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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgggtaaaatttagtcatctcatattgatgaactgctggaatttcaagtattttgccttatttgaaaaagactaatagtatgattccacctctgttgcagGTTTTCGTTATGTGGCTGGACTTTGTTACTTACTTGCATCACCATGGCTATGAGCAAAAACTTCCATGGTATCGGGGCAAG

Basic information

species Vitis vinifera
transcript Vv06s0004g06730.t01
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv06s0004g06730.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA14G37350.2 (Glycine max), 3'ss of exon 5
-gtgggtaaaatttagtcatctcatattgatgaactgctggaatttcaagtattttgccttatttgaaaaagactaatagtatgattccacctctgt-tgcagGTTTTCGTTATGTGGCTGGACTTTGTTACTTACTTGCATCACCATGGCTATGAGCAAAAACTTCCATGGTATCGGGGCAAG-------------------
  |   || ||| | || | |   | ||||   |    |  | | || | |        | |  |    |  | ||||  | | |||           ||||| | || |||||||||||||||||||| || |||||||||||||||||  || | || ||||| || |||||||| ||||||                   
tatatttagaatctggttaacattttttga---atatttcaattctccaattaaaaatttgaaatagtcaccattaattatgtaattgtttgaacacgtgcagATATTTGTTATGTGGCTGGACTTTGTCACATACTTGCATCACCATGGTCATCATCAGAAACTGCCTTGGTATCGCGGCAAGGTAACAAAAATAAATAGAA

upper sequence: Vv06s0004g06730.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA14G37350.1 (Glycine max), 3'ss of exon 5
-gtgggtaaaatttagtcatctcatattgatgaactgctggaatttcaagtattttgccttatttgaaaaagactaatagtatgattccacctctgt-tgcagGTTTTCGTTATGTGGCTGGACTTTGTTACTTACTTGCATCACCATGGCTATGAGCAAAAACTTCCATGGTATCGGGGCAAG
  |   || ||| | || | |   | ||||   |    |  | | || | |        | |  |    |  | ||||  | | |||           ||||| | || |||||||||||||||||||| || |||||||||||||||||  || | || ||||| || |||||||| ||||||
tatatttagaatctggttaacattttttga---atatttcaattctccaattaaaaatttgaaatagtcaccattaattatgtaattgtttgaacacgtgcagATATTTGTTATGTGGCTGGACTTTGTCACATACTTGCATCACCATGGTCATCATCAGAAACTGCCTTGGTATCGCGGCAAG

upper sequence: Vv06s0004g06730.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA02G39230.1 (Glycine max), 3'ss of exon 5
--------gtgggtaaaatttagtcatctcatattgatgaactgctggaatttcaagtattttgcctta--tttgaaaaagac----taatagtatgattccacctctgt-tgcagGTTTTCGTTATGTGGCTGGACTTTGTTACTTACTTGCATCACCATGGCTATGAGCAAAAACTTCCATGGTATCGGGGCAAG
         |   |   |  | || |  |  |  |  |    |  |   ||||||| | |        |  ||||||| ||      ||||  | | |||         | ||||| | || |||||||||||||||||||| || |||||||||||||||||  |  | || ||||| || ||||| || ||||||
gtaactaaattactcctacattgttactttttcctcctttttt-ttattatttcaattctccaattggaaatttgaaatagttaccataattatgtaattgtttgatcatgtgcagATATTTGTTATGTGGCTGGACTTTGTCACATACTTGCATCACCATGGTCACCACCAGAAACTGCCTTGGTACCGCGGCAAG

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|352768954|gb|FQ468145.1|FQ468145
EST:     TTGTAGTGGGTCTTCCCCAAGTGCTTAAGCTCTATGGGGTCCCATATCTG                         GTTTTCGTTATGTGGCTGGACTTTGTTACTTACTTGCATCACCATGGC
genomic: TTGTAGTGGGTCTTCCCCAAGTGCTTAAGCTCTATGGGGTCCCATATCTGgtgggtaaaa ... tctgttgcagGTTTTCGTTATGTGGCTGGACTTTGTTACTTACTTGCATCACCATGGC
EST: gi|110379212|gb|EC944392.1|EC944392
EST:     TTGTAGTGGGTCTTCCCCAAGTGCTTAAGCTCTATGGGGTCCCATATCTG                         GTTTTCGTTATGTGGCTGGACTTTGTTACTTACTTGCATCACCATGGCTAT
genomic: TTGTAGTGGGTCTTCCCCAAGTGCTTAAGCTCTATGGGGTCCCATATCTGgtgggtaaaa ... tctgttgcagGTTTTCGTTATGTGGCTGGACTTTGTTACTTACTTGCATCACCATGGCTAT
EST: gi|110377424|gb|EC942487.1|EC942487
EST:     TTGTAGTGGGTCTTCCCCAAGTGCTTAAGCTCTATGGGGTCCCATATCTG                         GTTTTCGTTATGTGGCTGGACTTTGTTACTTACTTGCATCACCATGGCTAT
genomic: TTGTAGTGGGTCTTCCCCAAGTGCTTAAGCTCTATGGGGTCCCATATCTGgtgggtaaaa ... tctgttgcagGTTTTCGTTATGTGGCTGGACTTTGTTACTTACTTGCATCACCATGGCTAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aagtattttgccttatttgaaaaagactaatagtatgattccacctctgttgcagGTTTTCGTTATGTGGCTGGACTTTGTTACTTACTTGCATCACCATGGCTATGAGCAAAAACTTCCATGGTATCGGGGCAAG
                        gactaat  putative branch site (score: 2)
                                      ttccacctct  putative PPT
            ttatttgaaaaaga  TA-rich tract