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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cttttactgatatcatgtttggtcaagtgtgcctagttgcacttgtatattgttttgtgaattcttgattgatctaacttaaaattgtcgatgactgtagATTCTATGCTGCAGAGGTAGTTGTTGCATTGGAGTACCTTCACTGTCAAG

Basic information

species Vitis vinifera
transcript Vv06s0004g03700.t01
intron # 16
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv06s0004g03700.t01 (Vitis vinifera), 3'ss of exon 16
lower sequence: GLYMA12G07890.2 (Glycine max), 3'ss of exon 17
cttttactgatatcatgtttggtcaagtgtgcctagttgcacttgtatattgttttgtgaattcttgattgatctaacttaaaattgtcgatgactgtagATTCTATGCTGCAGAGGTAGTTGTTGCATTGGAGTACCTTCACTGTCAAG
 | |  |   ||| |     | | |    |    |   |   | ||   | || ||        ||  || | || || |||  |  | ||| |   |||||| ||||| || || ||||||||||| |||||||| ||||| |||||||
atatacccactattaaagcagatgatccttcttcaacagtgttagttactagtgtttctctcctttcctttagctgacataatgtgcttgataataatagATTTTATGCCGCTGAAGTAGTTGTTGCGTTGGAGTATCTTCATTGTCAAG

upper sequence: Vv06s0004g03700.t01 (Vitis vinifera), 3'ss of exon 16
lower sequence: GLYMA15G04850.1 (Glycine max), 3'ss of exon 16
-cttttactgata--tcatgtttggtcaagtgtgcctagttgcacttgtatattgttttgtgaattcttgattgatctaacttaaaattgtcgatgactgtagATTCTATGCTGCAGAGGTAGTTGTTGCATTGGAGTACCTTCACTGTCAAG
  | ||    ||   |  ||  || | || |  |  ||  | | |  ||| ||  |      | |  |   ||   || || | || || |  ||   | |||||| ||||| || ||||||||  | ||||||||||||||||| |||||||
tttgttggaaatgatttttgcatgttaaaataaggttatctaccccagta-ataataacactattattctttta--ctgacattaagttcttaatatttatagATTTTATGCAGCTGAGGTAGTGATCGCATTGGAGTACCTTCATTGTCAAG
















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|30324849|gb|CD008111.1|CD008111
EST:     CTGCTTTTGGACAGGCAACCCACAAAAGTCCTGAAGGAAGATGCTGTGAG                         ATTCTATGCTGCAGAGGTAGTTGTTGCATTGGAGTACCTTCACTGTCAAG
genomic: CTGCTTTTGGACAGGCAACCCACAAAAGTCTTGAAGGAAGATGCTGTGAGgtatgcatgt ... atgactgtagATTCTATGCTGCAGAGGTAGTTGTTGCATTGGAGTACCTTCACTGTCAAG
EST: gi|32267450|gb|CD716413.1|CD716413
EST:     CTGCTTTTGGACAGGCAACCCACAAAAGTCCTGAAGGAAGATGCTGTGAG                         ATTCTATGCTGCAGAGGTAGTTGTTGCATTGGAGTACCTTCACTGTCAAG
genomic: CTGCTTTTGGACAGGCAACCCACAAAAGTCTTGAAGGAAGATGCTGTGAGgtatgcatgt ... atgactgtagATTCTATGCTGCAGAGGTAGTTGTTGCATTGGAGTACCTTCACTGTCAAG
EST: gi|30325883|gb|CD009145.1|CD009145
EST:     CTGCTTTTGGACAGGCAACCCACAAAAGTCCTGAAGGAAGATGCTGTGAG                         ATTCTATGCTGCAGAGGTAGTTGTTGCATT
genomic: CTGCTTTTGGACAGGCAACCCACAAAAGTCTTGAAGGAAGATGCTGTGAGgtatgcatgt ... atgactgtagATTCTATGCTGCAGAGGTAGTTGTTGCATT
EST: gi|351036173|gb|FQ464018.1|FQ464018
EST:     CTGCTTTTGGACAGGCAACCCACAAAAGTCCTGAAGGAAGATGCTGTGAG                         ATTCTATGCTGCACAGGTAGTTGTTGCATTGGAGTACCTTCACTGTCAAG
genomic: CTGCTTTTGGACAGGCAACCCACAAAAGTCTTGAAGGAAGATGCTGTGAGgtatgcatgt ... atgactgtagATTCTATGCTGCAGAGGTAGTTGTTGCATTGGAGTACCTTCACTGTCAAG
EST: gi|30325043|gb|CD008305.1|CD008305
EST:     CTGCTTTTGGACAGGCAACCCACAAAAGTCCTGAAGGAAGATGCTGTGAG                         ATTCTATGCTGCAGAGGTAGTTGTTGCATTGGAGTACCTTCACTGTCAAG
genomic: CTGCTTTTGGACAGGCAACCCACAAAAGTCTTGAAGGAAGATGCTGTGAGgtatgcatgt ... atgactgtagATTCTATGCTGCAGAGGTAGTTGTTGCATTGGAGTACCTTCACTGTCAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatattgttttgtgaattcttgattgatctaacttaaaattgtcgatgactgtagATTCTATGCTGCAGAGGTAGTTGTTGCATTGGAGTACCTTCACTGTCAAG
                          atctaac  putative branch site (score: 2)
                          atctaacttaaaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cttttactgatatcatgtttggtcaagtgtgcctagttgcacttgtatattgttttgtgaattcttgattgatctaacttaaaattgtcgatgactgtagATTCTATGCTGCAGAGGTAGTTGTTGCATTGGAGTACCTTCACTGTCAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - -tgtttgg
- - - - - - - - - - - - - - -tgcctag
- - - - - - - - - - - - - - - - - - - gcacttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cttaaaa