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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TATATACTTGAAACCAGTGTGTACCCAAGAGAGCCCGAATCCATGAAGGAGCTCAGAGAGTTGACTGCCCAGCATCCATGgtgagcttttcttgattcggattctcaaatctttgaatacccgttgtctatttgatgcttgtttgtaacgttagtgttggtttgaaaacgaaacag

Basic information

species Vitis vinifera
transcript Vv03s0063g00140.t01
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv03s0063g00140.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: GLYMA02G11530.1 (Glycine max), 5'ss of exon 2
TATATACTTGAAACCAGTGTGTACCCAAGAGAGCCCGAATCCATGAAGGAGCTCAGAGAGTTGACTGCCCAGCATCCATGgtgagcttttcttgattcggattctcaaat----ctttgaatacccgttgtctatttgat---gcttgtttgt--aacgttagtgttggttt-----gaaaacgaa--acag
||||| || || |||||||| ||||||||||| || ||||||||||| || || ||||||||||| ||  | || |||||||     | |    |||    || |||| |     ||||| | |   || | |  ||  |   | || | ||   |  |||| || |  |||     |||||| ||  ||||
TATATTCTGGAGACCAGTGTCTACCCAAGAGAACCTGAATCCATGAAAGAACTGAGAGAGTTGACAGCAAAACACCCATGgtatatatataactatttcatttttcaattgacattttgactcctatttatatgcttcgtttggtttctctgctcatggttactgattttttttgttgaaaacaaacaacag

upper sequence: Vv03s0063g00140.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: GLYMA07G33780.1 (Glycine max), 5'ss of exon 2
TATATACTTGAAACCAGTGTGTACCCAAGAGAGCCCGAATCCATGAAGGAGCTCAGAGAGTTGACTGCCCAGCATCCATGgtg-----agcttttcttgattcggattctcaa---atctttgaatacccgttg------tctatttgatgctt--gtttgtaac-gttagtgttggtttgaaaacgaaacag---
||||| || || || ||||| ||||||||||| || ||||||||||| || || ||||||||||| ||  | || |||||||      |  || | |   |||   || ||||   |  |||  | |||  ||       |   |||| |   |  | | ||      |  | ||   |||||||  |||||    
TATATTCTGGAGACAAGTGTCTACCCAAGAGAACCTGAATCCATGAAAGAACTGAGAGAGTTGACAGCAAAACACCCATGgtatatataatttatataatttcattttttcaattgacattttgacacctattaatatgattggtttggtttctctgctcgtggttactgattttttgttgaaaaaaaaacaacag
















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|161707477|gb|FC055995.1|FC055995
EST:     GAGCCCGAATCCATGAAGGAGCTCAGAGAGTTGACTGCCCAGCATCCATG                         GAACATCATGACTACGTCTGCTGATGAAGGGCAGTTCTTGAACATGCTTCT
genomic: GAGCCCGAATCCATGAAGGAGCTCAGAGAGTTGACTGCCCAGCATCCATGgtgagctttt ... aacgaaacagGAACATCATGACTACGTCTGCTGATGAAGGGCAGTTCTTGAACATGCTTCT
EST: gi|352795208|gb|FQ477318.1|FQ477318
EST:     GAGCCTGAATCCATGAAGGAGCTCATAGAGTTGACTGCCCAGCATCCATG                         GAACATCATGACTACGTCTGCTGATGAAGGGCAGTTCTTGACCATGCTTCT
genomic: GAGCCCGAATCCATGAAGGAGCTCAGAGAGTTGACTGCCCAGCATCCATGgtgagctttt ... aacgaaacagGAACATCATGACTACGTCTGCTGATGAAGGGCAGTTCTTGAACATGCTTCT
EST: gi|33409666|gb|CF215293.1|CF215293
EST:     GAGCCCGAATCCATGAAGGAGCTCAGAGAGTTGACTGCCCAGCATCCATG                         GAACATCATGACTACGTCTGCTGATGAAGGGCAGTTCTTGAACATGCTTCT
genomic: GAGCCCGAATCCATGAAGGAGCTCAGAGAGTTGACTGCCCAGCATCCATGgtgagctttt ... aacgaaacagGAACATCATGACTACGTCTGCTGATGAAGGGCAGTTCTTGAACATGCTTCT
EST: gi|110392855|gb|EC957377.1|EC957377
EST:     GAGCCCGAATCCATGAAGGAGCTCAGAGAGTTGACTGCCCAGCATCCATG                         GAACATCATGACTACGTCTGCTGATGAAGGGCAGTTCTTGAACATGCTTCT
genomic: GAGCCCGAATCCATGAAGGAGCTCAGAGAGTTGACTGCCCAGCATCCATGgtgagctttt ... aacgaaacagGAACATCATGACTACGTCTGCTGATGAAGGGCAGTTCTTGAACATGCTTCT
EST: gi|110392663|gb|EC956866.1|EC956866
EST:     GAGCCTGAATCCATGAAGGAGCTCAGAGAGTTGACTGCCCAGCATCCATG                         GAACATCATGACTACGTCTGCTGATGAAGGGCAGTTCTTGAACATGCTTCT
genomic: GAGCCCGAATCCATGAAGGAGCTCAGAGAGTTGACTGCCCAGCATCCATGgtgagctttt ... aacgaaacagGAACATCATGACTACGTCTGCTGATGAAGGGCAGTTCTTGAACATGCTTCT
EST: gi|77586769|gb|DV222527.1|DV222527
EST:     GAGCCTGAATCCATGAGGGAGCTCAGAGAGTTGACTGCCCAGCATCCATG                         GAACATCATGACTACGTCTGCTGATGAAGGGCAGTTCTTGAACATGCTTCT
genomic: GAGCCCGAATCCATGAAGGAGCTCAGAGAGTTGACTGCCCAGCATCCATGgtgagctttt ... aacgaaacagGAACATCATGACTACGTCTGCTGATGAAGGGCAGTTCTTGAACATGCTTCT
EST: gi|33407984|gb|CF213611.1|CF213611
EST:     GAGCCTGAATCCATGAAGGAGCTCAGAGAGTTGACTGCCCAGCATCCATG                         GAACATCATGACTACGTCTGCTGATGAAGGGCAGTTCTTGAACATGCTTCT
genomic: GAGCCCGAATCCATGAAGGAGCTCAGAGAGTTGACTGCCCAGCATCCATGgtgagctttt ... aacgaaacagGAACATCATGACTACGTCTGCTGATGAAGGGCAGTTCTTGAACATGCTTCT
EST: gi|34548696|gb|CF516928.1|CF516928
EST:     GAGCCTGAATCCATGAAGGAGCTCAGAGAGTTGACTGCCCAGCATCCATG                         GAACATCATGACTACGTCTGCTGATGAAGGGCAGTTCTTGAACATGCTTCT
genomic: GAGCCCGAATCCATGAAGGAGCTCAGAGAGTTGACTGCCCAGCATCCATGgtgagctttt ... aacgaaacagGAACATCATGACTACGTCTGCTGATGAAGGGCAGTTCTTGAACATGCTTCT
EST: gi|37185411|gb|CF604764.1|CF604764
EST:     GAGCCTGAATCCATGAAGGAGCTCAGAGAGTTGACTGCCCAGCATCCATG                         GAACATCATGACTACGTCTGCTGATGAAGGGCAGTTCTTGAACATGCTTCT
genomic: GAGCCCGAATCCATGAAGGAGCTCAGAGAGTTGACTGCCCAGCATCCATGgtgagctttt ... aacgaaacagGAACATCATGACTACGTCTGCTGATGAAGGGCAGTTCTTGAACATGCTTCT
EST: gi|110378003|gb|EC943111.1|EC943111
EST:     GAGCCTGAATCCATGAAGGAGCTCAGAGAGTTGACTGCCCAGCATCCATG                         GAACATCATGACTACGTCTGCTGATGAAGGGCAGTTCTTGAACATGCTTCT
genomic: GAGCCCGAATCCATGAAGGAGCTCAGAGAGTTGACTGCCCAGCATCCATGgtgagctttt ... aacgaaacagGAACATCATGACTACGTCTGCTGATGAAGGGCAGTTCTTGAACATGCTTCT
EST: gi|34550193|gb|CF518411.1|CF518411
EST:     GAGCCTGAATCCATGAAGGAGCTCAGAGAGTTGACTGCCCAGCATCCATG                         GAACATCATGACTACGTCTGCTGATGAAGGGCAGTTCTTGAACATGCTTCT
genomic: GAGCCCGAATCCATGAAGGAGCTCAGAGAGTTGACTGCCCAGCATCCATGgtgagctttt ... aacgaaacagGAACATCATGACTACGTCTGCTGATGAAGGGCAGTTCTTGAACATGCTTCT
EST: gi|110372307|gb|EC936462.1|EC936462
EST:     GAGCCTGAATCCATGAAGGAGCTCAGAGAGTTGACTGCCCAGCATCCATG                         GAACATCATGACTACGTCTGCTGATGAAGGGCAGTTCTTGAACATGCTTCT
genomic: GAGCCCGAATCCATGAAGGAGCTCAGAGAGTTGACTGCCCAGCATCCATGgtgagctttt ... aacgaaacagGAACATCATGACTACGTCTGCTGATGAAGGGCAGTTCTTGAACATGCTTCT
EST: gi|110378272|gb|EC943395.1|EC943395
EST:     GAGCCCGAATCCATGAAGGAGCTCAGAGAGTTGACTGCCCAGCATCCATG                         GAACATCATGACTACGTCTGCTGATGAAGGGCAGTTCTTGAACATGCTTCT
genomic: GAGCCCGAATCCATGAAGGAGCTCAGAGAGTTGACTGCCCAGCATCCATGgtgagctttt ... aacgaaacagGAACATCATGACTACGTCTGCTGATGAAGGGCAGTTCTTGAACATGCTTCT
EST: gi|110365089|gb|EC928834.1|EC928834
EST:     GAGCCCGAATCCATGAAGGAGCTCAGAGAGTTGACTGCCCAGCATCCATG                         GAACATCATGACTACGTCTGCTGATGAAGGGCAGTTCTTGAACATGCTTCT
genomic: GAGCCCGAATCCATGAAGGAGCTCAGAGAGTTGACTGCCCAGCATCCATGgtgagctttt ... aacgaaacagGAACATCATGACTACGTCTGCTGATGAAGGGCAGTTCTTGAACATGCTTCT
EST: gi|352794669|gb|FQ475167.1|FQ475167
EST:     GAGCCTGAATCCATGAAGGAGCTCAGAGAGTTGACTGCCCAGCATCCATG                         GAACATCATGACTACGTCTGCTGATGAAGGGCAGTTCTTGAACATGCTTCT
genomic: GAGCCCGAATCCATGAAGGAGCTCAGAGAGTTGACTGCCCAGCATCCATGgtgagctttt ... aacgaaacagGAACATCATGACTACGTCTGCTGATGAAGGGCAGTTCTTGAACATGCTTCT
EST: gi|34548780|gb|CF517012.1|CF517012
EST:     GAGCCTGAATCCATGAAGGAGCTCAGAGAGTTGACTGCCCAGCATCCATG                         GAACATCATGACTACGTCTGCTGATGAAGGGCAGTTCTTGAACATGCTTCT
genomic: GAGCCCGAATCCATGAAGGAGCTCAGAGAGTTGACTGCCCAGCATCCATGgtgagctttt ... aacgaaacagGAACATCATGACTACGTCTGCTGATGAAGGGCAGTTCTTGAACATGCTTCT
EST: gi|33409385|gb|CF215012.1|CF215012
EST:     GAGCCCGAATCCATGAAGGAGCTCAGAGAGTTGACTGCCCAGCATCCATG                         GAACATCATGACTACGTCTGCTGATGAAGGGCAGTTCTTGAACATGCTTCT
genomic: GAGCCCGAATCCATGAAGGAGCTCAGAGAGTTGACTGCCCAGCATCCATGgtgagctttt ... aacgaaacagGAACATCATGACTACGTCTGCTGATGAAGGGCAGTTCTTGAACATGCTTCT
EST: gi|33409469|gb|CF215096.1|CF215096
EST:     GAGCCCGAATCCATGAAGGAGCTCAGAGAGTTGACTGCCCAGCATCCATG                         GAACATCATGACTACGTCTGCTGATGAAGGGCAGTTCTTGAACATGCTTCT
genomic: GAGCCCGAATCCATGAAGGAGCTCAGAGAGTTGACTGCCCAGCATCCATGgtgagctttt ... aacgaaacagGAACATCATGACTACGTCTGCTGATGAAGGGCAGTTCTTGAACATGCTTCT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TATATACTTGAAACCAGTGTGTACCCAAGAGAGCCCGAATCCATGAAGGAGCTCAGAGAGTTGACTGCCCAGCATCCATGgtgagcttttcttgattcggattctcaaatctttgaatacccgttgtctatttgatgcttgtttgtaacgttagtgttggtttgaaaacgaaacag

- - - - - - - - - - - - - - - - - - - - - -  AAGGAG
- - - - - - - - - - - - - - - - - - - - - - -  GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - -  AGCTCA