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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttaggtgtttcacatgttttatttctttattgtgtatgtatatatatatattgtgtatctggtggaattttcttttgaattatggaagtaagttttatctaattcatgccttgtatgtctatcatctgaatgaggttactatttttcagCCTTGCAAGGGAATTCTTCTATTTGGGCCTCCTGGGACTGGAAAAACAATGCTTGCGAAGGCGGTTGCAACTGAGGCAGGTGCAAATTTTATCAACATAT

Basic information

species Vitis vinifera
transcript Vv07s0005g00200.t01
intron # 20
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv07s0005g00200.t01 (Vitis vinifera), 3'ss of exon 20
lower sequence: LOC_Os11g43970.1 (Oryza sativa), 3'ss of exon 21
gttaggtgtttcacatgttttatttctttattgtgtatgtatatatatatattgtgtatctggtggaattttct-tttgaattatggaagtaagttttatctaattcatgccttgtatgtctatcatctgaatgaggttactatttttcagCCTTGCAAGGGAATTCTTCTATTTGGGCCTCCTGGGACTGGAAAAACAATGCTTGCGAAGGCGGTTGCAACTGAGGCAGGTGCAAATTTTATCAACATAT
                                               |||||| ||   | | |||| | || | | |    ||   || |    | ||| ||| || |  |||  |  |    | ||||  | |   |  || ||  |||||||||||||||||  | || ||||| |||||||| ||||| ||||| |||||||| ||||| || |||||||| |||||||| || || || |||||||
----------------------------------------------ctatattttgggacggatggagtattatatgttggctacctaatttt-ctctatttaagtcctatcttaaaaattg--cctctgg-taaatctgttacttg-cagCCTTGCAAGGGAATATTGCTGTTTGGACCTCCTGGTACTGGGAAAACCATGCTTGCTAAGGCAGTAGCAACTGAAGCAGGTGCTAACTTCATTAACATAT

upper sequence: Vv07s0005g00200.t01 (Vitis vinifera), 3'ss of exon 20
lower sequence: GRMZM2G042074_T01 (Zea mays), 3'ss of exon 21
gttaggtgtttcacatgttttatttctttattgtgtatgtatatatatatattgtgtatctggtggaattttcttttgaattatggaa-gtaagttttatctaattcatgccttgtatgtctatcatctgaatgaggttactatttttcagCCTTGCAAGGGAATTCTTCTATTTGGGCCTCCTGGGACTGGAAAAACAATGCTTGCGAAGGCGGTTGCAACTGAGGCAGGTGCAAATTTTATCAACATAT
                                          |||   ||||| | ||| |  ||    |    |   |   ||||||   |  ||||| || |   |   ||    | |   |  | |  ||     || | | |  ||||| || || |||||| | || ||||| || ||||| |||||||| ||||||||||| ||||| || ||||||||||| ||||| ||||| || |||||||
------------------------------------------atagcaatattct-tattttttgatgctaagct---agcaatggaacacaccttttagctgacagaaagctaacttat--gttgtttatatt---ctattctataccagCCGTGTAAAGGAATTTTACTTTTTGGCCCACCTGGTACTGGAAAGACAATGCTTGCTAAGGCTGTGGCAACTGAGGCTGGTGCTAATTTCATAAACATAT

upper sequence: Vv07s0005g00200.t01 (Vitis vinifera), 3'ss of exon 20
lower sequence: GRMZM2G052403_T01 (Zea mays), 3'ss of exon 12
gttaggtgtttcacatgttttatttctttattgtgtatgtatatatatatattgtgtatctggtggaattttcttttgaattatggaagtaagttttatctaattcatgccttgtatgtctatcatctgaatgaggttactatttttcagCCTTGCAAGGGAATTCTTCTATTTGGGCCTCCTGGGACTGGAAAAACAATGCTTGCGAAGGCGGTTGCAACTGAGGCAGGTGCAAATTTTATCAACATAT
                                         | | |||||     || |  | |    |   | ||||||      |  | | || ||  | |||      |  ||||   || |||      |  ||| |  ||| |||||||||||||||||  | || || || |||||||| ||||| ||||| |||||||| || || || |||||||| |||||||| ||||| ||||| ||||
-----------------------------------------tttgtatattagtagtgttagatatgttgggcgtttgaa-----aacttcaattgtagattattttgatgtactatggtcatgatcc---ccaatttatt-ctttgcagCCTTGCAAGGGAATATTGCTTTTCGGACCTCCTGGCACTGGGAAAACTATGCTTGCCAAAGCAGTAGCAACTGAAGCAGGTGCTAATTTCATCAATATAT

upper sequence: Vv07s0005g00200.t01 (Vitis vinifera), 3'ss of exon 20
lower sequence: GRMZM2G126453_T02 (Zea mays), 3'ss of exon 6
gttaggtgtttcacatgttttatttctttattgtgtatgtatatatatatattgtgtatctggtggaattttcttttgaattatggaagtaagttttatctaattcatgccttgtatgtctatcatctgaat--gaggttactatttttcagCCTTGCAAGGGAATTCTTCTATTTGGGCCTCCTGGGACTGGAAAAACAATGCTTGCGAAGGCGGTTGCAACTGAGGCAGGTGCAAATTTTATCAACATAT
                                             || || ||   |||   || || ||||      || |      |||  |||| |  |  |  |    |  |  |||   | |||  |  |   ||  |  ||| |||||||||||||| ||  | || || || |||||||| ||||||||||| |||||||| || || || |||||||| ||||| || ||||| ||||| ||||
--------------------------------------------gta-atcttagatat---gtcgagtttta----aaacttcatctgtagattttcttgacctactatagtcaagatcttataactgcctccgcaattcattctttgcagCCTTGCAAGGGGATATTGCTTTTCGGACCTCCTGGCACTGGAAAAACTATGCTTGCCAAAGCAGTAGCAACTGAAGCAGGCGCTAATTTCATCAATATAT

upper sequence: Vv07s0005g00200.t01 (Vitis vinifera), 3'ss of exon 20
lower sequence: GRMZM2G435582_T01 (Zea mays), 3'ss of exon 1
gttaggtgtttcacatgttttatttctttattgtgtatgtatatatatatattgtgtatctggtggaattttcttttgaattatggaagtaagttttatctaattcatgccttgtatgtctatcatctgaatga--ggttactatttttcagCCTTGCAAGGGAATTCTTCTATTTGGGCCTCCTGGGACTGGAAAAACAATGCTTGCGAAGGCGGTTGCAACTGAGGCAGGTGCAAATTTTATCAACATAT
                                               || ||  |  || ||   || ||||      || |      |||  |||| |  |  |  |    |  |  |||   | |||  |      ||  |  ||| |||||||||||||| ||  | || || || |||||||| ||||||||||| |||||||| || || || |||||||| ||||| || ||||| ||||| ||||
-----------------------------------------------ta-atcttagatatgtcagagtttta----aaacttcatctgtagattttcttgacctactatggtcaagatcttataactgcctcctcaattcattctttgcagCCTTGCAAGGGGATATTGCTTTTCGGACCTCCTGGCACTGGAAAAACTATGCTTGCCAAAGCAGTAGCAACTGAAGCAGGCGCTAATTTCATCAATATAT

upper sequence: Vv07s0005g00200.t01 (Vitis vinifera), 3'ss of exon 20
lower sequence: GRMZM2G157621_T03 (Zea mays), 3'ss of exon 21
gttaggtgtttcacatgttttatttctttattgtgtatgtatatatatatattgtgtatctggtggaattttcttttgaattatggaagtaagttttatctaattcatgccttgtatgtctatcatc--tgaatgaggtta-ctattt--ttcagCCTTGCAAGGGAATTCTTCTATTTGGGCCTCCTGGGACTGGAAAAACAATGCTTGCGAAGGCGGTTGCAACTGAGGCAGGTGCAAATTTTATCAACATAT
                                                  | ||  ||  ||   || |   |      | || ||    |    |   ||  |    | |  |      |   |||  ||  |  | | | ||||||    ||||| || || || ||  | || ||||| || ||||| || || || || |||||||| || || |||||||| ||||| ||||| ||||||||||||||||
--------------------------------------------------agtgattaattgtccgagtaacc-----gactaggggtcgactagtcgcctggtcttcgaccaggcgacttgaaatcattggttctgatcatctatttgccccagCCATGTAAAGGGATATTGCTTTTTGGTCCACCTGGCACCGGTAAGACCATGCTTGCCAAAGCTGTTGCAACAGAGGCTGGTGCTAATTTTATCAACATAT

upper sequence: Vv07s0005g00200.t01 (Vitis vinifera), 3'ss of exon 20
lower sequence: GLYMA02G17410.1 (Glycine max), 3'ss of exon 16
gttaggtgtttcacatgttttatttctttattgtgtatgtatatatatatattgtgtatctggtggaattttcttttgaattatggaagtaagttttatctaattcatgcc----ttgtatgtctatcatctgaatgaggttactattt-ttcagCCTTGCAAGGGAATTCTTCTATTTGGGCCTCCTGGGACTGGAAAAACAATGCTTGCGAAGGCGGTTGCAACTGAGGCAGGTGCAAATTTTATCAACATAT
                                           |  ||| ||| | | | | || |    ||    ||| || |||||   | ||||   ||  ||||       |  | ||| || || || | ||   ||||| |   |  ||||||||||||||||  | || |||||||| ||||| || ||||||||||||||||| ||||| || |||||||| || || |||||||| || ||||| |
------------------------------------------gttgatagattttctttttagttg---ctttaaatgacttgtggaacacattttttagtagatcatattcgaatcatgtgtgtagcacctcattgtaattactttggatatagCCTTGCAAGGGAATATTGCTTTTTGGGCCCCCTGGCACAGGAAAAACAATGCTTGCAAAGGCTGTAGCAACTGAAGCTGGAGCAAATTTCATTAACATTT

upper sequence: Vv07s0005g00200.t01 (Vitis vinifera), 3'ss of exon 20
lower sequence: GLYMA02G17400.1 (Glycine max), 3'ss of exon 17
gttaggtgtttcacatgttttatttctttattgtgtatgtatatatatatattgtgtatctggtggaattttcttttgaattatggaagtaagttttatctaattcatgccttgtatgtctatcatctgaatgaggttactattttt-cagCCTTGCAAGGGAATTCTTCTATTTGGGCCTCCTGGGACTGGAAAAACAATGCTTGCGAAGGCGGTTGCAACTGAGGCAGGTGCAAATTTTATCAACATAT
                                         |  | | ||||| |   | | || |    ||    ||| || || |||  | | |||  ||  ||||||| ||  |||  | || || | ||   ||||| |   |  ||||||||||||||||  | || ||||| || ||||| || ||||||||||||||||| ||||| || |||||||| || || ||||||||||| ||||| |
----------------------------------------gtgaaaa-atattttcattttagttg----tttaaatgacttgtgaaagacattgttaagtagatcatgccatgcgtgt--agcacctaattgtaattactttgggtatagCCTTGCAAGGGAATATTGCTTTTTGGCCCCCCTGGCACAGGAAAAACAATGCTTGCAAAGGCTGTGGCAACTGAAGCTGGAGCAAATTTTATTAACATTT

upper sequence: Vv07s0005g00200.t01 (Vitis vinifera), 3'ss of exon 20
lower sequence: GLYMA10G02400.1 (Glycine max), 3'ss of exon 20
gttaggtgtttcacatgttttatttctttattgtgtatgtatatatatatattgtgtatctggtggaattttcttttgaattatggaagtaagttttatctaattcatgccttgtatgtctatcatctgaatgaggttactattt-ttcagCCTTGCAAGGGAATTCTTCTATTTGGGCCTCCTGGGACTGGAAAAACAATGCTTGCGAAGGCGGTTGCAACTGAGGCAGGTGCAAATTTTATCAACATAT
                                      ||   || || |  | | ||  || |  || |  |   || |  |      | |||   ||   ||||||  | ||| |||  | || || | ||   ||||| |   |  ||||||||||||||||  | || |||||||| ||||| || ||||||||||||||||| ||||| || |||||||| || || |||||||| || ||||| |
--------------------------------------gttggtagattttctttttagttgctttaaatgacaagtggaacacattttttagtag-atgatattcatatcatgtgtgt--agcacctcattgtaattactttggatatagCCTTGCAAGGGAATATTGCTTTTTGGGCCCCCTGGCACAGGAAAAACAATGCTTGCAAAGGCTGTAGCAACTGAAGCTGGAGCAAATTTCATTAACATTT

upper sequence: Vv07s0005g00200.t01 (Vitis vinifera), 3'ss of exon 20
lower sequence: GLYMA10G02410.1 (Glycine max), 3'ss of exon 17
gttaggtgtttcacatgttttatttctttattgtgtatgtatatatatatattgtgtatctggtggaattttcttttgaattatggaagtaagttttatctaattcatgccttgtatgtctatcatctgaatgaggttactattt-ttcagCCTTGCAAGGGAATTCTTCTATTTGGGCCTCCTGGGACTGGAAAAACAATGCTTGCGAAGGCGGTTGCAACTGAGGCAGGTGCAAATTTTATCAACATAT
                                           |  | | ||| |   | | || |    ||    ||| || || ||| || | ||   ||  ||||||| ||| |||  | || || | ||   ||||| |   |  |||||||||| |||||  | || ||||| |||||||| || ||||||||||||||||| ||||| || |||||||| || || ||||||||||| ||||| |
------------------------------------------gtgaa-agattttcattttagttg----tttaaatgacttgtgaaagaaattgttgagtagatcatgccatgtgtgt--agcacctaattgtaattactttgggtatagCCTTGCAAAGGAATATTGCTTTTTGGCCCTCCTGGCACAGGAAAAACAATGCTTGCAAAGGCTGTAGCAACTGAAGCTGGAGCAAATTTTATTAACATTT

upper sequence: Vv07s0005g00200.t01 (Vitis vinifera), 3'ss of exon 20
lower sequence: AT4G02480.1 (Arabidopsis thaliana), 3'ss of exon 20
gttaggtgtttcacatgttttatttctttattgtgtatgtatatatatatattgtgtatctggtggaattttcttttgaattatggaagtaagttttatctaattcatgccttgtatgtctatcatctga-atgaggttactattt--ttcagCCTTGCAAGGGAATTCTTCTATTTGGGCCTCCTGGGACTGGAAAAACAATGCTTGCGAAGGCGGTTGCAACTGAGGCAGGTGCAAATTTTATCAACATAT
                                                                 | |  || | |||   || |||  ||  | |||  |  | |    | |  ||  ||   | |  | ||    ||  | |||  | ||||||   || || || ||  | ||||| |||||||| |||||||| || ||||| || || || || ||||||||||| || |||||||| ||||| || |
-----------------------------------------------------------------gtaccttttattgctatacggatttatttgttagttgttac---tcctacataactgaaaccaaacatatatttgatgtttaatgcagCCTACGAAAGGTATACTGTTGTTTGGACCTCCTGGTACTGGAAAGACGATGCTGGCAAAAGCAGTAGCAACTGAGGCTGGCGCAAATTTCATCAATATCT

upper sequence: Vv07s0005g00200.t01 (Vitis vinifera), 3'ss of exon 20
lower sequence: EFJ31084 (Selaginella moellendorffii), 3'ss of exon 8
gttaggtgtttcacatgttttatttctttattgtgtatgtatatatatatattgtgtatctggtggaattttcttttgaattatggaagtaagttttatcta-attcatgccttgtatgtctatcatctgaatgaggttactatttttcagCCTTGCAAGGGAATTCTTCTATTTGGGCCTCCTGGGACTGGAAAAACAATGCTTGCGAAGGCGGTTGCAACTGAGGCAGGTGCAAATTTTATCAACATAT
                                                                                                  |||   |   ||   | |   | | |  | ||  | | |    ||| |  |||||||| | |||  | ||  ||||||| ||||| || ||||| || || |||||||| ||||||||||| || ||||| ||||||||||| ||||| || |
-------------------------------------------------------------------------------------------------gtctgtgtgtttgttatttgctttttttctttgtctaacgaatttatatggcagCCTTGTAGGGGCCTACTCTTATTTGGTCCTCCAGGAACTGGTAAGACCATGCTTGCTAAGGCGGTTGCTACAGAGGCTGGTGCAAATTTCATCAATATTT

upper sequence: Vv07s0005g00200.t01 (Vitis vinifera), 3'ss of exon 20
lower sequence: EFJ34631 (Selaginella moellendorffii), 3'ss of exon 10
gttaggtgtttcacatgttttatttctttattgtgtatgtatatatatatattgtgtatctggtggaattttcttttgaattatggaagtaagttttatcta-attcatgccttgtatgtctatcatctgaatgaggttactatttttcagCCTTGCAAGGGAATTCTTCTATTTGGGCCTCCTGGGACTGGAAAAACAATGCTTGCGAAGGCGGTTGCAACTGAGGCAGGTGCAAATTTTATCAACATAT
                                                                                                  |||   |   ||   | |   | | |  | ||  | | |   |||| |  |||||||| | |||  | ||  ||||||| ||||| || ||||| || || |||||||| ||||||||||| || ||||| ||||||||||| ||||| || |
-------------------------------------------------------------------------------------------------gtctgtgtgtttgttatttgctttttttctttgtctaacgaatctatatggcagCCTTGTAGGGGCCTACTCTTATTTGGTCCTCCAGGAACTGGTAAGACCATGCTTGCTAAGGCGGTTGCTACAGAGGCTGGTGCAAATTTCATCAATATTT

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|34547757|gb|CF515989.1|CF515989
EST:     TGCTTCCTCTTCAAAGGCCAGAACTATTTTGTAAGGGACAGCTGACTAAG                         CCTTGCAAGGGAATTCTTCTATTTGGGCCTCCTGGGACTGGAAAAACAATG
genomic: TGCTTCCTCTTCAAAGGCCAGAACTATTTTGTAAGGGACAGCTGACTAAGgttaggtgtt ... tatttttcagCCTTGCAAGGGAATTCTTCTATTTGGGCCTCCTGGGACTGGAAAAACAATG
EST: gi|71854977|gb|DT004032.1|DT004032
EST:     TGCTTCCTCTTCAAAGGCCAGAACTATTTTGTAAGGGACAGCTGACTGAG                         CCTTGCAAGGGAATTCTTCTATTTGGGCCTCCTGGGACTGGAAAAACAATG
genomic: TGCTTCCTCTTCAAAGGCCAGAACTATTTTGTAAGGGACAGCTGACTAAGgttaggtgtt ... tatttttcagCCTTGCAAGGGAATTCTTCTATTTGGGCCTCCTGGGACTGGAAAAACAATG
EST: gi|110727315|gb|EE103938.1|EE103938
EST:     TGCTTCCTCTTCAAAGGCCAGAACTATTTTGTAAGGGACAGCTGACTAAG                         CCTTGCAAGGGAATTCTTCTATTTGGGCCTCCTGGGACTGGAAAA-CAATG
genomic: TGCTTCCTCTTCAAAGGCCAGAACTATTTTGTAAGGGACAGCTGACTAAGgttaggtgtt ... tatttttcagCCTTGCAAGGGAATTCTTCTATTTGGGCCTCCTGGGACTGGAAAAACAATG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttatctaattcatgccttgtatgtctatcatctgaatgaggttactatttttcagCCTTGCAAGGGAATTCTTCTATTTGGGCCTCCTGGGACTGGAAAAACAATGCTTGCGAAGGCGGTTGCAACTGAGGCAGGTGCAAATTTTATCAACATAT
  atctaat  putative branch site (score: 3)
                                            ctatttttc  putative PPT
                                         ttactattttt  TA-rich tract