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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aaaaacagcatgttcttgtttgagtctactaaattggtcttgctgtattattttgccttcccgtgctttgttgatttccttcttggcttggtttaaccagGAAACAGCTGATCACCTACTCTACCCAAATCCTGGGTCAGGAATGATACACGAACAGCATCTCCAGTTTTTCCATTTTCTTGGAACTGTTCTTGGGAAG

Basic information

species Vitis vinifera
transcript Vv05s0077g00470.t01
intron # 17
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv05s0077g00470.t01 (Vitis vinifera), 3'ss of exon 17
lower sequence: LOC_Os05g06690.1 (Oryza sativa), 3'ss of exon 17
aaaaacagcatgttcttgtttgagtctactaaattg----gtcttgctgtattattttgccttcccgtgctttgttgatttccttcttggcttggtttaaccagGAAACAGCTGATCACCTACTCTACCCAAATCCTGGGTCAGGAATGATACACGAACAGCATCTCCAGTTTTTCCATTTTCTTGGAACTGTTCTTGGGAAG
 ||       | | |||   | | |    || | ||    |||| ||  | |   | |   || |   |  |      |||| || ||    |  ||    ||||| ||||| ||||| || ||||||||||||||||| || ||| || | || ||||||||||| || |  |||||||||||||| | | | |||||||||
-aagttcaagtctgctttcctaactggtttacagtgtgatgtctagcaatttgcatatcaattacaaaggctcacatgtttcgtttttaatctttttg---cagGAGACAGCCGATCATCTTCTCTACCCAAATCCTGGATCTGGATTGGTCCATGAACAGCATCTGCAATACTTCCATTTTCTTGGCAGTCTCCTTGGGAAG

upper sequence: Vv05s0077g00470.t01 (Vitis vinifera), 3'ss of exon 17
lower sequence: GLYMA09G03680.1 (Glycine max), 3'ss of exon 3
aaaaacagcatgttcttgtttgagtctactaaattggtcttgctgtattattttgccttcccgtgctttgttgatttcc----ttcttggcttggtt-taaccagGAAACAGCTGATCACCTACTCTACCCAAATCCTGGGTCAGGAATGATACACGAACAGCATCTCCAGTTTTTCCATTTTCTTGGAACTGTTCTTGGGAAG
                                             | ||| ||||  |||   || ||| | |   ||     ||||   | |  ||  | |||||||||||| |||||||| || || || ||||||||  ||||||||||||| ||||| ||| |||| |||||||| |||||||| ||| | ||||  |||
--------------------------------------------tttttactttgtgttctattggtttatggcaatctgaaattctgaacatcattgcatccaggaaacagcagatcacctgctttatcctaatcctgga-cagGAATGATACATGAACAACATTTCCAATTTTTCCACTTTCTTGGTACTCTCCTTGCAAAG

upper sequence: Vv05s0077g00470.t01 (Vitis vinifera), 3'ss of exon 17
lower sequence: GLYMA17G04180.1 (Glycine max), 3'ss of exon 16
aaaaacagcatgttcttgtttgagtctactaaattggtcttgctgta-ttattttgccttcccgtgctttgttgatttcc----ttcttggc-ttggtttaaccagGAAACAGCTGATCACCTACTCTACCCAAATCCTGGGTCAGGAATGATACACGAACAGCATCTCCAGTTTTTCCATTTTCTTGGAACTGTTCTTGGGAAG
   | ||| |     || ||| | | ||  |   || ||||| | |  |||| ||   | |    | |||  |||||  |    | ||     ||  | |  | |||||||||| |||||||| || || || |||||||| || ||||||||||| ||||| ||| |||| |||||||| || ||||| ||| |||| |  |||
--gatcagaag----ttatttcattttataatcctgctcttggtatccttatatttgttccttacgatttactgattctcggtatactgaatgttaatgtgtctagGAAACAGCGGATCACCTGCTTTATCCTAATCCTGGATCTGGAATGATACATGAACAACATTTCCAATTTTTCCACTTCCTTGGTACTCTTCTCGCAAAG

upper sequence: Vv05s0077g00470.t01 (Vitis vinifera), 3'ss of exon 17
lower sequence: GLYMA07G36390.1 (Glycine max), 3'ss of exon 16
aaaaacagcatgttcttgtttgagtctactaaattggtcttgctgta-ttattttgccttcccgtgctttgttgatttcc----ttcttggc-ttggtttaaccagGAAACAGCTGATCACCTACTCTACCCAAATCCTGGGTCAGGAATGATACACGAACAGCATCTCCAGTTTTTCCATTTTCTTGGAACTGTTCTTGGGAAG
    |  | | ||      || | | ||  |   ||  |||| | |  |||| ||   | |  | | |||  | |||  |    | ||     ||  |  |   |||||||||| |||||||| || ||  | |||||||| || ||||||||||| ||||| ||| |||| |||||||| || ||||| ||| ||||||  |||
---gatcgaaagtg---acttcattttataatcctgcccttggtatccttatatttgttgcttgagatttactaattctcggtatactgaatgttaatgcatttagGAAACAGCGGATCACCTGCTTTATGCTAATCCTGGATCTGGAATGATACATGAACAACATTTCCAATTTTTCCACTTCCTTGGTACTCTTCTTGCAAAG

upper sequence: Vv05s0077g00470.t01 (Vitis vinifera), 3'ss of exon 17
lower sequence: AT3G17205.1 (Arabidopsis thaliana), 3'ss of exon 16
----------aaaaacagcatgttcttgtttgagtctact---aaattggtcttgctgtattattttgccttcccgtgctttgttgatttcct---tcttg-gcttggtttaac-cagGAAACAGCTGATCACCTACTCTACCCAAATCCTGGGTCAGGAATGATACACGAACAGCATCTCCAGTTTTTCCATTTTCTTGGAACTGTTCTTGGGAAG
           |     ||     |  ||||  ||  | |    ||||   ||| ||  || || ||  | |   || | |   |  ||  ||   | |||  | || |||    ||||| || ||||||||| | || || || |||||||| |||||||||||||| ||||||||||||||||| || |||||||| || | | | || |  || 
gtcatatgtctagttttgctcacccaagtttttgtggatttgataatttaccttactccatcatctttgcatttagtacgtctatctttctctgaatattgtacatgctttctttcagGAGACCGCTGATCACATGCTTTATCCTAATCCTGGATCAGGAATGATACATGAACAGCATCTCCAGTTCTTTCATTTTCTCGGCAGTCTCCTCGCAAAA

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|71889221|gb|DT038276.1|DT038276
EST:     TGGAAAACATTACACGAGCAGCTTTTGACGTGCAGTATGGGTTGTTTAAG                         GAAACAGCTGATCACCTACTCTACCCAAATCCTGGGTCAGGAATGATACAC
genomic: TGGAAAACATTACACGAGCAGCTTTTGACGTGCAGTATGGGTTGTTTAAGgttgtaattt ... gtttaaccagGAAACAGCTGATCACCTACTCTACCCAAATCCTGGGTCAGGAATGATACAC
EST: gi|71884176|gb|DT033231.1|DT033231
EST:     TGGAAAACATTACACGAGCAGCTTTTGACGTGCAGTATGGGTTGTTTAAG                         GAAACAGCTGATCACCTACTCTACCCAAATCCTGGGTCAGGAATGATACAC
genomic: TGGAAAACATTACACGAGCAGCTTTTGACGTGCAGTATGGGTTGTTTAAGgttgtaattt ... gtttaaccagGAAACAGCTGATCACCTACTCTACCCAAATCCTGGGTCAGGAATGATACAC
EST: gi|71888019|gb|DT037074.1|DT037074
EST:     TGGAAAACATTACACGAGCAGCTTTTGACGTGCAGTATGGGTTGTTTAAG                         GAAACAGCTGATCACCTACTCTACCCAAATCCTGGGTCAGGAATGATACAC
genomic: TGGAAAACATTACACGAGCAGCTTTTGACGTGCAGTATGGGTTGTTTAAGgttgtaattt ... gtttaaccagGAAACAGCTGATCACCTACTCTACCCAAATCCTGGGTCAGGAATGATACAC
EST: gi|71881320|gb|DT030375.1|DT030375
EST:     TGGAAAACATTACACGAGCAGCTTTTGACGTGCAGTATGGGTTGTTTAAG                         GAAACAGCTGATCACCTACTCTACCCAAATCCTGGGTCAGGAATGATACAC
genomic: TGGAAAACATTACACGAGCAGCTTTTGACGTGCAGTATGGGTTGTTTAAGgttgtaattt ... gtttaaccagGAAACAGCTGATCACCTACTCTACCCAAATCCTGGGTCAGGAATGATACAC
EST: gi|110370035|gb|EC934210.1|EC934210
EST:     ACGAGCAGCTTTTGACGTGCAGTATGGGTTGTTTAAG                         GAAACAGCTGATCACCTACTCTACCCAAATCCTGGGTCAGGAATGATACAC
genomic: ACGAGCAGCTTTTGACGTGCAGTATGGGTTGTTTAAGgttgtaattt ... gtttaaccagGAAACAGCTGATCACCTACTCTACCCAAATCCTGGGTCAGGAATGATACAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tattattttgccttcccgtgctttgttgatttccttcttggcttggtttaaccagGAAACAGCTGATCACCTACTCTACCCAAATCCTGGGTCAGGAATGATACACGAACAGCATCTCCAGTTTTTCCATTTTCTTGGAACTGTTCTTGGGAAG
                       tgttgat  putative branch site (score: 4)
                         ttgattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aaaaacagcatgttcttgtttgagtctactaaattggtcttgctgtattattttgccttcccgtgctttgttgatttccttcttggcttggtttaaccagGAAACAGCTGATCACCTACTCTACCCAAATCCTGGGTCAGGAATGATACACGAACAGCATCTCCAGTTTTTCCATTTTCTTGGAACTGTTCTTGGGAAG

aaaaaca
- - - - catgttc
- - - - - - - - - - - - - - - - - - - cttgctg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgctttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tccttct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tggcttg