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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aataaagtactcatttttatttttagaagttagaacatgtctggattttgcttccctgataagtcaattaatgacttagtgctgattataatgtctacagTCCTGTTGGAGAGAATAAGAAAAGTGGCGAAGTATATAGATTATTCGATGTTGGAGGCCAGAGAAATGAAAGAAGGAAATGGATCCATTTATTTGAAGGT

Basic information

species Vitis vinifera
transcript Vv04s0008g02040.t01
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv04s0008g02040.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: GRMZM2G064732_T01 (Zea mays), 3'ss of exon 9
aataaagtactcatttttatttttagaagttagaacatgtctggattttgcttccctgataagtcaattaatgacttagtg-ctgattataatgtctacagTCCTGTTGGAGAGAATAAGAAAAGTGGCGAAGTATATAGATTATTCGATGTTGGAGGCCAGAGAAATGAAAGAAGGAAATGGATCCATTTATTTGAAGGT
                              ||   | ||  |    | |       | || ||| |  ||      || |      || |  |  || ||| ||| | |||||||  || | | | || || || |||||  | | |||||| |||||||||||||| || |||||||||||||||||| | || ||||||
-----------------------------gtattccttggttatgctatttgcttattattagttagatataactctaataatcagtttttttccctgcagCCCTCTAGGAGAGAGCAAAAGAGGCGGAGAGGTCTATAGGCTGTACGATGTAGGAGGCCAGAGAAACGAGAGAAGGAAATGGATCCATCTTTTCGAAGGT

upper sequence: Vv04s0008g02040.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: GLYMA04G05960.1 (Glycine max), 3'ss of exon 9
aataaagtactcatttttatttttagaagttagaacatgtctggattttgcttccc-tgataagtcaattaa-tgacttagtgc-tgattataatgtctacagTCCTGTTGGAGAGAATAAGAAAAGTGGCGAAGTATATAGATTATTCGATGTTGGAGGCCAGAGAAATGAAAGAAGGAAATGGATCCATTTATTTGAAGGT
   |   ||||||   ||  || |      | | |  | |       |    |    |  | |||  |  || |   |||||   |  ||   || |  |||| ||||||||||| ||||||| |||||| ||||| |||||| | || |||||||| |||||||||||||| ||||| |||||||||||| | |||||||| 
---atgttactcaacatttgttctgttccattgcattttttcaaccataatatgatatactgagtggaccaactttattagtatgtttttgctattttgacagCCCTGTTGGAGAAAATAAGAGAAGTGGTGAAGTCTATAGACTCTTTGATGTTGGTGGCCAGAGAAATGAGAGAAGAAAATGGATCCATCTTTTTGAAGGA

upper sequence: Vv04s0008g02040.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: GLYMA17G34450.1 (Glycine max), 3'ss of exon 8
aataaagtactcatttttatttttagaagttagaacatgtctggattttgcttccctgataagtcaattaatgacttagtgctgattataatgtct-acagTCCTGTTGGAGAGAATAAGAAAAGTGGCGAAGTATATAGATTATTCGATGTTGGAGGCCAGAGAAATGAAAGAAGGAAATGGATCCATTTATTTGAAGGT
  |  | ||||  |||  | |  |    ||||   |||     |   |    |     |    |||   |   |  | ||  ||  | |  | | |  |||||||||||| || |||||||||||||| ||||| |||||| | || |||||||| |||||||||||||| || || || ||||||||||| |||||||| 
-ttgcattacttttttcaagtgatctttgttatggcataatatggcatacagtgtagaactgctcatcaacatatattgttatgtatttgctattttgcagTCCTGTTGGGGAAAATAAGAAAAGTGGTGAAGTCTATAGACTCTTTGATGTTGGCGGCCAGAGAAATGAGAGGAGAAAGTGGATCCATTTGTTTGAAGGA

upper sequence: Vv04s0008g02040.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: GLYMA14G11140.1 (Glycine max), 3'ss of exon 8
---aataaagtactcatttttatttttagaagttagaacatgtctggattttgcttccctgataagtcaattaatgacttagtgctgattataatgtctacagTCCTGTTGGAGAGAATAAGAAAAGTGGCGAAGTATATAGATTATTCGATGTTGGAGGCCAGAGAAATGAAAGAAGGAAATGGATCCATTTATTTGAAGGT
    ||  | ||    |||   |||||       | || ||| |   |   ||     ||  | | ||||   || | |      |  ||   || |  |||| |||||||| || | |||||||||||| ||||| |||||| | || |||||||| |||||||||||||| || || |||||||||||||| |||||||| 
ttatatttactatcactttacttttttctttaacataatatggc-atacagtgtagaactactca-tcaacatat-attggtaagtctttgctattttgacagCCCTGTTGGGGAAAGTAAGAAAAGTGGTGAAGTCTATAGACTCTTTGATGTTGGCGGCCAGAGAAATGAGAGGAGAAAATGGATCCATTTGTTTGAAGGA

upper sequence: Vv04s0008g02040.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: GLYMA06G05960.1 (Glycine max), 3'ss of exon 10
aataaagtactcatttttatttttagaagttagaacatg--tctggattttgcttccctgata-----agtcaattaa-tgacttagtgctgattataatgtct--acagTCCTGTTGGAGAGAATAAGAAAAGTGGCGAAGTATATAGATTATTCGATGTTGGAGGCCAGAGAAATGAAAGAAGGAAATGGATCCATTTATTTGAAGGT
          |  ||||| |     |  |  ||| ||||  | |  || ||    |  |||||     |||  |  || |   |||||  || || |  | | |  |||| ||||||||||| ||||||| |||||| ||||| |||||| | || |||||||| || ||||||||||| || || |||||||||||| | |||||||| 
----------ttttttttgtggggtggggggagatcatgtatttttatattcacgctatgatatacagagtggaccaactttgttagtaatgtttttgctattttgacagCCCTGTTGGAGAAAATAAGAGAAGTGGTGAAGTCTATAGACTCTTTGATGTTGGTGGTCAGAGAAATGAGAGGAGAAAATGGATCCATCTTTTTGAAGGA

upper sequence: Vv04s0008g02040.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: AT2G26300.1 (Arabidopsis thaliana), 3'ss of exon 9
---aataaagtactcatttttatttttagaagttagaacatgtctggattttgcttccctgataagtcaattaatg--acttagtgctgattataatgtctacagTCCTGTTGGAGAGAATAAGAAAAGTGGCGAAGTATATAGATTATTCGATGTTGGAGGCCAGAGAAATGAAAGAAGGAAATGGATCCATTTATTTGAAGGT
   ||||    |||  || || |  |  |||  ||   | |||   |||       |   ||| | |  |  ||||  |  |       |   |  | | | ||| ||||| ||||||||||| |||||||| ||||| ||  |||| || || || || || ||||||||||| || ||||||||||| ||| | |||||||||
accaatatcaaacttgttgttgtggt--gaatcta---cttgtaatgatccgttaccaaagatgaattcacaaatggtatatgagataaagcttcgtttatgcagCCCTGTGGGAGAGAATAAAAAAAGTGGTGAAGTGTACCGATTGTTTGACGTGGGTGGACAGAGAAATGAGAGGAGGAAATGGATTCATCTGTTTGAAGGT

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|351055432|gb|FQ442030.1|FQ442030
EST:     GTTCTCTATGCAAGAATTCGTACAACAGGTGTCGTAGAAATCCAGTTCAG                         TCCTGTTGGAGAGAATAAGAAAAGTGGCGAAGTATATAGATTATTCGATGT
genomic: GTTCTCTATGCAAGAATTCGTACAACAGGTGTCGTAGAAATCCAGTTCAGgtatattttg ... atgtctacagTCCTGTTGGAGAGAATAAGAAAAGTGGCGAAGTATATAGATTATTCGATGT
EST: gi|351046433|gb|FQ453049.1|FQ453049
EST:     GTTCTCTATGCAAGAATTCGTACAACAGGTGTCGTAGAAATCCAGTTCAG                         TCCTGTTGGAGAGAATAAGAAAAGTGGCGAAGTATATAGATTATTCGATGT
genomic: GTTCTCTATGCAAGAATTCGTACAACAGGTGTCGTAGAAATCCAGTTCAGgtatattttg ... atgtctacagTCCTGTTGGAGAGAATAAGAAAAGTGGCGAAGTATATAGATTATTCGATGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttgcttccctgataagtcaattaatgacttagtgctgattataatgtctacagTCCTGTTGGAGAGAATAAGAAAAGTGGCGAAGTATATAGATTATTCGATGTTGGAGGCCAGAGAAATGAAAGAAGGAAATGGATCCATTTATTTGAAGGT
                                  tgctgat  putative branch site (score: 3)
             ataagtcaattaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aataaagtactcatttttatttttagaagttagaacatgtctggattttgcttccctgataagtcaattaatgacttagtgctgattataatgtctacagTCCTGTTGGAGAGAATAAGAAAAGTGGCGAAGTATATAGATTATTCGATGTTGGAGGCCAGAGAAATGAAAGAAGGAAATGGATCCATTTATTTGAAGGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
aataaag
- - - - - - - - - - - - - - - - - acatgtc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgctgat