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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aagaattcatggtgtcctctcttgaatgaatgattttgctcttaggttttgacacagaacagttgaggttacaaaacttttgtatttgactgatgtgcagCGCATCAATGAGAGTCGGAACAAGGTTGTGATAACCGACAGGATGTGGGCAAGGCTCCTTTCGTCAACAAACCAGCCAAGCTTCCAGAACCCCAAAGATG

Basic information

species Vitis vinifera
transcript Vv04s0008g00520.t01
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv04s0008g00520.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: LOC_Os01g53680.1 (Oryza sativa), 3'ss of exon 13
-----------------------------------------aagaattcatggtgtcctctcttgaatgaatgattttgctcttaggttttgacacagaacagttgaggttacaa-aacttttgtatttgactgatgtgcagCGCATCAATGAGAGTCGGAACAAGGTTGTGATAACCGACAGGATGTGGGCAAGGCTCCTTTCGTCAACAAACCAGCCAAGCTTCCAGAACCCCAAAGATG
                                             |||||     |  |  | | ||  ||| ||  ||   |||  | ||  |    |||||||    | |||  || |||||| ||   ||||    ||| |  | |     |   | |||||||||  |||||||||||||||||||||||||||  | || || || |||||||| ||||||| || ||  || ||  
gtgagtacaaatttttgtattaccttaattttctccggttcccagattca-aacatattaccctcaac-aattatcatgaa-ttaaatattaccctttaacagttcgcatgacatcaatttttgtgtt---ctgacaaacagAGGGTAACATCAACAAGAAACAAGGTTAAGATAACCGACAGGATGTGGGCAAGGCTGTTGTCCTCGACCAACCAGCCCAGCTTCCTGAGCCAGAAGGACA

upper sequence: Vv04s0008g00520.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: LOC_Os05g44922.2 (Oryza sativa), 3'ss of exon 11
--------------------------------------------------------------------aagaattcatggtgtcctctcttgaatgaatgattttgctcttaggttttgacacagaacagttgaggttacaaaacttttg-tatttgactgatgtgcagCGCATCAATGAGAGTCGGAACAAGGTTGTGATAACCGACAGGATGTGGGCAAGGCTCCTTTCGTCAACAAACCAGCCAAGCTTCCAGAACCCCAAAGATG
                                                                       |   |||  | | |    ||     |  | | ||  |  |   || | | ||  | ||   |     ||  ||| |    | ||    ||||| |||| |  | |     |  |||||||||||   ||| || || ||||||||||| ||||| || || ||||| ||||||||||||||||  | ||  || ||  
gtgagtaacttcaagtgatcttatttgttcacatggaaaatgcagaaatgtagtgctcgttacacccgggcatcccatttttttcctgattatccaagagctgttcttactgcattctcatactaagcatcagttccaacttaacgtgaaatcttcccttgatg-gcagAGGGTGACATCCACACGGAACAAGGTCAAGATCACTGATAGGATGTGGGCGAGGCTGCTATCATCAACCAACCAGCCAAGCTTCCTAAGCCAGAAGGACA

upper sequence: Vv04s0008g00520.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: GRMZM2G443985_T01 (Zea mays), 3'ss of exon 13
-----------------------------aagaattcatggtgtc-ctctcttgaatgaatgattttgctcttaggttttgacacagaacagttgaggt---tacaaaac-ttttgtatttgactgatgtgc---agCGCATCAATGAGAGTCGGAACAAGGTTGTGATAACCGACAGGATGTGGGCAAGGCTCCTTTCGTCAACAAACCAGCCAAGCTTCCAGAACCCCAAAGATG
                               |||||| |  |  | |  || | |    |  || |    | ||  | ||      ||||   ||   |   ||| ||   ||||| ||| |  | |    |   || | || |  ||||  | |||||  |||  ||||||||||||||||||||||||||| || ||||| || ||||||||||||||||    |  |||||  |
gtaagtcacacccctgccggagcagggcacggaattctttttaccgcattcatcatctcagcatctgagacctacttattctgcttgaactaatgccctccgtactaattgttttgcattcgcgtcactcacttcagAGGATAACAGAGAAGCAGAACAGAGTTTCGATAACCGACAGGATGTGGGCAAGGCTTCTCTCGTCGACGAACCAGCCAAGCTTCCTTTGCAACAAAGTCG

upper sequence: Vv04s0008g00520.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: GRMZM5G816636_T02 (Zea mays), 3'ss of exon 13
aagaattcatggtgtcctctcttgaatgaatga--ttttgctcttaggttttgacacagaacagttgaggttacaaaacttttgtatttgactgat--gtgcagCGCATCAATGAGAGTCGGAACAAGGTTGTGATAACCGACAGGATGTGGGCAAGGCTCCTTTCGTCAACAAACCAGCCAAGCTTCCAGAACCCCAAAGATG
   || |||   | |       ||    |  ||  | || ||  ||  ||      |  | ||  | |    ||  |    |||| ||  ||       | ||| | || |  ||||  | ||||| |||   ||||||||||||||||||||||||||| || ||||| || |||||||| |||||||    |  |||||   
-gtaagtcaccctatgaaggagtgggacacagaattctttctactaaattcaacatcgcagcatctaataagacctacacattgttttgaaccacccactccagAGGATAACAGAGAAGCAGAACAGGGTCTCGATAACCGACAGGATGTGGGCAAGGCTTCTGTCGTCGACCAACCAGCCGAGCTTCCTCTGCAACAAAGTCA

upper sequence: Vv04s0008g00520.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: GRMZM2G004932_T01 (Zea mays), 3'ss of exon 13
---------aagaattcatggtgtcctctcttgaatgaatgattttgctcttaggttttgacacagaacagttgaggttacaaaacttttgtatttgactgatgtgcagCGCATCAATGAGAGTCGGAACAAGGTTGTGATAACCGACAGGATGTGGGCAAGGCTCCTTTCGTCAACAAACCAGCCAAGCTTCCAGAACCCCAAAGATG
          |  |  |||       ||  || ||| ||  |   |||  |   | | || ||||     | ||||   || ||| | |||| | |||  |  | |     |||| |  ||     ||||||||||    | || |||||||||||||||||||| || ||||| || ||||||||||| |||| ||  |  || ||| 
gaaccatgtcacgaaacataactagatcaattaaattaaaaaaagtgcattactgatctg-cacactgatgatgag--caccaaattcttgt-tctgatggcagAGGGTGACATCCACAAG-----GAACAAGGTTAAAGTCACTGACAGGATGTGGGCAAGGCTTCTGTCGTCCACCAACCAGCCAAGTTTCCTGAGTCAGAAGGATA

upper sequence: Vv04s0008g00520.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: GLYMA06G09320.2 (Glycine max), 3'ss of exon 12
aagaattcatggtgtcctc--tcttgaatgaatgattttgctcttaggttttgacacagaacagttgag-gttacaaaacttttgtatttga---ctgatgtgcagCGCATCAATGAGAGTCGGAACAAGGTTGTGATAACCGACAGGATGTGGGCAAGGCTCCTTTCGTCAACAAACCAGCCAAGCTTCCAGAACCCCAAAGATG
     || || |  ||  |  | ||  ||  ||| |||   | ||           |||||  |||       |   |   ||| | ||  |    ||||   ||| | ||||||||||| | ||||||||||||||| || ||||| ||||||||||| |||||||| ||||| |||||||| |||||   || ||| |||||| 
---tttttattgcttctccaattttatattgatggtttgtatttt---cccaagatcagaattgttcttcacaattgagaatttatgttcaaattttgatacccagAGAATCAATGAGAGGCAGAACAAGGTTGTGATTACTGACAGAATGTGGGCAAGACTCCTTTCTTCAACCAACCAGCCTAGCTTTTTGAGCCCTAAAGATT

upper sequence: Vv04s0008g00520.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: GLYMA04G09180.1 (Glycine max), 3'ss of exon 12
aagaattcatggtgtcctc--tcttgaatgaatgattt-tgctcttaggttttgacacagaacagttgaggttacaaaacttttgtatttgactgatgtgcagCGCATCAATGAGAGTCGGAACAAGGTTGTGATAACCGACAGGATGTGGGCAAGGCTCCTTTCGTCAACAAACCAGCCAAGCTTCCAGAACCCCAAAGATG
     || || |  ||  |  | ||  ||   || ||| |  | |       | | |     |  |     ||   ||  | |  |       ||||   ||| | ||||||||||| | ||||||||||||||| || ||||| ||||||||||| |||||||| ||||| |||||||| |||||   || |||||||||| 
---tttttattgcttctccaattttatattggtggtttgtattttcccaagatcaaaattgtccttcacaattgagaatttatcttcaaattttgatacccagAGAATCAATGAGAGGCAGAACAAGGTTGTGATTACTGACAGAATGTGGGCAAGACTCCTTTCTTCAACCAACCAGCCTAGCTTTTTGAGCCCCAAAGATT

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|34362808|gb|CF404393.1|CF404393
EST:     GCTTCACGATTGGGATTGTCAATGGAAGACATGCATACATTCCTTTCCAT                         CGCATCAATGAGAGTCGGAACAAGGTTGTGATAACCGACAGGATGTGGGCA
genomic: GCTTCACGATTGGGATTGTCAATGGAAGACATGCATACATTCCTTTCCATgtacgttctt ... tgatgtgcagCGCATCAATGAGAGTCGGAACAAGGTTGTGATAACCGACAGGATGTGGGCA
EST: gi|110710754|gb|EE087164.1|EE087164
EST:     TTTC-CGAATTGGGAATGTCAATGGAAAACATGCATACATTCCTTTCCAT                         CGCATCAATGAAAGTCG
genomic: TT-CACGA-TTGGGATTGTCAATGGAAGACATGCATACATTCCTTTCCATgtacgttctt ... tgatgtgcagCGCATCAATGAGAGTCG
EST: gi|34544030|gb|CF512262.1|CF512262
EST:     GCTTCACGATTGGGATTGTCAATGGAAGACATGCATACATTCCTTTCCAT                         CGCATCAATGAGAGTCGGAACAAGGTTGTGATAACCGACAGGATGTGGGCA
genomic: GCTTCACGATTGGGATTGTCAATGGAAGACATGCATACATTCCTTTCCATgtacgttctt ... tgatgtgcagCGCATCAATGAGAGTCGGAACAAGGTTGTGATAACCGACAGGATGTGGGCA
EST: gi|110368437|gb|EC932413.1|EC932413
EST:     GCTTCACGATTGGGATTGTCAATGGAAGACATGCATACATTCCTTTCCAT                         CGCATCAATGAGAGTCGGAACAAGGTTGTGATAACCGACAGGATGTGGGCA
genomic: GCTTCACGATTGGGATTGTCAATGGAAGACATGCATACATTCCTTTCCATgtacgttctt ... tgatgtgcagCGCATCAATGAGAGTCGGAACAAGGTTGTGATAACCGACAGGATGTGGGCA
EST: gi|110417232|gb|EC983271.1|EC983271
EST:     GCTTCACGATTGGGATTGTCAATGGAAGACATGCATACATTCCTTTCCAT                         CGCATCAATGAGAGTCGGAACAAGGTTGTGATAACCGACAGGATGTGGGCA
genomic: GCTTCACGATTGGGATTGTCAATGGAAGACATGCATACATTCCTTTCCATgtacgttctt ... tgatgtgcagCGCATCAATGAGAGTCGGAACAAGGTTGTGATAACCGACAGGATGTGGGCA
EST: gi|110406376|gb|EC971947.1|EC971947
EST:     GCTTCACGATTGGGATTGTCAATGGAAGACATGCATACATTCCTTTCCAT                         CGCATCAATGAGAGTCGGAACAAGGTTGTGATAACCGACAGGATGTGGGCA
genomic: GCTTCACGATTGGGATTGTCAATGGAAGACATGCATACATTCCTTTCCATgtacgttctt ... tgatgtgcagCGCATCAATGAGAGTCGGAACAAGGTTGTGATAACCGACAGGATGTGGGCA
EST: gi|110717627|gb|EE093647.1|EE093647
EST:     GCTTCACGATTGGGATTGTCAATGGAAGACATGCATACATTCCTTTCCAT                         CGCATCAATGAGAGTCGGAACAAGGTTGTGATAACCGACAGGATGTGGGCA
genomic: GCTTCACGATTGGGATTGTCAATGGAAGACATGCATACATTCCTTTCCATgtacgttctt ... tgatgtgcagCGCATCAATGAGAGTCGGAACAAGGTTGTGATAACCGACAGGATGTGGGCA
EST: gi|34543942|gb|CF512174.1|CF512174
EST:     GCTTCACGATTGGGATTGTCAATGGAAGACATGCATACATTCCTTTCCAT                         CGCATCAATGAGAGTCGGAACAAGGTTGTGATAACCGACAGGATGTGGGCA
genomic: GCTTCACGATTGGGATTGTCAATGGAAGACATGCATACATTCCTTTCCATgtacgttctt ... tgatgtgcagCGCATCAATGAGAGTCGGAACAAGGTTGTGATAACCGACAGGATGTGGGCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttttgacacagaacagttgaggttacaaaacttttgtatttgactgatgtgcagCGCATCAATGAGAGTCGGAACAAGGTTGTGATAACCGACAGGATGTGGGCAAGGCTCCTTTCGTCAACAAACCAGCCAAGCTTCCAGAACCCCAAAGATG
                                          gactgat  putative branch site (score: 3)
                           aaaacttttgtattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aagaattcatggtgtcctctcttgaatgaatgattttgctcttaggttttgacacagaacagttgaggttacaaaacttttgtatttgactgatgtgcagCGCATCAATGAGAGTCGGAACAAGGTTGTGATAACCGACAGGATGTGGGCAAGGCTCCTTTCGTCAACAAACCAGCCAAGCTTCCAGAACCCCAAAGATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - -ttcatgg
- - - - - - - tcctctc
- - - - - - - - - - - -gaatgaat
- - - - - - - - - - - - - - - - - - - - - - - - - -acacaga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tacaaaa