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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagaacttcatggcgacctctagttttgccacctctatgcatatttctacctgtacacaagaatttatttctccatactcaggctttgttatccttacatgcccttctttgggtttacttatttttaactagTGCTCAAACTGCTGAGGAGTGGACAATTTATCCTTGGATCCACAGCAATTGCAATTCACTATCAGAAAACGACCAACTTCGTCCTGTTTCGATTCCTGAT

Basic information

species Vitis vinifera
transcript Vv18s0041g00100.t01
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv18s0041g00100.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: LOC_Os05g43560.1 (Oryza sativa), 3'ss of exon 11
gtgagaacttcatggcgacctctagttttgccacctctatgcatatttctacctgtacacaagaatttatttctccatactcaggctttgttatccttacatgcccttctttgggtttacttatttttaactagTGCTCAAACTGCTGAGGAGTGGACAATTTATCCTTGGATCCACAGCAATTGCAATTCACTATCAGAAAACGACCAACTTCGTCCTGTTTCGATTCCTGAT
                      ||| |    |    |||| ||||||| |   | || | || ||  ||   |   | | |      |||||  | | |||      | |||||      | || ||| |  ||  | |||    |  | |||||||| || ||||||||||| |||||||| |||||||| || ||||| || || |||||||| ||||||||  ||||||||
---------------------gtaggtcaatctaagctatacatattttt---tttaaaaaaaaaactagcaccttacattatcaagttgtt--catcacacaataatatttgg------tcatgttttatcagCACGCAAGAAACCAATGAGTGGACTATATATCCTTGGATACACAGCAACTGCAATTCTCTTTCAGACAATGATCAACTTCGCCCTGTTTCATTTCCTGAT

upper sequence: Vv18s0041g00100.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: GLYMA13G10730.1 (Glycine max), 3'ss of exon 13
------------gtgagaactt-catggcgacctc--tagttttgccacctctatgcatatttctacctgtacacaagaatttatttctccatactcaggctttgttatccttacatgcccttctt--tgggtttacttatttttaact---agTGCTCAAACTGCTGAGGAGTGGACAATTTATCCTTGGATCCACAGCAATTGCAATTCACTATCAGAAAACGACCAACTTCGTCCTGTTTCGATTCCTGAT
            || |   ||| ||||  || ||   |||| || | |    ||    | | | |    ||    |||  || ||| ||   | || |   |||| | |  || | |    ||||   |   ||  |||  |   |  |   ||| | ||||||||||  ||||||||||||||||||||||| |||||||||||||||||| ||||||| |  || ||||||||||||||||| || || |||
gtaagaataagggttatctctttcatgttgatcttgttagtgttacaatgattacttgtttgttttgaagtcacaaagtgttgattgct--gttctgattttttggtctttttgctttttgttctcaatcaattggcttgatggaacatttaagTTCCCAAACTGCTGGTGAGTGGACAATTTATCCTTGGATTCACAGCAATTGCAATTCATTATCAGACAGTGATCAACTTCGTCCTGTTTCAATACCAGAT

upper sequence: Vv18s0041g00100.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: GLYMA20G16030.1 (Glycine max), 3'ss of exon 11
------------gtgagaacttcatggcgacctctagttttgccacctctat-gcatatttctacctgtacacaagaat--ttatttctccatactcaggctttgttatccttacatgccc--ttctttgggtttacttatttttaactagTGCTCAAACTGCTGAGGAGTGGACAATTTATCCTTGGATCCACAGCAATTGCAATTCACTATCAGAAAACGACCAACTTCGTCCTGTTTCGATTCCTGAT
            || |   |||  | |       |  |  ||| ||  | ||  | ||||| |       ||||   ||  ||  |  ||     |   | | | || || ||   | | |  |   |||| || |   |   || |  ||| | ||||| ||||  ||||||||||||||||||||||| |||||||||||||||||| ||||||| |  || ||||||||||||||||| || || |||
gtaagattaagggttatctctttcttgtttatcttgttaatgctacagcaattacttatttgtttgaagtcacagtgatgattgctgttctgattttttggtcttttctctttttgttctcaatcgattggcttgatggaacattta--agTTCCCAAACGGCTGGCGAGTGGACAATTTATCCTTGGATTCACAGCAATTGCAATTCATTATCAGACAGTGATCAACTTCGTCCTGTTTCAATACCAGAT

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|34549600|gb|CF517832.1|CF517832
EST:     AACGAATTTTCATATTACATGATGATATGCTCCAGTTTTATTCTCAATAA                         TGCTCAAACTGCTGAGGAGTGGACAATTTATCCTTGGATCCACAGCAATTG
genomic: AACGAATTTTCATATTACATGATGATATGCTCAAGTTTTATTCTCAATAAgtgagaactt ... ttttaactagTGCTCAAACTGCTGAGGAGTGGACAATTTATCCTTGGATCCACAGCAATTG






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctcaggctttgttatccttacatgcccttctttgggtttacttatttttaactagTGCTCAAACTGCTGAGGAGTGGACAATTTATCCTTGGATCCACAGCAATTGCAATTCACTATCAGAAAACGACCAACTTCGTCCTGTTTCGATTCCTGAT
              tccttac  putative branch site (score: 2)
                                        cttattttt  putative PPT
                                    tttacttatttttaac  TA-rich tract