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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttttttttttttttctccatttgcccatacaatttgcaagacagtaataccaaatcctctttacatctatggcatgattcattatgttttgactcataccattcaaaatataatggttgctattttccttccattcgtcatctttcacaacccgtgcaccctgcagGACATAAAGTTTGCTGTTCATGCACATCCAACCTTGTCCGAGGTGCTTGACGAACTCTTCAAATCTGCTAAG

Basic information

species Vitis vinifera
transcript Vv14s0060g01330.t01
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv14s0060g01330.t01 (Vitis vinifera), 3'ss of exon 13
lower sequence: LOC_Os05g06460.1 (Oryza sativa), 3'ss of exon 13
gttttttttttttttctccatttgcccatacaatttgcaagacagtaataccaaatcctctttacatctatggcatgattcattatgttttgactcataccattcaaaatataatggttgctattttccttccattcgtcatctttcacaacccgtgcaccctgcagGACATAAAGTTTGCTGTTCATGCACATCCAACCTTGTCCGAGGTGCTTGACGAACTCTTCAAATCTGCTAAG
                                                                  |   |   |||||    | | | || |||     | |      ||   |    ||  | |  |||  ||| | |||  |   ||  ||   ||||  ||||||||| |||||||||||||||||||| ||||| |||||||||||||| ||||||||||| ||| | || |||
-----------------------------------------------------------------gtgagtataatgatattatttttcttcacttggttcgtctttgttagcctttcagcagtataacttgaatttgacatgat---cactcc---caccacgcagGACATCAAGTTTGCTGTTCATGCACACCCAACATTGTCCGAGGTGCTGGACGAACTCTTTAAAGCAGCCAAG

upper sequence: Vv14s0060g01330.t01 (Vitis vinifera), 3'ss of exon 13
lower sequence: LOC_Os01g23610.1 (Oryza sativa), 3'ss of exon 13
gttttttttttttttctccatttgcccatacaatttgcaagacagtaataccaaatcctctttacatctatggcatgattcattatgttttgactcataccattcaaaatataatggttgctattttccttccattcgtcatctttcacaacccgtgcaccctgcagGACATAAAGTTTGCTGTTCATGCACATCCAACCTTGTCCGAGGTGCTTGACGAACTCTTCAAATCTGCTAAG
                                                                                                  |      |  || | || |||  |   |   || |||| |      |  ||      | || ||  |||||||| |||||||||||||||||||| ||||| ||||| ||||| || || || ||||||||| |||| |||
-----------------------------------------------------------------------------------------------gtaagtgacgagcattttattgtttatgaatggattgcatttgc-----tcaacgctgtttacatcccccagGACATCAAGTTTGCTGTTCATGCACACCCAACTTTGTCTGAGGTTCTGGATGAGCTCTTCAAAGCTGCCAAG

upper sequence: Vv14s0060g01330.t01 (Vitis vinifera), 3'ss of exon 13
lower sequence: GRMZM2G145595_T01 (Zea mays), 3'ss of exon 13
gttttttttttttttctccatttgcccatacaatttgcaagacagtaataccaaatcctctttacatctatggcatgattcattatgttttgactcataccattcaaaatataatggttgctattttccttccattcgtcatctttcacaacccgtgcaccctgcagGACATAAAGTTTGCTGTTCATGCACATCCAACCTTGTCCGAGGTGCTTGACGAACTCTTCAAATCTGCTAAG
                                    |  ||   || || |   || || ||  | | | | ||||  |||   || |||            |||     |||||| |      ||   ||     | | | ||||         || |||||||||||||| |||||||||||||||||||| ||||| ||||| || || || || |||||||||||  |||| |||
------------------------------------gtgagtttgtcatgc---attctgttagc-tgtgtagcat--ttctgcattttt-----------gttctctgcataatgctaaacgcttaaattt-gcacataaccttt---------tgtaccctgcagGACATCAAGTTTGCTGTTCATGCACACCCAACGTTGTCTGAAGTTCTGGATGAACTCTTCAAGGCTGCCAAG

upper sequence: Vv14s0060g01330.t01 (Vitis vinifera), 3'ss of exon 13
lower sequence: GRMZM2G073774_T01 (Zea mays), 3'ss of exon 13
gttttttttttttttctccatttgcccatacaatttgcaagacagtaataccaa-atcctctttacatctatggcatgattcattatgttttgactc-ataccattcaaaatataatggttgctattttccttccattcgtcatctttcacaacccgtgcaccctgcagGACATAAAGTTTGCTGTTCATGCACATCCAACCTTGTCCGAGGTGCTTGACGAACTCTTCAAATCTGCTAAG
                                        |  |||    |  | |  || |||   | ||| |    ||||||  |  || || ||  |   | ||  |   ||   |||   || ||    |  | | | ||| ||      | ||      |||||||||| |||||||||||||| ||||| || || ||||| ||||| || || |||||||||||| | || |||
----------------------------------------gtgagtgtcgctgataatctattt---tttattgagc-attcatctttgttggattctgtcatactcgtagc-tagcagtt--catcttgaacctgtacataatcgttt-----ctgtat---ttgcagGACATCAAGTTTGCTGTTCACGCACACCCTACATTGTCTGAGGTCCTGGATGAACTCTTCAAAGCAGCCAAG

upper sequence: Vv14s0060g01330.t01 (Vitis vinifera), 3'ss of exon 13
lower sequence: GRMZM2G152958_T02 (Zea mays), 3'ss of exon 13
gttttttttttttttctccatttgcccatacaatttgcaagacagtaataccaa-atcctctttacatctatggcatgattcattatgttttgactc-ataccattcaaaatataatggttgctattttccttccattcgtcatctttcacaacccgtgcaccctgcagGACATAAAGTTTGCTGTTCATGCACATCCAACCTTGTCCGAGGTGCTTGACGAACTCTTCAAATCTGCTAAG
       |    |  | | |    | | |      ||||||  |||    |  | |  || |||   | ||| |    ||||||  |  || || ||  |   | ||  |   ||   |||   || ||    |  | | | ||| ||      | ||      |||||||||| |||||||||||||| ||||| || || ||||| ||||| || || |||||||||||| | || |||
------atgccatcgccctaggaactcgtg-----tgcaagtgagtgtcgctgataatctattt---tttattgagc-attcatctttgttggattctgtcatactcgtagc-tagcagtt--catcttgaacctgtacataatcgttt-----ctgtat---ttgcagGACATCAAGTTTGCTGTTCACGCACACCCTACATTGTCTGAGGTCCTGGATGAACTCTTCAAAGCAGCCAAG

upper sequence: Vv14s0060g01330.t01 (Vitis vinifera), 3'ss of exon 13
lower sequence: PP1S35_94V6.1 (Physcomitrella patens), 3'ss of exon 13
gttttttttttttttctccatttgcccatacaatttgcaagacagtaataccaaatcctctttacatctatggcatgattcattatgttttgactcataccattcaaaatataatggttgctattttccttccattcgtcatctttcacaacccgtgcaccctg--cagGACATAAAGTTTGCTGTTCATGCACATCCAACCTTGTCCGAGGTGCTTGACGAACTCTTCAAATCTGCTAAG
            |   |||||   | |||   |||  ||      |  | |  || | |  |||  ||   |  | ||| | | || |    |   |||    |||     |    | |     || |  |  |||| | |      ||     || |  | ||   ||||||| ||||||||||||||||| ||||| ||||| || || ||  | ||||| || |||||  | ||||||
-----------gtgagtccatgaactcatttgattcacag----ttgctgctgaacctt--ttaattcccagctaggatccttgatttaccaatcaatattcgtcacgtctt----gctatcgattgctgtgtattcctaaaaca--actggttgttcttcttgaatagGACATCAAGTTTGCTGTTCATGCCCATCCCACCTTATCTGAAGTTTTGGACGAGCTGTTCAAGGCAGCTAAG

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|110371471|gb|EC935522.1|EC935522
EST:     ACCTCATACACGAGGCATCCAATGCAATAGCTCTAGGGACACGTATACAG                         GACATAAAGTTTGCTGTTCATGCACATCCAACCTTGTCCGAGGTGCTTGAC
genomic: ACCTCATACACGAGGCATCCAATGCAATAGCTCTAGGGACACGTATACAGgttttttttt ... caccctgcagGACATAAAGTTTGCTGTTCATGCACATCCAACCTTGTCCGAGGTGCTTGAC






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aatggttgctattttccttccattcgtcatctttcacaacccgtgcaccctgcagGACATAAAGTTTGCTGTTCATGCACATCCAACCTTGTCCGAGGTGCTTGACGAACTCTTCAAATCTGCTAAG
         tatttt  TA-rich tract