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 5'  3'   		2  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttcaactgctcaatctcgatatgaaaatcggccagggaattctgctaagaatagtgcttgttgtttacaatctttttaacagctatttatttttatgcagCTGCATTTGGAGCCATTTTGCATGTGATATCCACTTCGCTTCTTGGTGTCACAGCAATCACCATGGCAAACAGTATTGCTGGGGAGGAAACAGTCCATAA

Basic information

species Vitis vinifera
transcript Vv06s0009g01580.t01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv06s0009g01580.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA02G44180.1 (Glycine max), 3'ss of exon 1
ttcaactgctcaatctcgatatgaaaatcg-gccagggaattctgctaagaatagtgcttgttgtttacaatctttttaacagctatttatttttatgcagCTGCATTTGGAGCCATTTTGCATGTGATATCCACTTCGCTTCTTGGTGTCACAGCAATCACCATGGCAAACAGTATTGCTGGGGAGGAAACAGTCCATAA
  | ||    ||| |||||||      | |  || |       ||| |   | ||  |||    ||| | | |||      |   ||||  ||| ||||||||||| ||||||| |||||||| || ||||||||||| || |||||| | |||||||| |||||||||||||  |||||||| || |||||||| |||||
aactacaaaccaagctcgataaattctttgtacctgtcctcattgccattgaaagctctttgaatttccta-cttaaccttattcattttatttcatgcagCTGCACTTGGAGCAATTTTGCACGTAATATCCACTTCACTGCTTGGTATAACAGCAATTACCATGGCAAACACCATTGCTGGTGAAGAAACAGTGCATAA

upper sequence: Vv06s0009g01580.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA14G04600.1 (Glycine max), 3'ss of exon 1
ttcaactgctcaatctcgatatgaaaatcggccagggaattctgctaagaatagtgcttg---ttgtttacaatctttttaacagctatttatttt----tatgcagCTGCATTTGGAGCCATTTTGCATGTGATATCCACTTCGCTTCTTGGTGTCACAGCAATCACCATGGCAAACAGTATTGCTGGGGAGGAAACAGTCCATAA
        |   ||  | ||||||      |       | || |   |   |  |    |    |||| | ||  ||||| |    |||| |||||     ||| ||||||| ||||||| |||||||| || ||||||||||| || |||||| | || ||||| |||||||||||||  |||||||| || ||||| || |||||
-------cccttattcccatatgatgtctagtgcaaagactcagaagactgtgttctcagattctgttcataaagttttttaaccttattcattttatttcatgtagCTGCACTTGGAGCAATTTTGCACGTAATATCCACTTCACTGCTTGGTATAACGGCAATTACCATGGCAAACACCATTGCTGGTGAAGAAACTGTGCATAA

upper sequence: Vv06s0009g01580.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: AT5G21070.1 (Arabidopsis thaliana), 3'ss of exon 1
----ttcaactgctcaatctcgatatgaaaatcggccagggaattctgctaagaatagtgcttgttgttta--caatctttttaacagctatttatttttatgcagCTGCATTTGGAGCCATTTTGCATGTGATATCCACTTCGCTTCTTGGTGTCACAGCAATCACCATGGCAAACAGTATTGCTGGGGAGGAAACAGTCCATAA
    |     |  ||||  |   | |   | | ||     ||  |  | ||   ||  ||   | |  |||    || ||||  |  |  |   |||||    ||||||||||||||||  |  | ||||| ||||||||||| || |||||| | ||||||||||| ||||| || |  || ||||| || || || || || ||
atcatgtttatcatcaacgtttttgttgcatttggtgtctga--tgggatatagatgatgtgagattcttatctgattttttctagtgtcacccatttt----cagCTGCATTTGGAGCAGTCCTACATGTTATATCCACTTCTCTCCTTGGTATAACAGCAATCACAATGGCGAATACCATCGCTGGTGAAGAGACTGTTCACAA

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|33407593|gb|CF213220.1|CF213220
EST:     CATCGTTGGCCGCGCCCAGAAATGGACTCTCTCCAAGACACTTTTCGTCA                         CTGCATTTGGAGCCATTTTGCATGTGATATCCACTTCGCTTCTTGGTGTAA
genomic: CATCGTTGGCCGCGCCCAGAAATGGACTCTCTCCAAGACACTTTTCGTCAgtgagttgac ... ttttatgcagCTGCATTTGGAGCCATTTTGCATGTGATATCCACTTCGCTTCTTGGTGTCA
EST: gi|110387190|gb|EC951840.1|EC951840
EST:     CATCGTTGGCCGCGCCCAGAAATGGACTCTCTCCAAGACACTTTTCGTCA                         CTGCATTTGGAGCCATTTTGCATGTGATATCCACTTCGCTTCTTGGTGTAA
genomic: CATCGTTGGCCGCGCCCAGAAATGGACTCTCTCCAAGACACTTTTCGTCAgtgagttgac ... ttttatgcagCTGCATTTGGAGCCATTTTGCATGTGATATCCACTTCGCTTCTTGGTGTCA
EST: gi|351036192|gb|FQ464037.1|FQ464037
EST:     CATCGTTGGCCGCGCCCAGAAATGGACTCTCTCCAAGACACTTTTCGTCA                         CTGCATTTGGAGCCATTTTGTATGTGATATCCACTTCGCTTCTTGGTGTCA
genomic: CATCGTTGGCCGCGCCCAGAAATGGACTCTCTCCAAGACACTTTTCGTCAgtgagttgac ... ttttatgcagCTGCATTTGGAGCCATTTTGCATGTGATATCCACTTCGCTTCTTGGTGTCA
EST: gi|30256230|gb|CB972073.1|CB972073
EST:     TCTCTCCAAGACACTTTTCGTCA                         CTGCATTNT-CAGCCATTTTGCATGTGATATCCACTTCGCTTCTTGGTGTC
genomic: TCTCTCCAAGACACTTTTCGTCAgtgagttgac ... ttttatgcagCTGCATT-TGGAGCCATTTTGCATGTGATATCCACTTCGCTTCTTGGTGTC
EST: gi|110724908|gb|EE101145.1|EE101145
EST:     CATCGTTGGCCGCGCCCAGAAATGGACTCTTTCCAAGACACTTTTCGTCA                         CTGCATTTGGAGCCATTTTGCATGTGATATCCACTTCGCTTCTTGGTGTAA
genomic: CATCGTTGGCCGCGCCCAGAAATGGACTCTCTCCAAGACACTTTTCGTCAgtgagttgac ... ttttatgcagCTGCATTTGGAGCCATTTTGCATGTGATATCCACTTCGCTTCTTGGTGTCA
EST: gi|351013366|gb|FQ425071.1|FQ425071
EST:     CATCGTTGGCCGCGCCCAGAAATGGACTCTCTCCAAGACACTTTTCGTCA                         CTGCATTTGGAGCCATTTTGCATGTGATATCCACTTCGCTTCTTGGTGTCA
genomic: CATCGTTGGCCGCGCCCAGAAATGGACTCTCTCCAAGACACTTTTCGTCAgtgagttgac ... ttttatgcagCTGCATTTGGAGCCATTTTGCATGTGATATCCACTTCGCTTCTTGGTGTCA
EST: gi|161721045|gb|FC069647.1|FC069647
EST:     CATCGTTGGCCGCGCCCAGAAATGGACTCTCTCCAAGACACTTTTCGTCA                         CTGCATTTGGAGCCATTTTGCATGTGATATCCACTTCGCTTCTTGGTGTAA
genomic: CATCGTTGGCCGCGCCCAGAAATGGACTCTCTCCAAGACACTTTTCGTCAgtgagttgac ... ttttatgcagCTGCATTTGGAGCCATTTTGCATGTGATATCCACTTCGCTTCTTGGTGTCA
EST: gi|30126352|gb|CB911691.1|CB911691
EST:     CATCGTTGGCCGCGCCCAGAAATGGACTCTCTCCAAGACACTTTTCGTCA                         CTGCATTTGGAGCCATTTTGCATGTGATATCCACTTCGCTTCTTGGTGTCA
genomic: CATCGTTGGCCGCGCCCAGAAATGGACTCTCTCCAAGACACTTTTCGTCAgtgagttgac ... ttttatgcagCTGCATTTGGAGCCATTTTGCATGTGATATCCACTTCGCTTCTTGGTGTCA
EST: gi|161716995|gb|FC069530.1|FC069530
EST:     CATCGTTGGCCGCGCCCAGAAATGGACTCTCTCCAAGACACTTTTCGTCA                         CTGCATTTGGAGCCATTTTGCATGTGATATCCACTTCGCTTCTTGGTGTAA
genomic: CATCGTTGGCCGCGCCCAGAAATGGACTCTCTCCAAGACACTTTTCGTCAgtgagttgac ... ttttatgcagCTGCATTTGGAGCCATTTTGCATGTGATATCCACTTCGCTTCTTGGTGTCA
EST: gi|30128699|gb|CB914038.1|CB914038
EST:     CATCGTTGGCCGCGCCCAGAAATGGACTCTCTCCAAGACACTTTTCGTCA                         CTGCATTTGGAGCCATTTTGCATGTGATATCCACTTCGCTTCTTGGTGTCA
genomic: CATCGTTGGCCGCGCCCAGAAATGGACTCTCTCCAAGACACTTTTCGTCAgtgagttgac ... ttttatgcagCTGCATTTGGAGCCATTTTGCATGTGATATCCACTTCGCTTCTTGGTGTCA
EST: gi|110389090|gb|EC953903.1|EC953903
EST:     GAAATGGACTCTCTCCAAGACACTTTTCGTCA                         CTGCATTTGGAGCCATTTTGCATGTGATATCCACTTCGCTTCTTGGTGTAA
genomic: GAAATGGACTCTCTCCAAGACACTTTTCGTCAgtgagttgac ... ttttatgcagCTGCATTTGGAGCCATTTTGCATGTGATATCCACTTCGCTTCTTGGTGTCA
EST: gi|110693601|gb|EE069985.1|EE069985
EST:     CATCGTTGGCCGCGCCCAGAAATGGACTCTCTCCAAGACACTTTTCGTCA                         CTGCATTTGGAGCCATTTTGCATGTGATATCCACTTCGCTTCTTGGTGTCA
genomic: CATCGTTGGCCGCGCCCAGAAATGGACTCTCTCCAAGACACTTTTCGTCAgtgagttgac ... ttttatgcagCTGCATTTGGAGCCATTTTGCATGTGATATCCACTTCGCTTCTTGGTGTCA
EST: gi|351031955|gb|FQ460212.1|FQ460212
EST:     CATCGTTGGCCGCGCCCAGAAATGGACTCTCTCCAAGACACTTTTCGTCA                         CTGCATTTGGAGCCATTTTGCATGTGATATCCACTTCGCTTCTTGGTGTCA
genomic: CATCGTTGGCCGCGCCCAGAAATGGACTCTCTCCAAGACACTTTTCGTCAgtgagttgac ... ttttatgcagCTGCATTTGGAGCCATTTTGCATGTGATATCCACTTCGCTTCTTGGTGTCA
EST: gi|161717560|gb|FC066258.1|FC066258
EST:     CATCGTTGGCCGCGCCCAGAAATGGACTCTCTCCAAGACACTTTTCGTCA                         CTGCATTTGGAGCCATTTTGCATGTGATATCCACTTCGCTTCTTGGTGTAA
genomic: CATCGTTGGCCGCGCCCAGAAATGGACTCTCTCCAAGACACTTTTCGTCAgtgagttgac ... ttttatgcagCTGCATTTGGAGCCATTTTGCATGTGATATCCACTTCGCTTCTTGGTGTCA
EST: gi|161716448|gb|FC064936.1|FC064936
EST:     CATCGTTGGCCGCGCCCAGAAATGGACTCTCTCCAAGACACTTTTCGTCA                         CTGCATTTGGAGCCATTTTGCATGTGATATCCACTTCGCTTCTTGGTGTAA
genomic: CATCGTTGGCCGCGCCCAGAAATGGACTCTCTCCAAGACACTTTTCGTCAgtgagttgac ... ttttatgcagCTGCATTTGGAGCCATTTTGCATGTGATATCCACTTCGCTTCTTGGTGTCA
EST: gi|352795616|gb|FQ480204.1|FQ480204
EST:     CATCGTTGGCCGCGCCCAGAAATGGACTCTCTCCAAGACACTTTTCGTCA                         CTGCATTTGGAGCCATTTTGCATGTGATATCCACTTCGCTTCTTGGTGTCA
genomic: CATCGTTGGCCGCGCCCAGAAATGGACTCTCTCCAAGACACTTTTCGTCAgtgagttgac ... ttttatgcagCTGCATTTGGAGCCATTTTGCATGTGATATCCACTTCGCTTCTTGGTGTCA
EST: gi|351026323|gb|FQ428335.1|FQ428335
EST:     CATCGTTGGCCGCGCCCAGAAATGGACTCTCTCCAAGACACTTTTCGTCA                         CTGCATTTGGAGCCATTTTGCATGTGATATCCACTTCGCTTCTTGGTGTCA
genomic: CATCGTTGGCCGCGCCCAGAAATGGACTCTCTCCAAGACACTTTTCGTCAgtgagttgac ... ttttatgcagCTGCATTTGGAGCCATTTTGCATGTGATATCCACTTCGCTTCTTGGTGTCA
EST: gi|161715249|gb|FC064867.1|FC064867
EST:     CATCGTTGGCCGCGCCCAGAAATGGACTCTCTCCAAGACACTTTTCGTCA                         CTGCATTTGGAGCCATTTTGCATGTGATATCCACTTCGCTTCTTGGTGTCA
genomic: CATCGTTGGCCGCGCCCAGAAATGGACTCTCTCCAAGACACTTTTCGTCAgtgagttgac ... ttttatgcagCTGCATTTGGAGCCATTTTGCATGTGATATCCACTTCGCTTCTTGGTGTCA
EST: gi|351018509|gb|FQ424616.1|FQ424616
EST:     CATCGTTGGCCGCGCCCAGAAATGGACTCTCTCCAAGACACTTTTCGTCA                         CTGCATTTGGAGCCATTTTGCATGTGATATCCACTTCGCTTCTTGGTGTCA
genomic: CATCGTTGGCCGCGCCCAGAAATGGACTCTCTCCAAGACACTTTTCGTCAgtgagttgac ... ttttatgcagCTGCATTTGGAGCCATTTTGCATGTGATATCCACTTCGCTTCTTGGTGTCA
EST: gi|351024928|gb|FQ433345.1|FQ433345
EST:     CATCGTTGGCCGCGCCCAGAAATGGACTCTCTCCAAGACACTTTTCGTCA                         CTGCATTTGGAGCCATTTTGCATGTGATATCCACTTCGCTTCTTGGTGTCA
genomic: CATCGTTGGCCGCGCCCAGAAATGGACTCTCTCCAAGACACTTTTCGTCAgtgagttgac ... ttttatgcagCTGCATTTGGAGCCATTTTGCATGTGATATCCACTTCGCTTCTTGGTGTCA
EST: gi|110388694|gb|EC953471.1|EC953471
EST:     CATCGTTGGCCGCGCCCAGAAATGGACTCTCTCCAAGACACTTTTTGTCA                         CTGCATTTGGAGCCATTTTGCATGTGATATCCACTTCGCTTCTTGGTGTAA
genomic: CATCGTTGGCCGCGCCCAGAAATGGACTCTCTCCAAGACACTTTTCGTCAgtgagttgac ... ttttatgcagCTGCATTTGGAGCCATTTTGCATGTGATATCCACTTCGCTTCTTGGTGTCA
EST: gi|349824308|gb|FQ417719.1|FQ417719
EST:     CATCGTTGGCCGCGCCCAGAAATGGACTCTCTCCAAGACACTTTTCGTCA                         CTGCATTTGGAGCCATTTTGCATGTGATATCCACTTCGCTTCTTGGTGTCA
genomic: CATCGTTGGCCGCGCCCAGAAATGGACTCTCTCCAAGACACTTTTCGTCAgtgagttgac ... ttttatgcagCTGCATTTGGAGCCATTTTGCATGTGATATCCACTTCGCTTCTTGGTGTCA
EST: gi|351033350|gb|FQ446582.1|FQ446582
EST:     CATCGTTGGCCGCGCCCAGAAATGGACTCTCTCCAAGACACTTTTCGTCA                         CTGCATTTGGAGCCATTTTGCATGTGATATCCACTTCGCTTCTTGGTGTCA
genomic: CATCGTTGGCCGCGCCCAGAAATGGACTCTCTCCAAGACACTTTTCGTCAgtgagttgac ... ttttatgcagCTGCATTTGGAGCCATTTTGCATGTGATATCCACTTCGCTTCTTGGTGTCA
EST: gi|161708343|gb|FC055292.1|FC055292
EST:     CATCGTTGGCCGCGCCCAGAAATGGACTCTCTCCAAGACACTTTTCGTCA                         CTGCATTTGGAGCCATTTTGCATGTGATATCCACTTCGCTTCTTGGTGTAA
genomic: CATCGTTGGCCGCGCCCAGAAATGGACTCTCTCCAAGACACTTTTCGTCAgtgagttgac ... ttttatgcagCTGCATTTGGAGCCATTTTGCATGTGATATCCACTTCGCTTCTTGGTGTCA
EST: gi|161708738|gb|FC057914.1|FC057914
EST:     CATCGTTGGCCGCGCCCAGAAATGGACTCTCTCCAAGACACTTTTCGTCA                         CTGCATTTGGAGCCATTTTGCATGTGATATCCACTTCGCTTCTTGGTGTCA
genomic: CATCGTTGGCCGCGCCCAGAAATGGACTCTCTCCAAGACACTTTTCGTCAgtgagttgac ... ttttatgcagCTGCATTTGGAGCCATTTTGCATGTGATATCCACTTCGCTTCTTGGTGTCA
EST: gi|110723263|gb|EE100373.1|EE100373
EST:     CATCGTTGGCCGCGCCCAGAAATGGACTCTTTCCAAGACACTTTTCGTCA                         CTGCATTTGGAGCCATTTTGCATGTGATATCCACTTCGCTTCTTGGTGTAA
genomic: CATCGTTGGCCGCGCCCAGAAATGGACTCTCTCCAAGACACTTTTCGTCAgtgagttgac ... ttttatgcagCTGCATTTGGAGCCATTTTGCATGTGATATCCACTTCGCTTCTTGGTGTCA
EST: gi|110686866|gb|EE063774.1|EE063774
EST:     CATCGTTGGCCGCGCCCAGAAATGGACTCTCTCCAAGACACTTTTCGTCA                         CTGCATTTGGAGCCATTTTGCATGTGATATCCACTTCGCTTCTTGGTGTAA
genomic: CATCGTTGGCCGCGCCCAGAAATGGACTCTCTCCAAGACACTTTTCGTCAgtgagttgac ... ttttatgcagCTGCATTTGGAGCCATTTTGCATGTGATATCCACTTCGCTTCTTGGTGTCA
EST: gi|349833056|gb|FQ416434.1|FQ416434
EST:     CATCGTTGGCCGCGCCCAGAAATGGACTCTCTCCAAGACACTTTTCGTCA                         CTGCATTTGGAGCCATTTTGCATGTGATATCCACTTCGCTTCTTGGTGTCA
genomic: CATCGTTGGCCGCGCCCAGAAATGGACTCTCTCCAAGACACTTTTCGTCAgtgagttgac ... ttttatgcagCTGCATTTGGAGCCATTTTGCATGTGATATCCACTTCGCTTCTTGGTGTCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taagaatagtgcttgttgtttacaatctttttaacagctatttatttttatgcagCTGCATTTGGAGCCATTTTGCATGTGATATCCACTTCGCTTCTTGGTGTCACAGCAATCACCATGGCAAACAGTATTGCTGGGGAGGAAACAGTCCATAA
                            ttttaac  putative branch site (score: 2)
                                        tttattttt  putative PPT
                       aatctttttaacagct  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttcaactgctcaatctcgatatgaaaatcggccagggaattctgctaagaatagtgcttgttgtttacaatctttttaacagctatttatttttatgcagCTGCATTTGGAGCCATTTTGCATGTGATATCCACTTCGCTTCTTGGTGTCACAGCAATCACCATGGCAAACAGTATTGCTGGGGAGGAAACAGTCCATAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- caactgc
- - - - - caatctc
- - - - - - - - - - - gaaaatc
- - - - - - - - - - - - - - - - - - - -ttctgct
- - - - - - - - - - - - - - - - - - - - - - - aagaata
- - - - - - - - - - - - - - - - - - - - - - - - - - -gtgcttg