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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgttgcatgtgaattatccacaaagataatagttttggaagcatagattttgtcccaaaatgaaagaatggatgcacgtgtacttatttattttgtttgatgcagGGTTTCGAAGTCGGGTTAAATACATAAGTGTTTTGGATCCAACAAATATGTCTTACTATGTCTCAGAAATTCTGGATGCAGGATTAGCTGGACCTCTGTT

Basic information

species Vitis vinifera
transcript Vv14s0036g00570.t01
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv14s0036g00570.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: AT1G08620.1 (Arabidopsis thaliana), 3'ss of exon 9
gtatgttgcatgtgaattatccacaaagataatagtt--ttggaagcatagattttgtcccaaaatgaaagaatggatgcacgtgtacttatttattttgtttgatgcagGGTTTCGAAGTCGGGTTAAATACATAAGTGTTTTGGATCCAACAAATATGTCTTACTATGTCTCAGAAATTCTGGATGCAGGATTAGCTGGACCTCTGTT
           ||||  | |   |||  ||  | | |  |||  | |||  |   |    || | || |||      |||   | |   ||||    || |||| |||||| ||||| || |||||||| |||||||   |||||||||||||||||||||  | |||  | ||||||||||||||||| |||       | ||  ||||
-----------gtgacatgtggtcaagtatttttgctacttgagaacattaacagttatacatattgcaag------tgcttat-tgtctattc---ttctttggtgcagGATTTCGTAGCCGGGTTAAGTACATAAACATTTTGGATCCAACAAATATGTGCTTCTACATTTCAGAAATTCTGGATGCTGGACGCAACAGTCCATTGTT
















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|56408484|gb|CX016736.1|CX016736
EST:     TGTGATTTCTGGAAAGTTGTGGTGCAACAGGCAGGCAGTTTTTCCCAAGG                         GGTTTCGAAGTCGGGTTAAATACATAAGTGTTTTGGATCCAACAAATATGT
genomic: TGTGATTTCTGGAAAGTTGTGGTGCAACAGGCAGGCAATTTTTCCCAAGGgtatgttgca ... tttgatgcagGGTTTCGAAGTCGGGTTAAATACATAAGTGTTTTGGATCCAACAAATATGT
EST: gi|56408652|gb|CX016904.1|CX016904
EST:     TGTGATTTCTGGAAAGTTGTGGTGCAACAGGCAGGCAGTTTTTCCCAAGG                         GGTTTCGAAGTCGGGTTAAATACATAAGTGTTTTGGATCCAACAAATATGT
genomic: TGTGATTTCTGGAAAGTTGTGGTGCAACAGGCAGGCAATTTTTCCCAAGGgtatgttgca ... tttgatgcagGGTTTCGAAGTCGGGTTAAATACATAAGTGTTTTGGATCCAACAAATATGT
EST: gi|161706481|gb|FC055002.1|FC055002
EST:     TGTGATTTCTGGAAAGTTGTGGTGCAACACGCAGGCAATTTTTCCCAAGG                         GGTTTCGAAGTCGGGTTAAATACATAAGTGTTTTGGATCCAACAAATATGT
genomic: TGTGATTTCTGGAAAGTTGTGGTGCAACAGGCAGGCAATTTTTCCCAAGGgtatgttgca ... tttgatgcagGGTTTCGAAGTCGGGTTAAATACATAAGTGTTTTGGATCCAACAAATATGT
EST: gi|110711369|gb|EE087767.1|EE087767
EST:     TGTGATTTCTGGAAAGTTGTGGTGCAACAGGCAGGCAATTTTTCCCAAGG                         GGTTTCGAAGTCGGGTTAAATACATAAGTGTTTTGGATCCAACAAATATGT
genomic: TGTGATTTCTGGAAAGTTGTGGTGCAACAGGCAGGCAATTTTTCCCAAGGgtatgttgca ... tttgatgcagGGTTTCGAAGTCGGGTTAAATACATAAGTGTTTTGGATCCAACAAATATGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtcccaaaatgaaagaatggatgcacgtgtacttatttattttgtttgatgcagGGTTTCGAAGTCGGGTTAAATACATAAGTGTTTTGGATCCAACAAATATGTCTTACTATGTCTCAGAAATTCTGGATGCAGGATTAGCTGGACCTCTGTT
                                            gtttgat  putative branch site (score: 5)
                                        ttttgttt  CT-rich tract
                              tacttatttattttgt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgttgcatgtgaattatccacaaagataatagttttggaagcatagattttgtcccaaaatgaaagaatggatgcacgtgtacttatttattttgtttgatgcagGGTTTCGAAGTCGGGTTAAATACATAAGTGTTTTGGATCCAACAAATATGTCTTACTATGTCTCAGAAATTCTGGATGCAGGATTAGCTGGACCTCTGTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA