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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttttgacgaattggaacccaagaaagcataggattatacgggttttaggattcgctcttttgaatcaagactcagatggtttgatggtgtgttgagtcagGTTTTGGAGCTTGCTGGAAATGCAGCGAGGGACAACAAAAAGAATCGCATTGTACCTCGCCACATACAGCTAGCAGTAAGGAATGACGAGGAGCTAAGCA

Basic information

species Vitis vinifera
transcript Vv14s0030g00450.t01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv14s0030g00450.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: PP1S55_112V6.1 (Physcomitrella patens), 3'ss of exon 2
ttttgacgaattggaacc-caagaaagcataggatt-atacgggttttagga--ttcgctcttttgaatcaagactcagatggtttgatggtgtgttgagtcagGTTTTGGAGCTTGCTGGAAATGCAGCGAGGGACAACAAAAAGAATCGCATTGTACCTCGCCACATACAGCTAGCAGTAAGGAATGACGAGGAGCTAAGCA
    | ||   ||  | | || | |    || |  | | | | ||   || |  |||  | | |  | |   |  ||  | |   |||  |  |||  |  |||||  | ||| | || |||||||| || || || ||||||||||||||||| ||||| ||||| || ||||| |||||| | || ||||||||| | ||||
ggacgccgtcgtgatatcacacgtatttctacgcctcaaaagcgtgcgagtaatttccgtttgtccattgttgtttctaacga--tgaaagcttgt--atgcagGTCCTTGAGTTGGCAGGAAATGCCGCCAGAGATAACAAAAAGAATCGCATAGTACCCCGCCATATTCAGCTGGCAGTACGAAACGACGAGGAGTTGAGCA

upper sequence: Vv14s0030g00450.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: PP1S452_4V6.1 (Physcomitrella patens), 3'ss of exon 1
----ttttgacgaattggaacccaagaaagcataggattatacgggttttaggattcgctct-tttgaatcaagactcagatggtttgatggtgtgttgagtcagGTTTTGGAGCTTGCTGGAAATGCAGCGAGGGACAACAAAAAGAATCGCATTGTACCTCGCCACATACAGCTAGCAGTAAGGAATGACGAGGAGCTAAGCA
     | |  | | || |    ||  |  ||    ||  |  ||| |    || |||  | | || |      |  || |  | |       |   ||    |||||  | ||  | || |||||||| || || || ||||| ||||||||||||||||| |||||||| ||||| ||||| || || ||||||||| ||||||
gcttctgtctccacttcgcgagcagcactgcgcctgaa-aagcggctaagtggtttcagtttgttcgtggtctgtttctggcgatcca----tacatttgtgcagGTACTTGAATTAGCAGGAAATGCCGCCAGAGATAACAAGAAGAATCGCATTGTACCCCGCCACATCCAGCTGGCAGTGAGAAACGACGAGGAGTTAAGCA

upper sequence: Vv14s0030g00450.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: PP1S188_35V6.1 (Physcomitrella patens), 3'ss of exon 1
ttttgacgaattggaacccaagaaagcataggattatacgggttttaggattcgctcttttgaatcaagactcaga--tggtttgatggtgtgttgagtcagGTTTTGGAGCTTGCTGGAAATGCAGCGAGGGACAACAAAAAGAATCGCATTGTACCTCGCCACATACAGCTAGCAGTAAGGAATGACGAGGAGCTAAGCA
 || | |    |  ||   ||| |    |     | |    |  |     || | |    |   |    ||       |   || |     |  || || ||||| | ||||| ||||||||||| ||||| |||||||| |||||||| || || ||||||||||| |||||||| ||  | || || ||||||||||| |
-ttcgtccctctccaattgaagtatatttcattctctggaagggtgcaagttggttaagatcgttagtaacgtgtgcctaactttagaacattatgcgt-agGTTCTTGAGCTGGCTGGAAATGCTGCGAGAGACAACAAGAAGAATCGTATCGTCCCTCGCCACATCCAGCTAGCGGTGCGAAACGATGAGGAGCTAAGTA

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|110377786|gb|EC942876.1|EC942876
EST:     CCGGCGCCCCCGTCTACCTGTCTGCTGTTCTTGAGTATCTCGCGGCCGAG                         GTTTTGGAGCTTGCTGGAAATGCAGCGAGGGACAACAAAAAGAATCGCATT
genomic: CCGGCGCCCCCGTCTACCTGTCTGCTGTTCTTGAGTATCTCGCGGCCGAGgtaaattagg ... gttgagtcagGTTTTGGAGCTTGCTGGAAATGCAGCGAGGGACAACAAAAAGAATCGCATT
EST: gi|34319769|gb|CF372523.1|CF372523
EST:     CCGCCGCCCCCGTCTACCTGTCTGCTGTTCTTGAGTATCTCGCGGCCGAG                         GTTTTGGAGCTTGCTGGAAATGCAGCGAGGGACAACAAAAAGAATCGCATT
genomic: CCGGCGCCCCCGTCTACCTGTCTGCTGTTCTTGAGTATCTCGCGGCCGAGgtaaattagg ... gttgagtcagGTTTTGGAGCTTGCTGGAAATGCAGCGAGGGACAACAAAAAGAATCGCATT
EST: gi|351015257|gb|FQ445541.1|FQ445541
EST:     CCGGCGCCCCCGTCTACCTGTCTGCTGTTCTTGAGTATCTCGCGGCCGAG                         GTTTTGGAGCTTGCTGGAAATGCAGCGAGGGACAACAAAAAGAATCGCATT
genomic: CCGGCGCCCCCGTCTACCTGTCTGCTGTTCTTGAGTATCTCGCGGCCGAGgtaaattagg ... gttgagtcagGTTTTGGAGCTTGCTGGAAATGCAGCGAGGGACAACAAAAAGAATCGCATT
EST: gi|22012727|gb|BQ797761.1|BQ797761
EST:     CCGGCGCCCCCGTCTACCTGTCTGCTGTTCTTGAGTATCTCGCGGCCGAG                         GTTTTGGAGCTTGCTGGAAATGCAGCGAGGGACAACAAAAAGAATCGCATT
genomic: CCGGCGCCCCCGTCTACCTGTCTGCTGTTCTTGAGTATCTCGCGGCCGAGgtaaattagg ... gttgagtcagGTTTTGGAGCTTGCTGGAAATGCAGCGAGGGACAACAAAAAGAATCGCATT
EST: gi|110710227|gb|EE086380.1|EE086380
EST:     CCGGCGCCCCCGTCTACCTGTCTGCTGTTCTTGAGTATCTCGCGGCCGAA                         GTTTTGGAGCTTGCTGGAAATGCAGCGAGGGACAACAAAAAGAATCGCATT
genomic: CCGGCGCCCCCGTCTACCTGTCTGCTGTTCTTGAGTATCTCGCGGCCGAGgtaaattagg ... gttgagtcagGTTTTGGAGCTTGCTGGAAATGCAGCGAGGGACAACAAAAAGAATCGCATT
EST: gi|110730861|gb|EE108425.1|EE108425
EST:     CCGGCGCCCCCGTCTACCTGTCTGCTGTTCTTGAGTATCTCGCGGCCGAG                         GTTTTGGAGCTTGCTGGAAATGCAGCGAGGGACAACAAAAAGAATCGCATT
genomic: CCGGCGCCCCCGTCTACCTGTCTGCTGTTCTTGAGTATCTCGCGGCCGAGgtaaattagg ... gttgagtcagGTTTTGGAGCTTGCTGGAAATGCAGCGAGGGACAACAAAAAGAATCGCATT
EST: gi|110428604|gb|EC995081.1|EC995081
EST:     CCGGCGCCCCCGTCTACCTGTCTGCTGTTCTTGAGTATCTCGCGGCCGAG                         GTTTTGGAGCTTGCTGGAAATGCAGCGAGGGATAACAAAAAGAATCGCATT
genomic: CCGGCGCCCCCGTCTACCTGTCTGCTGTTCTTGAGTATCTCGCGGCCGAGgtaaattagg ... gttgagtcagGTTTTGGAGCTTGCTGGAAATGCAGCGAGGGACAACAAAAAGAATCGCATT
EST: gi|37188443|gb|CF607792.1|CF607792
EST:     CCGGCGCCCCCGTCTACCTGTCTGCTGTTCTTGAGTATCTCGCGGCCGAG                         GTTTTGGAGCTTGCTGGAAATGCAGCGAGGGACAACAAAAAGAATCGCATT
genomic: CCGGCGCCCCCGTCTACCTGTCTGCTGTTCTTGAGTATCTCGCGGCCGAGgtaaattagg ... gttgagtcagGTTTTGGAGCTTGCTGGAAATGCAGCGAGGGACAACAAAAAGAATCGCATT
EST: gi|71883990|gb|DT033045.1|DT033045
EST:     CGGCGCCCCCGTCTACCTGTCTGCTGTTCTTGAGTATCTCGCGGCCGAG                         GTTTTGGAGCTTGCTGGAAATGCAGCGAGGGACAACAAAAAGAATCGCATT
genomic: CGGCGCCCCCGTCTACCTGTCTGCTGTTCTTGAGTATCTCGCGGCCGAGgtaaattagg ... gttgagtcagGTTTTGGAGCTTGCTGGAAATGCAGCGAGGGACAACAAAAAGAATCGCATT
EST: gi|110413602|gb|EC979394.1|EC979394
EST:     TATCTCGCGGCCGAG                         GTTTTGGAGCTTGCTGGAAATGCAGCGAGGGACAACAAAAAGAATCGCATT
genomic: TATCTCGCGGCCGAGgtaaattagg ... gttgagtcagGTTTTGGAGCTTGCTGGAAATGCAGCGAGGGACAACAAAAAGAATCGCATT
EST: gi|351031017|gb|FQ439053.1|FQ439053
EST:     CCGGCGCCCCCGTCTACCTGTCTGCTGTTCTTGAGTATCTCGCGGCCGAG                         GTTTTGGAGCTTGCTGGAAATGCAGCGAGGGACAACAAAAAGAATCGCATT
genomic: CCGGCGCCCCCGTCTACCTGTCTGCTGTTCTTGAGTATCTCGCGGCCGAGgtaaattagg ... gttgagtcagGTTTTGGAGCTTGCTGGAAATGCAGCGAGGGACAACAAAAAGAATCGCATT
EST: gi|71869485|gb|DT018540.1|DT018540
EST:     CCGGCGCCCCCGTCTACCTGTCTGCTGTTCTTGAGTATCTCGCGGCCGAG                         GTTTTGGAGCTTGCTGGAAATGCAGCGAGGGACAACAAAAAGAATCGCATT
genomic: CCGGCGCCCCCGTCTACCTGTCTGCTGTTCTTGAGTATCTCGCGGCCGAGgtaaattagg ... gttgagtcagGTTTTGGAGCTTGCTGGAAATGCAGCGAGGGACAACAAAAAGAATCGCATT
EST: gi|110686405|gb|EE064005.1|EE064005
EST:     CCGGCGCCCCCGTCTACCTGTCTGCTGTTCTTGAGTATCTCGCGGCCGAG                         GTTTTGGAGCTTGCTGGAAATGCAGCGAGGGACAACAAAAAGAATCGCATT
genomic: CCGGCGCCCCCGTCTACCTGTCTGCTGTTCTTGAGTATCTCGCGGCCGAGgtaaattagg ... gttgagtcagGTTTTGGAGCTTGCTGGAAATGCAGCGAGGGACAACAAAAAGAATCGCATT
EST: gi|110415214|gb|EC981095.1|EC981095
EST:     CCGGCGCCCCCGTCTACCTGTCTGCTGTTCTTGAGTATCTCGCGGCCGAG                         GTTTTGGAGCTTGCTGGAAATGCAGCGAGGGATAACAAAAAGAATCGCATT
genomic: CCGGCGCCCCCGTCTACCTGTCTGCTGTTCTTGAGTATCTCGCGGCCGAGgtaaattagg ... gttgagtcagGTTTTGGAGCTTGCTGGAAATGCAGCGAGGGACAACAAAAAGAATCGCATT
EST: gi|77582566|gb|DV220266.1|DV220266
EST:     CCGGCGCCCCCGTCTACCTGTCTGCTGTTCTTGAGTATCTCGCGGCCGAG                         GTTTTGGAGCTTGCTGGAAATGCAGCGAGGGACAACAAAAAGAATCGCATT
genomic: CCGGCGCCCCCGTCTACCTGTCTGCTGTTCTTGAGTATCTCGCGGCCGAGgtaaattagg ... gttgagtcagGTTTTGGAGCTTGCTGGAAATGCAGCGAGGGACAACAAAAAGAATCGCATT
EST: gi|71890496|gb|DT039551.1|DT039551
EST:     CCGGCGCCCCCGTCTACCTGTCTGCTGTTCTTGAGTATCTCGCGGCCGAG                         GTTTTGGAGCTTGCTGGAAATGCAGCGAGGGACAACAAAAAGAATCGCATT
genomic: CCGGCGCCCCCGTCTACCTGTCTGCTGTTCTTGAGTATCTCGCGGCCGAGgtaaattagg ... gttgagtcagGTTTTGGAGCTTGCTGGAAATGCAGCGAGGGACAACAAAAAGAATCGCATT
EST: gi|110714497|gb|EE091474.1|EE091474
EST:     CCGGCGCCCCCGTCTACCTGTCTGCTGTTCTTGAGTATCTCGCGGCCGAG                         GTTTTGGAGCTTGCTGGAAATGCAGCGAGGGACAACAAAAAGAATCGCATT
genomic: CCGGCGCCCCCGTCTACCTGTCTGCTGTTCTTGAGTATCTCGCGGCCGAGgtaaattagg ... gttgagtcagGTTTTGGAGCTTGCTGGAAATGCAGCGAGGGACAACAAAAAGAATCGCATT
EST: gi|110706497|gb|EE082076.1|EE082076
EST:     CCGGCGCCCCCGTCTACCTGTCTGCTGTTCTTGAGTATCTCGCGGCCGAG                         GTTTTGGAGCTTGCTGGAAATGCAGCGAGGGACAACAAAAAGAATCGCATT
genomic: CCGGCGCCCCCGTCTACCTGTCTGCTGTTCTTGAGTATCTCGCGGCCGAGgtaaattagg ... gttgagtcagGTTTTGGAGCTTGCTGGAAATGCAGCGAGGGACAACAAAAAGAATCGCATT
EST: gi|110374813|gb|EC939748.1|EC939748
EST:     CCGGCGCCCCCGTCTACCTGTCTGCTGTTCTTGAGTATCTCGCGGCCGAG                         GTTTTGGAGCTTGCTGGAAATGCAGCGAGGGACAACAAAAAGAATCGCATT
genomic: CCGGCGCCCCCGTCTACCTGTCTGCTGTTCTTGAGTATCTCGCGGCCGAGgtaaattagg ... gttgagtcagGTTTTGGAGCTTGCTGGAAATGCAGCGAGGGACAACAAAAAGAATCGCATT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taggattcgctcttttgaatcaagactcagatggtttgatggtgtgttgagtcagGTTTTGGAGCTTGCTGGAAATGCAGCGAGGGACAACAAAAAGAATCGCATTGTACCTCGCCACATACAGCTAGCAGTAAGGAATGACGAGGAGCTAAGCA
                                 gtttgat  putative branch site (score: 5)
            ttttgaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttttgacgaattggaacccaagaaagcataggattatacgggttttaggattcgctcttttgaatcaagactcagatggtttgatggtgtgttgagtcagGTTTTGGAGCTTGCTGGAAATGCAGCGAGGGACAACAAAAAGAATCGCATTGTACCTCGCCACATACAGCTAGCAGTAAGGAATGACGAGGAGCTAAGCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCT
- - - - - - - - cccaaga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gaatcaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cagatgg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gatggtg