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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatccgtcttagcaattatctatttgacatactcttatccattttttttggtatcacctgctgcctgtcaaagttgggtgttaatcaggccactaatgaaattttgtgattacagGCCATGTGTATTATATTCAGATAATTCATTACATAATTCAGCAGAGGTCGCAGATGATCTCTCCAAATGTTGCATTAAGGAAGTCGAGAAGCCACATATG

Basic information

species Vitis vinifera
transcript Vv05s0020g02530.t01
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv05s0020g02530.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: GLYMA15G10940.1 (Glycine max), 3'ss of exon 8
gtatccg---tcttagcaattatctatttgacatactc---------ttatccatt-ttttttggtatcacctgctgcc--tgtcaaag---------------ttgggtgttaatcaggccactaatgaaattttgtgattacagGCCATGTGTATTATATTCAGATAATTCATTACATAATTCAGCAGAGGTCGCAGATGATCTCTCCAAATGTTGCATTAAGGAAGTCGAGAAGCCACATATG
||||||    | |  |  | ||| | |||||  |  ||         || |||||| || |||  | |   |   | ||  | |  ||                || ||  ||    |  |  || ||    |  ||||  | ||| || ||||| || ||||||||  | ||| | || ||  || | ||||| ||||||||||| |||||||||||||| || ||||| ||||| | ||  || 
gtatcccaattttctgttactatttttttgaattgttcctttcttctttgtccattgttcttttatcttgtcaaattccaatatagaaaaatccctttatctgctttggaattgccaactctgctgatttgttgctgtgcatgcagACCTTGTGTGTTGTATTCAGACCACTCAATGCAGAACACATCTGAGGTTGCAGATGATCTATCCAAATGTTGCATCAAAGAAGTTGAGAAACAACCCATA
















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|71863134|gb|DT012189.1|DT012189
EST:     AATGGTGCAACTGTTGCTCCACCTGAGAGACAACATGCATCATTACCGAG                         GCCATGTGTATTATATTCAGATAATTCATTACATAATTCAGCAGAGGTCGC
genomic: AATGGTGCAACTGTTGCTCCACCTGAGAGACAACATGCATCATTACCAAGgtatccgtct ... gtgattacagGCCATGTGTATTATATTCAGATAATTCATTACATAATTCAGCAGAGGTCGC
EST: gi|294964202|gb|GW838005.1|GW838005
EST:     AATGGTGCAACTGTTGCTCCACCTGAGAGACAACATGCATCATTACCAAG                         GCCATGTGTATTATATTCAGATAATTCATTACATAATTCAGCAGAGGTCGC
genomic: AATGGTGCAACTGTTGCTCCACCTGAGAGACAACATGCATCATTACCAAGgtatccgtct ... gtgattacagGCCATGTGTATTATATTCAGATAATTCATTACATAATTCAGCAGAGGTCGC
EST: gi|110690752|gb|EE068184.1|EE068184
EST:     AATGGTGCAACTGTTGCTCCACCTGAGAGACAACATGCATCATTACCAAG                         GCCATGTGTATTATATTCAGATAATTCATTACATAATTCAGCAGAGGTCGC
genomic: AATGGTGCAACTGTTGCTCCACCTGAGAGACAACATGCATCATTACCAAGgtatccgtct ... gtgattacagGCCATGTGTATTATATTCAGATAATTCATTACATAATTCAGCAGAGGTCGC
EST: gi|161719505|gb|FC067398.1|FC067398
EST:     AATGGTGCAACTGTTGCTCCACCTGAGAGACAACATGCATCATTACCAAG                         GCCATGTGTATTATATTCAGATAATTCATTACATAATTCAGCAGAGGTCGC
genomic: AATGGTGCAACTGTTGCTCCACCTGAGAGACAACATGCATCATTACCAAGgtatccgtct ... gtgattacagGCCATGTGTATTATATTCAGATAATTCATTACATAATTCAGCAGAGGTCGC
EST: gi|33404616|gb|CF210243.1|CF210243
EST:     AATGGTGCAACTGTTGCTCCACCTGAGAGACAACATGCATCATTACCAAG                         GCCATGTGTATTATATTCAGATAATTCATTACATAATTCAGCAGAGGTCGC
genomic: AATGGTGCAACTGTTGCTCCACCTGAGAGACAACATGCATCATTACCAAGgtatccgtct ... gtgattacagGCCATGTGTATTATATTCAGATAATTCATTACATAATTCAGCAGAGGTCGC
EST: gi|156735426|gb|EV239547.1|EV239547
EST:     AATGGTGCAACTGTTGCTCCACCTGAGAGACAACATGCATCATTACCAAG                         GCCATGTGTATTATATTCAGATAATTCATTACATAATTCAGCAGAGGTCGC
genomic: AATGGTGCAACTGTTGCTCCACCTGAGAGACAACATGCATCATTACCAAGgtatccgtct ... gtgattacagGCCATGTGTATTATATTCAGATAATTCATTACATAATTCAGCAGAGGTCGC
EST: gi|71860512|gb|DT009567.1|DT009567
EST:     AATGGTGCAACTGTTGCTCCACCTGAGAGACAACATGCATCATTACCGAG                         GCCATGTGTATTATATTCAGATAATTCATTACATAATTCAGCAGAGGTCGC
genomic: AATGGTGCAACTGTTGCTCCACCTGAGAGACAACATGCATCATTACCAAGgtatccgtct ... gtgattacagGCCATGTGTATTATATTCAGATAATTCATTACATAATTCAGCAGAGGTCGC
EST: gi|37188545|gb|CF607894.1|CF607894
EST:     AATGGTGCAACTGTTGCTCCACCTGAGAGACAACATGCATCATTACCTAG                         GCCATGTGTATTATAT
genomic: AATGGTGCAACTGTTGCTCCACCTGAGAGACAACATGCATCATTACCAAGgtatccgtct ... gtgattacagGCCATGTGTATTATAT
EST: gi|110730439|gb|EE107523.1|EE107523
EST:     AATGGTGCAACTGTTGCTCCACCTGAGAGACAACATGCATCATTACCAAG                         GCCATGTGTATTATATTCAGATAATTCATTACATAATTCAGCAGAGGTCGC
genomic: AATGGTGCAACTGTTGCTCCACCTGAGAGACAACATGCATCATTACCAAGgtatccgtct ... gtgattacagGCCATGTGTATTATATTCAGATAATTCATTACATAATTCAGCAGAGGTCGC
EST: gi|110387017|gb|EC951656.1|EC951656
EST:     AATGGTGCAACTGTTGCTCCACCTGAGAGACAACATGCATCATTACCAAG                         GCCATGTGTATTATATTCAGATAATTCATTACATAATTCAGCAGAGGTCGC
genomic: AATGGTGCAACTGTTGCTCCACCTGAGAGACAACATGCATCATTACCAAGgtatccgtct ... gtgattacagGCCATGTGTATTATATTCAGATAATTCATTACATAATTCAGCAGAGGTCGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctgcctgtcaaagttgggtgttaatcaggccactaatgaaattttgtgattacagGCCATGTGTATTATATTCAGATAATTCATTACATAATTCAGCAGAGGTCGCAGATGATCTCTCCAAATGTTGCATTAAGGAAGTCGAGAAGCCACATATG
                              cactaat  putative branch site (score: 2)
                               actaatgaaatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatccgtcttagcaattatctatttgacatactcttatccattttttttggtatcacctgctgcctgtcaaagttgggtgttaatcaggccactaatgaaattttgtgattacagGCCATGTGTATTATATTCAGATAATTCATTACATAATTCAGCAGAGGTCGCAGATGATCTCTCCAAATGTTGCATTAAGGAAGTCGAGAAGCCACATATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC