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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtgagaattcaaatagtgattcttgttttattttacttacaatcaattttgattccatttttttttcttgtgtttcttttaattatcaagtggttgtgtttccatgcagTCACCGCCGCATTGTTCAGTACAAAACTGCTTATTACTCATTTTACCTTCCA

Basic information

species Vitis vinifera
transcript Vv19s0015g01010.t01
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv19s0015g01010.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: LOC_Os01g50760.1 (Oryza sativa), 3'ss of exon 5
gtaagtgagaattcaaatagtgattcttgttttattttacttacaatcaattttgattccatttttttttcttgtgtttcttttaattatcaagtggttgtgtttccatgcagTCACCGCCGCATTGTTCAGTACAAAACTGCTTATTACTCATTTTACCTTCCA
   ||   || ||  | | |   |   | ||||||||||         ||||  | |   || ||  |||  ||   ||||||||| |  ||  | ||           |||||||||||||||||||||||||||| || ||||| |||||||| || ||||| 
tctagaatgagttgtatttgcacta--tattttattttagcagttcagaattgggttatgatcttcatttaatggtgttcttttaactgacatattgt-----------gcagTCACCGCCGCATTGTTCAGTACAAGACAGCTTACTACTCATTCTATCTTCCG

upper sequence: Vv19s0015g01010.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GRMZM2G098569_T01 (Zea mays), 3'ss of exon 5
--------------------------------------------------------------gtaagtgagaattcaaatagtgattcttgttttattttacttacaatcaattttgattccatttttttttcttgtgtttcttttaattatcaagtggttgtgtttccatgcagTCACCGCCGCATTGTTCAGTACAAAACTGCTTATTACTCATTTTACCTTCCA
                                                               |   | ||  | || |  | | || || || | | ||    ||    ||||| |  |  | | |||| | ||||| |  |||    | |||| || || |  ||     ||||||||||||||| ||||||||||| || |||||||| ||||| |||||||| 
gtaagtttatgtttcgctgtatcagtaacataattcacacgctttgtttcctttcatggtttattgtttagtttccagaatgag-ttattattatgtgtttagcacctcaaatttaggataaaatcttttat-ttgtgctaatttc---tctcaa-tgattttcattttgcacagTCACCGCCGCATCGTTCAGTACAAGACAGCTTATTATTCATTCTACCTTCCT

upper sequence: Vv19s0015g01010.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GRMZM2G147721_T01 (Zea mays), 3'ss of exon 5
-------------------------------------------------------------gtaagtgagaattcaaatagtgattcttgttttattttacttacaatcaattttgattccatttttttttcttgtgtttcttttaattatcaagtggttgtgtttccatgcagTCACCGCCGCATTGTTCAGTACAAAACTGCTTATTACTCATTTTACCTTCCA
                                                              |   | ||  | || |  | ||   || |  |   ||    ||    ||||| |     | | ||| |||  |||||  ||     | ||||  | || |  ||     ||||| ||||| ||| ||||||||||| || |||||||| |||||||||||||| 
gtaagatcatgttcactgtatcagtaacataattcacacgctttgtttccttacatgatttattgtttagtttccagaatgagaca-ttatcatgcgtttagcacctcaaatttgggacataatctttattc--gtgttaattcc---tctcaa-cgattttcattttgcacagTCGCCGCCACATCGTTCAGTACAAGACAGCTTATTATTCATTTTACCTTCCT

upper sequence: Vv19s0015g01010.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA15G12780.1 (Glycine max), 3'ss of exon 6
gtaagtgagaattcaaatagtgattcttgttttattttacttacaatcaattttgattccatttttttttcttgt-----gtttcttttaattatcaagtggttgtgtttccatgcagTCACCGCCGCATTGTTCAGTACAAAACTGCTTATTACTCATTTTACCTTCCA
           |||||   |  ||| |   | ||||  |||| || |  || ||| |  || ||| |||  || |      |   |  |||| |  |       |   |    ||||| || || || |||||||||||||| ||||| ||||| || ||||||||||| 
-----------ttcaat--gcaatttta--tatattccactt-cagt--atcttgttcacaatttctttctttattggaaatcaatactaatgactagcaaacggacatcttctgcagGCATCGACGTATTGTTCAGTACAAGACTGCATATTATTCCTTTTACCTTCCG

upper sequence: Vv19s0015g01010.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: AT5G47770.1 (Arabidopsis thaliana), 3'ss of exon 6
gtaagtgagaattcaaatagtgattcttgtttta-ttttacttacaatcaattttgattccatttttttttcttgtgtttcttttaattatcaagtggttgtgtttc-catgcagTCACCGCCGCATTGTTCAGTACAAAACTGCTTATTACTCATTTTACCTTCCA
    |||||   |||| | |||    |||| | | |||||  |||  |   || ||||      ||   |    |    | || | |   | | |   | || ||   | ||||| ||||| || ||||| ||||||||||| ||||||||||||||||| || || 
----gtgag---tcaact-gtgggcattgtctaaattttagatacggtttcttctgatggttgattagatgaaaggcagtattctgacc-tgatgcaatggttttcaacttgcagCCACCGTCGTATTGTCCAGTACAAAACGGCTTATTACTCATTTTATCTCCCT

upper sequence: Vv19s0015g01010.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: AT4G17190.1 (Arabidopsis thaliana), 3'ss of exon 5
gtaagtgagaattcaaatagtgattcttgttttattttacttacaatcaattttgattccatttttttttcttgtgtttcttttaattatcaagtggttgtgtttccatgcagTCACCGCCGCATTGTTCAGTACAAAACTGCTTATTACTCATTTTACCTTCCA
    ||||||  |   ||    ||| ||  |  ||  |      | | || |  |||| ||| | |||  ||  ||         ||||| |  | | | |    |  ||||| || || || |||||| |||||||||| ||||||||||||||||| ||||| 
----gtgagagatatcattcaaatttttaatggatgatgt----agtgaagtaggattacatgtgtttgactgatg---------attat-agtttgctctaaaac-gtgcagCCATCGGCGTATTGTTGAGTACAAAACAGCTTATTACTCATTTTATCTTCCT

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|161718315|gb|FC067264.1|FC067264
EST:     ATCACGACTATTGAAGGAGAGAAAGATCTATCGAAGTATTCATTGCCTCT                         TCACCGCCGCATTGTTCAGTACAAAACTGCTTATTACTCATTTTACCTTCC
genomic: ATCACGACTATTGAAGGAGAGAAAGATCTATCAAAGTATTCATTGCCTCTgtaagtgaga ... ttccatgcagTCACCGCCGCATTGTTCAGTACAAAACTGCTTATTACTCATTTTACCTTCC
EST: gi|110702878|gb|EE079232.1|EE079232
EST:     ATCACGACTATTGAAGGAGAGAAAGATCTATCAAAGTATTCATTGCCTCT                         TCACCGCCGCATTGTTCAGTACAAAACTGCTTATTACTCATTTTACCTTCC
genomic: ATCACGACTATTGAAGGAGAGAAAGATCTATCAAAGTATTCATTGCCTCTgtaagtgaga ... ttccatgcagTCACCGCCGCATTGTTCAGTACAAAACTGCTTATTACTCATTTTACCTTCC
EST: gi|110396453|gb|EC962139.1|EC962139
EST:     ATCACGACTATTGAAGGAGAGAAAGATCTATCGAAGTATTCATTGCCTCT                         TCACCGCCGCATTGTTCAGTACAAAACTGCTTATTACTCATTTTACCTTCC
genomic: ATCACGACTATTGAAGGAGAGAAAGATCTATCAAAGTATTCATTGCCTCTgtaagtgaga ... ttccatgcagTCACCGCCGCATTGTTCAGTACAAAACTGCTTATTACTCATTTTACCTTCC
EST: gi|22013972|gb|BQ799006.1|BQ799006
EST:     ATCACGACTATTGAAGGAGAGAAAGATCTATCAAAGTATTCATTGCCTCT                         TCACCGCCGCATTGTTCAGTACAAAACTGCTTATTACTCATTTTACCTTCC
genomic: ATCACGACTATTGAAGGAGAGAAAGATCTATCAAAGTATTCATTGCCTCTgtaagtgaga ... ttccatgcagTCACCGCCGCATTGTTCAGTACAAAACTGCTTATTACTCATTTTACCTTCC
EST: gi|110729204|gb|EE105291.1|EE105291
EST:     ATCACGACTATTGAAGGAGAGAAAGATCTATCAAAGTATTCATTGCCTCT                         TCACCGCCGCATTGTTCAGTACAAAACTGCTTATTACTCATTTTACCTTCC
genomic: ATCACGACTATTGAAGGAGAGAAAGATCTATCAAAGTATTCATTGCCTCTgtaagtgaga ... ttccatgcagTCACCGCCGCATTGTTCAGTACAAAACTGCTTATTACTCATTTTACCTTCC
EST: gi|71877000|gb|DT026055.1|DT026055
EST:     ATCACGACTATTGAAGGAGAGAAAGATCTATCGAAGTATTCATTGCCTCT                         TCACCGCCGCATTGTTCAGTACAAAACTGCTTATTACTCATTTTACCTTCC
genomic: ATCACGACTATTGAAGGAGAGAAAGATCTATCAAAGTATTCATTGCCTCTgtaagtgaga ... ttccatgcagTCACCGCCGCATTGTTCAGTACAAAACTGCTTATTACTCATTTTACCTTCC
EST: gi|30256278|gb|CB972121.1|CB972121
EST:     ATCACGACTATTGAAGGAGAGAAAGATCTATCAAAGTATTCATTGCCTCT                         TCACCGCCGCATTGTTCAGTACAAAACTGCTTATTACTCATTTTACCTTCC
genomic: ATCACGACTATTGAAGGAGAGAAAGATCTATCAAAGTATTCATTGCCTCTgtaagtgaga ... ttccatgcagTCACCGCCGCATTGTTCAGTACAAAACTGCTTATTACTCATTTTACCTTCC
EST: gi|46917987|gb|CN547316.1|CN547316
EST:     ATCACGACTATTGAAGGAGAGAAAGATCTATCAAAGTATTCATTGCCTCT                         TCACCGCCGCATTGTTCAGTACAAAACTGCTTATTACTCATTTTACCTTCC
genomic: ATCACGACTATTGAAGGAGAGAAAGATCTATCAAAGTATTCATTGCCTCTgtaagtgaga ... ttccatgcagTCACCGCCGCATTGTTCAGTACAAAACTGCTTATTACTCATTTTACCTTCC
EST: gi|110698392|gb|EE075834.1|EE075834
EST:     ATC-CGACTATTGAAGGAGAGAAAGATCTATCAAAGTATTCATTGCCTCT                         TCACCGCCGCATTGTTCAGTACAAAACTGCTTATTACTCATTTTACCTTCC
genomic: ATCACGACTATTGAAGGAGAGAAAGATCTATCAAAGTATTCATTGCCTCTgtaagtgaga ... ttccatgcagTCACCGCCGCATTGTTCAGTACAAAACTGCTTATTACTCATTTTACCTTCC
EST: gi|77579770|gb|DV218763.1|DV218763
EST:     ATCACGACTATTGAAGGAGAGAAAGATCTATCAAAGTATTCATTGCCTCT                         TCACCGCCGCATTGTTCAGTACAAAACTGCTTATTACTCATTTTACCTTCC
genomic: ATCACGACTATTGAAGGAGAGAAAGATCTATCAAAGTATTCATTGCCTCTgtaagtgaga ... ttccatgcagTCACCGCCGCATTGTTCAGTACAAAACTGCTTATTACTCATTTTACCTTCC
EST: gi|110375001|gb|EC939952.1|EC939952
EST:     ATCACGACTATTGAAGGAGAGAAAGATCTATCAAAGTATTCATTGCCTCT                         TCACCGCCGCATTGTTCAGTACAAAACTGCTTATTACTCATTTTACCTTCC
genomic: ATCACGACTATTGAAGGAGAGAAAGATCTATCAAAGTATTCATTGCCTCTgtaagtgaga ... ttccatgcagTCACCGCCGCATTGTTCAGTACAAAACTGCTTATTACTCATTTTACCTTCC
EST: gi|30128757|gb|CB914096.1|CB914096
EST:     ATCACGACTATTGAAGGAGAGAAAGATCTATCAAAGTATTCATTGCCTCT                         TCACCGCCGCATTGTTCAGTACAAAACTGCTTATTACTCATTTTACCTTCC
genomic: ATCACGACTATTGAAGGAGAGAAAGATCTATCAAAGTATTCATTGCCTCTgtaagtgaga ... ttccatgcagTCACCGCCGCATTGTTCAGTACAAAACTGCTTATTACTCATTTTACCTTCC
EST: gi|110687343|gb|EE064671.1|EE064671
EST:     ATCACGACTATTGAAGGAGAGAAAGATCTATCGAAGTATTCATTGCCTCT                         TCACCGCCGCATTGTTCAGTACAAAACTGCTTATTACTCATTTTACCTTCC
genomic: ATCACGACTATTGAAGGAGAGAAAGATCTATCAAAGTATTCATTGCCTCTgtaagtgaga ... ttccatgcagTCACCGCCGCATTGTTCAGTACAAAACTGCTTATTACTCATTTTACCTTCC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccatttttttttcttgtgtttcttttaattatcaagtggttgtgtttccatgcagTCACCGCCGCATTGTTCAGTACAAAACTGCTTATTACTCATTTTACCTTCCA
                      ttttaat  putative branch site (score: 3)
                                          tgtttcc  putative PPT
     tttttttcttgtgttt  TA-rich tract