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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtttagaatttgatgtttctggctggaaaattattttccctttcatccaataaattttaattcatttgtccatgtattgccatgtttagGTTAATGCAAGTGGGCAGTTCTGTGGAGTAGCTGAGATGATTGGCCGAGTTGATTTTAATAAGAACATGGACTTCTGGCAACAGGATAAGTGGAATGGAT

Basic information

species Vitis vinifera
transcript Vv19s0085g01100.t01
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv19s0085g01100.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: LOC_Os01g48790.3 (Oryza sativa), 3'ss of exon 3
gtaagtttagaatttga----tgtttctggctggaaaattatttt--ccctttcatccaa-taaattttaattcatttgtccat-gtattgccatgtttagGTTAATGCAAGTGGGCAGTTCTGTGGAGTAGCTGAGATGATTGGCCGAGTTGATTTTAATAAGAACATGGACTTCTGGCAACAGGATAAGTGGAATGGAT
 | |||| |   ||       | ||| |||  |||||  || |||  ||  ||| |  || |   || |||  | | |    ||   | |   |||   |||| || |||||||| |||||||| || || ||||||||| | || |  || ||||| || | ||| ||| |||||||||| ||||| |||||||||||||
-tgagttcatggttcaccctttttttgtggggggaaatatacttttgccaattcttgtaactttgttgtaaaacttctaattattacactatgatgaccagGTGAACGCAAGTGGCCAGTTCTGCGGCGTGGCTGAGATGGTCGGTCCGGTAGATTTCAACAGGAATATGAACTTCTGGCAGCAGGACAAGTGGAATGGAT

upper sequence: Vv19s0085g01100.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GRMZM2G169116_T01 (Zea mays), 3'ss of exon 7
--gtaagtttag-------aatttgatgtttctggctggaaaattattttccctttcatccaataaattttaattcatttgtccatgtattgccatgtttagGTTAATGCAAGTGGGCAGTTCTGTGGAGTAGCTGAGATGATTGGCCGAGTTGATTTTAATAAGAACATGGACTTCTGGCAACAGGATAAGTGGAATGGAT
  | ||||| |        ||  ||    || |      |   ||   ||    |   |    | |  ||||  |   |||    |  | |   ||| | |||||||||||||||| ||||||||||| || ||||||||| |||||| ||| ||||| || | ||||||| |||||||||||||||| ||||||||||| |
tagcaagttgaattgcatcaaagtggcccttttatggaaagggttgcattattatctttattttgacctttacctg--ttgattgtaaactatgatggtcagGTTAATGCAAGTGGTCAGTTCTGTGGCGTGGCTGAGATGGTTGGCCCAGTAGATTTCAACAGGAACATGAACTTCTGGCAACAGGACAAGTGGAATGGTT

upper sequence: Vv19s0085g01100.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GRMZM2G127780_T02 (Zea mays), 3'ss of exon 6
-------gtaagtt---tagaatttgatgtttc-tggctggaaaattattttccctttcatccaataaattttaattcatttgtccatgtattgccatgtttagGTTAATGCAAGTGGGCAGTTCTGTGGAGTAGCTGAGATGATTGGCCGAGTTGATTTTAATAAGAACATGGACTTCTGGCAACAGGATAAGTGGAATGGAT
        | ||||   | |||   |   |||  |||   |      ||| |  | | |||       |||||    |  |||    | || |   ||||| |||||||||||||||| ||||||||||| || ||||||||| |||| | ||| ||||| || | ||||||| |||||||||||||||| ||||||||||| |
caagttaatgagttgcatcgaagcagcccttttatggaaagggtggcattattacctgcattttgaccatttt----ctgttgattgtataatatgatgttcagGTTAATGCAAGTGGTCAGTTCTGTGGCGTGGCTGAGATGGTTGGTCCAGTAGATTTCAACAGGAACATGAACTTCTGGCAACAGGACAAGTGGAATGGTT

upper sequence: Vv19s0085g01100.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA08G17240.1 (Glycine max), 3'ss of exon 6
----------------------gtaagtttagaatttgatgt-------ttctggctggaaaattattttcccttt--catccaataaat------tttaattcatttgtccatgtattgccatgtttagGTTAATGCAAGTGGGCAGTTCTGTGGAGTAGCTGAGATGATTGGCCGAGTTGATTTTAATAAGAACATGGACTTCTGGCAACAGGATAAGTGGAATGGAT
                        ||  ||   ||    ||        || |  |||   |  |||||||   ||  ||    |||| |       |||| |   ||     |   |     |||| |||| ||||| ||||| || || || |||||||||||||||| ||| ||||||||||| || || |  ||||| ||||||||||||||||||||||||||||
gtatgcaatttgggtccatcgcaaaaacttcagatcccctgcacccatgttttctctgcttatgtattttcagattgacaagtgataactgtgtttcttaacttcctttctggtaattgcttgtgttcagGTCAATGCTAGTGGTCAATTTTGCGGAGTAGCTGAGATGACTGGACGAGTTGATTTCAACAAAAGTATGGATTTCTGGCAACAGGATAAGTGGAATGGAT

upper sequence: Vv19s0085g01100.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA15G41960.1 (Glycine max), 3'ss of exon 6
-------------gtaagttt--agaatttgatgtttctggctggaaaattattttccctttcatccaataaattttaattcatttgtc-catgtattgccatgtttagGTTAATGCAAGTGGGCAGTTCTGTGGAGTAGCTGAGATGATTGGCCGAGTTGATTTTAATAAGAACATGGACTTCTGGCAACAGGATAAGTGGAATGGAT
              |  |||   | || || |  |  |  ||       || | ||  |||   |    |  |  || ||   | |||  |  ||| |  |||||| |||| ||||| || || || || |||||||| ||||||||||  || || |||||||| ||||| |  ||||| ||||||||||| ||||| ||||||||||
gtatgctgtttggttccgttgcaaaaacttaagatcccctgcatccttgttttatttgcttatgtatttttcagattgataactgtgtttctcgtaat-tcatgtt-agGTCAATGCTAGCGGTCAATTTTGTGGAGTGGCTGAGATGACCGGACGTGTTGATTTCAATAAAAGTATGGATTTCTGGCAACAAGATAAATGGAATGGAT

upper sequence: Vv19s0085g01100.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: AT1G79270.1 (Arabidopsis thaliana), 3'ss of exon 6
gtaagtttagaatttgatgtttctggctggaaaattattttccctttcatccaataaattttaattcatttgtccatgtattgccatgtttagGTTAATGCAAGTGGGCAGTTCTGTGGAGTAGCTGAGATGATTGGCCGAGTTGATTTTAATAAGAACATGGACTTCTGGCAACAGGATAAGTGGAATGGAT
    || |   ||| |   ||| | |||  | |  ||||     || |  |        || |     | ||  |   | ||      || |||| ||||||||||| || ||||| || ||||||||||||||||| |||||||||| | | || | |||||| ||||||||||| |||||||||| ||| |
----gtatgctattagg-atttttcgctatatacgtattcagttttgcgac-----gtcttcatggtctctgatcg-attttattggattcagGTGAATGCAAGTGGCCAATTCTGCGGTGTAGCTGAGATGATTGGACGAGTTGATTATGAGAAAAGCATGGAGTTCTGGCAACAAGATAAGTGGACTGGCT

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|110362572|gb|EC926115.1|EC926115
EST:     AAAGGATGGGAGACAGAGGCAGCAAGTGTCCCGTGTTTCTTTTCTTTTCG                         GTTAATGCAAGTGGGCAGTTCTGTGGAGTAGCTGAGATGATTGGCCGAGTT
genomic: AAAGGATGGGAGACAGAGGCAGCAAGTGTCCCGTGTTTCTTTTCTTTTCGgtaagtttag ... ccatgtttagGTTAATGCAAGTGGGCAGTTCTGTGGAGTAGCTGAGATGATTGGCCGAGTT
EST: gi|161716831|gb|FC068103.1|FC068103
EST:     AAAGGATGGGAGAGAGAGGCAGCAAGTGTCCCGTGTTTCTTTTCTTTTCG                         GTTAATGCAAGTGGGCAGTTCTGTGGAGTAGCTGAGATGATTGGCCGAGTT
genomic: AAAGGATGGGAGACAGAGGCAGCAAGTGTCCCGTGTTTCTTTTCTTTTCGgtaagtttag ... ccatgtttagGTTAATGCAAGTGGGCAGTTCTGTGGAGTAGCTGAGATGATTGGCCGAGTT
EST: gi|110361109|gb|EC924562.1|EC924562
EST:     AAAGGATGGGAGACAGAGGCAGCAAGTGTCCCGTGTTTCTTTTCTTTTCG                         GTTAATGCAAGTGGGCAGTTCTGTGGAGTAGCTGAGATGATTGGCCGAGTT
genomic: AAAGGATGGGAGACAGAGGCAGCAAGTGTCCCGTGTTTCTTTTCTTTTCGgtaagtttag ... ccatgtttagGTTAATGCAAGTGGGCAGTTCTGTGGAGTAGCTGAGATGATTGGCCGAGTT
EST: gi|110358581|gb|EC922894.1|EC922894
EST:     AAAGGATGGGAGAGAGAGGCAGCAAGTGTCCCGTGTTTCTTTTCTTTTCG                         GTTAATGCAAGTGGGCAGTTCTGTGGAGTAGCTGAGATGATTGGCCGAGTT
genomic: AAAGGATGGGAGACAGAGGCAGCAAGTGTCCCGTGTTTCTTTTCTTTTCGgtaagtttag ... ccatgtttagGTTAATGCAAGTGGGCAGTTCTGTGGAGTAGCTGAGATGATTGGCCGAGTT
EST: gi|30306091|gb|CB982885.1|CB982885
EST:     AAAGGATGGGAGACAGAGGCAGCAGGTGTCCCGTGTTTCTTTTCTTTTCG                         GTTAATGCAAGTGGGCAGTTCTGTGGAGTAGCTGAGATGATTGGCCGAGTT
genomic: AAAGGATGGGAGACAGAGGCAGCAAGTGTCCCGTGTTTCTTTTCTTTTCGgtaagtttag ... ccatgtttagGTTAATGCAAGTGGGCAGTTCTGTGGAGTAGCTGAGATGATTGGCCGAGTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttccctttcatccaataaattttaattcatttgtccatgtattgccatgtttagGTTAATGCAAGTGGGCAGTTCTGTGGAGTAGCTGAGATGATTGGCCGAGTTGATTTTAATAAGAACATGGACTTCTGGCAACAGGATAAGTGGAATGGAT
                    ttttaat  putative branch site (score: 3)
      tttcatccaataaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtttagaatttgatgtttctggctggaaaattattttccctttcatccaataaattttaattcatttgtccatgtattgccatgtttagGTTAATGCAAGTGGGCAGTTCTGTGGAGTAGCTGAGATGATTGGCCGAGTTGATTTTAATAAGAACATGGACTTCTGGCAACAGGATAAGTGGAATGGAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGTGGA