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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgactcgctcttcatcatctcatatccccttttggtgttttgatttttaccatgatctttagatctgtgttgagctggatactaactctcagcagtttggtttaacttcagtagtcactgtttttttcattaaatgtgttttcatggtttcagGGTGTTGTTTGAATTGATATGGAGAGATTACTTCAGGTTCCTGTCAGTTAAATACAGAAATTCTCTTTTTCATCTAG

Basic information

species Vitis vinifera
transcript Vv04s0008g02670.t01
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv04s0008g02670.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: LOC_Os06g45100.1 (Oryza sativa), 3'ss of exon 6
gtatgactcgctcttcatcatctcatatccccttttggtgttttgatttttaccatgatctttagatctgtgttgagc-tggatactaactctcagcagtttggtttaacttcagtagtcactgtttttttcattaaatgtgttttcatggtttcagGGTGTTGTTTGAATTGATATGGAGAGATTACTTCAGGTTCCTGTCAGTTAAATACAGAAATTCTCTTTTTCATCTAG
                                                         |   | | || | | | ||   | |  | |||   |   ||  ||  ||  |  ||| | || |   |    | | ||     | |    ||| ||||||||| || ||||| ||||||||||||||||||||| ||||| | ||||  |||||  | || ||  ||||||| ||||
---------------------------------------------------------agtgtgaaatatttatagattattgcaattaagggtttccaacttccttagaagtcaatggtgaaactgaaatactttcttgatatgacaatgttttcagGGTTTTATTTGAGTTGATATGGAGAGATTACTTCCGGTTCATATCAGCAAAATATGGGAACTCCATTTTTCACCTAG

upper sequence: Vv04s0008g02670.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GRMZM2G103897_T01 (Zea mays), 3'ss of exon 6
gtatgactcgctcttcatcatctcatatccccttttggtgttttgatttttaccatgatctttagatctgtgttgagctggatactaactctcagcagtttggtttaacttcagtagtca--ctgtttttttcattaaatgtgttttcatggtttcagGGTGTTGTTTGAATTGATATGGAGAGATTACTTCAGGTTCCTGTCAGTTAAATACAGAAATTCTCTTTTTCATCTAG
                                                   | |||   |||     |  |    | |   ||  |    | |     |   ||| |||||   |  | |    |  |||||| | | | ||      |||| |||||||| || ||||| |||||||||||||| |||||||| || || ||||  |||||  ||||  |  | ||||| || |
---------------------------------------------------aacataggcttgg---ccatacataacaatatgtttttaccctagtttcatgttgaacttgtttgattaaatcgcctttttcctgataagt----caatggcttcagGGTTTTATTTGAGTTGATATGGAGAGACTACTTCAGATTTCTATCAGCAAAATATGGAAACGCCATATTTCACCTGG

upper sequence: Vv04s0008g02670.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: AT5G24850.1 (Arabidopsis thaliana), 3'ss of exon 7
gtatgactcgctcttcatcatctcatatccccttttggtgttttgatttttaccatgatctttagatctgtgttgagctggatactaactctcagcagt-ttggtttaacttcagtagtcactgtttttttcattaaatgtgttttcatggtttcagGGTGTTGTTTGAATTGATATGGAGAGATTACTTCAGGTTCCTGTCAGTTAAATACAGAAATTCTCTTTTTCATCTAG
                                                              || ||||   |  | |||  || |   ||||  | |  ||   || |||    | |||      |  || |||| || |      ||| || ||||||  | |||||| | ||||||||||||||||||||||| || ||| |||| |   |||| || |||||||||||||
-------------------------------------------------------------gtatatcttcat--atctgagtattgtatctctactgcattctctttactct--tggtc-----ctaattgattagatat------atgtttccagGGTACTTTTTGAACTAATATGGAGAGATTACTTCAGGTTTCTTTCAATTAAGTGTGGAAACTCACTTTTTCATCTAG

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|71865775|gb|DT014830.1|DT014830
EST:     GTAAAGAGATATGAGAAAGAGAGGCAAGCAAACGATTCCACATACTG                         GGTGTTGTTTGAATTGATATGGAGAGATTACTTCAGGTTCCTGTCAGTTAA
genomic: GTAAAGAGATATGAGAAAGAGAGGCAAGCAAACGATTCCACATACTGgtatgactcg ... atggtttcagGGTGTTGTTTGAATTGATATGGAGAGATTACTTCAGGTTCCTGTCAGTTAA
EST: gi|77586218|gb|DV222205.1|DV222205
EST:     GTAAAGAGATATGAGAAAGAGAGGCAAGCAAACGATTCCACATACTG                         GGTGTTGTTTGAATTGATATGGAGAGATTACTTCAGGTTCCTGTCAGTTAA
genomic: GTAAAGAGATATGAGAAAGAGAGGCAAGCAAACGATTCCACATACTGgtatgactcg ... atggtttcagGGTGTTGTTTGAATTGATATGGAGAGATTACTTCAGGTTCCTGTCAGTTAA
EST: gi|110389719|gb|EC954579.1|EC954579
EST:     AGGTAAAGAGATATGAGAAAGAGAGGTTAAGCAAACGATTCCACATACTG                         GGTGTTGTTTGAATTGATATGGAGAGATTACTTCAGGTTCCTGTCAGTTAA
genomic: AGGTAAAGAGATATGAGAAAGAGAGG-CAAGCAAACGATTCCACATACTGgtatgactcg ... atggtttcagGGTGTTGTTTGAATTGATATGGAGAGATTACTTCAGGTTCCTGTCAGTTAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggtttaacttcagtagtcactgtttttttcattaaatgtgttttcatggtttcagGGTGTTGTTTGAATTGATATGGAGAGATTACTTCAGGTTCCTGTCAGTTAAATACAGAAATTCTCTTTTTCATCTAG
 gtttaac  putative branch site (score: 3)
                                        ttttcat  putative PPT
                      tttttttcattaaatg  TA-rich tract