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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTCAGGTTCTGTATGCTTGGATGTCATTAACCAATCATGGAGTCCAATGTTTGgtcagtattgcttgttagtcctccataaaaattttgagtatcatatgattgcaaaatatgtgcacatgtcttcttatatttccatgtcttcatgttcact...

Basic information

species Vitis vinifera
transcript Vv17s0000g07960.t01
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv17s0000g07960.t01 (Vitis vinifera), 5'ss of exon 6
lower sequence: GLYMA17G09940.1 (Glycine max), 5'ss of exon 5
GTCAGGTTCTGTATGCTTGGATGTCATTAACCAATCATGGAGTCCAATGTTTGgtcagtattgcttgttagtcctc-cataaaaattttgagtatcatatgattgcaa-----aatatgtgcacatgtcttcttatatttccatgtcttcatgttcact
 || || ||||||||||||||||||||||||||||| |||||||||||||||||| ||      || |      ||  || ||| ||   |||| |       |  |      | ||| |   ||| | ||||| | | || ||       | |     
ATCTGGCTCTGTATGCTTGGATGTCATTAACCAATCTTGGAGTCCAATGTTTGgtaagc--cagttatagactttcatattaaagttgcaagtacccaccatctaaaggttctattatttagtcatat-ttcttgtgtatctatactgaggtatat---

upper sequence: Vv17s0000g07960.t01 (Vitis vinifera), 5'ss of exon 6
lower sequence: GLYMA05G01980.1 (Glycine max), 5'ss of exon 5
GTCAGGTTCTGTATGCTTGGATGTCATTAACCAATCATGGAGTCCAATGTTTGgtcagtattgcttgttagtcctccataaaaattttgagtatcatatgattgcaaaatatgtgcacatgtcttcttatatttcc-atgtcttcatgttcact---
 || || ||||||||||||||||||||||||||||| |||||||||||||| ||| |||      |     | |    ||||| |||  |||| |  |  ||   ||  |   |  |    | || | |||||||   ||| || ||  | |     
ATCTGGCTCTGTATGCTTGGATGTCATTAACCAATCTTGGAGTCCAATGTTCGgtaagtcagttatagactttcatattaaaagtttcaagtacc-caccatctaaaggt---tctattatttttttcatatttcttgtgtatttatactgaggtat

upper sequence: Vv17s0000g07960.t01 (Vitis vinifera), 5'ss of exon 6
lower sequence: PP1S161_122V6.1 (Physcomitrella patens), 5'ss of exon 4
GTCAGGTTCTGTATGCTTGGATGTCATTAACCAATCATGGAGTCCAATGTTTGgtcagtattgcttgttagtcctccataaa-aattttgagtatcatatgattgc-aaaatatgtgcacatgtcttcttatatttccatgtcttcatgttcact
|||||| |||||||||||||||||||| || ||  | |||||||| ||||||||| ||| |    | ||  |        |  |||| | ||| |   |     ||   || |         |  |||      |        |  ||  | |  
GTCAGGATCTGTATGCTTGGATGTCATCAATCAGACTTGGAGTCCCATGTTTGgtgagtgtcctctcttcattgcagtcgattaattgtaagttttggacttcagctggaagacacctgatcgatttcgaggcctgatgctattctatcgtta--

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|32271062|gb|CD720221.1|CD720221
EST:     AGGTTCTGTATGCTTGGATGTTATTAACCAATCATGGAGTCCAATGTTTG                         ATCTTTTAAACGTCTTTGAAGTCTTTCTTCCACAGCTCTTGCTTTATCCAA
genomic: AGGTTCTGTATGCTTGGATGTCATTAACCAATCATGGAGTCCAATGTTTGgtcagtattg ... cttgtcacagATCTTTTAAACGTCTTTGAAGTCTTTCTTCCACAGCTCTTGCTTTATCCAA
EST: gi|32271807|gb|CD720966.1|CD720966
EST:     AGGTTCTGTATGCTTGGATGTTATTAACCAATCATGGAGTCCAATGTTTG                         ATCTTTTAAACGTCTTTGAAGTCTTTCTTCCACAGCTCTTGCTTTATCCAA
genomic: AGGTTCTGTATGCTTGGATGTCATTAACCAATCATGGAGTCCAATGTTTGgtcagtattg ... cttgtcacagATCTTTTAAACGTCTTTGAAGTCTTTCTTCCACAGCTCTTGCTTTATCCAA
EST: gi|32272372|gb|CD721531.1|CD721531
EST:     AGGTTCTGTATGCTTGGATGTTATTAACCAATCATGGAGTCCAATGTTTG                         ATCTTTTAAACGTCTTTGAAGTCTTTCTTCCACAGCTCTTGCTTTATCCAA
genomic: AGGTTCTGTATGCTTGGATGTCATTAACCAATCATGGAGTCCAATGTTTGgtcagtattg ... cttgtcacagATCTTTTAAACGTCTTTGAAGTCTTTCTTCCACAGCTCTTGCTTTATCCAA
EST: gi|87584867|gb|DY473862.1|DY473862
EST:     AGGTTCTGTATGCTTGGATGTCATTAACCAATCATGGAGTCCAATGTTTG                         ATCTTTTAAACGTCTTTGAAGTCTTTCTTCCACAGCTCTTGCTTTATCCAA
genomic: AGGTTCTGTATGCTTGGATGTCATTAACCAATCATGGAGTCCAATGTTTGgtcagtattg ... cttgtcacagATCTTTTAAACGTCTTTGAAGTCTTTCTTCCACAGCTCTTGCTTTATCCAA
EST: gi|161712684|gb|FC062256.1|FC062256
EST:     AGGTTCTGTATGCTTGGATGTCATTAACCAATCATGGAGTCCAATGTTTG                         ATCTTTTAAACGTCTTTGAAGTCTTTCTTCCACAGCTCTTGCTTTATCCAA
genomic: AGGTTCTGTATGCTTGGATGTCATTAACCAATCATGGAGTCCAATGTTTGgtcagtattg ... cttgtcacagATCTTTTAAACGTCTTTGAAGTCTTTCTTCCACAGCTCTTGCTTTATCCAA
EST: gi|30327528|gb|CD010790.1|CD010790
EST:     AGGTTCTGTATGCTTGGATGTTATTAACCAATCATGGAGTCCAATGTTTG                         ATCTTTTAAACGTCTTTGAAGTCTTTCTTCCACAGCTCTTGCTTTATCCAA
genomic: AGGTTCTGTATGCTTGGATGTCATTAACCAATCATGGAGTCCAATGTTTGgtcagtattg ... cttgtcacagATCTTTTAAACGTCTTTGAAGTCTTTCTTCCACAGCTCTTGCTTTATCCAA
EST: gi|32272391|gb|CD721550.1|CD721550
EST:     AGGTTCTGTATGCTTGGATGTTATTAACCAATCATGGAGTCCAATGTTTG                         ATCTTTTAAACGTCTTTGAAGTCTTTCTTCCACAGCTCTTGCTTTATCCAA
genomic: AGGTTCTGTATGCTTGGATGTCATTAACCAATCATGGAGTCCAATGTTTGgtcagtattg ... cttgtcacagATCTTTTAAACGTCTTTGAAGTCTTTCTTCCACAGCTCTTGCTTTATCCAA
EST: gi|32271578|gb|CD720737.1|CD720737
EST:     AGGTTCTGTATGCTTGGATGTTATTAACCAATCATGGAGTCCAATGTTTG                         ATCTTTTAAACGTCTTTGAAGTCTTTCTTCCACAGCTCTTGCTTTATCCAA
genomic: AGGTTCTGTATGCTTGGATGTCATTAACCAATCATGGAGTCCAATGTTTGgtcagtattg ... cttgtcacagATCTTTTAAACGTCTTTGAAGTCTTTCTTCCACAGCTCTTGCTTTATCCAA
EST: gi|32272363|gb|CD721522.1|CD721522
EST:     AGGTTCTGTATGCTTGGATGTTATTAACCAATCATGGAGTCCAATGTTTG                         ATCTTTTAAACGTCTTTGAAGTCTTTCTTCCACAGCTCTTGCTTTATCCAA
genomic: AGGTTCTGTATGCTTGGATGTCATTAACCAATCATGGAGTCCAATGTTTGgtcagtattg ... cttgtcacagATCTTTTAAACGTCTTTGAAGTCTTTCTTCCACAGCTCTTGCTTTATCCAA
EST: gi|30324813|gb|CD008075.1|CD008075
EST:     AGGTTCTGTATGCTTGGATGTTATTAACCAATCATGGAGTCCAATGTTTG                         ATCTTTTAAACGTCTTTGAAGTCTTTCTTCCACAGCTCTTGCTTTATCCAA
genomic: AGGTTCTGTATGCTTGGATGTCATTAACCAATCATGGAGTCCAATGTTTGgtcagtattg ... cttgtcacagATCTTTTAAACGTCTTTGAAGTCTTTCTTCCACAGCTCTTGCTTTATCCAA
EST: gi|27586958|gb|CB009653.1|CB009653
EST:     AGGTTCTGTATGCTTGGATGTCATTAACCAATCATGGAGTCCAATGTTTG                         ATCTTTTAAACGTCTTTGAAGTCTTTCTTCCACAGCTCTTGCTTTATCCAA
genomic: AGGTTCTGTATGCTTGGATGTCATTAACCAATCATGGAGTCCAATGTTTGgtcagtattg ... cttgtcacagATCTTTTAAACGTCTTTGAAGTCTTTCTTCCACAGCTCTTGCTTTATCCAA
EST: gi|32270967|gb|CD720126.1|CD720126
EST:     AGGTTCTGTATGCTTGGATGTTATTAACCAATCATGGAGTCCAATGTTTG                         ATCTTTTAAACGTCTTTGAAGTCTTTCTTCCACAGCTCTTGCTTTATCCAA
genomic: AGGTTCTGTATGCTTGGATGTCATTAACCAATCATGGAGTCCAATGTTTGgtcagtattg ... cttgtcacagATCTTTTAAACGTCTTTGAAGTCTTTCTTCCACAGCTCTTGCTTTATCCAA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTCAGGTTCTGTATGCTTGGATGTCATTAACCAATCATGGAGTCCAATGTTTGgtcagtattgcttgttagtcctccataaaaattttgagtatcatatgattgcaaaatatgtgcacatgtcttcttatatttccatgtcttcatgttcact

- - - - - - - - - - - - - - - - -  CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ataaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -caaaata