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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aatatttgctctaaggaaacaaaatatccattatgaacagatattaatgtattgctgaagattttacatcaatttagttttaaatctatggctctttaagTTTCAAGGTTTCAATTGGGAAAGCTGGAGGAGGCAGTGGTACCTGGAGTTAGCGCCTAAAGCTGCTGACTTATCCCAATGTGGGATAACAGCAGTGTGGT

Basic information

species Vitis vinifera
transcript Vv14s0068g00420.t01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv14s0068g00420.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA08G26860.1 (Glycine max), 3'ss of exon 2
aatatttgctctaaggaaacaaaatatccattatgaacagatattaatgtattgctgaagattttacatcaatttagttttaaatctatggctcttt-----aagTTTCAAGGTTTCAATTGGGAAAGCTGGAGGAGGCAGTGGTACCTGGAGTTAGCGCCTAAAGCTGCTGACTTATCCCAATGTGGGATAACAGCAGTGTGGT
  |    |   |    |     | | ||  ||      |  ||     |||| |  |||| |   |    ||   | |||| |||  ||     |||     |||||||||||||| || ||||| |||||||| ||||  ||||| ||||| |||||  ||||| | |||||||||||  | |||||| | |||||||||||||
--tgcaagtattttttatgtgcattttctgttgcatgtatttacct-cgtatagtggaaggtaaaaggggaag--aatttttaatgaatattcattttactcaagTTTCAAGGTTTTAACTGGGAGAGCTGGAGAAGGCGCTGGTATCTGGAATTAGCAGCTAAAACAGCTGACTTATCTAATTGTGGGGTGACAGCAGTGTGGT

upper sequence: Vv14s0068g00420.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: PP1S100_191V6.1 (Physcomitrella patens), 3'ss of exon 5
------------aatatttgctctaaggaaacaaaatatccattatgaacagatattaatgtattgctgaagatttt--acatcaat-ttagttttaaatctatggctcttta----agTTTCAAGGTTTCAATTGGGAAAGCTGGAGGAGGCAGTGGTACCTGGAGTTAGCGCCTAAAGCTGCTGACTTATCCCAATGTGGGATAACAGCAGTGTGGT
              |||  | |    |  |||   |  |  ||  || | |||  | | |    |  |  |  || |  |||||  | |||           || | | || |    |||||||||||||||| ||||| ||||||||  |||||||||  |||||| |  |  | |||||  | ||  | ||| |||| || || ||| |  | ||| 
gtacgtactcaccgtatccgattcctgcgaacttgaactatat-gtgcatagacctgacttctcttttatatcttatgtacatctgtgttaacaacgtgaacattgattttgatgccagTTTCAAGGTTTCAACTGGGAGAGCTGGAGACGGCAGTGGTGGCTGGAGATGTCAGCGAAAGCCTCAGATCTTTCCAAATGCGGAATCACAACTATCTGGC
















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|33404897|gb|CF210524.1|CF210524
EST:     AACCAGGAACTGGAACAGGTCGTGAGATTGTG                         TTTCAAGGTTTCAATTGGGAAAGCTGGAGGAGGCAGTGGTACCTGGAGTTA
genomic: AACCAGGAACTGGAACAGGTCGTGAGATTGTGgttagtatat ... gctctttaagTTTCAAGGTTTCAATTGGGAAAGCTGGAGGAGGCAGTGGTACCTGGAGTTA






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aatgtattgctgaagattttacatcaatttagttttaaatctatggctctttaagTTTCAAGGTTTCAATTGGGAAAGCTGGAGGAGGCAGTGGTACCTGGAGTTAGCGCCTAAAGCTGCTGACTTATCCCAATGTGGGATAACAGCAGTGTGGT
 tattaat  putative branch site (score: 2)
                                              ctcttt  putative PPT
               attttacatcaattta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aatatttgctctaaggaaacaaaatatccattatgaacagatattaatgtattgctgaagattttacatcaatttagttttaaatctatggctctttaagTTTCAAGGTTTCAATTGGGAAAGCTGGAGGAGGCAGTGGTACCTGGAGTTAGCGCCTAAAGCTGCTGACTTATCCCAATGTGGGATAACAGCAGTGTGGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - aaacaaa
- - - - - - - - - - - - - - - - - gaacaga
- - - - - - - - - - - - - - - - - - - - - - - - - - tgctgaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -acatcaa