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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gcatattcctgctgtaccccttgttctttaattgattgccttgtacttcattagaggatacaggtgatcaattgacatgatgttggatgtggatgcagGTGGGTAATGAAAAAGAGAGCGTCAGTTTTGACCTTCGACCTTCAGATGCCATTAACATTGCTGTTAGATGCAAG

Basic information

species Vitis vinifera
transcript Vv18s0001g12960.t01
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv18s0001g12960.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: LOC_Os08g26870.4 (Oryza sativa), 3'ss of exon 6
gcatattcctgctgtaccccttgttctttaattgattgccttgtacttcatta-----gaggatacaggtgatcaatt--gacatgatgttggatgtggatgcagGTGGGTAATGAAAAAGAGAGCGTCAGTTTTGACCTTCGACCTTCAGATGCCATTAACATTGCTGTTAGATGCAAG
   || |  ||| |  |   || ||    |    | ||   |  |||| | |       |   ||    | | || ||   ||  ||   ||  | |   ||||||| ||| |  | | ||| ||  |||  ||||| ||  |||||||||||||||| |||||||||||| | ||||||
--gtacttatgcagagcatttt-ttaaaaaggaaactgaactcaactttagtgtgtacaatactatcattaaccattttaaactagaaactgcctatac-tgcagGTAGGTGACCATACAGAAAGTATCACCTTTGATCTAAGACCTTCAGATGCCATAAACATTGCTGTTCGCTGCAAG

upper sequence: Vv18s0001g12960.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GRMZM2G053531_T02 (Zea mays), 3'ss of exon 6
gcatattcctgctgtaccccttgttctttaattgattgc---cttgtacttcattagaggatacaggtgatcaattgacatgatgttg-gatgtgga------------tgcagGTGGGTAATGAAAAAGAGAGCGTCAGTTTTGACCTTCGACCTTCAGATGCCATTAACATTGCTGTTAGATGCAAG
         | |    |  | |||    ||| | |  ||    |  | | |  |||| || | ||    || ||     || || ||   | || ||            |||||||   | ||   | ||| | | |||  || || ||||| |||||||||||||| |||||||||||| | ||||||
--------gtacaaatctacctgtctaataagtaagagcaaattaatgcatttttagtgggtgca--ccattaaccttaataatattctaaagtagaaacctcctgcactgcagGTCAATGATCCTACAGACAACATCACCTTCGATCTTCGGCCTTCAGATGCCATAAACATTGCTGTTCGTTGCAAG

upper sequence: Vv18s0001g12960.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GRMZM2G006468_T03 (Zea mays), 3'ss of exon 6
gcatattcctgctgtaccccttgttctttaattgattgccttgtacttcattagaggatacaggtgatcaattgacatgatgttgga-----tgtggatgcagGTGGGTAATGAAAAAGAGAGCGTCAGTTTTGACCTTCGACCTTCAGATGCCATTAACATTGCTGTTAGATGCAAG
     | ||            || ||| |||   |    ||  | | |  | || || ||  |   ||  |     || | || | |      |    ||||| | | | ||   | ||| ||| |||  || || ||||| |||||||||||||| |||||||||||| | ||||||
----gtaccaatctagttgactgatctgtaag-aacaaactaatgcattttcagtgggta--gaccattgacattaataaagtagaaacatccggcactgcagATTGATGATTCTACAGACAGCATCACCTTCGATCTTCGGCCTTCAGATGCCATAAACATTGCTGTTCGTTGCAAG

upper sequence: Vv18s0001g12960.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GLYMA17G37160.1 (Glycine max), 3'ss of exon 3
-----------------------------gcatattcctgctgtaccccttgttctttaattgattgccttgtacttcattagaggatacaggtgatcaattgacatgatgttggatgtggat--------------------------gcagGTGGGTAATGAAAAAGAGAGCGTCAGTTTTGACCTTCGACCTTCAGATGCCATTAACATTGCTGTTAGATGCAAG
                                                                                                                         ||                            |||| || |||||   |||    || || ||||| ||||||||||||||||| || |||||||| || |||||||||
gtttgagttaaagctaaaactnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnatcgtataacagttaaattatatttggtatagGTTGGAAATGAGGCAGAATATGTGAGCTTTGATCTTCGACCTTCAGATGCTATCAACATTGCAGTAAGATGCAAG

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|27578891|gb|CB001586.1|CB001586
EST:     TCACCAAGAGGGTACACGAGGCATATTTTGCTCAGTTATACCTCACAAAG                         GTGGGTAATGAAAAAGAGAGCGTCAGTTTTGACCTTCGACCTTCAGATGCC
genomic: TCACCAAGAGGGTACACGAGGCATATTTTGCTCAGTTATACCTCACAAAGgcatattcct ... gtggatgcagGTGGGTAATGAAAAAGAGAGCGTCAGTTTTGACCTTCGACCTTCAGATGCC
EST: gi|45770383|gb|CN006235.1|CN006235
EST:     TCACCAAGAGGGTACACGAGGCATATTTTGCTCAGTTATACCTCACAAAG                         GTGGGTAATGAAAAAGAGAGCGTCAGTTTTGACCTTCGACCTTCAGATGCC
genomic: TCACCAAGAGGGTACACGAGGCATATTTTGCTCAGTTATACCTCACAAAGgcatattcct ... gtggatgcagGTGGGTAATGAAAAAGAGAGCGTCAGTTTTGACCTTCGACCTTCAGATGCC
EST: gi|27580870|gb|CB003565.1|CB003565
EST:     TCACCAAGAGGGTACACGAGGCATATTTTGCTCAGTTATACCTCACAAAG                         GTGGGTAATGAAAAAGAGAGCGTCAGTTTTGACCTTCGACCTTCAGATGCC
genomic: TCACCAAGAGGGTACACGAGGCATATTTTGCTCAGTTATACCTCACAAAGgcatattcct ... gtggatgcagGTGGGTAATGAAAAAGAGAGCGTCAGTTTTGACCTTCGACCTTCAGATGCC
EST: gi|22007151|gb|BQ792185.1|BQ792185
EST:     TCACCAAGAGGGTACACGAGGCATATTTTGCTCAGTTATACCTCACAAAG                         GTGGGTAATGAAAAAGAGAGCGTCAGTTTTGACCTTCGACCTTCAGATGCC
genomic: TCACCAAGAGGGTACACGAGGCATATTTTGCTCAGTTATACCTCACAAAGgcatattcct ... gtggatgcagGTGGGTAATGAAAAAGAGAGCGTCAGTTTTGACCTTCGACCTTCAGATGCC
EST: gi|26261297|gb|CA812360.1|CA812360
EST:     TCACCAAGAGGGTACACGAGGCATATTTTGCTCAGTTATACCTCACAAAG                         GTGGGTAATGAAAAAGAGAGCGTCAGTTTTGACCTTCGACCTTCAGATGCC
genomic: TCACCAAGAGGGTACACGAGGCATATTTTGCTCAGTTATACCTCACAAAGgcatattcct ... gtggatgcagGTGGGTAATGAAAAAGAGAGCGTCAGTTTTGACCTTCGACCTTCAGATGCC
EST: gi|26260812|gb|CA811875.1|CA811875
EST:     TCACCAAGAGGGTACACGAGGCATATTTTGCTCAGTTATACCTCACAAAG                         GTGGGTAATGAAAAAGAGAGCGTCAGTTTTGACCTTCGACCTTCAGATGCC
genomic: TCACCAAGAGGGTACACGAGGCATATTTTGCTCAGTTATACCTCACAAAGgcatattcct ... gtggatgcagGTGGGTAATGAAAAAGAGAGCGTCAGTTTTGACCTTCGACCTTCAGATGCC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tacttcattagaggatacaggtgatcaattgacatgatgttggatgtggatgcagGTGGGTAATGAAAAAGAGAGCGTCAGTTTTGACCTTCGACCTTCAGATGCCATTAACATTGCTGTTAGATGCAAG
                          aattgac  putative branch site (score: 3)
                       atcaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gcatattcctgctgtaccccttgttctttaattgattgccttgtacttcattagaggatacaggtgatcaattgacatgatgttggatgtggatgcagGTGGGTAATGAAAAAGAGAGCGTCAGTTTTGACCTTCGACCTTCAGATGCCATTAACATTGCTGTTAGATGCAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT