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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaaatcagcaatacaatgcttaacttttattttcatacagagattgatgaatacttgattataatttatttgttggagaaagaaaaaactctaaaaagttctatttctcatctttgatcagGTCTCCTATTCCCTTTTGATTTTCTTCTGCGGAATGTTCATTACAGTTGATGGTTTCAACAAAACTGGAATCCCTAGCGCAGTATGGGACTTAATGGAGC

Basic information

species Vitis vinifera
transcript Vv16s0050g00780.t01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv16s0050g00780.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: LOC_Os03g05390.1 (Oryza sativa), 3'ss of exon 3
gtaaaatcagcaatacaatgcttaacttttatt-ttcatacagagattgatgaatacttgattataatttatttgttggagaaagaaaaaactctaaaaagttctatttctcatctttgat--cagGTCTCCTATTCCCTTTTGATTTTCTTCTGCGGAATGTTCATTACAGTTGATGGTTTCAACAAAACTGGAATCCCTAGCGCAGTATGGGACTTAATGGAGC
                   |  | | |||  ||  | || |    ||  |  |    ||   |  |   | ||  ||||   ||  |||   |  |      | | |||  ||| | ||||   |||| || || ||  |  |||| ||||||||||| ||||| ||||| || ||||| |||||||||||||| || || | | || | |||||  |  | || |
-------------------gtatgattttacttactgatgcctgaatcaacaa---tttatctgaatcatgttcattgggacaattaaa--tttca------tgtgtttgccatgtctgatgatagGTGTCATACTCATTGCTGATCTTCTTCTGCGGGATGTTTATTACGGTCGATGGCTTCAACAAAACTGGCATACCGAACACACTTTGGGAGCTCGTTGAAC

upper sequence: Vv16s0050g00780.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: LOC_Os10g31040.4 (Oryza sativa), 3'ss of exon 2
gtaaaatcagcaatacaatgcttaacttttattttcatacagagattgatgaatacttgattataatttatttgttggagaaagaaaaaactctaaaaagttctatttctcatctttgatcagGTCTCCTATTCCCTTTTGATTTTCTTCTGCGGAATGTTCATTACAGTTGATGGTTTCAACAAAACTGGAATCCCTAGCGCAGTATGGGACTTAATGGAGC
         | || |    |  ||||  ||  | |    | || |||  | ||   ||   |  |  | | || ||          |    | |   ||||  |  ||      ||||  ||||| || || || ||  |||| ||||||||||| |||||||| || || ||||| |||||||| |||||||| || | | |  | |||||  |  | ||||
---------ggaacagggagagtaacagtt--tcttgctctga-atttttcaactgttatcttgagctgaattattt---------actgttttgctaagtgattgttggtgaatttg--cagGTGTCATACTCGCTGCTGATCTTCTTCTGCGGGATGTTCATCACGGTGGATGGATTCAACAAGACTGGAATTCCAAACACTCTCTGGGAGCTCGTCGAGC

upper sequence: Vv16s0050g00780.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA16G29990.1 (Glycine max), 3'ss of exon 5
---------------gtaaaatc---agcaatacaatgcttaacttttattttcatacagagattgatgaatacttgattataatttatttgttggagaaagaaaaaactctaaaaagttctatttctcatcttt---gatcagGTCTCCTATTCCCTTTTGATTTTCTTCTGCGGAATGTTCATTACAGTTGATGGTTTCAACAAAACTGGAATCCCTAGCGCAGTATGGGACTTAATGGAGC
                 || |||     ||| |      || | || | ||    |  | | | |  | | ||  | ||| |  |||  |||    |    |||  | ||||   ||  | | ||| || | ||     | ||||| |||||||| || ||||| ||||| || ||||||||||| ||||| ||||| ||||||| |||||| || ||  | ||  | |||||  | |||||||
gtaaaacctatgaacacaacatcttgttcaagatttctttttatttctcttcctcttgaaacactagtaagtagct-attgttgttttgttgcaaaactttgaactatctcttggaatgtttttttttctttttcctgaaacagGTTTCCTATTCACTCTTGATATTCTTTTGTGGAATGTTCATCACAGTAGATGGCTTCAACAGAACTGGGATTCCAGGTGCTCTTTGGGATGTCATGGAGC

upper sequence: Vv16s0050g00780.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA09G24930.1 (Glycine max), 3'ss of exon 1
---------------------------gtaaaatcagcaatacaatgcttaacttttattttcatacagagattgatgaatacttgattataatttatttg----ttggagaaagaaaaaactctaaaaagttctatttctcatctttgatcagGTCTCCTATTCCCTTTTGATTTTCTTCTGCGGAATGTTCATTACAGTTGATGGTTTCAACAAAACTGGAATCCCTAGCGCAGTATGGGACTTAATGGAGC
                            ||| ||      |   ||  || | || | ||    |  | | | |    | ||  | ||| |  ||    ||    ||  |    ||| || |||| | ||  | | |||||  |||| || ||||| || ||||| || ||||| ||||| || ||||||||||| ||||| ||||| |||||||||||||| || ||  | ||  | |||||  | |||||||
gtaaaacctatgaacacaacatcttgtttaagatttctttttttattttttatttctcttcctcttgaaacactagcaagtagct-attgttgttctcgtgcaactttaactttgaacaatctcttagaatgtttttttct--tcttggaacagGTTTCTTATTCACTCTTGATATTCTTTTGTGGAATGTTCATCACAGTAGATGGCTTCAACAAAACTGGGATTCCAGGTGCTCTTTGGGATGTCATGGAGC

upper sequence: Vv16s0050g00780.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA16G30020.1 (Glycine max), 3'ss of exon 1
gtaaaatcagcaatacaatgcttaacttttattttcatacagagattgatgaatacttgattataatttatttgttggagaaagaaaaaactctaaaaagttctatttctcatctttgatcagGTCTCCTATTCCCTTTTGATTTTCTTCTGCGGAATGTTCATTACAGTTGATGGTTTCAACAAAACTGGAATCCCTAGCGCAGTATGGGACTTAATGGAGC
|||| |     | |||||  | |  ||||||| |   | | |   ||||  |    ||| |  || | | |   ||| |    ||| || | || |        |||  || |||| || |||||||| ||||| || ||||| ||||| || |||||||| || ||||| ||||| ||||| ||||||||||| ||  | ||  | ||||||||||||||||
gtaatacttata-tacaaaacctc-cttttatgtctcttccgt--ttgaaaagctattgttattattgtgtcaattgaactttgaacaatcacttatgg---tgattcttcttcttggaacagGTCTCTTATTCACTGTTGATATTCTTTTGTGGAATGTTTATCACAGTAGATGGATTCAAGAAAACTGGAATTCCAGGTGCTCTTTGGGACTTAATGGAGC

upper sequence: Vv16s0050g00780.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA10G37710.1 (Glycine max), 3'ss of exon 2
gtaaaatcagcaatacaatgcttaacttttattttcatacagagattgatgaatacttgattataatttatttgttggagaaagaaaaaactctaaaaagttctatttctcatctttgatcagGTCTCCTATTCCCTTTTGATTTTCTTCTGCGGAATGTTCATTACAGTTGATGGTTTCAACAAAACTGGAATCCCTAGCGCAGTATGGGACTTAATGGAGC
                   |  ||| | || | ||  ||       |  |  | |  |  | || ||   | || |  | |    | || |||| |  |||| | |||||   |||  | ||||| || ||||| |||||||| ||||| || |||||||| |||||||| |||||  |||| ||||||||||| || || ||  | |||||| |||||||||
-------------------gtctaaatattctctttctatttcttctccttgaaa--tactaattatgcttctgctcaatattttacaacctctcagtagtttt-tttcttcccttgtaacagGTTTCGTATTCACTTTTGATATTCTTTTGTGGAATGTTTATTACAGTGGATGGCCTCAATAAAACTGGAATTCCAAGTGCTCTGTGGGACATAATGGAGC

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|71871396|gb|DT020451.1|DT020451
EST:     TGGCTCTTGTAGTTCTTGATTTCAAGGATGCTCGGCCTTCCCTAGAGAAG                         GTCTCCTATTCCCTTTTGATTTTCTTCTGCGGAATGTTCATTACAGTTGAT
genomic: TGGCTCTTGTAGTTCTTGATTTCAAGGATGCTCGGCCTTCCCTAGAGAAGgtaaaatcag ... ctttgatcagGTCTCCTATTCCCTTTTGATTTTCTTCTGCGGAATGTTCATTACAGTTGAT
EST: gi|110360567|gb|EC923780.1|EC923780
EST:     TGGCTCTTGTAGTTCTTGATTTCAAGGATGCTCGGCCTTCCCTAGAGAAG                         GTCTCCTATTCCCTTTTGATTTTCTTCTGCGGAATGTTCATTACAGTTGAT
genomic: TGGCTCTTGTAGTTCTTGATTTCAAGGATGCTCGGCCTTCCCTAGAGAAGgtaaaatcag ... ctttgatcagGTCTCCTATTCCCTTTTGATTTTCTTCTGCGGAATGTTCATTACAGTTGAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatttgttggagaaagaaaaaactctaaaaagttctatttctcatctttgatcagGTCTCCTATTCCCTTTTGATTTTCTTCTGCGGAATGTTCATTACAGTTGATGGTTTCAACAAAACTGGAATCCCTAGCGCAGTATGGGACTTAATGGAGC
                      ctctaaa  putative branch site (score: 3)
                                ttctatttctcatctt  putative PPT
                aaaaaactctaaaaa  TA-rich tract