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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaccatgatgaaccaactttttacattcaagatcttttatgactattttgtcttactgccttgaaatttccattttgtagGAGCGCTCAGTTGCAACTATTCTGTATCTTGTTTCTCTACAAGATCTCACAAACTGCCCTTTTAGGGTGGTTGATGAGATAAATCAAG

Basic information

species Vitis vinifera
transcript Vv13s0064g00180.t01
intron # 25
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv13s0064g00180.t01 (Vitis vinifera), 3'ss of exon 25
lower sequence: LOC_Os05g51790.2 (Oryza sativa), 3'ss of exon 25
gtaccatgatgaaccaactttttacattcaagatcttttatgactattttgtcttactgccttgaaatttccattttgtagGAGCGCTCAGTTGCAACTATTCTGTATCTTGTTTCTCTACAAGATCTCACAAACTGCCCTTTTAGGGTGGTTGATGAGATAAATCAAG
|||  |  |  || | | |   | ||||| |||    | ||| ||  |   |  || |   ||    || |   ||| |||||||| |||||| |||| || ||||| ||||| || || |||||||| || |||||||| ||| |||| |||||||||||||||||||
gtatgaaaa--aaactattagatgcattctagaaaaat-atgccttatacttactattatttt----ttgctcctttatagGAGCGATCAGTTTCAACCATCCTGTACCTTGTATCACTTCAAGATCTTACCAACTGCCCCTTTCGGGTCGTTGATGAGATAAATCAAG

upper sequence: Vv13s0064g00180.t01 (Vitis vinifera), 3'ss of exon 25
lower sequence: GRMZM2G440916_T01 (Zea mays), 3'ss of exon 25
gtaccatg-atgaaccaacttt---ttacattcaagatcttttatgactattttgtcttactgccttgaaatttccattttgtagGAGCGCTCAGTTGCAACTATTCTGTATCTTGTTTCTCTACAAGATCTCACAAACTGCCCTTTTAGGGTGGTTGATGAGATAAATCAAG
|||  | | || ||| |   |    | | ||   | ||||||| |    |  ||  |||| |   |     || |  |||  |||||||| || ||  | || ||  |||||||||| || || |||||||| || |||||||||||| |||| |||||||||||||||||||
gtatgaaggatcaactagtgtcgagtcaaatgtgaaatcttttctcttcacctt--cttattatttcc---ttgctgtttcatagGAGCGATCTGTATCGACCATCTTGTATCTTGTGTCACTTCAAGATCTTACCAACTGCCCTTTTCGGGTTGTTGATGAGATAAATCAAG

upper sequence: Vv13s0064g00180.t01 (Vitis vinifera), 3'ss of exon 25
lower sequence: GLYMA20G34020.1 (Glycine max), 3'ss of exon 26
gtaccatgatgaaccaactttttacattcaagatcttttatgactattttgtcttactgccttgaaatttccattttgtagGAGCGCTCAGTTGCAACTATTCTGTATCTTGTTTCTCTACAAGATCTCACAAACTGCCCTTTTAGGGTGGTTGATGAGATAAATCAAG
|||  |  | |||     || |||  ||  |  | || ||||  |   |    | |    | |     ||  ||||| ||||| ||||||||| |||||||| | ||||||||||| || |||||||| ||||||||||| ||||| || ||||||||||| || ||||
gtattacaaagaatttgtttctta--ttacatttgttctatgttttcctcccttaatgaaccttggggtttgattttctagGAACGCTCAGTTTCAACTATTGTTTATCTTGTTTCCCTTCAAGATCTTACAAACTGCCCATTTAGAGTCGTTGATGAGATCAACCAAG

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|351031040|gb|FQ444867.1|FQ444867
EST:     GCAAGCAGGAGAACTTCAAGTTCTTAGCGCCCACCATCAATCTGGAGGG                         GAGCGCTCAGTTGCAACTATTCTGTATCTTGTTTCTCTACAAGATCTCACA
genomic: GCAAGCAGGAGAACTTCAAGTTCTTAGCGCCCACCATCAATCTGGAGGGgtaccatgat ... cattttgtagGAGCGCTCAGTTGCAACTATTCTGTATCTTGTTTCTCTACAAGATCTCACA
EST: gi|351032202|gb|FQ460459.1|FQ460459
EST:     GCAAGCAGGAGAACTTCAAGTTCTTAGCGCCCACCATCAATCTGGAGGG                         GAGCGCTCAGTTGCAACTATTCTGTATCTTGTTTCTCTACAAGATCTCACA
genomic: GCAAGCAGGAGAACTTCAAGTTCTTAGCGCCCACCATCAATCTGGAGGGgtaccatgat ... cattttgtagGAGCGCTCAGTTGCAACTATTCTGTATCTTGTTTCTCTACAAGATCTCACA
EST: gi|351031564|gb|FQ459821.1|FQ459821
EST:     GCAAGCAGGAGAACTTCAAGTTCTTAGCGCCCACCATCAATCTNNNNNN                         NAGCGCTCAGTTGCAACTATTCTGTATCTCGTTTCTCTACAAGATCTCACA
genomic: GCAAGCAGGAGAACTTCAAGTTCTTAGCGCCCACCATCAATCTGGAGGGgtaccatgat ... cattttgtagGAGCGCTCAGTTGCAACTATTCTGTATCTTGTTTCTCTACAAGATCTCACA
EST: gi|351037685|gb|FQ464126.1|FQ464126
EST:     GCAAGCAGGAGAACTTCAAGTTCTTAGCGCCCACCATCAATCTNNNNNN                         NAGCGCTCAGTTGCAACTATTCTGTATCTCGTTTCTCTACAAGATCTCACA
genomic: GCAAGCAGGAGAACTTCAAGTTCTTAGCGCCCACCATCAATCTGGAGGGgtaccatgat ... cattttgtagGAGCGCTCAGTTGCAACTATTCTGTATCTTGTTTCTCTACAAGATCTCACA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcaagatcttttatgactattttgtcttactgccttgaaatttccattttgtagGAGCGCTCAGTTGCAACTATTCTGTATCTTGTTTCTCTACAAGATCTCACAAACTGCCCTTTTAGGGTGGTTGATGAGATAAATCAAG
                        gtcttac  putative branch site (score: 3)
                                         tttccatttt  putative PPT
         ttttatgactatttt  TA-rich tract