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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tatttagagcatcgtttacttaccaaaagtaaataattttaaatactatatttactctcacaaactctaaaatgattacctttgttcccatcatttgcagAATTTTCTTGTGGACATCAAAGGACCTGCATTGGCATTTCTGCCTGTGCTTGCATTTGAAGGAGGAACAAGGAGAAATATACCCAAGTTTGAG

Basic information

species Vitis vinifera
transcript Vv17s0000g08490.t01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv17s0000g08490.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM2G540589_T01 (Zea mays), 3'ss of exon 3
---tatttagagcatcgtttacttaccaaaagtaaataattttaaata-ctatatttactctcacaaactctaaaatgattacctttgttcccatcatttgcagAATTTTCTTGTGGACATCAAAGGACCTGCATTGGCATTTCTGCCTGTGCTTGCATTTGAAGGAGGAACAAGGAGAAATATACCCAAGTTTGAG
      ||   | |     ||  ||      ||   | || |||||||  | | |||   ||   |     |    |   |    | | |  | | |||  ||||| ||| | || ||||| || || |||   ||| | || || || ||||||||||||||||| || ||||||||||| ||||| |||||||||
atgggcttttggtagaaactagatattt---gttttttatgttaaataattgtttttttcctgtgatgtgttttctttgctgaaatagctttcgttatt-acagAACTTTTTGGTAGACATAAAGGGTCCTAATTTGCCCTTCCTACCGGTGCTTGCATTTGAAGGTGGTACAAGGAGAAACATACCAAAGTTTGAG

upper sequence: Vv17s0000g08490.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM2G173989_T01 (Zea mays), 3'ss of exon 5
------------tatttagagcatcgtttacttaccaaaagtaaataattt-taaatactatatttactctcacaaactctaaaatgattacctttgttcccatcatttgcagAATTTTCTTGTGGACATCAAAGGACCTGCATTGGCATTTCTGCCTGTGCTTGCATTTGAAGGAGGAACAAGGAGAAATATACCCAAGTTTGAG
             |  ||||  |  ||||   |   ||  |||  |    | | |  |    || || | ||      ||| ||||   |   || |||        || ||||| ||| | || ||||| || || |||   ||||| ||||| || || ||| |||||||||| || ||||||||||| ||||||||||| |||
gggctttgcaagaagctagacgactgtttttatgttaattgtattttgcctgtgatcatgcgatgtattttctt---ttctgaaatagct---ttggtta-------ttacagAACTTTTTGGTAGACATAAAGGGTCCTAATTTGGCCTTTCTACCAGTACTTTCATTTGAAGGCGGTACAAGGAGAAACATACCCAAGTTCGAG

upper sequence: Vv17s0000g08490.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM5G802854_T01 (Zea mays), 3'ss of exon 5
tatttagagcatcgtttacttaccaaaagtaaataattttaaatactatatttactctcacaaactctaaaatgattaccttt--------gttcccatcatttgcagAATTTTCTTGTGGACATCAAAGGACCTGCATTGGCATTTCTGCCTGTGCTTGCATTTGAAGGAGGAACAAGGAGAAATATACCCAAGTTTGAG
      | || | | | |    | | | |    |  || |    | | |||||   ||   |   |  ||  |  || | |||        | |    | |||  ||||| ||| | || ||||| || || |||   ||||| ||||| || || ||| |||||||||| || ||||||||||| |||||||||||  ||
------gggctttgct-agaagctagatgactgtttttatgttaattgtattttgcctgcgatcatgcaatgtattttcttttctgaaatagctttggttatt-acagAACTTTTTGGTAGACATAAAGGGTCCTAATTTGGCCTTTCTACCAGTACTTTCATTTGAAGGCGGTACAAGGAGAAACATACCCAAGTTCAAG

upper sequence: Vv17s0000g08490.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA01G06540.1 (Glycine max), 3'ss of exon 6
tatttagagcatcgtttacttacc-aaaagtaaataattttaaatactatatttactctcacaaactctaaaatgattacctttgttcccatcatttgcagAATTTTCTTGTGGACATCAAAGGACCTGCATTGGCATTTCTGCCTGTGCTTGCATTTGAAGGAGGAACAAGGAGAAATATACCCAAGTTTGAG
  | ||     |  |||| || |   ||| ||| |||  |    | ||    |  ||||       ||||  || |  | ||   ||     | | ||||||| |||||||||||||| ||||||||  | || |||||| | || ||||||||||||||||||||||| || ||||||||||| | |||||||
gttgtacttttttttttaatttcttgaaaataattaaaatgtgtttcttacctagctctgtgtgtttctatgataaaaatctcaatttattgc-tgtgcagAACTTTCTTGTGGACATAAAAGGACCAACTTTAGCATTTTTACCGGTGCTTGCATTTGAAGGAGGAACTAGAAGAAATATACCTAGGTTTGAG

upper sequence: Vv17s0000g08490.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA02G12480.1 (Glycine max), 3'ss of exon 5
---tatttagagcatcgtttacttaccaaaagtaaataattttaaatactatatttactctcacaaactctaaaatgattacctttgttcccatcatttgcagAATTTTCTTGTGGACATCAAAGGACCTGCATTGGCATTTCTGCCTGTGCTTGCATTTGAAGGAGGAACAAGGAGAAATATACCCAAGTTTGAG
    || |   | |   |||  |     ||| ||| ||| |||   |    ||  ||             |   ||| | | ||   ||     | | ||||||| |||||||| ||||| ||||| || || || |||||| | || ||||||||||||||||||||||| || ||||||||||| | |||||||
tgtcatctgttgtactttttcttagttgaaaataattaaatttg--tttcttacctagctctgggtttctttctatggtaatctcaatttattgc-tgtgcagAACTTTCTTGTTGACATAAAAGGGCCAGCTTTAGCATTTTTACCAGTGCTTGCATTTGAAGGAGGAACTAGAAGAAATATACCTAGGTTTGAG

upper sequence: Vv17s0000g08490.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: AT4G32175.1 (Arabidopsis thaliana), 3'ss of exon 4
tatttagagcatcgtttacttaccaaaagtaaataattttaaat--actatatttactctcacaaactctaaaatgattacctttgttcccatcat-ttgcagAATTTTCTTGTGGACATCAAAGGACCTGCATTGGCATTTCTGCCTGTGCTTGCATTTGAAGGAGGAACAAGGAGAAATATACCCAAGTTTGAG
   ||      |   |||    |   |  |||    | ||  ||  ||||   |  |  |   ||   || || || ||   ||  |   |||    ||||||||||||   |||||||| |||||||||  ||| ||| || |||| || |||||||| |||||||||||| | |||||||| ||||||||||||
---ttgacttttaaattatcagctgcagttaagctttcttgcatgaactaacatcgccttagtaagtactgaattgtttcttttactcatcatgtcattgcagAATTTTTGGGTGGACATTAAAGGACCTCAATTAGCACTTTTGCCAGTTCTTGCATTCGAAGGAGGAACACGAAGAAATATTCCCAAGTTTGAG

upper sequence: Vv17s0000g08490.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: AT2G25355.2 (Arabidopsis thaliana), 3'ss of exon 4
tatttagagcatcgt---ttacttaccaaaagtaaataattttaaatactatatttactctcacaaactctaaaatgattacctttgttcccatcat-ttgcagAATTTTCTTGTGGACATCAAAGGACCTGCATTGGCATTTCTGCCTGTGCTTGCATTTGAAGGAGGAACAAGGAGAAATATACCCAAGTTTGAG
   ||||||  | |    |    | |  |    || | || ||  ||   | |       ||| ||  | |  ||  ||    ||    |   |    |||||||| | |    | ||||| ||||||||   ||||||  || |||||||||||||||||||||||| ||  || ||||||   ||||||||||||
---ttagagtgttgcccctagagttctcagccaaagtcatgttgcatgtaacaaagtagatcataatattttgaa-aatcgttttgacacatgtttcattgcagAACTATTGGATAGACATTAAAGGACCACAATTGGCTCTTTTGCCTGTGCTTGCATTTGAAGGAGCAAACAGAAGAAATTATCCCAAGTTTGAG

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|110419697|gb|EC985945.1|EC985945
EST:     CATGCGTGGAGGATACTGTTCTTGGAATTGTGGTAGATTCTAAAGCAGAT                         AATTTTCTTGTGGACATCAAAGGACCTGCATTGGCATTTCTGCCTGTGCTT
genomic: CATGCGTGGAGGATACTGTTCTTGGAATTGTGGTAGATTCTAAAGCAGATgtaagcactt ... tcatttgcagAATTTTCTTGTGGACATCAAAGGACCTGCATTGGCATTTCTGCCTGTGCTT
EST: gi|27755420|gb|CB036175.1|CB036175
EST:     CATGCGTGGAGGATACTGTTCTTGGAATTGTGGTAGATTCTAAAGCAGAT                         AATTTTCTTGTGGACATCAAAGGACCTGCATTGGCATTTCTGCCTGTGCTT
genomic: CATGCGTGGAGGATACTGTTCTTGGAATTGTGGTAGATTCTAAAGCAGATgtaagcactt ... tcatttgcagAATTTTCTTGTGGACATCAAAGGACCTGCATTGGCATTTCTGCCTGTGCTT
EST: gi|34550415|gb|CF518633.1|CF518633
EST:     CATGCGTGGAGGATACTGTTCTTGGAATTGTGGTAGATTCTAAAGCAGAT                         AATTTTCTTGTGGACATCAAAGGACCTGCATTGGCATTTCTGCCTGTGCTT
genomic: CATGCGTGGAGGATACTGTTCTTGGAATTGTGGTAGATTCTAAAGCAGATgtaagcactt ... tcatttgcagAATTTTCTTGTGGACATCAAAGGACCTGCATTGGCATTTCTGCCTGTGCTT
EST: gi|22015330|gb|BQ800364.1|BQ800364
EST:     TGGAATTG-GGTAGATT-TAAAGCAGAT                         AA-TTTCTTGTGGACATCAAAGGACCTGCA-TGGCA-TTCTGCCTGTGCTT
genomic: TGGAATTGTGGTAGATTCTAAAGCAGATgtaagcactt ... tcatttgcagAATTTTCTTGTGGACATCAAAGGACCTGCATTGGCATTTCTGCCTGTGCTT
EST: gi|110408373|gb|EC974008.1|EC974008
EST:     ATGCGTGGAAGATACTGTTC-TGGAAATTGTGGTAGATTCTAAAGCAGAT                         AATTTTCTTGTGGACATCAAAGGACCTGCATTGGCATTTCTGCCTGTGCTT
genomic: ATGCGTGGAGGATACTGTTCTTGG-AATTGTGGTAGATTCTAAAGCAGATgtaagcactt ... tcatttgcagAATTTTCTTGTGGACATCAAAGGACCTGCATTGGCATTTCTGCCTGTGCTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctatatttactctcacaaactctaaaatgattacctttgttcccatcatttgcagAATTTTCTTGTGGACATCAAAGGACCTGCATTGGCATTTCTGCCTGTGCTTGCATTTGAAGGAGGAACAAGGAGAAATATACCCAAGTTTGAG
                   ctctaaa  putative branch site (score: 3)
                                 cctttgttcccatc  putative PPT
                      taaaatgatta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tatttagagcatcgtttacttaccaaaagtaaataattttaaatactatatttactctcacaaactctaaaatgattacctttgttcccatcatttgcagAATTTTCTTGTGGACATCAAAGGACCTGCATTGGCATTTCTGCCTGTGCTTGCATTTGAAGGAGGAACAAGGAGAAATATACCCAAGTTTGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - taccaaa
- - - - - - - - - - - - - - - aaataat
- - - - - - - - - - - - - - - - - - - - - - - - - - - ctctcac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaaatga