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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgtgccgtcagtttagattacattgtttacagaagttaaaaactcattatgtgctgtcagtttatggttacatttatttcctgaagttaaaaattgtttatccatgagcctggatctttagctgatgttatattctttatctagGTGTTGTCCAGTGACAATCCAAAATATGGTTACAATGCTGCAACTGGAAAATACGAGGATTTGATGGCTGCTGGTATAATTGATCCCACGAAA

Basic information

species Vitis vinifera
transcript Vv09s0002g03930.t01
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv09s0002g03930.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: LOC_Os06g02380.1 (Oryza sativa), 3'ss of exon 12
gtgtgccgtcagtttagattacattgtttacagaagttaaaaactcattatgtgctgtcagtttatggttacatttatttcctgaagttaaaaattgtttatccatgagcctggatctttagctgatgttatattctttatctagGTGTTGTCCAGTGACAATCCAAAATATGGTTACAATGCTGCAACTGGAAAATACGAGGATTTGATGGCTGCTGGTATAATTGATCCCACGAAA
                                                                   |||| || |  |||   ||    |||||  | | | ||   |      |   || |  |    ||  | |||  | ||||  | || |  || ||    || | |||||||||||||||||||||| | |||||||||||||||||||||||||| ||||| ||||| || 
-------------------------------------------------------------------gttagatcttgttcactaa-cagaaaatcatatgttcacatgtacatctgaataacataaaagatgatgttttaccagGTTCTCTCTAACGATAACTTCAAGTTTGGTTACAATGCTGCAACTGGACAGTACGAGGATTTGATGGCTGCTGGTATCATTGACCCCACTAAG

upper sequence: Vv09s0002g03930.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: LOC_Os02g01280.1 (Oryza sativa), 3'ss of exon 12
gtgtgccgtcagtttagattacattgtttacagaagttaaaaactcattatgtgctgtcagtttatggttacatttatttcctgaagt-taaaaattgtttatccatgagcctggatctttagctgatgtt---atattctttatct-agGTGTTGTCCAGTGACAATCCAAAATATGGTTACAATGCTGCAACTGGAAAATACGAGGATTTGATGGCTGCTGGTATAATTGATCCCACGAAA
                                                            |||| |  |   |  | | | || ||||   |  | | |  |    ||   || | | | || |  || ||   | ||   | || | ||||  |  ||| ||| ||    |  |||||||||||||| || || |||||||| ||||||||||||||||||||||| ||||||||||| || 
------------------------------------------------------------gtttgtactctgacatttgttcttaagtacgatgaatatgcaattctgcagctcg-tgtgtaacgaatttttgaacatgtatgatttcagGTCCTTGCCAATGATAACTTCAGGTATGGTTACAATGCCGCTACAGGAAAATATGAGGATTTGATGGCTGCTGGTATTATTGATCCCACCAAG

upper sequence: Vv09s0002g03930.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: GRMZM2G095252_T02 (Zea mays), 3'ss of exon 6
gtgtgccgtcagtttagattacattgtttacagaagttaaaaactcattatgtgctgtcagtttatggttacatttatttcctgaagttaaaaattgtttatc-catgagcctggatctttagctgatgttatattctttatctagGTGTTGTCCAGTGACAATCCAAAATATGGTTACAATGCTGCAACTGGAAAATACGAGGATTTGATGGCTGCTGGTATAATTGATCCCACGAAA
                                                   || | || | | ||      ||   || ||   | ||  |  |  ||| ||  ||||   ||| |||||  ||  |  ||   | ||  | | ||||  | || |  || ||    || ||||||||||||||||| |||||| | |||||||| ||||||||||||||||| |||||||| || || 
---------------------------------------------------gtacagttattctac-----caaaaatctcac-acgtgtaccacagttcatggcatggatctgaatcttgtgcaaacatt---tgctgcacc-agGTCCTTTCTAACGATAACTTCAAGTATGGTTACAATGCTGCTACTGGACAGTACGAGGACTTGATGGCTGCTGGTATCATTGATCCTACTAAG

upper sequence: Vv09s0002g03930.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: GRMZM2G083716_T03 (Zea mays), 3'ss of exon 11
gtgtgccgtcagtttagattacattgtttacagaagttaaaaactcattatgtgctgtcagtttatggttacatttatttcctgaagttaaaaattgtttatccatgagcctggatctttagctgatgttatattctttatctagGTGTTGTCCAGTGACAATCCAAAATATGGTTACAATGCTGCAACTGGAAAATACGAGGATTTGATGGCTGCTGGTATAATTGATCCCACGAAA
                                                ||     ||       |  ||  ||   || | |   |||| ||           ||||   ||| |||||  |   |||||   ||||  | | ||||  | || | ||| ||    || ||||||||||||||||| |||||| | ||||||||  |||||||||||||||| ||||| ||||| || 
-----------------------------------------------gtacagcttgattaccaaaagtctcacgcatataccacagttcaagg---------catggatctgaatcttatgtaaatgtt---ttctacacc-agGTCCTTTCTAATGATAACTTCAAGTATGGTTACAATGCTGCTACTGGACAGTACGAGGACCTGATGGCTGCTGGTATCATTGACCCCACCAAG

upper sequence: Vv09s0002g03930.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: GRMZM2G015989_T01 (Zea mays), 3'ss of exon 12
gtgtgccgtcagtttagattacattgtttacagaagttaaaaactcattatgtgctgtcagtttatggttacatttatttcctgaagttaaaaattgtttatccatgagcctggatctttagctgatgttatattctttatctagGTGTTGTCCAGTGACAATCCAAAATATGGTTACAATGCTGCAACTGGAAAATACGAGGATTTGATGGCTGCTGGTATAATTGATCCCACGAAA
                                                  | ||   |||  || || |     ||| |   ||    |  || | ||   |  |  ||  |||| |||  | |||  ||             ||||  |  ||| ||| ||    |  ||||| |||||||| || || ||  | || ||||| ||||||||||||||||| ||||||||||| || 
-------------------------------------------------gtttgtgctcaaattgtgctcgttattagtctgtggctgtgcaactcgtgc-ttaacaagtttggaactt--gttgacatt------------cagGTTCTTGCCAATGAGAACTTCAGGTATGGGTACAATGCGGCTACAGGGGAGTATGAGGACTTGATGGCTGCTGGTATCATTGATCCCACCAAG

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|110363342|gb|EC926920.1|EC926920
EST:     AGTTAATCGCCAAGAATGCAGGGGTCAACGGAAGTGTTGTGATCGAAAAG                         GTGTTGTCCAGTGACAATCCAAAATATGGTTACAATGCTGCAACTGGAAAA
genomic: AGTTAATCGCCAAGAATGCAGGGGTCAACGGAAGTGTTGTGATCGAAAAGgtgtgccgtc ... ctttatctagGTGTTGTCCAGTGACAATCCAAAATATGGTTACAATGCTGCAACTGGAAAA
EST: gi|77586832|gb|DV222559.1|DV222559
EST:     AGTTAATCGCCAAGAATGCAGGGGTCAACGGAAGTGTTGTGATCGAAAAG                         GTGTTGTCCAGTGACAATCCAAAATATGGTTACAATGCTGCAACTGGAAAA
genomic: AGTTAATCGCCAAGAATGCAGGGGTCAACGGAAGTGTTGTGATCGAAAAGgtgtgccgtc ... ctttatctagGTGTTGTCCAGTGACAATCCAAAATATGGTTACAATGCTGCAACTGGAAAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaaattgtttatccatgagcctggatctttagctgatgttatattctttatctagGTGTTGTCCAGTGACAATCCAAAATATGGTTACAATGCTGCAACTGGAAAATACGAGGATTTGATGGCTGCTGGTATAATTGATCCCACGAAA
                              agctgat  putative branch site (score: 4)
                                           ttctttatct  putative PPT
                                   atgttatattctttat  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgtgccgtcagtttagattacattgtttacagaagttaaaaactcattatgtgctgtcagtttatggttacatttatttcctgaagttaaaaattgtttatccatgagcctggatctttagctgatgttatattctttatctagGTGTTGTCCAGTGACAATCCAAAATATGGTTACAATGCTGCAACTGGAAAATACGAGGATTTGATGGCTGCTGGTATAATTGATCCCACGAAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT