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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctcttctatcaattaagtcctgaattccttagcaagatttatttttctctgatcattgtcatttcatcaccccctttttttgtgttgtttattgaaacagGTTAGTCATCACCCAACACTCATTGCCTGCCATTGTGAAGGTAAAGGGTGGAAATTCTGGGCTGACAGTAACCTACGAACAAAATTTTGGGGACGATCAA

Basic information

species Vitis vinifera
transcript Vv02s0154g00250.t01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv02s0154g00250.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: LOC_Os08g05870.1 (Oryza sativa), 3'ss of exon 4
ctcttctatcaattaagtcctgaattccttagc-aagatttatt-tttctctgatcattgtcatttcatcac--cccctttttttgtgttgtttattgaaacagGTTAGTCATCACCCAACACTCATTGCCTGCCATTGTGAAGGTAAAGGGTGGAAATTCTGGGCTGACAGTAACCTACGAACAAAATTTTGGGGACGATCAA
       |         |  |  ||   | | | || ||||| | | |   |  |      ||||| ||  |  | | ||  |||  ||  |||     |  |||||||||||||||| |  || ||||||||||| |||||||| || || |||||||||||||  ||||| || ||   | | || |||||||| |  ||||
----gacacttgcctccttttctatctgtgaactaaaatttaatatcttgatagtgtgaagcatttaattgcaacacattgcttttcgtcattttcatcactagGTTAGTCATCACCCCATGCTGATTGCCTGCCACTGTGAAGGCAAGGGCTGGAAATTCTGGGGCGACAGCAATCTCAAATCCAAGTTTTGGGGGCAGTCAA

upper sequence: Vv02s0154g00250.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: LOC_Os10g40590.1 (Oryza sativa), 3'ss of exon 5
ctcttctatcaattaa-gtcctgaattccttagcaagatt-tatttttctctg-atcattgtcatttcatcaccccctttttttgtgttgtttattgaaacagGTTAGTCATCACCCAACACTCATTGCCTGCCATTGTGAAGGTAAAGGGTGGAAATTCTGGGCTGACAGTAACCTACGAACAAAATTTTGGGGACGATCAA
      |  ||   |  || ||||  | |   |||   |  |||| ||||||  ||      ||    || |     ||| || || || ||  |   | |||||||||||||| || |   |||| || |||||||||||||| ||||| |||||||| |||| |||||| || |||   |  ||||||||||| |  || |
taaaagtggcagacactgttctga--tgccaggcacattaatattcttctctacatttcacacaacatatgagttaatttgttagt-ttattcttgtcaccagGTTAGTCATCATCCGATGGTCATGGCATGCCATTGTGAAGGGAAAGGTTGGAAATTTTGGGGTGACAGCAATCTAAAGAGCAAATTTTGGGGGCAGTCCA

upper sequence: Vv02s0154g00250.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM2G402653_T03 (Zea mays), 3'ss of exon 4
---ctcttctatcaattaagtcctgaattccttagcaagatttatttttctctgatcattgtcatttcatcaccccctttttttgtgttgtttattgaaacagGTTAGTCATCACCCAACACTCATTGCCTGCCATTGTGAAGGTAAAGGGTGGAAATTCTGGGCTGACAGTAACCTACGAACAAAATTTTGGGGACGATCAA
    |    | |  | | |      | ||| | |    |   || |||    ||   | | | |||||||  |     | ||     || |  |    || ||||||||||||| ||||  || ||||||||||| |||||||| || || |||||||||||||  ||||| || ||   | | || ||||||||||  ||||
tcgtttacatttttactgatcatccatttcttaattttgtggtactttgaattggagactttaatttcattgcattgctattcaacatt-tccacc--aatagGTTAGTCATCATCCAATGCTGATTGCCTGCCACTGTGAAGGCAAGGGCTGGAAATTCTGGGGCGACAGCAATCTCAAATCCAAGTTTTGGGGACAGTCAA

upper sequence: Vv02s0154g00250.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM5G875564_T01 (Zea mays), 3'ss of exon 5
--ctcttctatcaattaagtcctgaattccttagcaagatttatttttctctgatcattgtcatttcatcaccccctttttttgtgttg--tttattgaaacagGTTAGTCATCACCCAACACTCATTGCCTGCCATTGTGAAGGTAAAGGGTGGAAATTCTGGGCTGACAGTAACCTACGAACAAAATTTTGGGGACGATCAA
      | | ||| || |      || |   ||      |||  |   ||| | |       ||  |   |   | | || |  || ||  ||| |||  | ||||||||||||| ||||   |||| || || ||||||||||| |||||||||||||| ||||  ||||| ||  ||   |  || || ||||| | | |||
aatcagtatttcagttgaaa---aaaataaatattgctgtttcatgacctcag-tagaaactatagctggagttcatgttatgatgctgtatttgttgcgatagGTTAGTCATCATCCAATGGTCATGGCTTGTCATTGTGAAGGAAAAGGGTGGAAATTTTGGGGAGACAGCAATGTAAAGAGCAAGTTCTGGGGGCAAACAA

upper sequence: Vv02s0154g00250.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA05G04340.2 (Glycine max), 3'ss of exon 6
ctcttctatcaattaagtcctgaattccttagcaagatttatttttctctgatcattgtcatttcatcaccccctttttttgtg-----ttgtttat---tgaaacagGTTAGTCATCACCCAACACTCATTGCCTGCCATTGTGAAGGTAAAGGGTGGAAATTCTGGGCTGACAGTAACCTACGAACAAAATTTTGGGGACGATCAA
        |    |  |   | | |   ||  |||    | |     |  ||  |||  | |  ||  |    || ||||          || ||||   |||||||||| ||||| || |||||  || |||||||||| |||||||||| ||| |||||||| ||||||||||||||| | ||  |||| ||||||||| | ||||
--------tttggtggggttttactgttttctcaaacaatgtgcaggtaagacaattaacctgccaatatttactgttttctcaaacaactgattatgtgtgaaacagGTGAGTCACCATCCAACTGTCGTTGCCTGCCACTGTGAAGGTAGAGGTTGGAAATTTTGGGCTGACAGTAACATTCGGTCAAAGTTTTGGGGAAGGTCAA

upper sequence: Vv02s0154g00250.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA01G41940.1 (Glycine max), 3'ss of exon 5
ctcttctatca-attaagtcctgaattccttagcaagatttatttttctctgatcattgtcatttcatcaccccctttttttgtgttgtttat---tgaaacagGTTAGTCATCACCCAACACTCATTGCCTGCCATTGTGAAGGTAAAGGGTGGAAATTCTGGGCTGACAGTAACCTACGAACAAAATTTTGGGGACGATCAA
   ||| |||  | || ||  |   |||  |||| ||  ||| | |   |   ||||   | |  ||  |    |  | || |      ||||   |||||||||| ||||| || ||||| |||||||||||||| || ||||||| ||| ||||| || ||||||||||| ||| | |   |||| ||||||||| | ||||
--attcgatcttagtatgtattt--ttctctagctagtcttaatatgtgcaattcatcagcctgccaatatattcgatattcgctgacattatgtgtgaaacagGTCAGTCACCATCCAACTCTCATTGCCTGCCACTGCGAAGGTAGAGGATGGAAGTTTTGGGCTGACAGCAACATCCATTCAAAGTTTTGGGGAAGGTCAA

upper sequence: Vv02s0154g00250.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA17G14820.1 (Glycine max), 3'ss of exon 6
ctcttctatcaattaagtcctgaattccttagcaagatttatttttctctgatcattgtcatttcatcaccccctttttttgtg-----ttgtttat---tgaaacagGTTAGTCATCACCCAACACTCATTGCCTGCCATTGTGAAGGTAAAGGGTGGAAATTCTGGGCTGACAGTAACCTACGAACAAAATTTTGGGGACGATCAA
            |    || |    ||  | |||     | |       |||  |||  | |  ||  |    || || |          || ||||   |||||||||| ||||| || |||||  || |||||||||| ||| |||||| ||| ||||| || ||||||||||||||| | ||  |||| ||||||||| | ||||
--------gtggtcctatcatacgctcagttgcatacaatgtgcaggcatgacaattaacctgccaatatttactgttctctcaaacaactgattatgtgtgaaacagGTGAGTCACCATCCAACTGTCGTTGCCTGCCACTGTCAAGGTAGAGGTTGGAAGTTTTGGGCTGACAGTAACATTCGGTCAAAGTTTTGGGGAAGGTCAA

upper sequence: Vv02s0154g00250.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA11G03420.2 (Glycine max), 3'ss of exon 7
ctcttctatcaattaagtcctgaattccttagcaagatttatttttctctgatcattgtcatttcatcac----cccctttttttgtgttgtttattgaaacagGTTAGTCATCACCCAACACTCATTGCCTGCCATTGTGAAGGTAAAGGGTGGAAATTCTGGGCTGACAGTAACCTACGAACAAAATTTTGGGGACGATCAA
   ||| |||   || ||  |   ||   |||| ||  ||| | |   |   ||||   | |  ||  |     | | ||   |    || | | | ||||||||| ||||| || || || |||||||||||||| || ||||||| ||| ||||| || ||||||||||  ||| | |   |||| ||||||||| | ||||
-aattcgatcttgtatgtattt--ttgtctagctagtcttaatatgtgcaattcatcaacctgccaatatatttcacgttccctgacattatgtgt-gaaacagGTCAGTCACCATCCGACTCTCATTGCCTGCCACTGCGAAGGTAGAGGATGGAAGTTTTGGGCTGACACCAACATCCATTCAAAGTTTTGGGGAAGGTCAA

upper sequence: Vv02s0154g00250.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: AT4G12460.1 (Arabidopsis thaliana), 3'ss of exon 5
ctcttctatcaattaagtcctgaattccttagcaagatttatttttctctgatcattgtcatttcatcaccccctttttttg--tgttgt-ttattgaaacagGTTAGTCATCACCCAACACTCATTGCCTGCCATTGTGAAGGTAAAGGGTGGAAATTCTGGGCTGACAGTAACCTACGAACAAAATTTTGGGGACGATCAA
   ||  |  || | |  | |    |    |  || | ||||     |||  || |    | ||   ||     ||  || |  | ||||  | |   || ||||||| || || |||||| | || ||||||||||| ||||||||||||||||| |||||||  ||||  ||||| ||  | || ||||||||  |||| |
gatttaaaaaaaatgaaacata---tggagaaaaaaaattatgagaatcttttcttaagaagtttggcatataattcgttagggtattgtactctcataatagGTTAGCCACCATCCAACAGTTATCGCCTGCCATTGCGAAGGTAAAGGGTGGAAGTTCTGGGGCGACACAAACCTCCGGTCGAAGTTTTGGGGGAGATCGA

upper sequence: Vv02s0154g00250.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: AT4G22540.3 (Arabidopsis thaliana), 3'ss of exon 5
--ctcttctatcaattaagtcctgaattccttagcaagatttatttttctctgatcattgtcatttcatcaccccctttttttgtgttgtttattgaaacagGTTAGTCATCACCCAACACTCATTGCCTGCCATTGTGAAGGTAAAGGGTGGAAATTCTGGGCTGACAGTAACCTACGAACAAAATTTTGGGGACGATCAA
   | |   |  ||||    |   ||||    |    |||  |  |   | | |  ||  | |   ||  ||       | |  |  | ||  ||  || |||| ||||| || |||||  | || |||||||| |||||||||||||||||||| || |||| ||||| ||||||  |  |||| ||||||||  | || |
gtatgtcacacaaattttaactcaaatttag-aatgtgatgaacataattgttagaatctttac--caagactagagaatatcattcttttggttataatagGTCAGTCACCATCCAACTGTTATCGCCTGCCACTGTGAAGGTAAAGGGTGGAAGTTTTGGGGTGACACTAACCTCAGGTCAAAGTTTTGGGGGAGGTCGA

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|110700214|gb|EE077994.1|EE077994
EST:     CTTATGAAGCTGATTTTCCTGATAAAGGAATTCGCTTTTTCTCTGAGAAG                         GTTAGTCATCACCCAACACTCATTGCCTGCCATTGTGAAGGTAAAGGGTGG
genomic: CTTATGAAGCTGATTTTCCTGATAAAGGAATTCGTTTTTTCTCTGAGAAGgtccgtagtt ... attgaaacagGTTAGTCATCACCCAACACTCATTGCCTGCCATTGTGAAGGTAAAGGGTGG






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctctgatcattgtcatttcatcaccccctttttttgtgttgtttattgaaacagGTTAGTCATCACCCAACACTCATTGCCTGCCATTGTGAAGGTAAAGGGTGGAAATTCTGGGCTGACAGTAACCTACGAACAAAATTTTGGGGACGATCAA
 ctctgat  putative branch site (score: 4)
                                          tttattgaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ctcttctatcaattaagtcctgaattccttagcaagatttatttttctctgatcattgtcatttcatcaccccctttttttgtgttgtttattgaaacagGTTAGTCATCACCCAACACTCATTGCCTGCCATTGTGAAGGTAAAGGGTGGAAATTCTGGGCTGACAGTAACCTACGAACAAAATTTTGGGGACGATCAA

- - -ctatcaa
- - - - - - - - -tcctgaa