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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...attgtggttaatctttattattattgttggtgttgtttttatgtgccctgttcatttgattggtaaaaagctgagttgcagtctctctttataatggcagAATAAGGATGTAACAGAAGCAATTCAGAAGGTTGCTGCTGCCTATGACTGCAAAATTGTCGAAGGTGTACTCAGCCACCAGCTAAAGCAGTTTGTGATAG

Basic information

species Vitis vinifera
transcript Vv08s0217g00020.t01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv08s0217g00020.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA18G43390.1 (Glycine max), 3'ss of exon 5
attgtggttaat-ctttattattattgttggtgttgtttttatgtgccctgttcatttg--attggtaaaaagctgagttgcagtctctctttataatggcagAATAAGGATGTAACAGAAGCAATTCAGAAGGTTGCTGCTGCCTATGACTGCAAAATTGTCGAAGGTGTACTCAGCCACCAGCTAAAGCAGTTTGTGATAG
  | |  | |   | ||||||  ||| ||  |  | |   ||  ||  ||  |  || |   | ||||   |  |    |  | | | |  || ||    ||||| ||||||||||  || |||||||| ||||||||||||||||||||||| |||||||| || ||||| || ||||||||  | ||||||||||| ||  
--tttaatcagcacgttattaaaattattattcgtatacataaatgatcttatttttagcagtgggtactcatttttaatatatttttttcttttatccacaGAACAAGGATGTAAGTGATGCAATTCAAAAGGTTGCTGCTGCCTATGACTGTAAAATTGTTGAGGGTGTTCTTAGCCACCAAATGAAGCAGTTTGTTATT-

upper sequence: Vv08s0217g00020.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA01G29420.1 (Glycine max), 3'ss of exon 5
attgtggttaatctttattatta--ttgttggtgttgttt-ttatgtgccctgttcatttgattggtaaaaagctgagttgcagtctctctttataatggcagAATAAGGATGTAACAGAAGCAATTCAGAAGGTTGCTGCTGCCTATGACTGCAAAATTGTCGAAGGTGTACTCAGCCACCAGCTAAAGCAGTTTGTGATAG
  ||  |  |  ||  |||  ||  || |||     |||  ||||||  |    | |   ||   ||| | |      | | | | | |  || |  || ||||| ||||||||||| ||||||||||| |||||||||||||| ||||| || |||||||| || ||||| || ||||||||  | || ||||||||||| |
tatgctgaaagactagatttgtaatttattgtcacagttagttatgtaactaaataagagga--agtacatattcttatgg-attttgttcttttcctgacagAACAAGGATGTAACTGAAGCAATTCAAAAGGTTGCTGCTGCGTATGATTGTAAAATTGTTGAGGGTGTTCTTAGCCACCAAATGAAACAGTTTGTGATTG

upper sequence: Vv08s0217g00020.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA07G18500.1 (Glycine max), 3'ss of exon 5
------attgtggttaa-tctttattattattgttggtgttgtttttatgtgccctgttcatttgattggtaaaaagctgagttgcagtctctctttataatggcagAATAAGGATGTAACAGAAGCAATTCAGAAGGTTGCTGCTGCCTATGACTGCAAAATTGTCGAAGGTGTACTCAGCCACCAGCTAAAGCAGTTTGTGATAG
      ||| |  | |  ||| ||||| |||| ||  |  |  ||| || | |     |    | |||  |||  ||      ||   | | |  || ||    ||||| ||||||||||  || |||||||| ||||||||||||||||||||||| ||||| || || ||||| || ||||||||  | ||||||||||| || |
ttgtctattttaatcagctctgtattaatattattattcataatttcatatacataaatggccttattt-taattag------tgtttttttttcttttatccacagAACAAGGATGTAAGTGATGCAATTCAAAAGGTTGCTGCTGCCTATGACTGTAAAATCGTTGAGGGTGTTCTTAGCCACCAAATGAAGCAGTTTGTTATTG

upper sequence: Vv08s0217g00020.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA03G07420.1 (Glycine max), 3'ss of exon 5
---attgtggttaatctttattattattgttggtgttgtttttatgtgccctgttcatttgattggtaaaaagctgagttgcagtctctctttataatggcagAATAAGGATGTAACAGAAGCAATTCAGAAGGTTGCTGCTGCCTATGACTGCAAAATTGTCGAAGGTGTACTCAGCCACCAGCTAAAGCAGTTTGTGATAG
     ||| |  |  ||  |||  || | ||  ||||    ||||||  | |   ||  ||   |   | |  || | |     | |||  || |  || ||||| ||||||||||| ||||||||||||||| |||| || || ||||| || |||||||| || ||||| || ||||||||  | || ||||||||||| |
ttgtatgttgaaaggctagatttgtaat-ttattgttacagttatgtaac-tacacaagtggccgtgcatattctta-tgcttttttcttcttttcctgacagAACAAGGATGTAACTGAAGCAATTCAGAAGATTGCCGCAGCGTATGATTGTAAAATTGTTGAGGGTGTTCTTAGCCACCAAATGAAACAGTTTGTGATTG

upper sequence: Vv08s0217g00020.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: PP1S264_34V6.1 (Physcomitrella patens), 3'ss of exon 4
----------attgtggttaatctttattattattgttggtgttgtttttat-gtgccctgttcatttgattggtaaaaagctgagttgcagtctctctttataatggcagAATAAGGATGTAACAGAAGCAATTCAGAAGGTTGCTGCTGCCTATGACTGCAAAATTGTCGAAGGTGTACTCAGCCACCAGCTAAAGCAGTTTGTGATAG
           ||    | | |   |||||   |   |||| ||   || ||  ||   ||||||  |  ||   | |    |||      |  |||||||      |||||| ||||| || || || |||||||||||||| || |||||||| || ||||| |||| ||| |||||  | || || ||||| ||||||||||| || |
gtatgcttctgtttgtctcacttcatattaaactcactggtttttgcttcattatggtttgttcaaatatttatgatagtaatgaaaaaatgattctctttc-----gcagAACAAGGACGTGACCGATGCAATTCAGAAGGTAGCGGCTGCCTACGATTGCAAGATTGCCGAGGGTGTGTTGAGTCATCAGCTCAAGCAGTTTGTCATCG

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|294966210|gb|GW839433.1|GW839433
EST:     CAAATACTGCTGCTGAAGTTGCTCTGAGGCTTGTAAGGCCAGGAAGAAAG                         AATAAGGATGTAACAGAAGCAATTCAGAAGGTTGCTGCTGCCTATGACTGC
genomic: CAAATACTGCTGCTGAAGTTGCTCTGAGGCTTGTAAGGCCAGGAAGAAAGgtaattccgt ... ataatggcagAATAAGGATGTAACAGAAGCAATTCAGAAGGTTGCTGCTGCCTATGACTGC
EST: gi|71875961|gb|DT025016.1|DT025016
EST:     CAAATACTGCTGCTGAAGTTGCTCTGAGGCTTGTAAGGCCAGGAAGAAAG                         AATAAGGATGTAACAGAAGCAATTCAGAAGGTTGCTGCTGCCTATGACTGC
genomic: CAAATACTGCTGCTGAAGTTGCTCTGAGGCTTGTAAGGCCAGGAAGAAAGgtaattccgt ... ataatggcagAATAAGGATGTAACAGAAGCAATTCAGAAGGTTGCTGCTGCCTATGACTGC
EST: gi|22007317|gb|BQ792351.1|BQ792351
EST:     CAAATACTGCTGCTGAAGTTGCTCTGAGGCTTGTAAGGCCAGGAAGAAAG                         AATAAGGATGTAACAGAAGCAATTCAGTAGGTTGCTGCTGCCTATGACTGC
genomic: CAAATACTGCTGCTGAAGTTGCTCTGAGGCTTGTAAGGCCAGGAAGAAAGgtaattccgt ... ataatggcagAATAAGGATGTAACAGAAGCAATTCAGAAGGTTGCTGCTGCCTATGACTGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccctgttcatttgattggtaaaaagctgagttgcagtctctctttataatggcagAATAAGGATGTAACAGAAGCAATTCAGAAGGTTGCTGCTGCCTATGACTGCAAAATTGTCGAAGGTGTACTCAGCCACCAGCTAAAGCAGTTTGTGATAG
        atttgat  putative branch site (score: 5)
                                    tctctctttat  putative PPT
                                        tctttataat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
attgtggttaatctttattattattgttggtgttgtttttatgtgccctgttcatttgattggtaaaaagctgagttgcagtctctctttataatggcagAATAAGGATGTAACAGAAGCAATTCAGAAGGTTGCTGCTGCCTATGACTGCAAAATTGTCGAAGGTGTACTCAGCCACCAGCTAAAGCAGTTTGTGATAG

-ttgtggt
- - - - - - - - - - - - -gttggtg
- - - - - - - - - - - - - - - - - - - -tatgtgc
- - - - - - - - - - - - - - - - - - - - - - - cctgttc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gtaaaaa