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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cacaatatttacaatataagagaagaaaaaaaaacggagtacttaacatatagtgtaattataatgaggagttccaactaaaaaatgttttattttgcagCAACGGCCTCATCATCCGGTTCGGCCAATTCCTTCACAGCTCTGGTGCAAGAATTTTGGAAATAAGGAATACTGATTTCTCTGCTGCTGTGTGATAAAAT

Basic information

species Vitis vinifera
transcript Vv16s0100g01290.t01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv16s0100g01290.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA18G46330.1 (Glycine max), 3'ss of exon 1
caca-atatttacaatataagagaagaaaaaaaaacggagtacttaacatatagtgtaattataatg-aggagttccaactaaaaaatgtttt----attttgcagCAACGGCCTCATCATCCGGTTCGGCCAATTCCTTCACAGCTCTGGTGCAAGAATTTTGGAAATAAGGAATACTGATTTCTCTGCTGC-TGTGTGATAAAAT
 ||| | || |||  |     |         || |    || | ||  |   | | ||  |  |||| | || ||    |||| |  |  |||    || || ||||||||||| ||||| || ||||| || || ||||| || |||||||||||||| ||||||| ||| || ||      ||  || | | |   |   | || 
tacatagatgtactctcctc-atttttttttaacattttgttcgtagta---attttagcttgaatgcatgaatt--ggctaagagtttcttttttgatctttcagCAACGGCCACATCACCCTGTTCGCCCCATCCCTTCTCAACTCTGGTGCAAGAACTTTGGAACTAAAGACTATAATGATCCATGATTCATCAATTGCATAA-

upper sequence: Vv16s0100g01290.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: AT4G00585.1 (Arabidopsis thaliana), 3'ss of exon 2
cacaatatttacaatataagagaagaaaaaaaaacggagtacttaacatatagtgtaattataatgaggagttc-caact----aaaaaatgttttattttgcagCAACGGCCTCATCATCCGGTTCGGCCAATTCCTTCACAGCTCTGGTGCAAGAATTTTGGAAATAAGGAATACTGATTTCTCTGCTGCTGTGTGATAAAAT
      | ||  | | | |          |    ||   ||||  | |||   |  | || |  |  |  |||| ||| |    ||||    |||    || |||||| |||| ||    || || || ||||||||||||||| ||||||||||||| |||||||  |||||  | |              |    | |    |
---tgcacttgaattgttatgttttgtgtatgtccgtgctact--atatagtttccacttcttgtttgatgttcacaatttgagaaaagccctttctgatttcagCAAAGGCCACACATGCCAGTACGCCCAATTCCTTCACAGATCTGGTGCAAGAACTTTGGAACCAAGGACGATTACGAAAAAGAGCATTAAAAGTTTTTTT
















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|37190617|gb|CF609966.1|CF609966
EST:     GCGTCTTTCTCATTTGCATCCCAATCGCTATGAAATCTGCCGAGCTCGAG                         CAACGGCCTCATCATCCGGTTCGGCCAATTCCTTCACAGCTCTGGTGCAAG
genomic: GCGTCTTTCTCATTTGCATCCCAATCGCTATGAAATCTGCCGAGCTCGAGgtctctctct ... tattttgcagCAACGGCCTCATCATCCGGTTCGGCCAATTCCTTCACAGCTCTGGTGCAAG
EST: gi|37188117|gb|CF607468.1|CF607468
EST:     GCGTCTTTCTCATTTGCATCCCAATCGCTATGAAATCTGCCGAGCTCGAG                         CAACGGCCTCATCATCCGGTTCGGCCAATTCCTTCACAGCTCTGGTGCAAG
genomic: GCGTCTTTCTCATTTGCATCCCAATCGCTATGAAATCTGCCGAGCTCGAGgtctctctct ... tattttgcagCAACGGCCTCATCATCCGGTTCGGCCAATTCCTTCACAGCTCTGGTGCAAG
EST: gi|110408102|gb|EC973725.1|EC973725
EST:     GCGTCTTTCTCATTTGCATCCCAATCGCTATGAAATCTGCCGAGCTCGAG                         CAACGGCCTCATCATCCGGTTCGGCCAATTCCTTCACAGCTCTGGTGCAAG
genomic: GCGTCTTTCTCATTTGCATCCCAATCGCTATGAAATCTGCCGAGCTCGAGgtctctctct ... tattttgcagCAACGGCCTCATCATCCGGTTCGGCCAATTCCTTCACAGCTCTGGTGCAAG
EST: gi|110394096|gb|EC958577.1|EC958577
EST:     GCGTCTTTCTCATTTGCATCCCAATCGCTATGAAATCTGCCGAGCTCGAG                         CAACGGCCTCATCATCCGGTTCGGCCAATTCCTTCACAGCTCTGGTGCAAG
genomic: GCGTCTTTCTCATTTGCATCCCAATCGCTATGAAATCTGCCGAGCTCGAGgtctctctct ... tattttgcagCAACGGCCTCATCATCCGGTTCGGCCAATTCCTTCACAGCTCTGGTGCAAG
EST: gi|110426582|gb|EC992995.1|EC992995
EST:     GCGTCTTTCTCATTTGCATCCCAATCGCTATGAAATCTGCCGAGCTCGAG                         CAACGGCCTCATCATCCGGTTCGGCCAATTCCTTCACAGCTCTGGTGCAAG
genomic: GCGTCTTTCTCATTTGCATCCCAATCGCTATGAAATCTGCCGAGCTCGAGgtctctctct ... tattttgcagCAACGGCCTCATCATCCGGTTCGGCCAATTCCTTCACAGCTCTGGTGCAAG
EST: gi|110428631|gb|EC995108.1|EC995108
EST:     GCGTCTTTCTCATTTGCATCCCAATCGCTATGAAATCTGCCGAGCTCGAG                         CAACGGCCTCATCATCCGGTTCGGCCAATTCCTTCACAGCTCTGGTGCAAG
genomic: GCGTCTTTCTCATTTGCATCCCAATCGCTATGAAATCTGCCGAGCTCGAGgtctctctct ... tattttgcagCAACGGCCTCATCATCCGGTTCGGCCAATTCCTTCACAGCTCTGGTGCAAG
EST: gi|71881494|gb|DT030549.1|DT030549
EST:     GCGTTTTTCTCATTTGCATCCCAATCGCTATGAAATCTGCCGAGCTCGAG                         CAACGGCCTCATCATCCGGTTCGGCCAATTCCTTCACAGCTCTGGTGCAAG
genomic: GCGTCTTTCTCATTTGCATCCCAATCGCTATGAAATCTGCCGAGCTCGAGgtctctctct ... tattttgcagCAACGGCCTCATCATCCGGTTCGGCCAATTCCTTCACAGCTCTGGTGCAAG
EST: gi|110724815|gb|EE100975.1|EE100975
EST:     GCGTTTTTCTCATTTGCATCCCAATCGCTATGAAATCTGCCGAGCTCGAG                         CAACGGCCTCATCATCCGGTTCGGCCAATTCCTTCACAGCTCTGGTGCAAG
genomic: GCGTCTTTCTCATTTGCATCCCAATCGCTATGAAATCTGCCGAGCTCGAGgtctctctct ... tattttgcagCAACGGCCTCATCATCCGGTTCGGCCAATTCCTTCACAGCTCTGGTGCAAG
EST: gi|110415282|gb|EC981171.1|EC981171
EST:     GCGTCTTTCTCATTTGCATCCCAATCGCTATGAAATCTGCCGAGCTCGAG                         CAACGGCCTCATCATCCGGTTCGGCCAATTCCTTCACAGCTCTGGTGCAAG
genomic: GCGTCTTTCTCATTTGCATCCCAATCGCTATGAAATCTGCCGAGCTCGAGgtctctctct ... tattttgcagCAACGGCCTCATCATCCGGTTCGGCCAATTCCTTCACAGCTCTGGTGCAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acatatagtgtaattataatgaggagttccaactaaaaaatgttttattttgcagCAACGGCCTCATCATCCGGTTCGGCCAATTCCTTCACAGCTCTGGTGCAAGAATTTTGGAAATAAGGAATACTGATTTCTCTGCTGCTGTGTGATAAAAT
                              aactaaa  putative branch site (score: 2)
                                          ttttatttt  putative PPT
                              aactaaaaaatgtttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cacaatatttacaatataagagaagaaaaaaaaacggagtacttaacatatagtgtaattataatgaggagttccaactaaaaaatgttttattttgcagCAACGGCCTCATCATCCGGTTCGGCCAATTCCTTCACAGCTCTGGTGCAAGAATTTTGGAAATAAGGAATACTGATTTCTCTGCTGCTGTGTGATAAAAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
cacaata
- - - - - - - - - - agaagaa
- - - - - - - - - - - - -aaaaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tccaact
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaaaaat