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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agtgaaaacttttcctccattcatatatttgctcttttcacagctgctttgttaatttagtcttgagttctcattttaactacccaactgtcgattgcagCCACAACTTTAACTAGCTGGCATCTTCTGGTCACATTTTGTTCTCTTCATGTGGCACTATGGATGAAATTATTTGAGCACAAGCCTTTTGACGCTAGAGC

Basic information

species Vitis vinifera
transcript Vv06s0004g07960.t01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv06s0004g07960.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: LOC_Os01g07310.4 (Oryza sativa), 3'ss of exon 2
agtgaaaacttttcctccattcatatatttgctcttttcacagctgctttgttaatttagtcttgagttctcatt--ttaactacccaactgtcgattgcagCCACAACTTTAACTAGCTGGCATCTTCTGGTCACATTTTGTTCTCTTCATGTGGCACTATGGATGAAATTATTTGAGCACAAGCCTTTTGACGCTAGAGC
 ||   ||  | |    || |  ||  |    |        || | | |   ||     || |   || |  |||  | ||||  |   ||||   |||||||||| ||||| || ||||||||||| || || |||||||| |||||||| |||||| |||| |||||  | ||||||||||| |||||||| || ||  |
ggttctaaagtgtgtgacaatactaggtaacgtaaaaagttag-tacataaatagacgtgtttcctgtccaaattactcaact-tcggtctgtgttttgcagCCACTACTTTGACAAGCTGGCATCTCCTCGTTACATTTTGCTCTCTTCACGTGGCATTATGTATGAAGCTCTTTGAGCACAAACCTTTTGATGCAAGGAC

upper sequence: Vv06s0004g07960.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: LOC_Os05g07670.1 (Oryza sativa), 3'ss of exon 2
agtgaaaacttttcctccattcat------atatttgctcttttcacagctgctttgttaatttagtcttgagttctcattttaactacccaactgtcgattgcagCCACAACTTTAACTAGCTGGCATCTTCTGGTCACATTTTGTTCTCTTCATGTGGCACTATGGATGAAATTATTTGAGCACAAGCCTTTTGACGCTAGAGC
        ||||||    || |||       |||| |   || |   |  | | |   ||     | |   |  | |  ||  |   |   || |||   |||||||||| || || || || ||||||||||| ||||||||||| || || ||||| ||| |||||||||| || || |||||||||||||| ||| | ||| |
------ttcttttctcaaatgcattgcaatgtattagtgtttgtagaatttacatgaatataaatgacaccaactgtttttccatacatggaattgtattttgcagCCACTACCTTGACGAGTTGGCATCTTCTTGTCACATTTTGCTCCCTCCATGTAGCATTATGGATGAAGTTCTTCGAGCACAAGCCTTTCGACTCGAGAAC

upper sequence: Vv06s0004g07960.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: LOC_Os01g60780.2 (Oryza sativa), 3'ss of exon 1
agtgaaaacttttcctccattcatat-atttgctctt-ttcacagctgctttgttaatttagtcttg-agttctcattttaactacccaactgtcgattgcagCCACAACTTTAACTAGCTGGCATCTTCTGGTCACATTTTGTTCTCTTCATGTGGCACTATGGATGAAATTATTTGAGCACAAGCCTTTTGACGCTAGAGC
  |||  ||  |    | |   |||  |  ||       | || | | | |     || ||  | || |    |||    |    || || |     || |||| || ||  | || ||||||||||| ||||| ||||||||||| ||||||||||| ||   ||||||  | || ||| ||||   ||| ||| | |   |
tatgagtacaatatgacgaacaataccacctgagaaaactaactgtttcctaagctatataaccatgcaaaaatcacagcactctcctaatttc---tttcagCTACTACGCTGACAAGCTGGCATCTCCTGGTGACATTTTGTTCCCTTCATGTGGCTCTTCAGATGAAGCTTTTCGAGAACAAAGATTTAGACCCCAAGAC

upper sequence: Vv06s0004g07960.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GRMZM2G063511_T02 (Zea mays), 3'ss of exon 2
agtgaaaacttttcctccattcatatatt-tgctcttttcacagctgctttgttaatttagtcttgagttctcatt-ttaactacccaactgtcgattgcagCCACAACTTTAACTAGCTGGCATCTTCTGGTCACATTTTGTTCTCTTCATGTGGCACTATGGATGAAATTATTTGAGCACAAGCCTTTTGACGCTAGAGC
    |   |  ||  |  ||  | || |  ||   | | ||   ||| |||     | |  |  ||   | |  || | || ||   |  ||||   ||||||||| || || || ||||||||||| ||||| ||||| || || |||||||||||| ||||||||||||| |||||||| |||||||||||  | ||| |
--acacgccccttattttatcaacatgtggtggagtatgcaagtctgatttaaatgtcttcttatggactatggttgtgaaatatgtatttgtcttctgcagCCACTACCTTGACAAGCTGGCATCTGCTGGTTACATTCTGCTCCCTTCATGTGGCATTATGGATGAAATTCTTTGAGCATAAGCCTTTTGATTCAAGAAC

upper sequence: Vv06s0004g07960.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GRMZM2G116053_T01 (Zea mays), 3'ss of exon 2
----agtga-aaacttttcctccattcatatatttgctcttttcacagctgctttgttaatttagtcttgagttctcattttaactacccaactgtcgattgcagCCACAACTTTAACTAGCTGGCATCTTCTGGTCACATTTTGTTCTCTTCATGTGGCACTATGGATGAAATTATTTGAGCACAAGCCTTTTGACGCTAGAGC
     |||   |  |     | | |  ||| |       |  | | |||      |  |  ||   ||  |  | | | |  ||      |    |   |||||||||| ||||| || ||||||||||| ||||| ||||| |||||||| ||||||||| |||| |||||  | ||||||||||| ||||| || || ||  |
caagtgtggtgaggtgacagtgcgtctataaacaga---taatgatagcaaagaaggcaggttttcctccaagtgttaataaaatgtggtattcatt--ttgcagCCACTACTTTGACAAGCTGGCATCTCCTGGTTACATTCTGTTCTCTCCATGTGGCATTATGTATGAAGCTGTTTGAGCACAAACCTTTCGATGCAAGGAC

upper sequence: Vv06s0004g07960.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GRMZM2G081848_T05 (Zea mays), 3'ss of exon 2
agtgaaaacttttcctccattcatatatttgctcttttcacagctgct-ttgttaatttagtcttgagttctcattttaactacccaactgtcga-------ttgcagCCACAACTTTAACTAGCTGGCATCTTCTGGTCACATTTTGTTCTCTTCATGTGGCACTATGGATGAAATTATTTGAGCACAAGCCTTTTGACGCTAGAGC
       || | ||||| | | | |  |  | ||| |  |||| |  | ||   ||   || |  |  |||     |   |||   || | |||        |||||||||| ||||| || |||||||||||||||||||| || || ||||| ||||| ||| |||| |||||| | ||||||||||| ||||| || || ||  |
------cacgtgtcctcaagtgaca-gtccg-tctataaacagataatattagcaaagaaggcaggttttcctccatatgctaataaaatctcgtattcattttgcagCCACCACTTTGACAAGCTGGCATCTTCTGGTCACCTTCTGCTCTCTCCATGTAGCATTATGTATGAAACTCTTTGAGCACAAACCTTTCGATGCAAGGAC

upper sequence: Vv06s0004g07960.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GRMZM2G063253_T09 (Zea mays), 3'ss of exon 1
---agtgaaaacttttcctccattcatatatttgctcttttcacagctgctttg--ttaatttagtcttgagttctcattttaactacccaactgtcgattgcagCCACAACTTTAACTAGCTGGCATCTTCTGGTCACATTTTGTTCTCTTCATGTGGCACTATGGATGAAATTATTTGAGCACAAGCCTTTTGACGCTAGAGC
   |||   |  | ||     ||  | || | ||   |       |    | ||  |||| | | |  | |  |||    | || ||   |  ||||  |||||||||| || || || ||||||||||| ||||| ||||| || || |||||||| ||| |||||||||| || |||||||| |||||||||||  | ||| |
cagagtactagatcttatattatcaacatgtatgtagtgaagtatgtaagtctgatttaaatgacttctaatatctg---tgaaatatgta--tgtcttttgcagCCACTACCTTGACGAGCTGGCATCTGCTGGTTACATTCTGCTCCCTTCATGTAGCATTATGGATGAAGTTCTTTGAGCATAAGCCTTTTGATTCAAGAAC

upper sequence: Vv06s0004g07960.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GRMZM2G063253_T08 (Zea mays), 3'ss of exon 1
agtgaaaacttttcctccattcatatatttgctcttttcacagctgctttgttaatttagtcttgagttctcattttaactacccaactgtcgattgcagCCACAACTTTAACTAGCTGGCATCTTCTGGTCACATTTTGTTCTCTTCATGTGGCACTATGGATGAAATTATTTGAGCACAAGCCTTTTGACGCTAGAGC
                      || || | |   | |  |   ||| |||   || | | |  | |  |||    | || ||   |  ||||  |||||||||| || || || ||||||||||| ||||| ||||| || || |||||||| ||| |||||||||| || |||||||| |||||||||||  | ||| |
--------------------gtatgtagt-gaagtatgtaagtctgattt---aaatgacttctaatatctg---tgaaatatgta--tgtcttttgcagCCACTACCTTGACGAGCTGGCATCTGCTGGTTACATTCTGCTCCCTTCATGTAGCATTATGGATGAAGTTCTTTGAGCATAAGCCTTTTGATTCAAGAAC

upper sequence: Vv06s0004g07960.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: AT2G30460.1 (Arabidopsis thaliana), 3'ss of exon 3
---agtgaaaacttttcctccattcatatatttgctcttttcacagctgctttgttaatttagtcttgagttctcattttaactacccaactgtcga-ttgcagCCACAACTTTAACTAGCTGGCATCTTCTGGTCACATTTTGTTCTCTTCATGTGGCACTATGGATGAAATTATTTGAGCACAAGCCTTTTGACGCTAGAGC
        |    |   ||||||||||        | | | ||  |    | |  || | ||    || ||  ||||||  | |||   |   |  | || |||| || ||||| || |||||||||||| |||| ||||||||||| |||||||||||| |||||||||| || ||||||||||||||||||||  |  ||||
tctttaccatgggtgaactccattcatgataacagtttatgcatgg--aatctcatagtctatctgtgtgtaatcattt--attactttatattgaacttacagCAACTACTTTGACAAGCTGGCATCTTTTGGTGACATTTTGTTCACTTCATGTGGCATTATGGATGAAGTTTTTTGAGCACAAGCCTTTTGATCCACGAGC

upper sequence: Vv06s0004g07960.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: AT1G06890.2 (Arabidopsis thaliana), 3'ss of exon 2
agtgaaaacttttcctccattcatatatttgctcttttcacagctgctttgttaatttagtct--tgagttctc-attttaactacc-caactgtcgat-tgcagCCACAACTTTAACTAGCTGGCATCTTCTGGTCACATTTTGTTCTCTTCATGTGGCACTATGGATGAAATTATTTGAGCACAAGCCTTTTGACGCTAGAGC
    |      |  ||   ||   |||   ||| || |  || ||  | ||  | |||  |||  | || | ||  || | |||      | | |  || | |||| || ||||| || || ||||||||| |||||||||||||||| |||||||||||| ||||||||||  | || || ||||||||||||||  |  ||||
---cattttgatgtctgtgttgccataacagcttttatgtcatct--tatgcaattttgatctcataagctatctgttcttactcttgttattttgtatgtacagCGACTACTTTGACAAGTTGGCATCTTTTGGTCACATTTTGTTCCCTTCATGTGGCATTATGGATGAAGATGTTCGAACACAAGCCTTTTGATCCACGAGC

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|110699675|gb|EE076891.1|EE076891
EST:     GATTGTGATTTGCAATAAGGCGCTTATTAGCTCGCTTGGCTTCTCTTTCG                         CCACAACTTTAACTAGCTGGCATCTTCTGGTCACATTTTGTTCTCTTCATG
genomic: GATTGTGATTTGCAATAAGGCGCTTATTAGCTCGCTTGGCTTCTCTTTCGgtgagtggtt ... tcgattgcagCCACAACTTTAACTAGCTGGCATCTTCTGGTCACATTTTGTTCTCTTCATG
EST: gi|110699527|gb|EE076603.1|EE076603
EST:     GATTGTGATTTGCAATAAGGCGCTTATTAGCTCGCTTGGCTTCTCTTTCG                         CCACAACTTTAACTAGCTGGCATCTTCTGGTCACATTTTGTTCTCTTCATG
genomic: GATTGTGATTTGCAATAAGGCGCTTATTAGCTCGCTTGGCTTCTCTTTCGgtgagtggtt ... tcgattgcagCCACAACTTTAACTAGCTGGCATCTTCTGGTCACATTTTGTTCTCTTCATG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gctttgttaatttagtcttgagttctcattttaactacccaactgtcgattgcagCCACAACTTTAACTAGCTGGCATCTTCTGGTCACATTTTGTTCTCTTCATGTGGCACTATGGATGAAATTATTTGAGCACAAGCCTTTTGACGCTAGAGC
                            ttttaac  putative branch site (score: 2)
      ttaatttagt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
agtgaaaacttttcctccattcatatatttgctcttttcacagctgctttgttaatttagtcttgagttctcattttaactacccaactgtcgattgcagCCACAACTTTAACTAGCTGGCATCTTCTGGTCACATTTTGTTCTCTTCATGTGGCACTATGGATGAAATTATTTGAGCACAAGCCTTTTGACGCTAGAGC

- tgaaaac
- - - - - - tcctcca
- - - - - - - - - - - - - - - - - - - - cagctgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctaccca