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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgctatacaatgccgttttcttgttaatattcttagttgggctctgatattcgtactgttttatatctcaattctaacaatattcattccaatttttaagGTTGAATCTGAAATATTTTGCCTGCATGGTGGGTTGTCCCCATCTATCGAGACCCTTGATAACATACGCAATTTTGACCGTGTTCAAGAAGTTCCTCATG

Basic information

species Vitis vinifera
transcript Vv06s0004g00830.t01
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv06s0004g00830.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: LOC_Os03g59060.1 (Oryza sativa), 3'ss of exon 7
tgctatacaatgccgttttcttgttaatattcttagttgggctctgatattcgtactgttttatatctcaattctaacaatattcattc--caatttttaagGTTGAATCTGAAATATTTTGCCTGCATGGTGGGTTGTCCCCATCTATCGAGACCCTTGATAACATACGCAATTTTGACCGTGTTCAAGAAGTTCCTCATG
              || |  |    | | ||| ||  |     |  | || | | |    |||| |    | ||| |||  |    |||     || |  ||||||| || ||||||||||||||||||||||| || || ||||| || ||||| |||||||||||||| || || || ||||| ||||||||||| ||||
------------gtgtgtattcagcatt-ttcatatgtatatgccaacatccttcccacattatctagtgaatctgacagaagctgttcatttgttctgtagGTTGAGTCAGAAATATTTTGCCTGCATGGTGGATTATCGCCATCCATTGAGACACTTGATAACATACGTAACTTCGATCGTGTCCAAGAAGTTCCCCATG

upper sequence: Vv06s0004g00830.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GRMZM2G108355_T01 (Zea mays), 3'ss of exon 7
tgctatacaatgccgttttcttgttaatatt-cttagttgggct--ctgatattcgtactgttttatatctcaattctaacaatattcattccaatttttaagGTTGAATCTGAAATATTTTGCCTGCATGGTGGGTTGTCCCCATCTATCGAGACCCTTGATAACATACGCAATTTTGACCGTGTTCAAGAAGTTCCTCATG
                    |   || | || |||| || || |   | | ||  | |     | |  | || ||||      | ||  |||   ||||  |||| || || |||||||||||| |||||||||| || || ||||| || |||||||| || ||||| ||||| |||||||| || |||||||||||||| |
-------------------gtgagtattgtttcttaattaggatgatttacatgtgcatctagtgaattttccattcagtt--tgtttgttct--ttttctagGTCGAGTCAGAAATATTTTGCTTGCATGGTGGATTATCGCCATCCATTGAGACCCTCGACAACATCCGCAACTTTGACCGCGTCCAAGAAGTTCCTCACG

upper sequence: Vv06s0004g00830.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GRMZM2G062394_T01 (Zea mays), 3'ss of exon 7
tgctatacaatgccgttttcttgttaatattcttagttgggctctgat-attcgtactgttttatatctcaattctaacaatattcattccaattttta-agGTTGAATCTGAAATATTTTGCCTGCATGGTGGGTTGTCCCCATCTATCGAGACCCTTGATAACATACGCAATTTTGACCGTGTTCAAGAAGTTCCTCATG
                      || | |||| |   ||   ||  ||| ||| | |    | | ||    || |  |   |  ||  ||    |||| | |||| || || |||||||||||  |||||||||| || || ||||| || |||||||| || ||||| ||||| || |||||||| ||||||||||||||||
----------------------gtgagtattgtcccttat-ctaggatgatttgcatgcgtatctagtgaaactacattcagtttgtttgttcttttcatagGTCGAGTCAGAAATATTTTGTTTGCATGGTGGATTATCGCCATCCATTGAGACCCTCGACAACATCCGCAACTTCGACCGTGTCCAAGAAGTTCCTCATG

upper sequence: Vv06s0004g00830.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GLYMA08G11940.2 (Glycine max), 3'ss of exon 7
---tgctatacaatgccgttttcttgttaatattcttagttgggctctgatattcgtactgttttatatctcaattctaacaatattcattccaattttta-agGTTGAATCTGAAATATTTTGCCTGCATGGTGGGTTGTCCCCATCTATCGAGACCCTTGATAACATACGCAATTTTGACCGTGTTCAAGAAGTTCCTCATG
    |||     ||    |  ||     |||    ||   |||  |   |  ||   | |  || |      | | ||||        ||   || ||| | |||||||||||||||||||||| || |||||||||||||| |||||||| || ||||| ||||||||||| |||||||| || || ||||||||||||||||
ttaagcttcgtgatatgctgctcaatcaaatgcatttcactggatttctagtttttcaataattgag----tattgctaaagtgtgatatgttaactttcatagGTTGAATCTGAAATATTTTGTCTTCATGGTGGGTTGTCGCCATCTATTGAAACCCTGGATAACATACGTAATTTTGATCGCGTACAAGAAGTTCCTCATG

upper sequence: Vv06s0004g00830.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GLYMA05G28790.2 (Glycine max), 3'ss of exon 7
tgctatacaatgccgttttcttgttaatattcttagttgggctctgatattcgtactgttttatatctcaattctaacaatattc---attccaattttta-agGTTGAATCTGAAATATTTTGCCTGCATGGTGGGTTGTCCCCATCTATCGAGACCCTTGATAACATACGCAATTTTGACCGTGTTCAAGAAGTTCCTCATG
     |   |||| | |   |   |   | |     |    | |||  |||  || | ||  |||  | | |  |   ||  |     || | || ||| | |||||||||||||||||||||| || |||||||||||||| |||||||| || ||||| ||||||||||| |||||||| || || |||||||||||||| |
---cgtgatatgctgctcaatcaattgcagttcacatatttcactgg-atttctagttttcaataattgagtgttgctaaagtgtgatatgctaactttcatagGTTGAATCTGAAATATTTTGTCTTCATGGTGGGTTGTCACCATCTATTGAAACCCTGGATAACATACGTAATTTTGATCGCGTACAAGAAGTTCCTCACG

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|30131760|gb|CB917099.1|CB917099
EST:     TTTGGAAGATCTTTACAGATTTATTTGATTATTTCCCACTGACAGCATTG                         GTTGAATCTGAAATATTTTGCCTGCATGGTGGGTTGTCCCCATCTATCGAG
genomic: TTTGGAAGATCTTTACAGATTTATTTGATTATTTCCCACTGACAGCATTGgttagtattt ... aatttttaagGTTGAATCTGAAATATTTTGCCTGCATGGTGGGTTGTCCCCATCTATCGAG
EST: gi|33404623|gb|CF210250.1|CF210250
EST:     TTTGGAAGATCTTTACAGATTTATTTGATTATTTCCCACTGACAGCATTG                         GTTGAATCTGAAATATTTTGCCTGCATGGTGGGTTGTCCCCATCTATCGGG
genomic: TTTGGAAGATCTTTACAGATTTATTTGATTATTTCCCACTGACAGCATTGgttagtattt ... aatttttaagGTTGAATCTGAAATATTTTGCCTGCATGGTGGGTTGTCCCCATCTATCGAG
EST: gi|110684715|gb|EE062310.1|EE062310
EST:     TTTGGAAGATCTTTACAGATTTATTTGATTATTTCCCACTGACAGCATTG                         GTTGAATCTGAAATATTTTGCCTGCATGGTGGGTTGTCCCCATCTATCGAG
genomic: TTTGGAAGATCTTTACAGATTTATTTGATTATTTCCCACTGACAGCATTGgttagtattt ... aatttttaagGTTGAATCTGAAATATTTTGCCTGCATGGTGGGTTGTCCCCATCTATCGAG
EST: gi|161716085|gb|FC065837.1|FC065837
EST:     TTTGGAAGATCTTTACAGATTTATTTGATTATTTCCCACTGACAGCATTG                         GTTGAATCTGAAATATTTTGCCTGCATGGTGGGTTGTCCCCATCTATCGAG
genomic: TTTGGAAGATCTTTACAGATTTATTTGATTATTTCCCACTGACAGCATTGgttagtattt ... aatttttaagGTTGAATCTGAAATATTTTGCCTGCATGGTGGGTTGTCCCCATCTATCGAG
EST: gi|110379397|gb|EC944588.1|EC944588
EST:     TTTGGAAGATCTTTACAGATTTATTTGATTATTTCCCACTGACAGCATTG                         GTTGAATCTGAAATATTTTGCCTGCATGGTGGGTTGTCCCCATCTATCGAG
genomic: TTTGGAAGATCTTTACAGATTTATTTGATTATTTCCCACTGACAGCATTGgttagtattt ... aatttttaagGTTGAATCTGAAATATTTTGCCTGCATGGTGGGTTGTCCCCATCTATCGAG
EST: gi|71854856|gb|DT003911.1|DT003911
EST:     TTTGGAAGATCTTTACAGATTTATTTGATTATTTCCCACTGACAGCATTG                         GTTGAATCTGAAATATTTTGCCTGCATGGTGGGTTGTCCCCATCTATCGAG
genomic: TTTGGAAGATCTTTACAGATTTATTTGATTATTTCCCACTGACAGCATTGgttagtattt ... aatttttaagGTTGAATCTGAAATATTTTGCCTGCATGGTGGGTTGTCCCCATCTATCGAG
EST: gi|110380939|gb|EC946242.1|EC946242
EST:     TTTGGAAGATCTTTACAGATTTATTTGATTATTTCCCACTGACAGCATTG                         GTTGAATCTGAAATATTTTGCCTGCATGGTGGGTTGTCCCCATCTATCGAG
genomic: TTTGGAAGATCTTTACAGATTTATTTGATTATTTCCCACTGACAGCATTGgttagtattt ... aatttttaagGTTGAATCTGAAATATTTTGCCTGCATGGTGGGTTGTCCCCATCTATCGAG
EST: gi|30134848|gb|CB920186.1|CB920186
EST:     TTTGGAAGATCTTTACAGATTTATTTGATTATTTCCCACTGACAGCATTG                         GATGAATCTGAAATATTTTGCCTGCATGGTGGGTTGTCCCCATCTATCGAG
genomic: TTTGGAAGATCTTTACAGATTTATTTGATTATTTCCCACTGACAGCATTGgttagtattt ... aatttttaagGTTGAATCTGAAATATTTTGCCTGCATGGTGGGTTGTCCCCATCTATCGAG
EST: gi|110377055|gb|EC942116.1|EC942116
EST:     TTTGGAAGATCTTTACAGATTTATTTGATTATTTCCCACTGACAGCATTG                         GTTGAATCTGAAATATTTTGCCTGCATGGTGGGTTGTCCCCATCTATCGAG
genomic: TTTGGAAGATCTTTACAGATTTATTTGATTATTTCCCACTGACAGCATTGgttagtattt ... aatttttaagGTTGAATCTGAAATATTTTGCCTGCATGGTGGGTTGTCCCCATCTATCGAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gatattcgtactgttttatatctcaattctaacaatattcattccaatttttaagGTTGAATCTGAAATATTTTGCCTGCATGGTGGGTTGTCCCCATCTATCGAGACCCTTGATAACATACGCAATTTTGACCGTGTTCAAGAAGTTCCTCATG
                          ttctaac  putative branch site (score: 1)
                                               ttttt  putative PPT
                                 aatattcattccaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgctatacaatgccgttttcttgttaatattcttagttgggctctgatattcgtactgttttatatctcaattctaacaatattcattccaatttttaagGTTGAATCTGAAATATTTTGCCTGCATGGTGGGTTGTCCCCATCTATCGAGACCCTTGATAACATACGCAATTTTGACCGTGTTCAAGAAGTTCCTCATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT
- - - -caatgcc
- - - - - - - - - - - - - - - - -tagttgg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aacaata