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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgcctttttacatatgaaattctggaggttgtatgatggaactggttggttaaatgatttgggatgtaaaattttctgaatgcattttttaattatgcagGTATGATTATTCTGGCTATGGGCAGTCTTCAGGAAAG

Basic information

species Vitis vinifera
transcript Vv17s0000g09740.t01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv17s0000g09740.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GRMZM2G039214_T01 (Zea mays), 3'ss of exon 1
tgcctttttacatatgaaattctggaggttgtatgatggaactggttggttaaatgatttgggatgtaaaattttctgaatgca-ttttttaattatgcagGTATGATTATTCTGGCTATGGGCAGTCTTCAGGAAAG
         | |||||  | | || |     ||      |  |   | ||||  ||||||       |  |    || |  | |  |||  |||||||||||||||| ||||| || |||||||| || |||||||||
-tttgaggaaaatatgttactttgtaaacaatacatcttatgtaacttgttacttgattttcctgtcatcagaggctaatagtagctttgaaattatgcagGTATGACTATTCAGGATATGGGCAATCATCAGGAAAG
















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|71888035|gb|DT037090.1|DT037090
EST:     TACGAGCTCTTCATCGAGTTGAGCATTCACTTGCGGGTTAATCTCATGGG                         GTATGATTATTCTGGCTATGGGCAGTCTTCAGGAAAG
genomic: TACGAGCTCTTCATCGAGTTGAGCATTCACTTGCGGGTTAATCTCATGGGgtacttcgtt ... aattatgcagGTATGATTATTCTGGCTATGGGCAGTCTTCAGGAAAG
EST: gi|110732441|gb|EE107729.1|EE107729
EST:     TACGAGCTCTTCATCGAGTTGAGCATTCACTTGCGGGTTAATCTCATGGG                         GTATGATTATTCTGGCTATGGGCAGTCTTCAGGAAAG
genomic: TACGAGCTCTTCATCGAGTTGAGCATTCACTTGCGGGTTAATCTCATGGGgtacttcgtt ... aattatgcagGTATGATTATTCTGGCTATGGGCAGTCTTCAGGAAAG
EST: gi|110711539|gb|EE088132.1|EE088132
EST:     TACGAGCTCTTCATCGAGTTGAGCATTCACTTGCGGGTTAATCTCATGGG                         GTATGATTATTCTGGCTATGGGCAGTCTTCAGGAAAG
genomic: TACGAGCTCTTCATCGAGTTGAGCATTCACTTGCGGGTTAATCTCATGGGgtacttcgtt ... aattatgcagGTATGATTATTCTGGCTATGGGCAGTCTTCAGGAAAG
EST: gi|71858447|gb|DT007502.1|DT007502
EST:     TACGAGCTTTTCATCGAGTTGAGCATTCACTTGCGGGTTAATCTCATGGG                         GTATGATTATTCTGGCTATGGGCAGTCTTCAGGAAAG
genomic: TACGAGCTCTTCATCGAGTTGAGCATTCACTTGCGGGTTAATCTCATGGGgtacttcgtt ... aattatgcagGTATGATTATTCTGGCTATGGGCAGTCTTCAGGAAAG
EST: gi|110684904|gb|EE062715.1|EE062715
EST:     TACGAGCTCTTCATCGAGTTGAGCATTCACTTGCGGGTTAATCTCATGGG                         GTATGATTATTCTGGCTATGGGCAGTCTTCAGGAAAG
genomic: TACGAGCTCTTCATCGAGTTGAGCATTCACTTGCGGGTTAATCTCATGGGgtacttcgtt ... aattatgcagGTATGATTATTCTGGCTATGGGCAGTCTTCAGGAAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttggttaaatgatttgggatgtaaaattttctgaatgcattttttaattatgcagGTATGATTATTCTGGCTATGGGCAGTCTTCAGGAAAG
                                         ttttaat  putative branch site (score: 3)
                                       tttttta  CT-rich tract
                     taaaattttctgaatg  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgcctttttacatatgaaattctggaggttgtatgatggaactggttggttaaatgatttgggatgtaaaattttctgaatgcattttttaattatgcagGTATGATTATTCTGGCTATGGGCAGTCTTCAGGAAAG

tgccttt
- - - - - - - - - attctgg
- - - - - - - - - - - - - - - - -tgatgga
- - - - - - - - - - - - - - - - - - - - - tggttgg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -atgtaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctgaatg