACTAGGCATGGAGAG
EST: gi|110360631|gb|EC923892.1|EC923892
EST:     GTCAACAATATCAGTGGCTATCTTCCTGGGCGGATTGTGTTTTTCTTG                         GTTAATACACACCTCACACCCCGACCAATTTTACTTACTAGGCATGGAGAG
genomic: GTCAACAATATCAGTGGCTATCTTCCTGGGCGGATTGTGTTTTTCTTGgtatgttgcc ... tgttttgcagGTTAATACACATCTCACACCCCGACCAATTTTACTTACTAGGCATGGAGAG
EST: gi|30321898|gb|CD005160.1|CD005160
EST:     GTCAACAATATCAGTGGCTATCTTCCTGGGCGGATTGTGTTTTTCTTG                         GTTAATACACACCTCACACCCCGACCAATTTTACTTACTAGGCATGGAGAG
genomic: GTCAACAATATCAGTGGCTATCTTCCTGGGCGGATTGTGTTTTTCTTGgtatgttgcc ... tgttttgcagGTTAATACACATCTCACACCCCGACCAATTTTACTTACTAGGCATGGAGAG
EST: gi|30321402|gb|CD004664.1|CD004664
EST:     GTCAACAATATCAGTGGCTATCTTCCTGGGCGGATTGTGTTTTTCTTG                         GTTAATACACACCTCACACCCCGACCAATTTTACTTACTAGGCATGGAGAG
genomic: GTCAACAATATCAGTGGCTATCTTCCTGGGCGGATTGTGTTTTTCTTGgtatgttgcc ... tgttttgcagGTTAATACACATCTCACACCCCGACCAATTTTACTTACTAGGCATGGAGAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttaaatactattgctctttaacatagaacatgaactcttaataatgttttgcagGTTAATACACATCTCACACCCCGACCAATTTTACTTACTAGGCATGGAGAGAGTCGGGATAATGTTAGAGGTAGAATTGGGGGTGACACTGCATTAAG
                                    tcttaat  putative branch site (score: 3)
                                    tcttaataatgtttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
acagggtgtcattataactaattttccttttctctgcttttcatttttaaatactattgctctttaacatagaacatgaactcttaataatgttttgcagGTTAATACACATCTCACACCCCGACCAATTTTACTTACTAGGCATGGAGAGAGTCGGGATAATGTTAGAGGTAGAATTGGGGGTGACACTGCATTAAG

- - - - - - - -aactaat
- - - - - - - - - - - - - - - tctctgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aacataga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - catgaac