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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tttttcgtagatttctgatgatcctttgatatttgggagttcctttcagatagattctcttcatattcttattgtgctgatgaaaaatgtacttgtccagCAACTGGTAATATACGAGACATCTGCTTCAGAATTGGATATAATTCGAGATATTTCTCGTACCTTCCCATCACATGTTTTCTTCCAGCAGAGACATGGAC

Basic information

species Vitis vinifera
transcript Vv14s0083g00540.t01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv14s0083g00540.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: LOC_Os08g31840.2 (Oryza sativa), 3'ss of exon 3
--------------------------------------------------------------------tttttcgtagatttc-tgatgatcctttgat-atttgggagttcctttcagatagattc---tcttcatattcttattgtgctgatgaaaaatgtacttgtccagCAACTGGTAATATACGAGACATCTGCTTCAGAATTGGATATAATTCGAGATATTTCTCGTACCTTCCCATCACATGTTTTCTTCCAGCAGAGACATGGAC
                                                                     |||  || |  ||  |  | ||   |  || ||  ||   ||   || |||   || |   ||||   |   |||||    |  |  |  || |  |||  |||  |||||| ||||||||||||||||| ||||||||||| |||||||| || || || ||||| || ||||||||| |||||||||| ||||||||||| |
gtacctataacaattgtgaaagaactgcttgccctgatttttgttgaatgttccctattattttttaactttctgttgtcttagtagttatttctaaattatcaggatattgtcttaagagtcatacatatcttgtcaacattattacatttctatactattt-tttggacagACACTGGTCATATACGAGACATCTGCATCAGAATTGGAAATAATTCGTGACATATCACGTACTTTTCCATCACATATTTTCTTCCAACAGAGACATGGTC

upper sequence: Vv14s0083g00540.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA13G07090.1 (Glycine max), 3'ss of exon 2
tttttcgtagatttctgatg-atcctttgatatt-tgggagttcctttcagatagattctcttcatattcttat-tgtgctgatgaaa-aatgtacttgtc-cagCAACTGGTAATATACGAGACATCTGCTTCAGAATTGGATATAATTCGAGATATTTCTCGTACCTTCCCATCACATGTTTTCTTCCAGCAGAGACATGGAC
      |  | || ||  |  |   ||||| ||| |    | |  |   |      |  ||  | | ||    | ||   |||  | | | | ||| | |  |||||||| || ||||||||||||||||| || ||| ||||||||||||||||||||||||| |||||||| |||||||| |||||||| |||||||||||||
-----tgaggtttcctcctttactttttgaaattatcttgggttttaataccctactattccacgttttggagtctgcattgacaagacattatacctattgcagCAACTAGTCATATACGAGACATCTGCCTCTGAACTGGATATAATTCGAGATATTTCTCGAACCTTCCCTTCACATGTATTCTTCCAACAGAGACATGGAC

upper sequence: Vv14s0083g00540.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA19G05360.1 (Glycine max), 3'ss of exon 3
-------tttttcgtagatttctgatgatcctttgatatttgggagttcctttcagatagattctcttcatattcttattgtgctgatgaaaaatgtacttgtc-cagCAACTGGTAATATACGAGACATCTGCTTCAGAATTGGATATAATTCGAGATATTTCTCGTACCTTCCCATCACATGTTTTCTTCCAGCAGAGACATGGAC
       |  | | |   ||| |||   |   ||||  |||   | | || | | | |  ||  | |  |  ||   ||||      |  | | | ||| | |  |||||||| || ||||| ||||||||||| || ||| ||||||||||||||||||||||||| |||||||| |||||||| ||||| || |||||||||||||
tgaggtttcctcctttactttttgaaattatcttgaggttt---actaccctactgttccatgttttgga-gtttgcattg----actagacattatacctattgcagCAACTAGTCATATATGAGACATCTGCCTCTGAACTGGATATAATTCGAGATATTTCTCGAACCTTCCCTTCACATGTATTCTTTCAACAGAGACATGGAC

upper sequence: Vv14s0083g00540.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: AT5G15930.1 (Arabidopsis thaliana), 3'ss of exon 3
tttttcgtagatttctgatgatcctttgatatttgggagttcctttcagatagattctcttcatattcttattgtgctgatgaaaaatgtactt---gtccagCAACTGGTAATATACGAGACATCTGCTTCAGAATTGGATATAATTCGAGATATTTCTCGTACCTTCCCATCACATGTTTTCTTCCAGCAGAGACATGGAC
    |  ||  ||  |     |||||   | ||| |   ||| |||    | | |||  | |        |     || |  |         ||    |  |||||||||| || || ||||| || || |||||| | ||||| ||||| ||||| |||||||| ||||| |||||||||||||||||| ||||||||||||
---gtaataacttattatc--tccttgtgtgttttgttattcattttctttggcttcattgctggaaagaaaaaaacttacaattctctcgatttcattatagCAACTGGTGATTTATGAGACGTCGGCATCAGAACTCGATATCATTCGGGATATATCTCGTACTTTCCCGTCACATGTTTTCTTCCAGAAGAGACATGGAC

upper sequence: Vv14s0083g00540.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: AT3G02460.1 (Arabidopsis thaliana), 3'ss of exon 3
tttttcgtagatttctgatgatcctttgatatttgggagttcctttcagatagattctcttcatattcttattgtgctgatg-aaaaatgtacttgtccagCAACTGGTAATATACGAGACATCTGCTTCAGAATTGGATATAATTCGAGATATTTCTCGTACCTTCCCATCACATGTTTTCTTCCAGCAGAGACATGGAC
                  | ||| || |   |||      |    | | || | ||||  ||  | || |||| || | ||  |   || | | | |  ||||| |||| || || || |||||||| |||||  | ||||| |||||||| || || ||||| |||||||||||||||||||| ||| ||||||||||||
-----------------gtaatc-ttcgccgttta-----tatccttacattgtttcttctctgagtcatattctgatcatctatcgattttcctatgaagCAATTGGTGATTTATGAAACATCTGCATCAGAGCTTGATATCATTCGAGACATATCCCGTACTTTCCCATCACATGTTTTCTTTCAGAAGAGACATGGAC

upper sequence: Vv14s0083g00540.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: PP1S263_22V6.1 (Physcomitrella patens), 3'ss of exon 3
tttttcgtagatttctgatgatc-ctttgatatttgggagttcctttcagatagattctcttcat-attcttattgtgctgatgaaaaatg--tacttgtccagCAACTGGTAATATACGAGACATCTGCTTCAGAATTGGATATAATTCGAGATATTTCTCGTACCTTCCCATCACATGTTTTCTTCCAGCAGAGACATGGAC
   || ||    | |||| | |  |  ||   |  ||  |   |||| | |   |     |  || |  |   ||||| | |  |  |     |   | | |||||| ||||  | || || || |||||| ||||| ||||||||||  |||| || ||  | || |||||||| ||||||||||||||||| |||||||| |
-catttgtg---tcctgaagtttacaatggggtacggaggaatctttgaaaacaacgtcatggatgacacggcttgtgttcacaagtatctcttggatttgcagCAATTGGTGCTTTATGAAACTTCTGCTGCAGAACTGGATATAATAAGAGACATCTCGAGAACTTTCCCATCGCATGTTTTCTTCCAGCAAAGACATGGGC

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|161719620|gb|FC067048.1|FC067048
EST:     TGATCTCAGGAAGTCGTGACCTCTTGCTGATGAACCCTGGAGTTTATGAG                         CAACTGGTAATATACGAGACATCTGCTTCAGAATTGGATATAATTCGAGAT
genomic: TGATCTCAGGAAGTCGTGACCTCTTGCTGATGAACCCTGGAGTTTATGAGgtataccttt ... acttgtccagCAACTGGTAATATACGAGACATCTGCTTCAGAATTGGATATAATTCGAGAT
EST: gi|349829177|gb|FQ419687.1|FQ419687
EST:     TGATCTCAGGAAGTCGTGACCTCTTGCTGATGAACCCTGGAGTTTATGAG                         CAACTGGTAATGTACGAGACATCTGCTTCAGAATTGGATATAATTCGAGAT
genomic: TGATCTCAGGAAGTCGTGACCTCTTGCTGATGAACCCTGGAGTTTATGAGgtataccttt ... acttgtccagCAACTGGTAATATACGAGACATCTGCTTCAGAATTGGATATAATTCGAGAT
EST: gi|351012823|gb|FQ430386.1|FQ430386
EST:     TGATCTCAGGAAGTCGTGACCTCTTGCTGATGAACCCTGGAGTTTATGAG                         CAACTGGTAATGTACGAGACATCTGCTTCAGAATTGGATATAATTCGAGAT
genomic: TGATCTCAGGAAGTCGTGACCTCTTGCTGATGAACCCTGGAGTTTATGAGgtataccttt ... acttgtccagCAACTGGTAATATACGAGACATCTGCTTCAGAATTGGATATAATTCGAGAT
EST: gi|349827061|gb|FQ421334.1|FQ421334
EST:     TGATCTCAGGAAGTCGTGACCTCTTGCTGATGAACCCTGGAGTTTATGAG                         CAACTGGTAATGTACGAGACATCTGCTTCAGAATTGGATATAATTCGAGAT
genomic: TGATCTCAGGAAGTCGTGACCTCTTGCTGATGAACCCTGGAGTTTATGAGgtataccttt ... acttgtccagCAACTGGTAATATACGAGACATCTGCTTCAGAATTGGATATAATTCGAGAT
EST: gi|349829128|gb|FQ419660.1|FQ419660
EST:     TGATCTCAGGAAGTCGTGACCTCTTGCTGATGAACCCTGGAGTTTATGAG                         CAACTGGTAATGTACGAGACATCTGCTTCAGAATTGGATATAATTCGAGAT
genomic: TGATCTCAGGAAGTCGTGACCTCTTGCTGATGAACCCTGGAGTTTATGAGgtataccttt ... acttgtccagCAACTGGTAATATACGAGACATCTGCTTCAGAATTGGATATAATTCGAGAT
EST: gi|351038918|gb|FQ457593.1|FQ457593
EST:     TGATCTCAGGAAGTCGTGACCTCTTGCTGATGAACCCTGGAGTTTATGAG                         CAACTGGTAATGTACGAGACATCTGCTTCACAATTGGATATAATTCGAGAT
genomic: TGATCTCAGGAAGTCGTGACCTCTTGCTGATGAACCCTGGAGTTTATGAGgtataccttt ... acttgtccagCAACTGGTAATATACGAGACATCTGCTTCAGAATTGGATATAATTCGAGAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcagatagattctcttcatattcttattgtgctgatgaaaaatgtacttgtccagCAACTGGTAATATACGAGACATCTGCTTCAGAATTGGATATAATTCGAGATATTTCTCGTACCTTCCCATCACATGTTTTCTTCCAGCAGAGACATGGAC
                             tgctgat  putative branch site (score: 3)
                                              cttgtcc  putative PPT
              ttcatattcttatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tttttcgtagatttctgatgatcctttgatatttgggagttcctttcagatagattctcttcatattcttattgtgctgatgaaaaatgtacttgtccagCAACTGGTAATATACGAGACATCTGCTTCAGAATTGGATATAATTCGAGATATTTCTCGTACCTTCCCATCACATGTTTTCTTCCAGCAGAGACATGGAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CATGGA
- - - - - - - ctgatga
- - - - - - - - - - - - - - - - - - - - -cctttca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gtgctga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgaaaaa