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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gaatagttcctggtgataagtgataaacccattctcttatttgcattattgagttaacaagtctgtgtcatgatcaagatgtgttgccttctctgtgcagCTTATACTGGAAAATCAAGTATGTCAGCCGCCTGCAGTACCTTTGGGAAGATGTAAAGAAGGGAGAGGTCGAGATTCCTGAATTTGTGCAAAGCCATGAT

Basic information

species Vitis vinifera
transcript Vv08s0007g05700.t01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv08s0007g05700.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA19G31200.1 (Glycine max), 3'ss of exon 2
gaatagttcctgg--tgataagtgataaacccattctcttatttgcattattgagttaacaagtctgtgtcatgatcaagatg-tgttgccttctctgtgcagCTTATACTGGAAAATCAAGTATGTCAGCCGCCTGCAGTACCTTTGGGAAGATGTAAAGAAGGGAGAGGTCGAGATTCCTGAATTTGTGCAAAGCCATGAT
 || |  | ||    || |      |  ||||||| | | | ||     ||  | |   |   | ||| |  || |     || ||     || |  ||  || ||||| ||||| ||||||||||| ||||| || |||||||||||||| ||| ||||||| |||||| | ||||| || || |||||  |||| ||||||
-aacatgtgctaaattggttgacagttgacccattgtatcactttttacatataatc--cctttttgttttttggtttgcttgctgacttgttgttggtttagATTATATTGGAAGATCAAGTATGTAAGCCGGCTTCAGTACCTTTGGGATGATATAAAGAAAGGAGAGATTGAGATACCAGATTTTGTTAAAAGTCATGAT

upper sequence: Vv08s0007g05700.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA03G28460.2 (Glycine max), 3'ss of exon 3
gaatagttcctggtgataagtgataaacccattctcttatttgcattattgagttaacaagtc-tgtgtcatgatcaagatgtgttgccttctctgtg----cagCTTATACTGGAAAATCAAGTATGTCAGCCGCCTGCAGTACCTTTGGGAAGATGTAAAGAAGGGAGAGGTCGAGATTCCTGAATTTGTGCAAAGCCATGAT
    | | |   || | | | | ||||     |  |  | |||    ||||  | |     |      | ||  |   | | ||||| |||   |||      || ||||| ||||| ||||||||||| ||||| || |||||||||||||| ||  ||||||| |||||| | ||||| || || |||||| |||| ||||||
---caatacaaagtaacatgcgctaaattggctgac--aattgacccattgtatcacttttttgcacttaatcctttgggtttgttgactttgttgttggtttagATTATATTGGAAGATCAAGTATGTAAGCCGGCTTCAGTACCTTTGGGATGACATAAAGAAAGGAGAGATTGAGATACCGGATTTTGTGAAAAGTCATGAT
















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|294965821|gb|GW837304.1|GW837304
EST:     CGTTCAAGGCTTCTCTTTGCCACTCTTGGACGATTCTTCTTAAGTGGAGG                         CTTATACTGGA
genomic: CGTTCAAGGCTTCTCTTTGCCACTCTTGGACGATTCTTCTTAAGTGGAGGgtgagtagtt ... ctctgtgcagCTTATACTGGA
EST: gi|30252080|gb|CB968719.1|CB968719
EST:     CGTTCAAGGCTTCTCTTTGCCACTCTTGGACGATTCTTCTTAAGTGGAGG                         CTTATACTGGAAAATCAAGTATGTTAGCCGCCTGCAGTACCTTTGGGAAGA
genomic: CGTTCAAGGCTTCTCTTTGCCACTCTTGGACGATTCTTCTTAAGTGGAGGgtgagtagtt ... ctctgtgcagCTTATACTGGAAAATCAAGTATGTCAGCCGCCTGCAGTACCTTTGGGAAGA
EST: gi|110428334|gb|EC994803.1|EC994803
EST:     CGTTCAAGGCTTCTCTTTGCCACTCTTGGACGATTCTTCTTAAGTGGAGG                         CTTATACTGGAAAATCAAGTATGTTAGCCGCCTGCAGTACCTTTGGGAAGA
genomic: CGTTCAAGGCTTCTCTTTGCCACTCTTGGACGATTCTTCTTAAGTGGAGGgtgagtagtt ... ctctgtgcagCTTATACTGGAAAATCAAGTATGTCAGCCGCCTGCAGTACCTTTGGGAAGA
EST: gi|71882792|gb|DT031847.1|DT031847
EST:     CGTTCAAGGCTTCTCTTTGCCACTCTTGGACGATTCTTCTTAAGTGGAGG                         CTTATACTGGAAAATCAAGTATGTTAGCCGCCTGCAGTACCTTTGGGAAGA
genomic: CGTTCAAGGCTTCTCTTTGCCACTCTTGGACGATTCTTCTTAAGTGGAGGgtgagtagtt ... ctctgtgcagCTTATACTGGAAAATCAAGTATGTCAGCCGCCTGCAGTACCTTTGGGAAGA
EST: gi|30252166|gb|CB969717.1|CB969717
EST:     CGTTCAAGGCTTCTCTTTGCCACTCTTGGACGATTCTTCTTAAGTGGAGG                         CTTATACTGGAAAATCAAGTATGTTAGCCCCCTGCAGTACCTTTGGGAAGA
genomic: CGTTCAAGGCTTCTCTTTGCCACTCTTGGACGATTCTTCTTAAGTGGAGGgtgagtagtt ... ctctgtgcagCTTATACTGGAAAATCAAGTATGTCAGCCGCCTGCAGTACCTTTGGGAAGA
EST: gi|22012593|gb|BQ797627.1|BQ797627
EST:     CGTTCAAGGCTTCTCTTTGCCACTCTTGGACGATTCTTCTTAAGTGGAGG                         CTTATACTGGAAAATCAAGTATGTCAGCCGCCTGCAGTACCTTTGGGAAGA
genomic: CGTTCAAGGCTTCTCTTTGCCACTCTTGGACGATTCTTCTTAAGTGGAGGgtgagtagtt ... ctctgtgcagCTTATACTGGAAAATCAAGTATGTCAGCCGCCTGCAGTACCTTTGGGAAGA
EST: gi|349825796|gb|FQ423091.1|FQ423091
EST:     CGTTCAAGGCTTCTCTTTGCCACTCTTGGACGATTCTTCTTAAGTGGAGG                         CTTATACTGGAAAATCAAGTATGTCAGCCGCCTGCAGTACCTTTGGGAAGA
genomic: CGTTCAAGGCTTCTCTTTGCCACTCTTGGACGATTCTTCTTAAGTGGAGGgtgagtagtt ... ctctgtgcagCTTATACTGGAAAATCAAGTATGTCAGCCGCCTGCAGTACCTTTGGGAAGA
EST: gi|77582450|gb|DV220202.1|DV220202
EST:     CGTTCAAGGCTTCTCTTTGCCACTCTTGGACGATTCTTCTTAAGTGGAGG                         CTTATACTGGAAAATCAAGTATGTTAGCCGCCTGCAGTACCTTTGGGAAGA
genomic: CGTTCAAGGCTTCTCTTTGCCACTCTTGGACGATTCTTCTTAAGTGGAGGgtgagtagtt ... ctctgtgcagCTTATACTGGAAAATCAAGTATGTCAGCCGCCTGCAGTACCTTTGGGAAGA
EST: gi|30329703|gb|CD012965.1|CD012965
EST:     CGTTCAAGGCTTCTCTTTGCCACTCTTGGACGATTCTTCTTAAGTGGAGG                         CTTATACTGGAAAATCAAGTATGTCAGCCGCCTGCAGTACCTTTGGGAAGA
genomic: CGTTCAAGGCTTCTCTTTGCCACTCTTGGACGATTCTTCTTAAGTGGAGGgtgagtagtt ... ctctgtgcagCTTATACTGGAAAATCAAGTATGTCAGCCGCCTGCAGTACCTTTGGGAAGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttattgagttaacaagtctgtgtcatgatcaagatgtgttgccttctctgtgcagCTTATACTGGAAAATCAAGTATGTCAGCCGCCTGCAGTACCTTTGGGAAGATGTAAAGAAGGGAGAGGTCGAGATTCCTGAATTTGTGCAAAGCCATGAT
      agttaac  putative branch site (score: 3)
                                      ttgccttctct  putative PPT
        ttaacaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gaatagttcctggtgataagtgataaacccattctcttatttgcattattgagttaacaagtctgtgtcatgatcaagatgtgttgccttctctgtgcagCTTATACTGGAAAATCAAGTATGTCAGCCGCCTGCAGTACCTTTGGGAAGATGTAAAGAAGGGAGAGGTCGAGATTCCTGAATTTGTGCAAAGCCATGAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAAG
- - - ttcctgg
- - - - - - - - - - - - aaaccca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - catgatc