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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGTGAGGAGGGTTTGGTCCATTTTCAGTGGCTTGATAGAACCAACAATGTCCTTGAAGATgtatcctagtttttaaattttccattttactatggtattactcagctttaatccattttcttatccttcacacatgcaaaaatgtgtttcattttttttt...

Basic information

species Vitis vinifera
transcript Vv11s0065g00450.t01
intron # 4
splice site 5'
intron type U12 (go to U12 genes for details)

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv11s0065g00450.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: GLYMA08G03080.3 (Glycine max), 5'ss of exon 4
GGTGAGGAGGGTTTGGTCCATTTTCAGTGGCTTGATAGAACCAACAATGTCCTTGAAGATgtatcctagtttttaaattttccattttactatggtattactcagctt-taatccattttcttatccttcacacatgcaaaaatgtgtttcattttttttt
||||||||||| || ||||||||||||||||||||| | ||  | ||| |  |||||||||||||||   |||| | |       |  |  ||  | | |          |||    || ||| |  |   ||   |     || | ||| |  | |||  
GGTGAGGAGGGATTAGTCCATTTTCAGTGGCTTGATCGCACACAAAATATTGTTGAAGATgtatcctttgttttcagtggcttggta-atcatcatttaaggggatgcacaattaggttccttcttttgttcaggagttttcatttattttacatgtttaa

upper sequence: Vv11s0065g00450.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: GLYMA05G36490.2 (Glycine max), 5'ss of exon 4
GGTGAGGAGGGTTTGGTCCATTTTCAGTGGCTTGATAGAACCAACAATGTCCTTGAAGATgtatcctagtttttaaattttccattttac---tatggtattactcagct---ttaatccattttcttatccttcacacatgcaaaaatgtgtttcattttttttt
||||||||||| || || |||||||||||||||||| | ||  | |||||  |||||||||||||||   ||||   |  || |||||       ||||  |  |||  |   |  || ||   |    | | |  |   |      | || |||  |        
GGTGAGGAGGGATTAGTACATTTTCAGTGGCTTGATCGCACACAAAATGTTGTTGAAGATgtatcctttgttttccctcctcaattttgtacacttggtcatcatcatttaagtggatgcacaattaggttccttcctttttggtgcaagtattttgtac------

upper sequence: Vv11s0065g00450.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: GLYMA05G36490.1 (Glycine max), 5'ss of exon 4
------------------GGTGAGGAGGGTTTGGTCCATTTTCAGTGGCTTGATAGAACCAACAATGTCCTTGAAGATgtatcctagtttttaaattttccattttac---tatggtattactcagct---ttaatccattttcttatccttcacacatgcaaaaatgtgtttcattttttttt
                  ||||||||||| || || |||||||||||||||||| | ||  | |||||  |||||||||||||||   ||||   |  || |||||       ||||  |  |||  |   |  || ||   |    | | |  |   |      | || |||  |        
TGTTTGCTTCTGTTTCAGGGTGAGGAGGGATTAGTACATTTTCAGTGGCTTGATCGCACACAAAATGTTGTTGAAGATgtatcctttgttttccctcctcaattttgtacacttggtcatcatcatttaagtggatgcacaattaggttccttcctttttggtgcaagtattttgtac------

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|87584845|gb|DY473849.1|DY473849
EST:     GTTTGGTCCATTTTCAGTGGCTTGATAGAACCAACAATGTCCTTGAAGAT                         GACCAGATTGTTTTTCCTGATGAAGCAGTTTTTGAGAAG
genomic: GTTTGGTCCATTTTCAGTGGCTTGATAGAACCAACAATGTCCTTGAAGATgtatcctagt ... tgtaccatagGACCAGATTGTTTTTCCTGATGAAGCAGTTTTTGAGAAG
EST: gi|294964296|gb|GW838099.1|GW838099
EST:     GTTTGGTCCATTTTCAGTGGCTTGATAGAACCAACAATGTCCTTGAAGAT                         GACCAGATTGTCTTTCCTGATGAAGCAGTTTTTGAGAAG
genomic: GTTTGGTCCATTTTCAGTGGCTTGATAGAACCAACAATGTCCTTGAAGATgtatcctagt ... tgtaccatagGACCAGATTGTTTTTCCTGATGAAGCAGTTTTTGAGAAG
EST: gi|33405732|gb|CF211359.1|CF211359
EST:     GTTTGGTCCATTTTCAGTGGCTTGATAGAACCAACAATGTCCTTGAAGAT                         GACCAGATTGTTTTTCCTGATGAAGCAGTTTTTGAGAAG
genomic: GTTTGGTCCATTTTCAGTGGCTTGATAGAACCAACAATGTCCTTGAAGATgtatcctagt ... tgtaccatagGACCAGATTGTTTTTCCTGATGAAGCAGTTTTTGAGAAG
EST: gi|351028718|gb|FQ433148.1|FQ433148
EST:     GTTTGGTCCATTTTCAGTGGCTTGATAGAACCAACAATGTCCTTGAAGAT                         GACCAGATTGTTTTTCCTGATGAAGCAGTTTTTGAGAAG
genomic: GTTTGGTCCATTTTCAGTGGCTTGATAGAACCAACAATGTCCTTGAAGATgtatcctagt ... tgtaccatagGACCAGATTGTTTTTCCTGATGAAGCAGTTTTTGAGAAG
EST: gi|22011495|gb|BQ796529.1|BQ796529
EST:     GTTTGGTCCATTTTCAGTGGCTTGATAGAACCAACAATGTCCTTGAAGAT                         GACCAGATTGTTTTTCCTGATGAAGCAGTTTTTGAGAAG
genomic: GTTTGGTCCATTTTCAGTGGCTTGATAGAACCAACAATGTCCTTGAAGATgtatcctagt ... tgtaccatagGACCAGATTGTTTTTCCTGATGAAGCAGTTTTTGAGAAG
EST: gi|110377829|gb|EC942921.1|EC942921
EST:     GTTTGGTCCATTTTCAGTGGCTTGATAGAACCAACAATGTCCTTGAAGAT                         GACCAGATTGTTTTTCCTGATGAAGCAGTTTTTGAGAAG
genomic: GTTTGGTCCATTTTCAGTGGCTTGATAGAACCAACAATGTCCTTGAAGATgtatcctagt ... tgtaccatagGACCAGATTGTTTTTCCTGATGAAGCAGTTTTTGAGAAG
EST: gi|161716363|gb|FC068095.1|FC068095
EST:     GTTTGGTCCATTTTCAGTGGCTTGATAGAACCAACAATGTCCTTGAAGAT                         GACCAGATTGTTTTTCCTGATGTAGCAGTTTTTGAGAAG
genomic: GTTTGGTCCATTTTCAGTGGCTTGATAGAACCAACAATGTCCTTGAAGATgtatcctagt ... tgtaccatagGACCAGATTGTTTTTCCTGATGAAGCAGTTTTTGAGAAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGTGAGGAGGGTTTGGTCCATTTTCAGTGGCTTGATAGAACCAACAATGTCCTTGAAGATgtatcctagtttttaaattttccattttactatggtattactcagctttaatccattttcttatccttcacacatgcaaaaatgtgtttcattttttttt

- - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gcaaaaa