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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtagaacatgtgctacattgctgaacacccatttttgtgttcttgaaatattttatagcattctttaatctcttgacattggtttgtttctatggttctcatcttcttttttgtgttttagTTCAAGAGTGAGATCAGAACAGTCACTTGTGAGATGGGCTACTCCCCAACTTCATGATATAGATGCCCTGGCAAAAATGGTTGATCCTTCCCTAAATGGC

Basic information

species Vitis vinifera
transcript Vv10s0116g00100.t01
intron # 14
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv10s0116g00100.t01 (Vitis vinifera), 3'ss of exon 14
lower sequence: LOC_Os02g09740.2 (Oryza sativa), 3'ss of exon 14
gtagaacatgtgctacattgctgaacacccatttttgtgttcttgaaatattttatagcattctttaatctcttgacattg-gtttgtttctatggttctcatcttcttttttgtgttttagTTCAAGAGTGAGATCAGAACAGTCACTTGTGAGATGGGCTACTCCCCAACTTCATGATATAGATGCCCTGGCAAAAATGGTTGATCCTTCCCTAAATGGC
                                            | |   || ||    ||  |  |||| |    ||||| ||||  |    ||    | | |||||  |   | ||  ||||| |||| |||||||||||| || |||||  ||||||||||||| || ||||||||||| ||||| || || || ||||| |||||  |  ||||||| 
--------------------------------------------gtatgcttctagtttatattcaaatcccggtgcattgcgttttataaattgaaaatgaccttctgatggatattgcagTTCTAGAGAGAGATCAGAACAATCTCTTGTTCGATGGGCTACTCCACAGCTTCATGATATCGATGCGCTTGCTAAGATGGTGGATCCAGCATTAAATGGA

upper sequence: Vv10s0116g00100.t01 (Vitis vinifera), 3'ss of exon 14
lower sequence: LOC_Os06g42800.1 (Oryza sativa), 3'ss of exon 14
gtagaacatgtgctacattgctgaacacccatttttgtgttcttgaaatattttatagcattctttaatctcttgacattggtttgtttctatggttctcatcttcttttttgtgttttagTTCAAGAGTGAGATCAGAACAGTCACTTGTGAGATGGGCTACTCCCCAACTTCATGATATAGATGCCCTGGCAAAAATGGTTGATCCTTCCCTAAATGGC
   | |||| | |   |||  |  | | | | |   ||  |    ||||   | ||    |||||||   |  | ||     ||     |  |  |||   |||| | ||      |  || || |||| ||| || |||||||| ||||| | |||||||||||| || |||||||| || ||||| || || || |||||||||||  |  |  |||| 
---gtacat-taccttattatttcagagctagtaa-gtagtaagaaaatgagtaatgtatttcttta--ttagtaac-----ttcaaggccgtcattcat-tcttgtgttgcaatgtgcagCTCTAGAGAGAGGTCCGAACAGTCTCTTGTCACATGGGCTACTCCACAGCTTCATGACATCGATGCGCTTGCCAAGATGGTTGATCCAGCAATGGATGGG

upper sequence: Vv10s0116g00100.t01 (Vitis vinifera), 3'ss of exon 14
lower sequence: GRMZM2G103070_T01 (Zea mays), 3'ss of exon 14
gtagaacatgtgctacattgctgaacacccatttttgtgttcttgaaatattttatagcattctttaatctcttgacattggtttgtttctatggttctcatcttcttttttgtgttttagTTCAAGAGTGAGATCAGAACAGTCACTTGTGAGATGGGCTACTCCCCAACTTCATGATATAGATGCCCTGGCAAAAATGGTTGATCCTTCCCTAAATGGC
                                 | |||| ||| ||    || |||  || || |   || ||| |  || |   ||   | | |   |   |||    |     ||  ||||| |||| ||| ||||||||||| ||||| ||||||||||| || |||||||||||||| ||||| || || |  |||||||||||  |  |||| || 
--------------------------------gtatgtgatctaga----ttgtatc-caatcctggttcgcttcagcttcgaa-gtggttgttgaaatagcctttggatgatcattgcagTTCCAGAGAGAGGTCAGAACAGTCTCTTGTTAGATGGGCTACCCCTCAACTTCATGATATTGATGCACTTGCTAGGATGGTTGATCCAGCATTAAACGGA

upper sequence: Vv10s0116g00100.t01 (Vitis vinifera), 3'ss of exon 14
lower sequence: GLYMA15G11820.1 (Glycine max), 3'ss of exon 14
gtagaacatgtgctacat--tgctgaacacccatttttgtgttcttgaaatattttatagcattctttaatctcttgacattggtttgtttctatggttctcatcttcttttttgtgttttagTTCAAGAGTGAGATCAGAACAGTCACTTGTGAGATGGGCTACTCCCCAACTTCATGATATAGATGCCCTGGCAAAAATGGTTGATCCTTCCCTAAATGGC
|| || | | |  |||||  ||   |  |  ||| |   |    || |  | |    |  |||| ||  |||| |      ||  | | ||||    |||   | |  |||||     |||||||   | ||  |||| || |||||||||||||| |||||||| |||||||| ||||||||||||||| |||| ||||||||||||||| |  | || |||
gt-gagcctatcgtacatgatgtaaagtaatcatgtccatcactttaatgtttaccctt-cattatt--atctttcttttctgtatggcttcttacattcatttgtaatttttgcaagtttagTTTGCGGGTTCGATCGGAGCAGTCACTTGTGAGGTGGGCTACACCCCAACTCCATGATATAGATGCCTTGGCCAAAATGGTTGATCCTACTTTGAACGGC

upper sequence: Vv10s0116g00100.t01 (Vitis vinifera), 3'ss of exon 14
lower sequence: GLYMA09G00970.1 (Glycine max), 3'ss of exon 14
gtagaacatgtgctacattgctgaacacccatttt-tgtgttcttgaaatattttatagcattctttaatctcttgacattggtttgtttctatggttctcatcttcttttttgtgttttagTTCAAGAGTGAGATCAGAACAGTCACTTGTGAGATGGGCTACTCCCCAACTTCATGATATAGATGCCCTGGCAAAAATGGTTGATCCTTCCCTAAATGGC
|| || | |    ||| ||| || | |   ||  | |   |   | |||| ||| ||       | | |||| |      ||  | | ||||    |||   | |  |||||     ||||||||| | ||  ||||||| |||||||||||||| |||||||| || ||||| ||||||||||||||| |||| ||||||||||||||| |  | || |||
gt-gagcctaccatac-ttgatgtaaagaaatcatgtccatcacttaaatgttt-atccttcattattatctttcttttctgtatggcttcttacattcatttgtaatttttgcaagtttagTTCACGGGTTCGATCAGAGCAGTCACTTGTGAGGTGGGCTACACCACAACTCCATGATATAGATGCCTTGGCCAAAATGGTTGATCCTACTTTGAACGGC

upper sequence: Vv10s0116g00100.t01 (Vitis vinifera), 3'ss of exon 14
lower sequence: AT4G22130.2 (Arabidopsis thaliana), 3'ss of exon 9
gtagaacatgtgctacattgctgaacacccatttttgtgttcttg--aaatattttatagcattctttaatctcttgacattggtttgtttctatggttctcatct----tcttttttgtgt---tttagTTCAAGAGTGAGATCAGAACAGTCACTTGTGAGATGGGCTACTCCCCAACTTCATGATATAGATGCCCTGGCAAAAATGGTTGATCCTTCCCTAAATGGC
                               ||||  | || ||   |   | | |  |||| |    ||| |     ||   |  || ||  |   | || || |    | |  |||||||   | ||| || ||   |||| |||| || ||||| ||||||||||| || || || ||||| |||||||||||  || | ||||||||||||||||| || ||||||
--------------------------gtttcttttcatatttttagtagccaatgttgagcaatagccaatgtg--agcaaaagcctgatttgagtttccttatgtaaaatgtgctttgtgtatgtgtagCTCGAGGACGAGAGCAGAGCAATCACTAGTGAGATGGGCAACACCGCAGCTTCACGATATAGATGCTTTGTCTAAAATGGTTGATCCTTCTCTTAATGGC

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|33410441|gb|CF216068.1|CF216068
EST:     TTTGGGGTGGTGATGTTGGAGCTGTTGACAGGTCGGAAGCCCCTGGACAG                         TTCAAGGGTGAGATCAGAACAGTCACTTGTGAGATGGGCTACTCCCCAACT
genomic: TTTGGGGTGGTGATGTTGGAGCTGTTGACAGGTCGGAAGCCCCTGGACAGgtagaacatg ... tgtgttttagTTCAAGAGTGAGATCAGAACAGTCACTTGTGAGATGGGCTACTCCCCAACT






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aatctcttgacattggtttgtttctatggttctcatcttcttttttgtgttttagTTCAAGAGTGAGATCAGAACAGTCACTTGTGAGATGGGCTACTCCCCAACTTCATGATATAGATGCCCTGGCAAAAATGGTTGATCCTTCCCTAAATGGC
    tcttgac  putative branch site (score: 3)
                             ttctcatcttcttttt  putative PPT
                                        ttttttgtgtttta  TA-rich tract