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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tctgtttgttagatgttgaattagtaatgatggttattgcaaatgaaattctgaaactaaaatttcatattgtcatgacgtctcacatctgggtttgcagGTGTGTTATCCGTGGTTGTGTTCCTAAAAAGATTTTGGTGTATGGAGCATCTTTTAGAGGTGAAATTGAG

Basic information

species Vitis vinifera
transcript Vv05s0051g00870.t01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv05s0051g00870.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: LOC_Os02g56850.1 (Oryza sativa), 3'ss of exon 3
------------------------------------------tctgtttgttagatgttgaattag--taatgatggttattgc--aaatgaaattctgaaa-----ctaaaatttcatattgtcatgacgtctcacatctgggtt-tgc-agGTGTGTTATCCGTGGTTGTGTTCCTAAAAAGATTTTGGTGTATGGAGCATCTTTTAGAGGTGAAATTGAG
                                            ||  || | |||  ||| |||    ||   |  | ||  |     ||| | | ||| |     ||  |   | | |    ||||     |    |    ||| ||| |||||||| || ||||||||||| |||||||||||  ||||||||||  |||||||  | || ||| |||||
gtaagcatctgccgattacttgtctgcgtttacatttctgtcgttgaatgcttgattatgatttaaaccaactctcctcatcccctgggtgagaatgtgagatgttgctgcatcctaaaacccgcatgctcattattgtacatgttgtgctagGTGTGTGATACGTGGTTGTGTGCCTAAAAAGATACTGGTGTATGGTTCATCTTTCCGCGGAGAATTTGAG

upper sequence: Vv05s0051g00870.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA16G27210.1 (Glycine max), 3'ss of exon 3
-tctgtttgttaga--tgttgaattagtaatgatggttattgcaaatgaaattctgaaactaaaatttcatattgtcatgacgtctcacatctgggtttgcagGTGTGTTATCCGTGGTTGTGTTCCTAAAAAGATTTTGGTGTATGGAGCATCTTTTAGAGGTGAAATTGAG
   ||| |  ||||     |       ||   ||   ||||  |  | || | ||||   ||     | | | ||   |    | |    | |   ||   ||||||||||| |||||||||||||| |||||||||||||| ||||||||||||||| |||||||  |||||
aattgtgtaatagagtcacttctactctataaatatctattctagttcaactactgag--tagttaatgaaaatgcttttttctttttt-tttaatttcaaagGTGTGTTATTCGTGGTTGTGTTCCCAAAAAGATTTTGGTCTATGGAGCATCTTTTGGAGGTGATCTTGAG

upper sequence: Vv05s0051g00870.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA02G08180.1 (Glycine max), 3'ss of exon 2
tctgtttgttagatgttgaattagtaatgatggttattgcaaatgaaattctgaa-----actaaaatttcatattgtcatgacgtctcacatctgggtttgcagGTGTGTTATCCGTGGTTGTGTTCCTAAAAAGATTTTGGTGTATGGAGCATCTTTTAGAGGTGAAATTGAG
    |||  |   |  |    |  | ||||| | || |  |  | || | || |        | ||| | | |||| |  | |  | | |  | |   ||   ||||||||||| |||||||||||||| |||||||||||||| ||||||||||||||| |||||||  || ||
----tttcctcactcctct-ctgctgatgatagctaatcaagttcaactactaagtagttgatgaaaatgcttattttttttattttttatttttaatttcaaagGTGTGTTATTCGTGGTTGTGTTCCCAAAAAGATTTTGGTCTATGGAGCATCTTTTGGAGGTGATCTTCAG

upper sequence: Vv05s0051g00870.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: AT3G24170.1 (Arabidopsis thaliana), 3'ss of exon 3
tctgtttgttagatgttgaattagtaatgatg-gttattgcaaatgaaattctgaaactaaaatttcatattgtcatgacgtctcacatctg--ggtttgcagGTGTGTTATCCGTGGTTGTGTTCCTAAAAAGATTTTGGTGTATGGAGCATCTTTTAGAGGTGAAATTGAG
              ||    |   |  |||||  ||||   |  |   | ||| | ||    || | |||   | ||    |  ||| | |   || || ||| ||||||||||||||||||||||||||||||||| | || ||||||||  |||   | |||||| |||||
--------------gtaagttccttgttgatgcattatcaaacgttggaatcttacac---gatcttatacctttatttgtttccactttttttggctttcagCTGTGTTATCCGTGGTTGTGTTCCTAAAAAGATTCTCGTCTATGGAGCTACTTACGGTGGTGAACTTGAG

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|161717161|gb|FC065924.1|FC065924
EST:     CTTCCCTTTCACCCAGTCAGCTCAGAAGTAATTGGAGGGGTTGGTGGCAC                         GTGTGTTATCCGTGGTTGTGTTCCTAAAAAGATTTTGGTGTATGGAGCATC
genomic: CTTCCCTTTCACCCAGTCAGCTCAGAAGTAATTGGAGGGGTTGGTGGCACgtaagtttat ... gggtttgcagGTGTGTTATCCGTGGTTGTGTTCCTAAAAAGATTTTGGTGTATGGAGCATC
EST: gi|71857814|gb|DT006869.1|DT006869
EST:     CTTCCCTTTCACCCAGTCAGCTCAGAAGTAATTGGAGGGGTTGGTGGCAC                         GTGTGTTATCCGTGGTTGTGTTCCTAAAAAGATTTTGGTGTATGGAGCATC
genomic: CTTCCCTTTCACCCAGTCAGCTCAGAAGTAATTGGAGGGGTTGGTGGCACgtaagtttat ... gggtttgcagGTGTGTTATCCGTGGTTGTGTTCCTAAAAAGATTTTGGTGTATGGAGCATC
EST: gi|161715993|gb|FC068764.1|FC068764
EST:     CTTCCCTTTCACCCAGTCAGCTCAGAAGTAATTGGAGGGGTTGGTGGCAC                         GTGTGTTATCCGTGGTTGTGTTCCTAAAAAGATTTTGGTGTATGGAGCATC
genomic: CTTCCCTTTCACCCAGTCAGCTCAGAAGTAATTGGAGGGGTTGGTGGCACgtaagtttat ... gggtttgcagGTGTGTTATCCGTGGTTGTGTTCCTAAAAAGATTTTGGTGTATGGAGCATC
EST: gi|110699093|gb|EE077335.1|EE077335
EST:     CTTCCCTTTCACCCAGTCAGCTCAGAAGTAATTGGAGGGGTTGGTGGCAC                         GTGTGTTATCCGTGGTTGTGTTCCTAAAAAGATTTTGGTGTATGGAGCATC
genomic: CTTCCCTTTCACCCAGTCAGCTCAGAAGTAATTGGAGGGGTTGGTGGCACgtaagtttat ... gggtttgcagGTGTGTTATCCGTGGTTGTGTTCCTAAAAAGATTTTGGTGTATGGAGCATC
EST: gi|37187518|gb|CF606871.1|CF606871
EST:     CTTCCCTTTCACCCAGTCAGCTCAGAAGTAATTGGAGGGGTTGGTGGCAC                         GTGTGTTATCCGTGGTTGTGTTCCTAAAAAGATTTTGGTGTATGGAGCATC
genomic: CTTCCCTTTCACCCAGTCAGCTCAGAAGTAATTGGAGGGGTTGGTGGCACgtaagtttat ... gggtttgcagGTGTGTTATCCGTGGTTGTGTTCCTAAAAAGATTTTGGTGTATGGAGCATC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaattctgaaactaaaatttcatattgtcatgacgtctcacatctgggtttgcagGTGTGTTATCCGTGGTTGTGTTCCTAAAAAGATTTTGGTGTATGGAGCATCTTTTAGAGGTGAAATTGAG
        aaactaaaatttcata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tctgtttgttagatgttgaattagtaatgatggttattgcaaatgaaattctgaaactaaaatttcatattgtcatgacgtctcacatctgggtttgcagGTGTGTTATCCGTGGTTGTGTTCCTAAAAAGATTTTGGTGTATGGAGCATCTTTTAGAGGTGAAATTGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCA
-ctgtttg
- - - - - - - - - - - - - -tgatggt
- - - - - - - - - - - - - - - - - - - - aaatgaa
- - - - - - - - - - - - - - - - - - - - - - - - - - -aaactaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tcatgac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctcacat