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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaccattttcttgaaattcgtcccttttttattttatttgaatttgaaacattgtttagggctgcatttttttgcaactggtatcatttttgtatgagctcatgatgaaggtttatcttgcagATGGTTGCATCAGAAGATATAGGTAGACAAATCTTGACATATGGAGAGAG

Basic information

species Vitis vinifera
transcript Vv11s0016g02870.t01
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv11s0016g02870.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: GLYMA08G03580.1 (Glycine max), 3'ss of exon 9
gtaaccattttcttgaaattcgtcccttttttattttatttgaatttgaaacattgtttagggctgcatttttttgcaactggtatcatttttgtatgagctcatgatgaaggtttatcttgcagATGGTTGCATCAGAAGATATAGGTAGACAAATCTTGACATATGGAGAGAG
||||  |  | | |   |   |    |||| | | | | ||  | | ||||  || ||||    |   |||||| | ||||      || |||   ||| || |      | ||||   || ||||||||||  |||||||||||||| |||||||| ||||||||||| |||||
gtaagtaaatacatctcaaatgaaaattttatttgtaaattacaatggaaattttttttaaattt---ttttttggtaact------atctttac-tgaactta------atgttt---tttcagATGGTTGTTTCAGAAGATATAGGAAGACAAATTTTGACATATGGTGAGAG

upper sequence: Vv11s0016g02870.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: GLYMA05G36040.1 (Glycine max), 3'ss of exon 10
----gtaaccattttcttgaaattcgtcccttttttattttatttgaatttgaaacattgtttagggctgcatt---tttttgcaactg-gtatcatttttg-----tatgagctcatgatgaaggtttat----cttgcagATGGTTGCATCAGAAGATATAGGTAGACAAATCTTGACATATGGAGAGAG
    ||||  |  | ||  ||     |    | |  |  |||          ||    | |||     | ||||   |||||   | || |  |  ||||||     |||    |||  |   |  |||||     || ||||||||||  |||||||||||||| |||||||| ||||||||||| |||||
gtaagtaaatacat-ctcaaatgaaattttatatggaaattacaatggcaaaaatttatttttcaattttcattcagtttttcttattgtgctttttttttggtaactatctaatcactactgaactttatgtttttttcagATGGTTGTTTCAGAAGATATAGGAAGACAAATTTTGACATATGGTGAGAG
















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|22013320|gb|BQ798354.1|BQ798354
EST:     GTGCCAAACAGACCACGAAGACTGCTGTTCTGATGAACTTGGAATCTAGA                         ATGGTTGCATCAGAAGATATAGGTAGACAAATCTTGACATATGGAGAGAG
genomic: GTGCCAAACAGACCACGAAGACTGCTGTTCTGATGAACTTGGAATCTAGAgtaaccattt ... tatcttgcagATGGTTGCATCAGAAGATATAGGTAGACAAATCTTGACATATGGAGAGAG
EST: gi|22013547|gb|BQ798581.1|BQ798581
EST:     GTGCCAAACAGACCACGAAGACTGCTGTTCTGATGAACTTGGAATCTAGA                         ATGGTTGCATCAGAAGATATAGGTAGACAAATCTTGACATATGGAGAGAG
genomic: GTGCCAAACAGACCACGAAGACTGCTGTTCTGATGAACTTGGAATCTAGAgtaaccattt ... tatcttgcagATGGTTGCATCAGAAGATATAGGTAGACAAATCTTGACATATGGAGAGAG
EST: gi|46910215|gb|CN545590.1|CN545590
EST:     GTGCCAAACAGACCACGAAGACTGCTGTTCTGATGAACTTGGAATCTAGA                         ATGGTTGCATCAGAAGATATAGGTAGACAAATCTTGACATATGGAGAGAG
genomic: GTGCCAAACAGACCACGAAGACTGCTGTTCTGATGAACTTGGAATCTAGAgtaaccattt ... tatcttgcagATGGTTGCATCAGAAGATATAGGTAGACAAATCTTGACATATGGAGAGAG
EST: gi|110716318|gb|EE091196.1|EE091196
EST:     GTGCCAAACAGACCACGAAGACTGCTGTTCTGATGAACTTGGAATCTAGA                         ATGGTTGCATCAGAAGATATAGGTAGACAAATCTTGACATATGGAGAGAG
genomic: GTGCCAAACAGACCACGAAGACTGCTGTTCTGATGAACTTGGAATCTAGAgtaaccattt ... tatcttgcagATGGTTGCATCAGAAGATATAGGTAGACAAATCTTGACATATGGAGAGAG
EST: gi|110382252|gb|EC938898.1|EC938898
EST:     GTGCCAAACAGACCACGAAGACTGCTGTTCTGATGAACTTGGAATCTAGA                         ATGGTTGCATCAGAAGATATAGGTAGACAAATCTTGACATATGGAGAGAG
genomic: GTGCCAAACAGACCACGAAGACTGCTGTTCTGATGAACTTGGAATCTAGAgtaaccattt ... tatcttgcagATGGTTGCATCAGAAGATATAGGTAGACAAATCTTGACATATGGAGAGAG
EST: gi|22014250|gb|BQ799284.1|BQ799284
EST:     GTGCCAAACAGACCACGAAGACTGCTGTTCTGATGAACTTGGAATCTAGA                         ATGGTTGCATCAGAAGATATAGGTAGACAAATCTTGACATATGGAGAGAG
genomic: GTGCCAAACAGACCACGAAGACTGCTGTTCTGATGAACTTGGAATCTAGAgtaaccattt ... tatcttgcagATGGTTGCATCAGAAGATATAGGTAGACAAATCTTGACATATGGAGAGAG
EST: gi|352763498|gb|FQ473201.1|FQ473201
EST:     GTGCCAAACAGACCACGAAGACTGCTGTTTTGATGAACTTGGAATCTAGA                         ATGGTTGCATCAGAAGATATAGGTAGACAAATCTTGACATATGGAGAGAG
genomic: GTGCCAAACAGACCACGAAGACTGCTGTTCTGATGAACTTGGAATCTAGAgtaaccattt ... tatcttgcagATGGTTGCATCAGAAGATATAGGTAGACAAATCTTGACATATGGAGAGAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttttgcaactggtatcatttttgtatgagctcatgatgaaggtttatcttgcagATGGTTGCATCAGAAGATATAGGTAGACAAATCTTGACATATGGAGAGAG
                                           tttatctt  CT-rich tract
             tatcatttttgtat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaccattttcttgaaattcgtcccttttttattttatttgaatttgaaacattgtttagggctgcatttttttgcaactggtatcatttttgtatgagctcatgatgaaggtttatcttgcagATGGTTGCATCAGAAGATATAGGTAGACAAATCTTGACATATGGAGAGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA