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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagaattccatcttactgcctatgctattcctttttttttttttccctttgatttgattgttttcatgtcactattggattgcattttgatgcagGCCTTGGTCCTACCATAATGCAGGTTCCTGGCCAACTTTGCTCTGGCAG

Basic information

species Vitis vinifera
transcript Vv13s0074g00720.t01
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv13s0074g00720.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: LOC_Os04g33490.1 (Oryza sativa), 3'ss of exon 4
gtaagaattccatcttactgcctatgctattcctttttttttttttccctttgatttgattgttttcatgtcactattggattgcattttgatgcagGCCTTGGTCCTACCATAATGCAGGTTCCTGGCCAACTTTGCTCTGGCAG
|| ||    || | | | |  | ||| ||  || | |  |||       || ||||| ||  | ||  | |   |  |        |||  ||||||| ||||||| |||||||||| |||||||||||||||  |  | ||||||
gtgag----ccctatgattatc-atg-taacccgtgtaatttagactgtttggatttcatcttatttgttttttttctc-------tttcaatgcagGGCTTGGTCTTACCATAATGGAGGTTCCTGGCCAACACTATTGTGGCAG

upper sequence: Vv13s0074g00720.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: LOC_Os02g32730.1 (Oryza sativa), 3'ss of exon 5
gtaagaattccatcttactgcctatgctattcctttttttttttttccctttgatttgattgttttcatgtcactattggattgcattttgatgcagGCCTTGGTCCTACCATAATGCAGGTTCCTGGCCAACTTTGCTCTGGCAG
|| ||  |||    | | |  || |||   ||  | |   | ||     |   ||  ||   | ||| |   | |||         | ||||| |||||||||||| || ||||||| ||| ||||||||||| ||| | ||||||
gtgagttttcggaataattatctttgca--tctatgtacatgttcaagttccaat--gagcatcttcttagtaatatc--------tattgattcagGCCTTGGTCATATCATAATGGAGGATCCTGGCCAACATTGTTATGGCAG

upper sequence: Vv13s0074g00720.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA08G15220.1 (Glycine max), 3'ss of exon 5
gtaagaattccatcttac--tgcctatgctattcctttttttttttttccctttgatttgattgttttcatgtcactattggattgcattttgatgcagGCCTTGGTCCTACCATAATGCAGGTTCCTGGCCAACTTTGCTCTGGCAG
|||     || |  || |  ||  |||| | |||  || | || || |   ||| ||   ||  ||||        ||||  |||   |||||  |||||||||||||||||||||||||||| |||||||||||  |||||||||||
gtactgtatctaatttgccgtgtttatgtttttctgttatcttattatatttttcatcaaatgattttt------ttatttaattattttttg--gcagGCCTTGGTCCTACCATAATGCAGGCTCCTGGCCAACACTGCTCTGGCAG

upper sequence: Vv13s0074g00720.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA05G31920.1 (Glycine max), 3'ss of exon 4
gtaagaattccatcttactgcctatgctattcctttttttttt-tttccctttgatttgattgttttcatgtcactattggattgcattttgatgcagGCCTTGGTCCTACCATAATGCAGGTTCCTGGCCAACTTTGCTCTGGCAG
    | |    |||| | |  || || || |  ||||| | || | |   | |  |||   |    | || |   |||| | ||   |||||  ||||||| |||||||||||||||||||| |||||||||||  |||||||||||
----gtacagtatctaatttgctgtgttaatgttttttctattatcttattatatttttcatcaaatgatttttttatttgtttattttttg--gcagGCCATGGTCCTACCATAATGCAGGCTCCTGGCCAACACTGCTCTGGCAG

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|294964217|gb|GW838020.1|GW838020
EST:     TGAAGGTCCAGGAATTGGCAA-TTATCACCGGTAGTGATCCTAAAAACAC                         GCCTTGGTCCTACCAT
genomic: TGAAGGTC-AGGAAT-GGCAAATTATCACCGGTAGTGATCCTAAGAACACgtaagaattc ... tttgatgcagGCCTTGGTCCTACCAT
EST: gi|110382317|gb|EC939148.1|EC939148
EST:     CTTGAAGGTCAGGAATGGCAAATTATCACCGGTAGTGATCCTAAGAACAC                         GCCTTGGTCCTACCATAATGCAGGTTCCTGGCCAACTTTGCTCTGGCAG
genomic: CTTGAAGGTCAGGAATGGCAAATTATCACCGGTAGTGATCCTAAGAACACgtaagaattc ... tttgatgcagGCCTTGGTCCTACCATAATGCAGGTTCCTGGCCAACTTTGCTCTGGCAG
EST: gi|110687834|gb|EE065698.1|EE065698
EST:     CTTGAAGGTCAGGAATGGCAAATTATCACCGGTAGTGATCCTAAGAACAC                         GCCTTGGTCCTACCATAATGCAGGTTCCTGGCCAACTTTGCTCTGGCAG
genomic: CTTGAAGGTCAGGAATGGCAAATTATCACCGGTAGTGATCCTAAGAACACgtaagaattc ... tttgatgcagGCCTTGGTCCTACCATAATGCAGGTTCCTGGCCAACTTTGCTCTGGCAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttccctttgatttgattgttttcatgtcactattggattgcattttgatgcagGCCTTGGTCCTACCATAATGCAGGTTCCTGGCCAACTTTGCTCTGGCAG
                                            ttttgat  putative branch site (score: 4)
       tttgattt  TA-rich tract