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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...catatggttagcacttgcaggttgtaaaatattatgacaaatgttttacctgcattatatctattgttatatcattgataagatacttttaactgcagagTTTTGACCCAGATTCTGATTATGTTCCAACTCCGATGGTTCTGATAGATCAAGATTCAGATTCTGTTGCAACAATTGTACAGCTTAGTTTTGGAGATCGA

Basic information

species Vitis vinifera
transcript Vv13s0147g00220.t01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv13s0147g00220.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GRMZM2G066496_T01 (Zea mays), 3'ss of exon 2
catatggttagcacttgcaggttgtaaaatattatgacaaatgttttacctgcattatatctattgttatatcattgataagatacttttaactgcagagTTTTGACCCAGAT-TCTGATTATG---TTCCAACTCCGATGGTTCTGATAGATCAAGATTCAGATTCTGTTGCAACAATTGTACAGCTTAGTTTTGGAGATCGA-------
     |     || || |   ||||    |||| |  || |   |        |||  || ||||| |  ||   |  |||  |   ||       | | | |   ||||||  |||||| | |   | |||   ||  | || | |||||||||||| |||||   || |||||| ||||| ||||| ||||||||||||||        
----agaactccattttccc-ttgtgctttattcttgcacacactgc-----tattcaatttattgatg-attgcttttaacgtgtattcttggtaaaattctcaccccagACATCTGATGAGGCAATCCCAGTCCCAGTTGTCCAGATAGATCAAGACTCAGACCGTGATGCAACCATTGTGCAGCTAAGTTTTGGAGATCGTTTGGGGG

upper sequence: Vv13s0147g00220.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA10G42580.4 (Glycine max), 3'ss of exon 2
catatggttagcacttgcaggttgtaaaatattatgacaaatgttttacctgcat-tatatctattgttat-atcattgataagatacttttaact--gcagagTTTTGACCCAGATTCTGATTATGTTCCAACTCCGATGGTTCTGATAGATCAAGATTCAGATTCTGTTGCAACAATTGTACAGCTTAGTTTTGGAGATCGA
  | || | |  | |       | |    |  | | |   |||   | | |  || || || ||||  ||  ||  |||||  |||| || | |||  ||||   | ||      || |||||  |||||| |  || || ||||| ||||||||||| ||||||||||  ||||||||||| |||||||| ||||| ||||  
--tttgttaattattcattacatatgccctgcttttatgtatgccatgcttttatgtacatatatttataggatgtttgattggataattcttactgtgcagCAATCTGGTGACAATCCTGATAGTGTTCCTATGCCAATAGTTCTAATAGATCAAGAATCAGATTCTGAAGCAACAATTGTGCAGCTTAGCTTTGGGGATC--

upper sequence: Vv13s0147g00220.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA20G24450.1 (Glycine max), 3'ss of exon 2
catatggttagcacttgcaggttgtaaaatatt-atgacaaatgttttacctgcat-tatatctattgttatatcatt-gataagatacttttaact--gcagagTTTTGACCCAGATTCTGATTATGTTCCAACTCCGATGGTTCTGATAGATCAAGATTCAGATTCTGTTGCAACAATTGTACAGCTTAGTTTTGGAGATCGA
    || | |  | |       | |    | |  ||     |||   | | |  || || || |||| || ||   || ||   | || || |  ||  ||||   | ||      || |||||  | |||| |  || || ||||| ||||||||||| ||||||||||  ||||||||||| |||||||| |||||  |||  
---ttgttaattattcattaaatatgccctctggattttgtatgccgtgcttttatgtacatatatttttgtaatgtttgaatggttaattcttgctgtgcagCAATCTGGTGACAATCCTGATAGTCTTCCTATGCCAATAGTTCTAATAGATCAAGAATCAGATTCTGAAGCAACAATTGTGCAGCTTAGCTTTGGGAATC--

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|110392201|gb|EC957452.1|EC957452
EST:     AGATTCAGTTCCTTCAATATCACTGAG                        
genomic: AGATTCAGTTCCTTCAATATCACT--Ggtcagtaaca ... aactgcaga
EST: gi|22014843|gb|BQ799877.1|BQ799877
EST:     TCAGTTCC-TCAATATCACTG                         A
genomic: TCAGTTCCTTCAATATCACTGgtcagtaaca ... aactgcagag-
EST: gi|22014843|gb|BQ799877.1|BQ799877
EST:     TCAGTTCC-TCAATATCACTG                         A
genomic: TCAGTTCCTTCAATATCACTGgtcagtaaca ... aactgcagag-
EST: gi|110430431|gb|EC996990.1|EC996990
EST:     AGATTCAGTTCCTTCAATATCACTGAG                        
genomic: AGATTCAGTTCCTTCAATATCACT--Ggtcagtaaca ... aactgcaga
EST: gi|110394001|gb|EC958326.1|EC958326
EST:     AGATTCAGTTCCTTCAATATCACTGAG                        
genomic: AGATTCAGTTCCTTCAATATCACT--Ggtcagtaaca ... aactgcaga
EST: gi|110358677|gb|EC923071.1|EC923071
EST:     CTTCAATATCACTGAG                        
genomic: CTTCAATATCACT--Ggtcagtaaca ... aactgcaga


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttacctgcattatatctattgttatatcattgataagatacttttaactgcagagTTTTGACCCAGATTCTGATTATGTTCCAACTCCGATGGTTCTGATAGATCAAGATTCAGATTCTGTTGCAACAATTGTACAGCTTAGTTTTGGAGATCGA
                                         ttttaac  putative branch site (score: 2)
        attatatctattgtta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
catatggttagcacttgcaggttgtaaaatattatgacaaatgttttacctgcattatatctattgttatatcattgataagatacttttaactgcagagTTTTGACCCAGATTCTGATTATGTTCCAACTCCGATGGTTCTGATAGATCAAGATTCAGATTCTGTTGCAACAATTGTACAGCTTAGTTTTGGAGATCGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC
- - tggttag
- - - - - -cacttgc
- - - - - - - - - - - - -aaaatat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gataaga