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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgaataagcgattggtttatttgatgcaatattgatctttatttttgggactctatatattgatgtttttcttccattcttcagGTTTATGCAAAGGTAAGTGGGGAACCTTCTTTGGAGGTACCAACTGTGGATGTAAGCTCCAAAGAATTCTATGGTGAGGGATATGATGACAGTGACAAGA

Basic information

species Vitis vinifera
transcript Vv06s0061g01120.t01
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv06s0061g01120.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GLYMA12G30490.1 (Glycine max), 3'ss of exon 7
-----gtgaataagc--gattggtt-tatttgatgcaatattgatctttatttttgggactctatatattgatgtttttcttccattcttcagGTTTATGCAAAGGTAAGTGGGGAACCTTCTTTGGAGGTACCAACTGTGGATGTAAGCTCCAAAGAATTCTATGGTGAGGGATATGATGACAGTGACAAGA
       || ||||   ||||| || ||  |  |  ||| |  | | |  | ||||||||  |  | |    | ||||  ||| ||||| ||||||||| ||||||||||||| ||| |  || ||||   ||| ||| | ||||| |||||||||||||| |||||||||||||||||||| ||||||||||
gttagaggattaagtttgattgtttgtacctattagaatttcaa-catggtatttgggaccattca-acatttattttcgttcaattctgcagGTTTATTCAAAGGTAAGTGGAGAAGCACCTCTGGAAAAACCTACTATTGATGTGAGCTCCAAAGAATTTTATGGTGAGGGATATGATGATAGTGACAAGA

upper sequence: Vv06s0061g01120.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GLYMA11G19550.2 (Glycine max), 3'ss of exon 6
---gtgaataagcgattggtttat-----ttgatgcaatattgatctttatttttgggactctatatattgat-gtttttcttccattctt------cagGTTTATGCAAAGGTAAGTGGGGAACCTTCTTTGGAGGTACCAACTGTGGATGTAAGCTCCAAAGAATTCTATGGTGAGGGATATGATGACAGTGACAAGA
    | ||      |||| | | |      || |  ||| | |   | |  || ||||| |  ||  ||  || ||| |||    ||| |       ||||||||  ||||||||||||| ||||   ||   ||   ||| ||  | ||||| ||||| |||||||| |||||||||||||||||||||||||||||||
atgatcaactttttattgttatgtgactactgttagaatttaggcatgttgttatgggaattcatgaatcaattgttattccattattttctatatacagGTTTACTCAAAGGTAAGTGGAGAACAAACTGCTGAAACACCTACCATTGATGTGAGCTCAAAAGAATTTTATGGTGAGGGATATGATGACAGTGACAAGA

upper sequence: Vv06s0061g01120.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GLYMA11G19550.1 (Glycine max), 3'ss of exon 7
--------gtgaataagcgattggtttat-----ttgatgcaatattgatctttatttttgggactctatatattgat-gtttttcttccattctt------cagGTTTATGCAAAGGTAAGTGGGGAACCTTCTTTGGAGGTACCAACTGTGGATGTAAGCTCCAAAGAATTCTATGGTGAGGGATATGATGACAGTGACAAGA
         | ||      |||| | | |      || |  ||| | |   | |  || ||||| |  ||  ||  || ||| |||    ||| |       ||||||||  ||||||||||||| ||||   ||   ||   ||| ||  | ||||| ||||| |||||||| |||||||||||||||||||||||||||||||
gtggaatgatcaactttttattgttatgtgactactgttagaatttaggcatgttgttatgggaattcatgaatcaattgttattccattattttctatatacagGTTTACTCAAAGGTAAGTGGAGAACAAACTGCTGAAACACCTACCATTGATGTGAGCTCAAAAGAATTTTATGGTGAGGGATATGATGACAGTGACAAGA

upper sequence: Vv06s0061g01120.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GLYMA17G05440.1 (Glycine max), 3'ss of exon 5
-----gtgaataagc--gattggtttatttgatgcaatattgatctttatttttgggactctatatattgatgtttttcttccattcttcagGTTTATGCAAAGGTAAGTGGGGAACCTTCTTTGGAGGTACCAACTGTGGATGTAAGCTCCAAAGAATTCTATGGTGAGGGATATGATGACAGTGACAAGA
       || ||||   ||||| || |     |   |  || | | |  | ||||||||  |  | |    | ||||| ||| ||| | ||||||||| ||||||| || || ||| |  || ||||   ||| ||| | ||||| || ||||||||||| |||||||||||||||||||| ||||||||||
gttagaggattaagtttgattgtttgacccttttagaatttcaacatggtatttgggaccgttca-acatttatttttgttcaattatgcagGTTTATTCAAAGGTTAGCGGAGAAGCACCTCTGGAAAAACCTACTATTGATGTGAGTTCCAAAGAATTTTATGGTGAGGGATATGATGATAGTGACAAGA

upper sequence: Vv06s0061g01120.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GLYMA12G08930.1 (Glycine max), 3'ss of exon 7
----------------gtgaataagcgattggtttatttgatgcaatattgatctttatttttgggactctatatattgat-gtttttc--ttccattct----tcagGTTTATGCAAAGGTAAGTGGGGAACCTTCTTTGGAGGTACCAACTGTGGATGTAAGCTCCAAAGAATTCTATGGTGAGGGATATGATGACAGTGACAAGA
                     | |    |||  |    || |  ||| |||   | |  |||||||| |  ||  ||  || ||| |||  |||||||||     ||||||||| ||||||||||||| ||||   ||   ||   ||| || || ||||| ||||| |||||||| |||||||||||||||||||| ||||||||||
gtgaaatgatcaagtttctttttattatttgactctactgttagaattttggcatgttgttttgggaattcatgaatcaattgttattccattccattctatatacagGTTTATTCAAAGGTAAGTGGCGAACAAACTCCTGAAACACCTACCGTTGATGTGAGCTCAAAAGAATTTTATGGTGAGGGATATGATGATAGTGACAAGA

upper sequence: Vv06s0061g01120.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: AT2G27860.1 (Arabidopsis thaliana), 3'ss of exon 7
gtgaataag--cgattggtttatttgatgcaatattgatctttatttttgggactctatatattgatgttt---ttcttccattcttcagGTTTATGCAAAGGTAAGTGGGGAACCTTCTTTGGAGGTACCAACTGTGGATGTAAGCTCCAAAGAATTCTATGGTGAGGGATATGATGACAGTGACAAGA
||||  |||   |||  |||       |   | | |  | || |||| |  | | ||   | |  ||  |          |||  |||||||||| ||||| || ||||| |||    |  | |||   ||||| || ||||| ||||||||||| || || || || || |||||||||||||||||||
gtgaggaagatggatcagttaggaaactatgaaaatagt-ttgatttctctgtcgctggttctcaattctcaaaacgaatcatgtttcagGTTTACGCAAAAGTGAGTGGAGAAGGAGCCATTGAGAGCCCAACGGTTGATGTTAGCTCCAAAGAGTTTTACGGGGAAGGTTATGATGACAGTGACAAGA

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|33402337|gb|CF207964.1|CF207964
EST:     ACCCCAACAATGAGGTTACTGTTAGGCAGCTTGCAGAAATGATGACTGAG                         GTTTATGCAAAGGTAAGTGGGGAACCTTCTTTGGAGGTACCAACTGTGGAT
genomic: ACCCCAACAATGAGGTTACTGTTAGGCAGCTTGCAGAAATGATGACTGAGgtgaataagc ... cattcttcagGTTTATGCAAAGGTAAGTGGGGAACCTTCTTTGGAGGTACCAACTGTGGAT
EST: gi|110405386|gb|EC970927.1|EC970927
EST:     ACCCCAACAATGAGGTTACTGTTAGGCAGCTTGCAGAAATGATGACTGAG                         GTTTATGCAAAGGTAAGTGGGGAACCTTCTTTGGAGGTACCAACTGTGGAT
genomic: ACCCCAACAATGAGGTTACTGTTAGGCAGCTTGCAGAAATGATGACTGAGgtgaataagc ... cattcttcagGTTTATGCAAAGGTAAGTGGGGAACCTTCTTTGGAGGTACCAACTGTGGAT
EST: gi|30298239|gb|CB975033.1|CB975033
EST:     ACCCCAACAATGAGGTTACTGTTAGGCAGCTTGCAGAAATGATGACTGAG                         GTTCATGCAAAGGTAAGTGGGGAACCTTCTTTGGAGGTACCAACTGTGGAT
genomic: ACCCCAACAATGAGGTTACTGTTAGGCAGCTTGCAGAAATGATGACTGAGgtgaataagc ... cattcttcagGTTTATGCAAAGGTAAGTGGGGAACCTTCTTTGGAGGTACCAACTGTGGAT
EST: gi|71884664|gb|DT033719.1|DT033719
EST:     ACCCCAACAATGAGGTTACTGTTAGGCAGCTTGCAGAAATGATGACTGAG                         GTTTATGCAAAGGTAAGTGGGGAACCTTCTTTGGAGGTACCAACTGTGGAT
genomic: ACCCCAACAATGAGGTTACTGTTAGGCAGCTTGCAGAAATGATGACTGAGgtgaataagc ... cattcttcagGTTTATGCAAAGGTAAGTGGGGAACCTTCTTTGGAGGTACCAACTGTGGAT
EST: gi|33401793|gb|CF207420.1|CF207420
EST:     ACCCCAACAATGAGGTTACTGTTAGGCAGCTTGCAGAAATGATGACTGAG                         GTTTATGCAAAGGTAAGTGGGGAACCTTCTTTGGAG
genomic: ACCCCAACAATGAGGTTACTGTTAGGCAGCTTGCAGAAATGATGACTGAGgtgaataagc ... cattcttcagGTTTATGCAAAGGTAAGTGGGGAACCTTCTTTGGAG
EST: gi|33402259|gb|CF207886.1|CF207886
EST:     ACCCCAACAATGAGGTTACTGTTAGGCAGCTTGCAGAAATGATGACTGAG                         GTTTATGCAAAGGTAAGTGGGGAACCTTCTTTGGAGGTACCAACTGTGGAT
genomic: ACCCCAACAATGAGGTTACTGTTAGGCAGCTTGCAGAAATGATGACTGAGgtgaataagc ... cattcttcagGTTTATGCAAAGGTAAGTGGGGAACCTTCTTTGGAGGTACCAACTGTGGAT
EST: gi|349828491|gb|FQ417233.1|FQ417233
EST:     ACCCCAACAATGAGGTTACTGTTAGGCAGCTTGCAGAAATGATGACTGAG                         GTTTATGCAAAGGTAAGTGGGGAACCTTCTTTGGAGGTACCAACTGTGGAT
genomic: ACCCCAACAATGAGGTTACTGTTAGGCAGCTTGCAGAAATGATGACTGAGgtgaataagc ... cattcttcagGTTTATGCAAAGGTAAGTGGGGAACCTTCTTTGGAGGTACCAACTGTGGAT
EST: gi|71884313|gb|DT033368.1|DT033368
EST:     ACCCCAACAATGAGGTTACTGTTAGGCAGCTTGCAGAAATGATGACTGAG                         GTTTATGCAAAGGTAAGTGGGGAACCTTCTTTGGAGGTACCAACTGTGGAT
genomic: ACCCCAACAATGAGGTTACTGTTAGGCAGCTTGCAGAAATGATGACTGAGgtgaataagc ... cattcttcagGTTTATGCAAAGGTAAGTGGGGAACCTTCTTTGGAGGTACCAACTGTGGAT
EST: gi|22007527|gb|BQ792561.1|BQ792561
EST:     ACCCCAACAATGAGGTTACTGTTAGGCAGCTTGCAGAAATGATGACTGAG                         GTTTATGCAAAGGTAAGTGGGGAACCTTCTTTGGAGGTACCAACTGTGGAT
genomic: ACCCCAACAATGAGGTTACTGTTAGGCAGCTTGCAGAAATGATGACTGAGgtgaataagc ... cattcttcagGTTTATGCAAAGGTAAGTGGGGAACCTTCTTTGGAGGTACCAACTGTGGAT
EST: gi|33404942|gb|CF210569.1|CF210569
EST:     ACCCCAACAATGAGGTTACTGTTAGGCAGCTTGCAGAAATGATGACTGAG                         GTTTATGCAAAGGTAAGTGGGGAACCTTCTTTGGAGGTACCAACTGTGGAT
genomic: ACCCCAACAATGAGGTTACTGTTAGGCAGCTTGCAGAAATGATGACTGAGgtgaataagc ... cattcttcagGTTTATGCAAAGGTAAGTGGGGAACCTTCTTTGGAGGTACCAACTGTGGAT
EST: gi|110397475|gb|EC963215.1|EC963215
EST:     ACCCCAACAATGAGGTTACTGTTAGGCAGCTTGCAGAAATGATGACTGAG                         GTTTATGCAAAGGTAAGTGGGGAACCTTCTTTGGAGGTACCAACTGTGGAT
genomic: ACCCCAACAATGAGGTTACTGTTAGGCAGCTTGCAGAAATGATGACTGAGgtgaataagc ... cattcttcagGTTTATGCAAAGGTAAGTGGGGAACCTTCTTTGGAGGTACCAACTGTGGAT
EST: gi|110420047|gb|EC986308.1|EC986308
EST:     ACCCCAACAATGAGGTTACTGTTAGGCAGCTTGCAGAAATGATGACTGAG                         GTTTATGCAAAGGTAAGTGGGGAACCTTCTTTGGAGGTACCAACTGTGGAT
genomic: ACCCCAACAATGAGGTTACTGTTAGGCAGCTTGCAGAAATGATGACTGAGgtgaataagc ... cattcttcagGTTTATGCAAAGGTAAGTGGGGAACCTTCTTTGGAGGTACCAACTGTGGAT
EST: gi|71890357|gb|DT039412.1|DT039412
EST:     ACCCCAACAATGAGGTTACTGTTAGGCAGCTTGCAGAAATGATGACTGAG                         GTTTATGCAAAGGTAAGTGGGGAACCTTCTTTGGAGGTACCAACTGTGGAT
genomic: ACCCCAACAATGAGGTTACTGTTAGGCAGCTTGCAGAAATGATGACTGAGgtgaataagc ... cattcttcagGTTTATGCAAAGGTAAGTGGGGAACCTTCTTTGGAGGTACCAACTGTGGAT
EST: gi|110396028|gb|EC961702.1|EC961702
EST:     ACCCCAACAATGAGGTTACTGTTAGGCAGCTTGCAGAAATGATGACTGAG                         GTTTATGCAAAGGTAAGTGGGGAACCTTCTTTGGAGGTACCAACTGTGGAT
genomic: ACCCCAACAATGAGGTTACTGTTAGGCAGCTTGCAGAAATGATGACTGAGgtgaataagc ... cattcttcagGTTTATGCAAAGGTAAGTGGGGAACCTTCTTTGGAGGTACCAACTGTGGAT
EST: gi|110371215|gb|EC935056.1|EC935056
EST:     ACCCCAACAATGAGGTTACTGTTAGGCAGCTTGCAGAAATGATGACTGAG                         GTTTATGCAAAGGTAAGTGGGGAACCTTCTTTGGAGGTACCAACTGTGGAT
genomic: ACCCCAACAATGAGGTTACTGTTAGGCAGCTTGCAGAAATGATGACTGAGgtgaataagc ... cattcttcagGTTTATGCAAAGGTAAGTGGGGAACCTTCTTTGGAGGTACCAACTGTGGAT
EST: gi|71888796|gb|DT037851.1|DT037851
EST:     ACCCCAACAATGAGGTTACTGTTAGGCAGCTTGCAGAAATGATGACTGAG                         GTTTATGCAAAGGTAAGTGGGGAACCTTCTTTGGAGGTACCAACTGTGGAT
genomic: ACCCCAACAATGAGGTTACTGTTAGGCAGCTTGCAGAAATGATGACTGAGgtgaataagc ... cattcttcagGTTTATGCAAAGGTAAGTGGGGAACCTTCTTTGGAGGTACCAACTGTGGAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tattgatctttatttttgggactctatatattgatgtttttcttccattcttcagGTTTATGCAAAGGTAAGTGGGGAACCTTCTTTGGAGGTACCAACTGTGGATGTAAGCTCCAAAGAATTCTATGGTGAGGGATATGATGACAGTGACAAGA
                            tattgat  putative branch site (score: 3)
                                  tgtttttcttccattc  CT-rich tract
                        tatatattgatgtttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgaataagcgattggtttatttgatgcaatattgatctttatttttgggactctatatattgatgtttttcttccattcttcagGTTTATGCAAAGGTAAGTGGGGAACCTTCTTTGGAGGTACCAACTGTGGATGTAAGCTCCAAAGAATTCTATGGTGAGGGATATGATGACAGTGACAAGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA