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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gagaagcaaaatgaactttcaaattaggagaacaatacgaattttgtttggttttatatgatgttttacattgaactctaacaacttcaagcatgatcagGAAGAATTGGAGAAGAAGAAGGCAGAATATGCAGAGAAAATGAAAAACAAAGTAGCATTGATTCACAAGCAAGCAGAAGAAAAGAAGGCAATGATTGAAG

Basic information

species Vitis vinifera
transcript Vv15s0046g03180.t01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv15s0046g03180.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: LOC_Os04g45070.1 (Oryza sativa), 3'ss of exon 4
-gagaagcaaaatgaactttcaaattaggagaaca-atacgaattttgtttggttttatatgatgttttacattgaactctaacaacttcaagcatgatcagGAAGAATTGGAGAAGAAGAAGGCAGAATATGCAGAGAAAATGAAAAACAAAGTAGCATTGATTCACAAGCAAGCAGAAGAAAAGAAGGCAATGATTGAAG
      | ||  || || || |   |||||  ||| ||   |   |||| |  | | ||   ||  |||  | | ||  |||   | ||  | | |  ||||||  || |||| ||||||||||| |||||||||||||| ||||| |||||||| ||  |  | |||||| |||| || || ||||  |||||| | || |
tatagggaaagctgtaccttaactataggactacacatgtcatacttgtatcatgt-atggcatcctttgaactaaagcctatgcatttgcaccctt-tcagGAGCAACTGGAAAAGAAGAAGGCTGAATATGCAGAGAAGATGAAGAACAAAGTCGCGATCGTCCACAAGGAAGCTGAGGAGAAGAGAGCAATGGTCGAGG

upper sequence: Vv15s0046g03180.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM2G122937_T01 (Zea mays), 3'ss of exon 4
gagaagcaaaatgaactttcaaattaggagaacaatacgaattttgtttggttttatatgatgttttacattgaactctaacaacttcaagcatgatcagGAAGAATTGGAGAAGAAGAAGGCAGAATATGCAGAGAAAATGAAAAACAAAGTAGCATTGATTCACAAGCAAGCAGAAGAAAAGAAGGCAATGATTGAAG
|  ||  || |    |  |  || ||  |   ||   |   |              |   ||  | |    |  |   ||     || |  |||| ||||||| || |||| ||||||||||| |||||||||||||| ||||| ||||| || ||| |||| |||||| |||| ||||| |||   || ||| | || |
ggaaaagaatagatccagtggaactaatatgccaccccccctccccccctaaaaggtgatatcctcttagctacagcttatatggtttattcatgttcagGAACAACTGGAAAAGAAGAAGGCTGAATATGCAGAGAAGATGAAGAACAAGGTTGCAATGATACACAAGGAAGCCGAAGAGAAGCGAGCGATGGTGGAGG

upper sequence: Vv15s0046g03180.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM2G116538_T02 (Zea mays), 3'ss of exon 4
--gagaagcaaaatgaactttcaaatt-aggagaac-aatacgaattttgtttggttttatatgatgttttacattgaactctaacaacttcaagcatgatcagGAAGAATTGGAGAAGAAGAAGGCAGAATATGCAGAGAAAATGAAAAACAAAGTAGCATTGATTCACAAGCAAGCAGAAGAAAAGAAGGCAATGATTGAAG
  |     |      ||     | ||  || ||||| |||| |       |      | |||| ||  |    | |   |||  | || || |  |||| ||||||| || |||| |||||||| || |||||||| ||||| ||||||||||| || ||| |||| |||| | |||| ||||| |||   || ||| | || |
atggaggacgccgcaaaaggatagatccagtagaactaatatgccacccctaaaaggtgatatcatcata---actatgctcatataattt-attcatgttcagGAACAACTGGAAAAGAAGAAAGCTGAATATGCTGAGAAGATGAAAAACAAGGTTGCAATGATCCACAGGGAAGCCGAAGAGAAGCGAGCGATGGTGGAGG

upper sequence: Vv15s0046g03180.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM2G066997_T01 (Zea mays), 3'ss of exon 4
gagaagcaaaatgaactttcaaattaggaga-acaatacga-attttgtttggttttatatgatgttttacattgaactctaacaacttcaagca--tgatcagGAAGAATTGGAGAAGAAGAAGGCAGAATATGCAGAGAAAATGAAAAACAAAGTAGCATTGATTCACAAGCAAGCAGAAGAAAAGAAGGCAATGATTGAAG
  || |  ||   ||     | || |  | | |   |  |  |  |||| || ||||  ||||      | |   ||   |||   |||  |||   ||||||||||||| | |||||||| | ||| |||||||| ||||| |||||||||||    ||| | || || ||| | || || |||||||  || ||| ||   |
ttgatgttaatgtaataggtatatcataaaatatggtgtgggaaattgtgtgctttttaatgaaa----ataaaaaatattaatctctttgagctactgatcagGAAGAACTAGAGAAGAAAATGGCTGAATATGCTGAGAAGATGAAAAACAAGAAGGCAATCATCCATAAGAAGGCCGAGGAAAAGAGAGCGATGGTTATGG

upper sequence: Vv15s0046g03180.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA18G46470.1 (Glycine max), 3'ss of exon 4
gagaagcaaaatgaactttcaaattaggagaacaatacgaattttgtttggtttta--tatgatgttttacattgaactctaacaacttcaagcatgatcagGAAGAATTGGAGAAGAAGAAGGCAGAATATGCAGAGAAAATGAAAAACAAAGTAGCATTGATTCACAAGCAAGCAGAAGAAAAGAAGGCAATGATTGAAG
 | ||   ||| | |  | | |   |  ||   |  ||  |||||   | ||  ||  | || || || | || |   | ||| ||||||  |  ||| |||||| || ||||||| ||||| ||||||||||  || |||||||| ||||| || || ||  |||||||| ||||||| || |||| ||||||||||||||
-ataacttaaaagcatgtgctatgaaatagtttagaacagattttaacttgtaatacttttgctgattaatatagc-ttttaataacttcttgtgtgagcagGAACAACTGGAGAAAAAGAAAGCAGAATATGGTGAAAAAATGAAGAACAAGGTGGCCTTAGTTCACAAGGAAGCAGAGGAGAAGAGGGCAATGATTGAAG

upper sequence: Vv15s0046g03180.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA07G07970.1 (Glycine max), 3'ss of exon 4
gagaagcaaa--atgaactttcaaattaggagaacaatacgaattttgtttggttttatatgatgttttacattgaactctaacaacttcaagcatgatcagGAAGAATTGGAGAAGAAGAAGGCAGAATATGCAGAGAAAATGAAAAACAAAGTAGCATTGATTCACAAGCAAGCAGAAGAAAAGAAGGCAATGATTGAAG
 | |  ||||  ||| |  |  | ||| | | | ||     ||   |    |   ||| |   | ||  |        | ||| |   || ||  | | |||||| || | ||||| ||||| ||||||||||  || ||||||||||||||| |||| ||  |||||||||||||||| || ||||  |||||| ||||||
-atattcaaataatggaactcaacatt-gaataccacataaaaacatacaagcacttaaagagtattgcattcatctttttaatactctcgagtctaagcagGAACAACTAGAGAAAAAGAAAGCAGAATATGGTGAAAAAATGAAAAACAAAATAGCCTTAGTTCACAAGCAAGCAGAGGAGAAGAGAGCAATGGTTGAAG

upper sequence: Vv15s0046g03180.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA03G01550.1 (Glycine max), 3'ss of exon 4
gagaagcaaaatgaactttcaaattaggagaacaatacgaat-tttgtttggttttatatgat---------gttttacattgaact--ctaacaacttcaagcatgatcagGAAGAATTGGAGAAGAAGAAGGCAGAATATGCAGAGAAAATGAAAAACAAAGTAGCATTGATTCACAAGCAAGCAGAAGAAAAGAAGGCAATGATTGAAG
               |||  ||||||  | |  ||||    | ||||  |      |||  |          || ||||||| | ||  ||||||   || ||  | | |||||| || ||||||| ||||| || |||||||  || || |||||||||||| |||  ||  |||||||||||||||| || ||||  |||||| ||||||
------------tttcttgtaaattaaaaaatgaatagatctctttgcataaaaacatacaagcacttcagagtattacattcatctatctaacactctcgagtctaagcagGAACAAATGGAGAAAAAGAAAGCCGAATATGGTGAAAAGATGAAAAACAAAATAGTCTTAGTTCACAAGCAAGCAGAGGAGAAGAGAGCAATGGTTGAAG

upper sequence: Vv15s0046g03180.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: AT3G61260.1 (Arabidopsis thaliana), 3'ss of exon 4
gagaagcaaaatgaactttcaaattaggagaacaatacgaattttgtttggttttatatgatgttttacattgaactctaacaacttcaagcatgatcagGAAGAATTGGAGAAGAAGAAGGCAGAATATGCAGAGAAAATGAAAAACAAAGTAGCATTGATTCACAAGCAAGCAGAAGAAAAGAAGGCAATGATTGAAG
     | | ||| |||||   |||   |||   || |||  |||  | || ||      || ||      || |  | | |    ||     |||  |||||  || | ||||||||||| ||||| ||||||||||  ||||| || || || |||  |||||||||| |||||||||| |  |  |||||||||||||
-----gtataataaacttagcaatagagaggtgaa-acggttttaatgtgatt----gagaagtgaagtgttaatttgtgagttttttctcaatg--cagGAGCAACTAGAGAAGAAGAAAGCAGAGTATGCAGAGAGGATGAAGAATAAGGTTGCAGCGATTCACAAGGAAGCAGAAGAGAGAAGAGCAATGATTGAAG

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|33409095|gb|CF214722.1|CF214722
EST:     GGGAAAACAGCAAGAAAGCAGCTGTTGAAGCTAATCTGAAGAAGATTGAG                         GAAGAATTGGAGAAGAAGAAGGCAGAATATGC
genomic: GGGAAAACAGCAAGAAAGCAGCTGTTGAAGCTAATCTGAAGAAGATTGAGgttactgccc ... gcatgatcagGAAGAATTGGAGAAGAAGAAGGCAGAATATGC






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtttggttttatatgatgttttacattgaactctaacaacttcaagcatgatcagGAAGAATTGGAGAAGAAGAAGGCAGAATATGCAGAGAAAATGAAAAACAAAGTAGCATTGATTCACAAGCAAGCAGAAGAAAAGAAGGCAATGATTGAAG
                              ctctaac  putative branch site (score: 2)
      ttttatatgatgtttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gagaagcaaaatgaactttcaaattaggagaacaatacgaattttgtttggttttatatgatgttttacattgaactctaacaacttcaagcatgatcagGAAGAATTGGAGAAGAAGAAGGCAGAATATGCAGAGAAAATGAAAAACAAAGTAGCATTGATTCACAAGCAAGCAGAAGAAAAGAAGGCAATGATTGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- -aagcaaa
- - - - - - - - - -caaatta
- - - - - - - - - - - - - - - aacaata
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -caacttc