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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatgagcttggtcttttctaggggatgtatggacatcggccatataaattttatttatttatttatttttaggctgcaataatcgtcaatagttttgctgatttagagttctacttttcagGGAGCTGGCTTGGTTGTTCATGATGCGGGTGCTTACTGCATGAGCATGGCATCAACTTACAATCTCAAGATGCGCCCACCTGAGTACTGG

Basic information

species Vitis vinifera
transcript Vv03s0038g04490.t01
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv03s0038g04490.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: LOC_Os02g24354.1 (Oryza sativa), 3'ss of exon 6
gtaatgagcttggtcttttctaggggatgtatggacatcggccatataaattttatttatttatttatttttaggctgcaataatcgtcaatagttttgctgatttagagttctacttttcagGGAGCTGGCTTGGTTGTTCATGATGCGGGTGCTTACTGCATGAGCATGGCATCAACTTACAATCTCAAGATGCGCCCACCTGAGTACTGG
                                                  ||| |     |  | | ||||     ||  ||  | ||   ||    | |  |  ||   ||   ||| | |||||||||| ||||| |||||||| || || || ||||||||||||||||| ||||| |||||  | ||| |||| |||||||| || |||
-------------------------------------------------gtttgaccatatcttgtgttttctttttgatatccttgttggta-ccctacaaacata---ttgcgcttgt-agGGAGCTGGTTTGGTGGTTCATGACGCAGGAGCCTACTGCATGAGCATGGCTTCAACCTACAACTTGAAGTTGCGACCACCTGAATATTGG

upper sequence: Vv03s0038g04490.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GRMZM2G090722_T02 (Zea mays), 3'ss of exon 6
gtaatgagcttggtcttttctaggggatgtatggacatcggccatataaattttatttatttatttatttttaggctgcaataatcgtcaatagttttgctgatttagagttctacttttcagGGAGCTGGCTTGGTTGTTCATGATGCGGGTGCTTACTGCATGAGCATGGCATCAACTTACAATCTCAAGATGCGCCCACCTGAGTACTGG
                                                  ||||    |   | |   |||||       || | |||      | || |    | | |  |   | ||  ||||||||||  |||||||||||||||| ||||| ||||||||||||||||| || || ||||| || ||| || | || || |||||||||
-----------------------------------------------gtctttttcaaagccactatattttatttgatgattagcgtttcctctgtttcgttgtgatatattgtccttgtagGGAGCTGGACTGGTTGTTCATGATGCAGGTGCCTACTGCATGAGCATGGCTTCCACCTACAACCTGAAGTTGAGGCCGCCAGAGTACTGG

upper sequence: Vv03s0038g04490.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GRMZM2G020446_T01 (Zea mays), 3'ss of exon 6
gtaatgagcttggtcttttctaggggatgtatggacatcggccatataaattttatttatttatttatttttaggctgcaataatcgtcaatagtt-ttgctgatttagagttctacttttcagGGAGCTGGCTTGGTTGTTCATGATGCGGGTGCTTACTGCATGAGCATGGCATCAACTTACAATCTCAAGATGCGCCCACCTGAGTACTGG
                                     ||      | |    |||| | ||  || ||  ||||||         | || ||  || || ||||  |   || ||    |  ||||||||||  |||||||||||||||| ||||| ||||||||||||||||| || || ||||| || ||| || | ||||| || ||||||
------------------------------------gtctctttcaaagccattatattttatttgatgattaggc---------cttctatgtttctttctgacatgttgtcct----tgtagGGAGCTGGACTGGTTGTTCATGATGCAGGTGCCTACTGCATGAGCATGGCTTCCACCTACAACCTGAAGTTGAGGCCACCGGAATACTGG

upper sequence: Vv03s0038g04490.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: EFJ12224 (Selaginella moellendorffii), 3'ss of exon 5
gtaatgagcttggtcttttctaggggatgtatggacatcggccatataaattttatttatttatttatttttaggctgcaataatcgtcaatagttttgctgatttagagttctacttttcagGGAGCTGGCTTGGTTGTTCATGATGCGGGTGCTTACTGCATGAGCATGGCATCAACTTACAATCTCAAGATGCGCCCACCTGAGTACTGG
                                                                    |   | | |   ||||   |   |     || |||| || |    | |    ||||| | |||  | |||||||| || || || || ||||||||||| |||||||| ||||||||  | || ||||| ||||| |||||||||
-------------------------------------------------------------------gtaagatgttcatataaggttttctttccgtggtgatctaaaaccttgcg--acagGGCGATGGAATCGTTGTTCACGACGCCGGAGCGTACTGCATGAGTATGGCATCGACTTACAACTTGAAAATGCGGCCACCAGAGTACTGG

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|110389892|gb|EC954765.1|EC954765
EST:     AATCTGCAGATTTCTTGGGGAAGGATAGAGAACTTCCCACTCCACCTAGG                         GGAGCTGGCCTGGTTGTTCATGATGCGGGTGCTTACTGCATGAGCATGGCA
genomic: AATCTGCAGATTTCTTGGGGAAGGATAGAGAACTTCCCACTCCACCTAGGgtaatgagct ... tacttttcagGGAGCTGGCTTGGTTGTTCATGATGCGGGTGCTTACTGCATGAGCATGGCA
EST: gi|71867276|gb|DT016331.1|DT016331
EST:     AATCTGCAGATTTCTTGGGGAAGGATAGAGAACTTCCCACTCCACCTAGG                         GGAGCTGGCCTGGTTGTTCATGATGCGGGTGCTTACTGCATGAGCATGGCA
genomic: AATCTGCAGATTTCTTGGGGAAGGATAGAGAACTTCCCACTCCACCTAGGgtaatgagct ... tacttttcagGGAGCTGGCTTGGTTGTTCATGATGCGGGTGCTTACTGCATGAGCATGGCA
EST: gi|30256339|gb|CB972182.1|CB972182
EST:     AATCTGCAGATTTCTTGGGGAAGGATAGAGAACTTCCCACTCCACCTAGG                         GGAGCTGGCCTGGTTGTTCATGATGCGGGTGCTTACTGCATGAGCATGGCA
genomic: AATCTGCAGATTTCTTGGGGAAGGATAGAGAACTTCCCACTCCACCTAGGgtaatgagct ... tacttttcagGGAGCTGGCTTGGTTGTTCATGATGCGGGTGCTTACTGCATGAGCATGGCA
EST: gi|110373051|gb|EC937258.1|EC937258
EST:     AATCTGCAGATTTCTTGGGGAAGGATAGAGAACTTCCCACTCCACCTAGG                         GGAGCTGGCCTGGTTGTTCATGATGCGGGTGCTTACTGCATGAGCATGGCA
genomic: AATCTGCAGATTTCTTGGGGAAGGATAGAGAACTTCCCACTCCACCTAGGgtaatgagct ... tacttttcagGGAGCTGGCTTGGTTGTTCATGATGCGGGTGCTTACTGCATGAGCATGGCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttaggctgcaataatcgtcaatagttttgctgatttagagttctacttttcagGGAGCTGGCTTGGTTGTTCATGATGCGGGTGCTTACTGCATGAGCATGGCATCAACTTACAATCTCAAGATGCGCCCACCTGAGTACTGG
                             tgctgat  putative branch site (score: 3)
                                          ttctacttttc  putative PPT
                     aatagtttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaatgagcttggtcttttctaggggatgtatggacatcggccatataaattttatttatttatttatttttaggctgcaataatcgtcaatagttttgctgatttagagttctacttttcagGGAGCTGGCTTGGTTGTTCATGATGCGGGTGCTTACTGCATGAGCATGGCATCAACTTACAATCTCAAGATGCGCCCACCTGAGTACTGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG