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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tttgtttctgctaccaaactggctgctaagctttgtcagtgtttgtgtatatactgatggttggtgatgtttcataattcatgggaatctttttctgcagCTGGCCAACAGTGAAGAATACATTGATGGACAGTTCACTGGAAACCTTGGAGAGATTTTGATCAG

Basic information

species Vitis vinifera
transcript Vv00s0220g00030.t01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv00s0220g00030.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GRMZM2G058252_T01 (Zea mays), 3'ss of exon 3
---------------tttgtttctgctaccaaactggctgctaagctttg-----------tcagtgtttgtgtatatactgatggttggtgatgtttcataattcatgggaatctttttct------------gcagCTGGCCAACAGTGAAGAATACATTGATGGACAGTTCACTGGAAACCTTGGAGAGATTTTGATCAG
               ||||  | |  ||| | |  ||  |    |  |||           | | |   |    || || ||     ||       | || ||||||| |    || ||| |            |||||| ||||||| ||| || ||||||||||| || ||| |||||||||| ||||||||| |||||||
gtactaatttggcagtttggctgtcatactataagggtggtggtgtattgaatgcgtgagatgaatagctaatcatctattgggtactgaatgacatacaaaattcattgctgcctcttttttttctactgcgtgcagCTTGCCAACACTGAGGAGTACATTGATGGTCAATTCTCTGGAAACCTGGGAGAGATTCTGATCAG

upper sequence: Vv00s0220g00030.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GRMZM2G168252_T01 (Zea mays), 3'ss of exon 3
tttgtttctgctaccaaactggctgctaagctttgtcagtgtttgtgtata---tactga-tggttggtgatgtttcataattcatgggaatctttttctgcagCTGGCCAACAGTGAAGAATACATTGATGGACAGTTCACTGGAAACCTTGGAGAGATTTTGATCAG
  |  |  |  |  ||   | |||| |   || |   |||| |  |   ||   |||| | ||       |  ||   |  | | |     |  |  | ||||||| ||||| | ||| || ||||||||||| || ||| |||||||||| ||||||||| |||||||
-gtactaat-ttgacagtttagctgttgtactgttagagtgatcatcactagggtactaaatgacatacaaaattcattgctgccttatttttgtactgtgcagCTTGCCAATACTGAGGAGTACATTGATGGGCAATTCTCTGGAAACCTGGGAGAGATTCTGATCAG

upper sequence: Vv00s0220g00030.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA20G21250.1 (Glycine max), 3'ss of exon 3
tttgtttctgctaccaaactggctgctaagc-tttgt-cagtgtttgtgtatatactgat-----ggttggtgatgtttcataattcatgggaatctttttctgcagCTGGCCAACAGTGAAGAATACATTGATGGACAGTTCACTGGAAACCTTGGAGAGATTTTGATCAG
     || |    | ||| |   |  || |  ||||| | || | ||  |    | |||      | |  | | |  ||  ||||   || |||| | |  ||| |||||||||||| |||||| |||||||| |||||||| ||||||||  | ||||||||||| |||||
----gttatatatctaaattaatttttaggtgtttgttccgtatatgaatgatcattgacttggggctctgggcttgtttttaatatctgtgaatatct--ctgtagCTGGCCAACACTGAAGAGTACATTGAGGGACAGTTTACTGGAAATTTGGGAGAGATTTTAATCAG

upper sequence: Vv00s0220g00030.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: AT2G14285.1 (Arabidopsis thaliana), 3'ss of exon 3
-------------------------------------------------------------------tttgtttctgctaccaaactggctgctaagct-ttgtcagtgtttgtgtatatactgat---ggttggtgatgtttcataattcatgggaatct---------ttttctgcagCTGGCCAACAGTGAAGAATACATTGATGGACAGTTCACTGGAAACCTTGGAGAGATTTTGATCAG
                                                                     |||||         ||      |  || || || | || || | |||||| |   |    | | | | ||   |  || |   || || | |         |||| || |||| |  ||||  || |||||||||||||| || || || ||||||||||||||||||||||||||
gtatggtcttagcttctatgttcaactcaagatcatgttcttgtcattgaagttttaaacagagattgatgttttcaaatttcaatgcttagaaaatctattcttagagtctatgtatagagatacatagatcgtttattcattgtagtcattgagattttccatgcttgttttttgtagCTAGGAAACACCGAGGAATACATTGATGGGCAATTGACAGGAAACCTTGGAGAGATTTTGATCAG

upper sequence: Vv00s0220g00030.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: AT4G30220.2 (Arabidopsis thaliana), 3'ss of exon 3
------------------------------------------------------------------------------------------tttgtttctgctaccaaactggctgctaagctttgtcagtgtttgtgtatatactgatggttggtgatgtttcataattcatgggaatctttttctgcagCTGGCCAACAGTGAAGAATACATTGATGGACAGTTCACTGGAAACCTTGGAGAGATTTTGATCAG
                                                                                            |||| ||  | | | ||  | |   | ||  ||    |  |  |||| | |   || | | || |||  |    |||      | | ||||| | |||||||  ||||  |||||||| ||||||||||| || || || |||||||||||||| ||||||||
gtgcgttatttcctgaattacaaagttagataagatagctttttgattaaacagagagattgatgttattttgtccaaaaccacctgctaaatgttccttgtgc-atacaagtttagaggcaatgctgataatc-tgtacagatacatagattgttatgcattgacattttccatattgtttttgt-cagCTGGGAAACACCGAAGAATATATTGATGGACAATTGACAGGGAACCTTGGAGAGATCTTGATCAG

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|27585892|gb|CB008587.1|CB008587
EST:     GTTATCTCGTATCAGTGGATTCATACATGAACTTGCAG                         CTGGCCAACAGTGAAGAATACATTGATGGACAGTTCACTGGAAACCTTGGA
genomic: GTTATCTCGTATCAGTGGATTCATACATGAACTTGCAGgtgcttcctc ... ttttctgcagCTGGCCAACAGTGAAGAATACATTGATGGACAGTTCACTGGAAACCTTGGA
EST: gi|34319677|gb|CF372431.1|CF372431
EST:     GTTATCTCGTATCAGTGGATTCATACATGAACTTGCAG                         CTGGCCAACAGTGAAGAATACATTGATGGACAGTTCACTGGAAACCTTGGA
genomic: GTTATCTCGTATCAGTGGATTCATACATGAACTTGCAGgtgcttcctc ... ttttctgcagCTGGCCAACAGTGAAGAATACATTGATGGACAGTTCACTGGAAACCTTGGA
EST: gi|27580636|gb|CB003331.1|CB003331
EST:     GTTATCTCGTATCAGTGGATTCATACATGAACTTGCAG                         CTGGCCAACAGTGAAGAATACATTGATGGACAGTTCACTGGAAACCTTGGA
genomic: GTTATCTCGTATCAGTGGATTCATACATGAACTTGCAGgtgcttcctc ... ttttctgcagCTGGCCAACAGTGAAGAATACATTGATGGACAGTTCACTGGAAACCTTGGA
EST: gi|32246334|gb|CD712153.1|CD712153
EST:     GTTATCTCGTATCAGTGGATTCATACATGAACTTGCAG                         CTGGCCAACAGTGAAGAATACATTGATGGACAGTTCACTGGAAACCTTGGA
genomic: GTTATCTCGTATCAGTGGATTCATACATGAACTTGCAGgtgcttcctc ... ttttctgcagCTGGCCAACAGTGAAGAATACATTGATGGACAGTTCACTGGAAACCTTGGA
EST: gi|110730178|gb|EE106958.1|EE106958
EST:     GTTATCTCGTATCAGTGGATTCATACATGAACTTGCAG                         CTGGCCAACAGTGAAGAATACATTGATGGACAGTTCACTGGAAACCTTGGA
genomic: GTTATCTCGTATCAGTGGATTCATACATGAACTTGCAGgtgcttcctc ... ttttctgcagCTGGCCAACAGTGAAGAATACATTGATGGACAGTTCACTGGAAACCTTGGA
EST: gi|110383296|gb|EC947661.1|EC947661
EST:     GTTATCTCGTATCAGTGGATTCATACATGAACTTGCAG                         CTGGCCAACAGTGAAGAATACATTGATGGACAGTTCACTGGAAACCTTGGA
genomic: GTTATCTCGTATCAGTGGATTCATACATGAACTTGCAGgtgcttcctc ... ttttctgcagCTGGCCAACAGTGAAGAATACATTGATGGACAGTTCACTGGAAACCTTGGA
EST: gi|110419842|gb|EC986096.1|EC986096
EST:     GTTATCTCGTATCAGTGGATTCATACATGAACTTGCAG                         CTGGCCAACAGTGAAGAATACATTGATGGACAGTTCACTGGAAACCTTGGA
genomic: GTTATCTCGTATCAGTGGATTCATACATGAACTTGCAGgtgcttcctc ... ttttctgcagCTGGCCAACAGTGAAGAATACATTGATGGACAGTTCACTGGAAACCTTGGA
EST: gi|77578909|gb|DV218261.1|DV218261
EST:     GTTATCTCGTATCAGTGGATTCATACATGAACTTGCAG                         CTGGCCAACAGTGAAGAATACATTGATGGACAGTTCACTGGAAACCTTGGA
genomic: GTTATCTCGTATCAGTGGATTCATACATGAACTTGCAGgtgcttcctc ... ttttctgcagCTGGCCAACAGTGAAGAATACATTGATGGACAGTTCACTGGAAACCTTGGA
EST: gi|110426527|gb|EC992940.1|EC992940
EST:     GTTATCTCGTATCAGTGGATTCATACATGAACTTGCAG                         CTGGCCAACAGTGAAGAATACATTGATGGACAGTTCACTGGAAACCTTGGA
genomic: GTTATCTCGTATCAGTGGATTCATACATGAACTTGCAGgtgcttcctc ... ttttctgcagCTGGCCAACAGTGAAGAATACATTGATGGACAGTTCACTGGAAACCTTGGA
EST: gi|110686902|gb|EE063845.1|EE063845
EST:     GTTATCTCGTATCAGTGGATTCATACATGAACTTGCAG                         CTGGCCAACAGTGAAGAATACATTGATGGACAGTTCACTGGAAACCTTGGA
genomic: GTTATCTCGTATCAGTGGATTCATACATGAACTTGCAGgtgcttcctc ... ttttctgcagCTGGCCAACAGTGAAGAATACATTGATGGACAGTTCACTGGAAACCTTGGA
EST: gi|110380052|gb|EC945289.1|EC945289
EST:     GTTATCTCGTATCAGTGGATTCATACATGAACTTGCAG                         CTGGCCAACAGTGAAGAATACATTGATGGACAGTTCACTGGAAACCTTGGA
genomic: GTTATCTCGTATCAGTGGATTCATACATGAACTTGCAGgtgcttcctc ... ttttctgcagCTGGCCAACAGTGAAGAATACATTGATGGACAGTTCACTGGAAACCTTGGA
EST: gi|27579125|gb|CB001820.1|CB001820
EST:     GTTATCTCGTATCAGTGGATTCATACATGAACTTGCAG                         CTGGCCAACAGTGAAGAATACATTGATGGACAGTTCACTGGAAACCTTGGA
genomic: GTTATCTCGTATCAGTGGATTCATACATGAACTTGCAGgtgcttcctc ... ttttctgcagCTGGCCAACAGTGAAGAATACATTGATGGACAGTTCACTGGAAACCTTGGA
EST: gi|110731217|gb|EE109189.1|EE109189
EST:     GTTATCTCGTATCAGTGGATTCATACATGAACTTGCAG                         CTGGCCAACAGTGAAGAATACATTGATGGACAGTTCACTGGAAACCTTGGA
genomic: GTTATCTCGTATCAGTGGATTCATACATGAACTTGCAGgtgcttcctc ... ttttctgcagCTGGCCAACAGTGAAGAATACATTGATGGACAGTTCACTGGAAACCTTGGA
EST: gi|27580948|gb|CB003643.1|CB003643
EST:     GTTATCTCGTATCAGTGGATTCATACATGAACTTGCAG                         CTGGCCAACAGTGAAGAATACATTGATGGACAGTTCACTGGAAACCTTGGA
genomic: GTTATCTCGTATCAGTGGATTCATACATGAACTTGCAGgtgcttcctc ... ttttctgcagCTGGCCAACAGTGAAGAATACATTGATGGACAGTTCACTGGAAACCTTGGA
EST: gi|30125982|gb|CB911321.1|CB911321
EST:     GTTATCTCGTATCAGTGGATTCATACATGAACTTGCAG                         CTGGCCAACAGTGAAGAATACATTGATGGACAGTTCACTGGAAACCTTGGA
genomic: GTTATCTCGTATCAGTGGATTCATACATGAACTTGCAGgtgcttcctc ... ttttctgcagCTGGCCAACAGTGAAGAATACATTGATGGACAGTTCACTGGAAACCTTGGA
EST: gi|34549721|gb|CF517953.1|CF517953
EST:     GTTATCTCGTATCAGTGGATTCATACATGAACTTGCAG                         CTGGCCAACAGTGAAGAATACATTGATGGACAGTTCACTGGAAACCTTGGA
genomic: GTTATCTCGTATCAGTGGATTCATACATGAACTTGCAGgtgcttcctc ... ttttctgcagCTGGCCAACAGTGAAGAATACATTGATGGACAGTTCACTGGAAACCTTGGA
EST: gi|34544804|gb|CF513036.1|CF513036
EST:     GTTATCTCGTATCAGTGGATTCATACATGAACTTGCAG                         CTGGCCAACAGTGAAGAATACATTGATGGACAGTTCACTGGAAACCTTGGA
genomic: GTTATCTCGTATCAGTGGATTCATACATGAACTTGCAGgtgcttcctc ... ttttctgcagCTGGCCAACAGTGAAGAATACATTGATGGACAGTTCACTGGAAACCTTGGA
EST: gi|27586320|gb|CB009015.1|CB009015
EST:     GTTATCTCGTATCAGTGGATTCATACATGAACTTGCAG                         CTGGCCAACAGTGAAGAATACATTGATGGACAGTTCACTGGAAACCTTGGA
genomic: GTTATCTCGTATCAGTGGATTCATACATGAACTTGCAGgtgcttcctc ... ttttctgcagCTGGCCAACAGTGAAGAATACATTGATGGACAGTTCACTGGAAACCTTGGA
EST: gi|34544882|gb|CF513114.1|CF513114
EST:     GTTATCTCGTATCAGTGGATTCATACATGAACTTGCAG                         CTGGCCAACAGTGAAGAATACATTGATGGACAGTTCACTGGAAACCTTGGA
genomic: GTTATCTCGTATCAGTGGATTCATACATGAACTTGCAGgtgcttcctc ... ttttctgcagCTGGCCAACAGTGAAGAATACATTGATGGACAGTTCACTGGAAACCTTGGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtatatactgatggttggtgatgtttcataattcatgggaatctttttctgcagCTGGCCAACAGTGAAGAATACATTGATGGACAGTTCACTGGAAACCTTGGAGAGATTTTGATCAG
      tactgat  putative branch site (score: 2)
                                          tctttttctgc  putative PPT
                        tttcataatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tttgtttctgctaccaaactggctgctaagctttgtcagtgtttgtgtatatactgatggttggtgatgtttcataattcatgggaatctttttctgcagCTGGCCAACAGTGAAGAATACATTGATGGACAGTTCACTGGAAACCTTGGAGAGATTTTGATCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - -ttctgct
- - - - - - -ccaaact
- - - - - - - - - - - ctgctaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -tggttgg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ttcatgg