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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...catccattcataatattttctggttccatgacttcttccgaaggctcaggcatttggtcgaattaattcagataatatgttctctatttatattgcatagGTGGCTGTTTCGTTGAAGGTGATTGGTTAAGAAATGCATTTCGCTGGAAACAGACAATTGGGCCCTGGGAGGAGAGACCTGGACACTTTGGTGATGTTTG

Basic information

species Vitis vinifera
transcript Vv08s0040g00320.t01
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv08s0040g00320.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: GRMZM2G006130_T01 (Zea mays), 3'ss of exon 7
catccattcataatattttctggttccatgacttcttccgaaggctcaggcatttggt-cgaattaat-------tcagataat--atgttctctatttatattgcatagGTGGCTGTTTCGTTGAAGGTGATTGGTTAAGAAATGCATTTCGCTGGAAACAGACAATTGGGCCCTGGGAGGAGAGACCTGGACACTTTGGTGATGTTTG
     || ||   | |||||   ||  |   |   |||   | | |  | ||| |  |  |  || ||       ||||||| |  ||    || ||     |    |||| || ||||| || |||||||| ||| |||||||||||||  | |||| | || ||||||| || ||||| ||||| ||||||||||| || ||||||||
---gtatgcactgtgttttcacatttaaaatcaagttcttcatgtttggacatatattatgtgttcatagatgtttcagatatttgatagattccatgcgactactgtagGAGGTTGTTTTGTAGAAGGTGACTGGCTAAGAAATGCATTCAGATGGAGAGAGTCAATTGGTCCATGGGAAGAGAGGCCTGGACACTTCGGGGATGTTTG

upper sequence: Vv08s0040g00320.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: GRMZM2G077299_T03 (Zea mays), 3'ss of exon 6
--------------catccattcataat--attttctggttccatgacttcttccgaaggctcaggcat-ttggtcgaattaat--tcagataatatgttctctatttatattgcatagGTGGCTGTTTCGTTGAAGGTGATTGGTTAAGAAATGCATTTCGCTGGAAACAGACAATTGGGCCCTGGGAGGAGAGACCTGGACACTTTGGTGATGTTTG
                   ||| | |||    || |   | | | ||  | |     |   |     || ||  |  | ||||   | |   | ||  ||   |  |  |||||  |||| ||||| || || |||||||  |||||||||||||| ||| | |||| | |  | ||||| || ||||| ||||||||||||||||| || ||||||||
gtatgctccgtgttttcttatttagaatcaggttcccaatgctaagatgtatatgatatattgcaatatattaatacatttaaggataatggactagattgcatgatgctattg--tagGAGGCTGCTTTGTAGAAGGTGGCTGGTTAAGAAATGCCTTTAGGTGGAGAGAATCTATTGGTCCATGGGAAGAGAGACCTGGACACTTCGGGGATGTTTG

upper sequence: Vv08s0040g00320.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: GRMZM2G006130_T05 (Zea mays), 3'ss of exon 19
catccattcataatattttctggttccatgacttcttccgaaggctcaggcatttggt-cgaattaat-------tcagataat--atgttctctatttatattgcatagGTGGCTGTTTCGTTGAAGGTGATTGGTTAAGAAATGCATTTCGCTGGAAACAGACAATTGGGCCCTGGGAGGAGAGACCTGGACACTTTGGTGATGTTTG
     || ||   | |||||   ||  |   |   |||   | | |  | ||| |  | ||  || ||       ||||||| |  ||    || ||     |    |||| || ||||| || |||||||| ||| |||||||||||||  | |||| | |  ||||||| || ||||| ||||| ||||||||||| || ||||||||
---gtatgcactgtgttttcacatttaaaatcaagttcttcatgtttggacatatattacgtgttcatagatgtttcagatatttgatagattccatgcgactactgtagGAGGTTGTTTTGTAGAAGGTGACTGGCTAAGAAATGCATTCAGATGGAGAGAATCAATTGGTCCATGGGAAGAGAGGCCTGGACACTTCGGGGATGTTTG

upper sequence: Vv08s0040g00320.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: GRMZM2G006130_T02 (Zea mays), 3'ss of exon 7
-catccattcataatattttctggttccatgacttcttccgaaggctcaggcatttggtcgaattaattcagataat--atgttctctatttatattgcatagGTGGCTGTTTCGTTGAAGGTGATTGGTTAAGAAATGCATTTCGCTGGAAACAGACAATTGGGCCCTGGGAGGAGAGACCTGGACACTTTGGTGATGTTTG
   |   |||| | |          | | | |  | |    |    | | |  ||      |  |  |||||||| |  ||    || ||     |    |||| || ||||| || |||||||| ||| |||||||||||||  | |||| | |  ||||||| || ||||| ||||| ||||||||||| || ||||||||
ctgtgttttcacatttaaaatcaagttcttcatgtttggacatatattacgtgttcat---agatgtttcagatatttgatagattccatgcgactactgtagGAGGTTGTTTTGTAGAAGGTGACTGGCTAAGAAATGCATTCAGATGGAGAGAATCAATTGGTCCATGGGAAGAGAGGCCTGGACACTTCGGGGATGTTTG

upper sequence: Vv08s0040g00320.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: GLYMA03G27460.3 (Glycine max), 3'ss of exon 7
-catccattcataatattttctggttccatgacttcttccgaaggctcaggcatttggtcgaattaattcagataatatgttctctatttatattgcatagGTGGCTGTTTCGTTGAAGGTGATTGGTTAAGAAATGCATTTCGCTGGAAACAGACAATTGGGCCCTGGGAGGAGAGACCTGGACACTTTGGTGATGTTTG
   |   |    |  ||||  |  |  | ||   |  |   |    ||  |  | |     | | || | | ||       | |   |||| |||||||||| || ||||| |||||||| || |||||||||||||||||||| ||||||    |  |||| || ||||||||||||||||| |||||||||||||||||
gtttgagtaagcatcatttgataataacgtgttctagttt-actcttctagtttgtatgtaactcaactaacatctaggaatgttattttacattgcatagGCGGTTGTTTTGTTGAAGGAGAATGGTTAAGAAATGCATTTCGATGGAAAGCATCTGTTGGACCATGGGAGGAGAGACCTGGGCACTTTGGTGATGTTTG

upper sequence: Vv08s0040g00320.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: GLYMA19G30450.1 (Glycine max), 3'ss of exon 7
--------catccattcataatattttctggttccatgacttcttccgaaggctcaggcatttggtcgaattaat-tcagataatatgttctctatttatattgcat-agGTGGCTGTTTCGTTGAAGGTGATTGGTTAAGAAATGCATTTCGCTGGAAACAGACAATTGGGCCCTGGGAGGAGAGACCTGGACACTTTGGTGATGTTTG
          |      |||||   |||| ||||  |  |||||     ||  |   | ||       || |||  || |  | | |  | | |  ||| ||||||| ||| || ||||| |||||||| || |||||||||||||||||||| ||||||    | ||||| || ||||||||||||||||| |||||||||||||||||
gtaagcatagtttgacaataatgcattctagttcact--cttct-----agttt---gtatgcaactcaactaacatctgggagtgttatttttcattacattgcattagGCGGTTGTTTTGTTGAAGGAGAATGGTTAAGAAATGCATTTCGATGGAAAACATCCATTGGACCATGGGAGGAGAGACCTGGGCACTTTGGTGATGTTTG

upper sequence: Vv08s0040g00320.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: GLYMA03G27490.1 (Glycine max), 3'ss of exon 6
--catccattcataatattttctggttccatgacttcttccgaaggc-tcaggcatttggtcgaattaattcagataatatgttctctatttatattgcatagGTGGCTGTTTCGTTGAAGGTGATTGGTTAAGAAATGCATTTCGCTGGAAACAGACAATTGGGCCCTGGGAGGAGAGACCTGGACACTTTGGTGATGTTTG
   ||||||   |  |    | |  | |    | || |    | | | ||| || ||      | ||    || ||   |||   | | ||    ||  | |||||||||||| ||||||||  |    ||||||||||||||||| |||||| | |   |||| |||||||| ||||||||||| |||||||||||||||||
atgatccatcttttttccaatttcttcctcgaatttgtctttatgtcatcaagcgttcaaataactt---ccaaatttaatgcaattttttatctttcaagagGTGGCTGTTTTGTTGAAGGACAAACATTAAGAAATGCATTTCGGTGGAAAGATAGTGTTGGACCCTGGGAAGAGAGACCTGGTCACTTTGGTGATGTTTG

upper sequence: Vv08s0040g00320.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: GLYMA19G30470.1 (Glycine max), 3'ss of exon 6
--catccattcataatattttctggttccatgacttcttccgaaggc-tcaggcatttggtcgaattaattcagataatatgttctctatttatattgcat-agGTGGCTGTTTCGTTGAAGGTGATTGGTTAAGAAATGCATTTCGCTGGAAACAGACAATTGGGCCCTGGGAGGAGAGACCTGGACACTTTGGTGATGTTTG
   ||| ||   |  |    | |  | |  | | || |    ||| | | |  ||||    | ||| | |||| |   ||       | ||||| |||||  ||||||||||||  |||||||  |    ||||||||||||||||| |||||| | | | |||| ||||||||  |||||||||| |||||||||||||||||
atgatctatctcttttccaatttcttcctctaatttgtcttcaagtcatgaaacatt----caaataacttcaaaatttaacgcaaatttttatcttgcaagagGTGGCTGTTTTATTGAAGGACAAACATTAAGAAATGCATTTCGGTGGAAAGATAGAGTTGGACCCTGGGAACAGAGACCTGGGCACTTTGGTGATGTTTG

upper sequence: Vv08s0040g00320.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: GLYMA03G00630.1 (Glycine max), 3'ss of exon 6
catccattcata-atattttctgg-ttccatgacttcttccgaaggctcaggcatttggtcgaattaattcagataatatgttctctatttatattgcatagGTGGCTGTTTCGTTGAAGGTGATTGGTTAAGAAATGCATTTCGCTGGAAACAGACAATTGGGCCCTGGGAGGAGAGACCTGGACACTTTGGTGATGTTTG
  |  || |||| |  |||| ||  ||   | |          |        |  || | |  | |||||   ||  |      |     |  |||   ||||||| ||||  |||||||| ||||  ||||||||||||||| | |||||| | ||| |||| || ||||| |||||||| ||||||| ||| ||||| ||
tgtgtatccatacaagttttgtgaatttagttatgcaaatattaaatagtttctcttagacctactaatttt-atgttgaaactttggcatgcattat-tagGTGGGTGTTATGTTGAAGGAGATTATTTAAGAAATGCATTTAGGTGGAAAGACACAGTTGGACCATGGGAAGAGAGACCAGGACACTATGGAGATGTATG

upper sequence: Vv08s0040g00320.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: GLYMA19G30460.1 (Glycine max), 3'ss of exon 6
-catccattcataatattttctggttccatgacttcttccgaaggctcaggcatttggtcgaattaattcagataatatgttctctattta---tattgcat-agGTGGCTGTTTCGTTGAAGGTGATTGGTTAAGAAATGCATTTCGCTGGAAACAGACAATTGGGCCCTGGGAGGAGAGACCTGGACACTTTGGTGATGTTTG
  | || ||  ||||    |    || |     |  ||| |||   | | | |        |||    | ||||   |   | | |||  |    ||||||| |||||| ||||  ||||||||  |||   | |||||   |||||  |||||| | || ||||| || ||||||||||||||||| ||| |||||||||||||
ttaacc-tttgtaatggaataatatttc----ttctttctgaactttgatgtaaaaaaaaaaatcctcttagatctaactctatttatcaaaatcattgcattagGTGGTTGTTATGTTGAAGGAAATTATCTGAGAAACCGATTTCAATGGAAAGATACTATTGGACCATGGGAGGAGAGACCTGGGCACCTTGGTGATGTTTG

upper sequence: Vv08s0040g00320.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: AT3G10740.1 (Arabidopsis thaliana), 3'ss of exon 7
--------------------------------------catccattcataa---tattttctggttccatgacttcttccgaaggctcaggcatttggtcgaattaattcagataatatgttctctatttatatt-----gcatagGTGGCTGTTTCGTTGAAGGTGATTGGTTAAGAAATGCATTTCGCTGGAAACAGACAATTGGGCCCTGGGAGGAGAGACCTGGACACTTTGGTGATGTTTG
                                        || || ||||    ||  |  | |||| ||      |  | ||      | | |  | |  ||| |  | |  |    | ||  || |  |||||        ||||||| ||||| || || ||||| |||||||| ||||| || ||||||||| | ||  | || || ||||| |||||||| || || ||||||||||||||
gtacgtattatttaaggctagtagcatttttgttacttattctatccatagacgtacctcttagttcaata-----tgacaaaaagcatgacttaagatgaaataagctaaagtctattctttactctggatatttgtgaatttagGTGGTTGTTTTGTCGAGGGTGAATGGTTAAGTAATGCCTTCCGCTGGAAAGAAACCGTAGGACCTTGGGAAGAGAGACCGGGCCATTTTGGTGATGTTTG

upper sequence: Vv08s0040g00320.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: AT5G26120.1 (Arabidopsis thaliana), 3'ss of exon 7
catccattcataatattttctg-gttccatgacttcttccgaaggctcaggcatttggtcgaattaattcagataa--tatgttctctatttatattgca-----tagGTGGCTGTTTCGTTGAAGGTGATTGGTTAAGAAATGCATTTCGCTGGAAACAGACAATTGGGCCCTGGGAGGAGAGACCTGGACACTTTGGTGATGTTTG
          |||| | |   | ||   ||  | | |  |   |    |    | ||  |  |  || | ||| ||  ||       ||   || ||        ||||||| ||||| || || |||||||||||| | |||||||| ||||||||| | ||  |  |  | ||||| ||||||||||| || | ||||||||||||
---------gtaatttctagagagtaaaatagcatttcacttggtaaaatatgtatgaacataaaaaatgagaaaagctaaaagaattagcaatgttttgggagttagGTGGTTGTTTTGTGGAGGGTGATTGGTTAGGCAATGCATTCCGCTGGAAAGAAACCGTGAGAGCTTGGGAAGAGAGACCTGGCCATTATGGTGATGTTTG

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|161713110|gb|FC062474.1|FC062474
EST:     TCTTTCACAAATGATAGCCGATTTTAAACCTCGATTTCTTAGGTTTCCAG                         GTGGCTGTTTCGTTGAAGGTGATTGGTTAAGAAATGCATTTCGCTGGAAAC
genomic: TCTTTCACAAATGATAGCCGATTTGAAACCTCGATTTCTTAGGTTTCCAGgtatgcatta ... tattgcatagGTGGCTGTTTCGTTGAAGGTGATTGGTTAAGAAATGCATTTCGCTGGAAAC
EST: gi|161713404|gb|FC062796.1|FC062796
EST:     TCGATTTCTTAGGTTTCCAG                         GTGGCTGTTTCGTTGAAGGTGATTGGTTAAGAAATGCATTTCGCTGGAAAC
genomic: TCGATTTCTTAGGTTTCCAGgtatgcatta ... tattgcatagGTGGCTGTTTCGTTGAAGGTGATTGGTTAAGAAATGCATTTCGCTGGAAAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcaggcatttggtcgaattaattcagataatatgttctctatttatattgcatagGTGGCTGTTTCGTTGAAGGTGATTGGTTAAGAAATGCATTTCGCTGGAAACAGACAATTGGGCCCTGGGAGGAGAGACCTGGACACTTTGGTGATGTTTG
               aattaat  putative branch site (score: 3)
               aattaattcagataat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
catccattcataatattttctggttccatgacttcttccgaaggctcaggcatttggtcgaattaattcagataatatgttctctatttatattgcatagGTGGCTGTTTCGTTGAAGGTGATTGGTTAAGAAATGCATTTCGCTGGAAACAGACAATTGGGCCCTGGGAGGAGAGACCTGGACACTTTGGTGATGTTTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA
- -ccattca
- - - - - - - - tttctgg
- - - - - - - - - - - - -ccatgac
- - - - - - - - - - - - - - - - ttcttcc
- - - - - - - - - - - - - - - - - - - - - - -tcaggca