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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTTAGCATGCTGTGGCTTTTTGTGTGGAAGTGGTTGTGATGGGGGTTATCCTCTTTATGCATGGCGATATTTTATTCACCATGGTGTTGTCACTGAGGAGgttattttcttttttcagcctattacaattattcattagttattccggcacctttttcttattgcaaataattcttcttgcactctatgttatatggtct...

Basic information

species Vitis vinifera
transcript Vv07s0005g02820.t01
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv07s0005g02820.t01 (Vitis vinifera), 5'ss of exon 6
lower sequence: GLYMA03G38520.1 (Glycine max), 5'ss of exon 7
CTTAGCATGCTGTGGCTTTTTGTGTGGAAGTGGTTGTGATGGGGGTTATCCTCTTTATGCATGGCGATATTTTATTCACCATGGTGTTGTCACTGAGGAGgttattttcttttttcagcctattacaattattcattagttatt---------ccggcacctt---tttcttattgcaaataattcttcttgcactctatgttatatggtct---------------------------------------------------------------
  | ||||||||||||||| ||||||||  ||| |||||||| || |||||  | |||||||||||||| ||    |||||||||||||||||||| ||||| ||    ||   |    |  |   ||| ||  | | ||||||         | |  | |||    ||||| |  |  | |  ||  ||| ||||  ||| ||  |  |                                                                 
TCTTGCATGCTGTGGCTTTCTGTGTGGATCTGGCTGTGATGGAGGATATCCCTTATATGCATGGCGATACTTAGCCCACCATGGTGTTGTCACTGAAGAGgtaatacatttccattttgccttggtaatcataaaatggttatttgtcagagacagaaatcttaggcttcttttcacctagatctcccctt-cacttgatgctaatttttgctgaagacttatatttcacaacttacccaactctcttacactcagcatttttattatgtggcag

upper sequence: Vv07s0005g02820.t01 (Vitis vinifera), 5'ss of exon 6
lower sequence: GLYMA19G41120.1 (Glycine max), 5'ss of exon 7
CTTAGCATGCTGTGGCTTTTTGTGTGGAAGTGGTTGTGATGGGGGTTATCCTCTTTATGCATGGCGATATTTTATTCACCATGGTGTTGTCACTGAGGAGgttattttcttttttcagcctattacaattattcattagttattccggcacctttttcttattgcaaataattcttcttgcactct-atgttatatggtct
  | ||||||||||||||| ||||||||  ||||||||||||||| |||||  | ||||| |||| ||| ||    ||||| |||||||||||||| ||||| ||    ||   |    |  |   | ||     || || ||       | |     |  || |   | |  ||  ||  |  |  |  |  |||| || 
TCTTGCATGCTGTGGCTTTCTGTGTGGATCTGGTTGTGATGGGGGATATCCCTTGTATGCGTGGCAATACTTAGCCCACCACGGTGTTGTCACTGAAGAGgtaatgcatttccattttgccttggtagtttccacttggtaatcataattcataagaatggttactggttagactcgttagagacagaaatcttatgctc-
















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|22010916|gb|BQ795950.1|BQ795950
EST:     TATGCATGGCGATATTTTATTCACCATGGTGTTGTCACTGAGGAG                         TGTGACCCATACTTTGATGCTACTGGCTGTTCTCACCCTGGTTGTGAACCT
genomic: TATGCATGGCGATATTTTATTCACCATGGTGTTGTCACTGAGGAGgttattttct ... tacttggcagTGTGACCCATACTTTGATGCTACTGGCTGTTCTCACCCTGGTTGTGAACCT
EST: gi|110716152|gb|EE090883.1|EE090883
EST:     CTCTTTATGCATGGCGATATTTTATTCACCATGGTGTTGTCACTGAGGAG                         TGTGACCCATACTTTGATGCTACTGGCTGTTCTCACCCTGGTTGTGAACCT
genomic: CTCTTTATGCATGGCGATATTTTATTCACCATGGTGTTGTCACTGAGGAGgttattttct ... tacttggcagTGTGACCCATACTTTGATGCTACTGGCTGTTCTCACCCTGGTTGTGAACCT
EST: gi|110717706|gb|EE093795.1|EE093795
EST:     CTCTTTATGCATGGCGATATTTTATTCACCATGGTGTTGTCACTGAGGAG                         TGTGACCCATACTTTGATGCTACTGGCTGTTCTCACCCTGGTTGTGAACCT
genomic: CTCTTTATGCATGGCGATATTTTATTCACCATGGTGTTGTCACTGAGGAGgttattttct ... tacttggcagTGTGACCCATACTTTGATGCTACTGGCTGTTCTCACCCTGGTTGTGAACCT
EST: gi|30302325|gb|CB979119.1|CB979119
EST:     CGATATTTTATTCACCATGGTGTTGTCACTGAGGAG                         TGTGACCCATACTTTGATGCTACTGGCTGTTCTCACCCTGGTTGTGAACCT
genomic: CGATATTTTATTCACCATGGTGTTGTCACTGAGGAGgttattttct ... tacttggcagTGTGACCCATACTTTGATGCTACTGGCTGTTCTCACCCTGGTTGTGAACCT
EST: gi|110375663|gb|EC940672.1|EC940672
EST:     CTCTTTATGCATGGCGATATTTTATTCACCATGGTGTTGTCACTGAGGAG                         TGTGACCCATACTTTGATGCTACTGGCTGTTCTCACCCTGGTTGTGAACCT
genomic: CTCTTTATGCATGGCGATATTTTATTCACCATGGTGTTGTCACTGAGGAGgttattttct ... tacttggcagTGTGACCCATACTTTGATGCTACTGGCTGTTCTCACCCTGGTTGTGAACCT
EST: gi|26262146|gb|CA813209.1|CA813209
EST:     CTCTTTATGCATGGCGATATTTTATTCACCATGGTGTTGTCACTGAGGAG                         TGTGACCCATACTTTGATGCTACTGGCTGTTCTCACCCTGGTTGTGAACCT
genomic: CTCTTTATGCATGGCGATATTTTATTCACCATGGTGTTGTCACTGAGGAGgttattttct ... tacttggcagTGTGACCCATACTTTGATGCTACTGGCTGTTCTCACCCTGGTTGTGAACCT
EST: gi|110703469|gb|EE080340.1|EE080340
EST:     CTCTTTATGCATGGCGATATTTTATTCACCATGGTGTTGTCACTGAGGAG                         TGTGACCCATACTTTGATGCTACTGGCTGTTCTCACCCTGGTTGTGAACCT
genomic: CTCTTTATGCATGGCGATATTTTATTCACCATGGTGTTGTCACTGAGGAGgttattttct ... tacttggcagTGTGACCCATACTTTGATGCTACTGGCTGTTCTCACCCTGGTTGTGAACCT
EST: gi|110731310|gb|EE105611.1|EE105611
EST:     CTCTTTATGCATGGCGATATTTTATTCACCATGGTGTTGTCACTGAGGAG                         TGTGACCCATACTTTGATGCTACTGGCTGTTCTCACCCTGGTTGTGAACCT
genomic: CTCTTTATGCATGGCGATATTTTATTCACCATGGTGTTGTCACTGAGGAGgttattttct ... tacttggcagTGTGACCCATACTTTGATGCTACTGGCTGTTCTCACCCTGGTTGTGAACCT
EST: gi|351041020|gb|FQ443796.1|FQ443796
EST:     CTCTTTATGCATGGCGATATTTTATTCACCATGGTGTTGTCACTGAGGAG                         TGTGACCCATACTTTGATGCTACTGGCTGTTCTCACCCTGGTTGTGAACCT
genomic: CTCTTTATGCATGGCGATATTTTATTCACCATGGTGTTGTCACTGAGGAGgttattttct ... tacttggcagTGTGACCCATACTTTGATGCTACTGGCTGTTCTCACCCTGGTTGTGAACCT
EST: gi|110420331|gb|EC986603.1|EC986603
EST:     CTCTTTATGCATGGCGATATTTTATTCACCATGGTGTTGTCACTGAGGAG                         TGTGACCCATACTTTGATGCTACTGGCTGTTCTCACCCTGGTTGTGAACCT
genomic: CTCTTTATGCATGGCGATATTTTATTCACCATGGTGTTGTCACTGAGGAGgttattttct ... tacttggcagTGTGACCCATACTTTGATGCTACTGGCTGTTCTCACCCTGGTTGTGAACCT
EST: gi|110406529|gb|EC972106.1|EC972106
EST:     CTCTTTATGCATGGCGATATTTTATTCACCATGGTGTTGTCACTGAGGAG                         TGTGACCCATACTTTGATGCTACTGGCTGTTCTCACCCTGGTTGTGAACCT
genomic: CTCTTTATGCATGGCGATATTTTATTCACCATGGTGTTGTCACTGAGGAGgttattttct ... tacttggcagTGTGACCCATACTTTGATGCTACTGGCTGTTCTCACCCTGGTTGTGAACCT
EST: gi|110406274|gb|EC971841.1|EC971841
EST:     CTCTTTATGCATGGCGATATTTTATTCACCATGGTGTTGTCACTGAGGAG                         TGTGACCCATACTTTGATGCTACTGGCTGTTCTCACCCTGGTTGTGAACCT
genomic: CTCTTTATGCATGGCGATATTTTATTCACCATGGTGTTGTCACTGAGGAGgttattttct ... tacttggcagTGTGACCCATACTTTGATGCTACTGGCTGTTCTCACCCTGGTTGTGAACCT
EST: gi|351027477|gb|FQ444726.1|FQ444726
EST:     CTCTTTATGCATGGCGATATTTTATTCACCATGGTGTTGTCACTGAGGAG                         TGTGACCCATACTTTGATGCTACTGGCTGTTCTCACCCTGGTTGTGAACCT
genomic: CTCTTTATGCATGGCGATATTTTATTCACCATGGTGTTGTCACTGAGGAGgttattttct ... tacttggcagTGTGACCCATACTTTGATGCTACTGGCTGTTCTCACCCTGGTTGTGAACCT
EST: gi|110426643|gb|EC993059.1|EC993059
EST:     GTTGTCACTGAGGAG                         TGTGACCCATACTTTGATGCTACTGGCTGTTCTCACCCTGGTTGTGAACCT
genomic: GTTGTCACTGAGGAGgttattttct ... tacttggcagTGTGACCCATACTTTGATGCTACTGGCTGTTCTCACCCTGGTTGTGAACCT
EST: gi|110360706|gb|EC924023.1|EC924023
EST:     CTCTTTATGCATGGCGATATTTTATTCACCATGGTGTTGTCACTGAGGAG                         TGTGACCCATACTTTGATGCTACTGGCTGTTCTCACCCTGGTTGTGAACCT
genomic: CTCTTTATGCATGGCGATATTTTATTCACCATGGTGTTGTCACTGAGGAGgttattttct ... tacttggcagTGTGACCCATACTTTGATGCTACTGGCTGTTCTCACCCTGGTTGTGAACCT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTTAGCATGCTGTGGCTTTTTGTGTGGAAGTGGTTGTGATGGGGGTTATCCTCTTTATGCATGGCGATATTTTATTCACCATGGTGTTGTCACTGAGGAGgttattttcttttttcagcctattacaattattcattagttattccggcacctttttcttattgcaaataattcttcttgcactctatgttatatggtct

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - caaataa