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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aaacatggattattctattatatgtacataatatattatttttcttgttcatctgactgtcactgattttttctctattcctttatgtgcaattgatcagAATTTGCAGGTTGATGAATTAAATTTAGCTGACATTGGTCCAAAATTTGAGCATCATGCTATGTTTCCTGCTCGAACTAATACAG

Basic information

species Vitis vinifera
transcript Vv08s0040g02540.t01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv08s0040g02540.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GRMZM2G130332_T03 (Zea mays), 3'ss of exon 5
aaacatggattatt-ctattatatgtacataatatattatttttcttgttcatctgactgtcactgattttttctctattcctttatgtgcaattgatcagAATTTGCAGGTTGATGAATTAAATTTAGCTGACATTGGTCCAAAATTTGAGCATCATGCTATGTTTCCTGCTCGAACTAATACAG
   |  |  | ||  | ||||   |    || |        ||      |||| ||| ||| |      |    |||| || |   ||  |   ||  ||||  |||||| | || || |||||  |    || ||||| || ||||||||||||||||  |||||||||||||| || || ||||
--gcccgactaatcgcgattaatcgcgattagtcggacgacttga--aatcat-tgattgtaatca---tagattctagtcttgactggactcctg--cagaccttgcagATCGACGATTTAAAACTCAGCGAAATTGGGCCTAAATTTGAGCATCATGAAATGTTTCCTGCTCGCACAAACACAG

upper sequence: Vv08s0040g02540.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: AC182617.3_FGT001 (Zea mays), 3'ss of exon 5
------aaacatg-gattattctattatatgtacataatatattatttttcttgttcatctgactgtcactgattttttctctattcctttatgtgcaattgatcagAATTTGCAGGTTGATGAATTAAATTTAGCTGACATTGGTCCAAAATTTGAGCATCATGCTATGTTTCCTGCTCGAACTAATACAG
      ||  ||| |  |  |  ||||||  |  || |  | | |       ||| ||| | | ||| ||     |    |||| || |   | | |   ||  |||   |||||||| || || |||||  |    || ||||| || ||||||||||||||||  |||||||||||||| || || ||||
tagttgaactatgtgcatgatgaattatacctttatca-gtctaaccaagggtgtccatat-attgtaacca---taaattctagtcttgactatactcctg--cagGTATTGCAGGTCGACGATTTAAAACTTAGCGAAATTGGGCCTAAATTTGAGCATCATGAAATGTTTCCTGCTCGCACAAACACAG

upper sequence: Vv08s0040g02540.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GRMZM2G130332_T04 (Zea mays), 3'ss of exon 5
aaacatggatta-ttctattatatgtacataatatattatttttcttgttcatctgactgtcactgatttt--ttctctattc---ctttatgtgcaattgatcagAATTTGCAGGTTGATGAATTAAATTTAGCTGACATTGGTCCAAAATTTGAGCATCATGCTATGTTTCCTGCTCGAACTAATACAG
    |  ||  |   | | ||   |    ||||     |||  ||  |  |  ||     ||| ||||| |  |  |  ||||     ||   || | |    ||||  |||||| | || || |||||  |    || ||||| || ||||||||||||||||  |||||||||||||| || || ||||
---taccgaccagcccgactaatcgcgattaat-cgcgattagtc--ggacgacttgaaatcattgattgtaatcatagattctagtcttgactggactcctgcagACCTTGCAGATCGACGATTTAAAACTCAGCGAAATTGGGCCTAAATTTGAGCATCATGAAATGTTTCCTGCTCGCACAAACACAG

upper sequence: Vv08s0040g02540.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA03G33080.1 (Glycine max), 3'ss of exon 5
-----aaacatggattattctattatatgtacataatatattatttttcttgttcatctgactgtcactgattttttctctattcctttatgtgcaattgatcagAATTTGCAGGTTGATGAATTAAATTTAGCTGACATTGGTCCAAAATTTGAGCATCATGCTATGTTTCCTGCTCGAACTAATACAG-------------
     |||     ||| || |  | |  ||  ||||  |   ||   | |    ||| |   ||   |  || |  | | | ||  || ||      |  | ||||||||||  ||||||||||| ||  |||| || ||||| ||||||||||| |||||||   |||| ||||| |||||||| ||||             
tgttaaaatgccaatttttat-ctgttggtcaataactttacatgaatttaa--catttttttgctgcatatatgatgtttgtt--ttaatccttgttgcaacagAATTTGCTTGTTGATGAATTGAAGCTAGCAGAAATTGGCCCAAAATTTGAACATCATGAGGTGTTCCCTGCACGAACTAACACAGGCAAGATTTGTTT

upper sequence: Vv08s0040g02540.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA19G35780.1 (Glycine max), 3'ss of exon 5
aaacatggattatt--ctattatatgtacataatatattatttttcttgttcatctgactgtcactgattttttctctattcctttatgtgcaattgatcagAATTTGCAGGTTGATGAATTAAATTTAGCTGACATTGGTCCAAAATTTGAGCATCATGCTATGTTTCCTGCTCGAACTAATACAG
| |  |  | | ||  || || ||         || |  | |||     ||  ||||  | || |||  | | ||    ||  ||||       |  | ||||||||||  ||||||||||| ||  |||| || ||||| ||||||||||| |||||||   |||| ||||| |||||||| ||||
acatgtcaacttttatctgttgtacagcaggtttacaccaatttaac-atttttctgcttttc-ctgcatatatcatgtttgttttaatcttgttgcaacagAATTTGCTTGTTGATGAATTGAAGCTAGCAGAAATTGGGCCAAAATTTGAACATCATGAGGTGTTCCCTGCACGAACTAACACAG

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|110423566|gb|EC989913.1|EC989913
EST:     TTTTGGAACAAAAGGAGGCCAG                         AATTTGCAGGTTGATGAATTAAATTTAGCTGACATTGGTCCAAAATTTGAG
genomic: TTTTGGAACAAAAGGAGGCCAGgtatggattt ... aattgatcagAATTTGCAGGTTGATGAATTAAATTTAGCTGACATTGGTCCAAAATTTGAG
EST: gi|110379227|gb|EC944409.1|EC944409
EST:     TTAGTATGGGAAATCCTCACTGTGTAACTTTTGGAACAAAAGGAGGCCAG                         AATTTGCAGGTTGATGAATTAAATTTAGCTGACATTGGTCCAAAATTTGAG
genomic: TTAGTATGGGAAATCCTCACTGTGTAACTTTTGGAACAAAAGGAGGCCAGgtatggattt ... aattgatcagAATTTGCAGGTTGATGAATTAAATTTAGCTGACATTGGTCCAAAATTTGAG
EST: gi|110363795|gb|EC927411.1|EC927411
EST:     TTAGTATGGGAAATCCTCACTGTGTAACTTTTGGAACAAAAGGAGGCCAG                         AATTTGCAGGTTGATGAATTAAATTTAGCTGACATTGGTCCAAAATTTGAG
genomic: TTAGTATGGGAAATCCTCACTGTGTAACTTTTGGAACAAAAGGAGGCCAGgtatggattt ... aattgatcagAATTTGCAGGTTGATGAATTAAATTTAGCTGACATTGGTCCAAAATTTGAG
EST: gi|34549331|gb|CF517563.1|CF517563
EST:     TTAGTATGGGAAATCCTCACTGTGTAACTTTTGGAACAAAAGGAGGCCAG                         AATTTGCAGGTTGATGAATTAAATTTAGCTGACATTGGTCCAAAATTTGAG
genomic: TTAGTATGGGAAATCCTCACTGTGTAACTTTTGGAACAAAAGGAGGCCAGgtatggattt ... aattgatcagAATTTGCAGGTTGATGAATTAAATTTAGCTGACATTGGTCCAAAATTTGAG
EST: gi|30131639|gb|CB916978.1|CB916978
EST:     TTAGTATGGGAAATCCTCACTGTGTAACTTTTGGAACAAAAGGAGGCCAG                         AATTTGCAGGTTGATGAATTAAATTTAGCTGACATTGGTCCAAAATTTGAG
genomic: TTAGTATGGGAAATCCTCACTGTGTAACTTTTGGAACAAAAGGAGGCCAGgtatggattt ... aattgatcagAATTTGCAGGTTGATGAATTAAATTTAGCTGACATTGGTCCAAAATTTGAG
EST: gi|32458996|gb|CD800170.1|CD800170
EST:     TTAGTATGGGAAATCCTCACTGTGTAACTTTTGGAACAAAAGGAGGCCAG                         AATTTGCAGGTTGATGAATTAAATTTAGCTGACATTGGTCCAAAATTTGAG
genomic: TTAGTATGGGAAATCCTCACTGTGTAACTTTTGGAACAAAAGGAGGCCAGgtatggattt ... aattgatcagAATTTGCAGGTTGATGAATTAAATTTAGCTGACATTGGTCCAAAATTTGAG
EST: gi|110382285|gb|EC939068.1|EC939068
EST:     TTAGTATGGGAAATCCTCACTGTGTAACTTTTGGAACAAAAGGAGGCCAG                         AATTTGCAGGTTGATGAATTAAATTTAGCTGACATTGGTCCAAAATTTGAG
genomic: TTAGTATGGGAAATCCTCACTGTGTAACTTTTGGAACAAAAGGAGGCCAGgtatggattt ... aattgatcagAATTTGCAGGTTGATGAATTAAATTTAGCTGACATTGGTCCAAAATTTGAG
EST: gi|110728275|gb|EE103711.1|EE103711
EST:     TTAGTATGGGAAATCCTCACTGTGTAACTTTTGGAACAAAAGGAGGCCAG                         AATTTGCAGGTTGATGAATTAAATTTAGCTGACATTGGTCCAAAATTTGAG
genomic: TTAGTATGGGAAATCCTCACTGTGTAACTTTTGGAACAAAAGGAGGCCAGgtatggattt ... aattgatcagAATTTGCAGGTTGATGAATTAAATTTAGCTGACATTGGTCCAAAATTTGAG
EST: gi|110717263|gb|EE092967.1|EE092967
EST:     TTAGTATGGGAAATCCTCACTGTGTAACTTTTGGAACAAAAGGAGGCCAG                         AATTTGCAGGTTGATGAATTAAATTTAGCTGACATTGGTCCAAAATTTGAG
genomic: TTAGTATGGGAAATCCTCACTGTGTAACTTTTGGAACAAAAGGAGGCCAGgtatggattt ... aattgatcagAATTTGCAGGTTGATGAATTAAATTTAGCTGACATTGGTCCAAAATTTGAG
EST: gi|110423955|gb|EC990308.1|EC990308
EST:     TTAGTATGGGAAATCCTCACTGTGTAACTTTTGGAACAAAAGGAGGCCAG                         AATTTGCAGGTTGATGAATTAAATTTAGCTGACATTGGTCCAAAATTTGAG
genomic: TTAGTATGGGAAATCCTCACTGTGTAACTTTTGGAACAAAAGGAGGCCAGgtatggattt ... aattgatcagAATTTGCAGGTTGATGAATTAAATTTAGCTGACATTGGTCCAAAATTTGAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgttcatctgactgtcactgattttttctctattcctttatgtgcaattgatcagAATTTGCAGGTTGATGAATTAAATTTAGCTGACATTGGTCCAAAATTTGAGCATCATGCTATGTTTCCTGCTCGAACTAATACAG
               cactgat  putative branch site (score: 3)
                    attttttctctatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aaacatggattattctattatatgtacataatatattatttttcttgttcatctgactgtcactgattttttctctattcctttatgtgcaattgatcagAATTTGCAGGTTGATGAATTAAATTTAGCTGACATTGGTCCAAAATTTGAGCATCATGCTATGTTTCCTGCTCGAACTAATACAG

- -catggat
- - - - - - - - - - tatgtac
- - - - - - - - - - - - - - - - - - - - - - - - - - -tgactgt