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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aaacccaaccaaaaaaaataaaattgaaaacaagtcttgagagtcgccatggagattgaattttctgtaaattgatgtgtcgtttgataatcaatggcagATAGATGAAAAATTAGCAAGGCAGAAGGAGATCGATGATTGGCTGCCCATTTCTTCCTCCAGGAATGCAAAATGGTGGTATTCAGCATTCCACAATGTTA

Basic information

species Vitis vinifera
transcript Vv14s0171g00400.t01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv14s0171g00400.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA19G22590.1 (Glycine max), 3'ss of exon 1
---aaacccaaccaaaaaaaataaaattgaaaacaagtcttgagagtcgccatggagattgaattttctg-taaattgatgtgtcgtttgataatcaatggcagATAGATGAAAAATTAGCAAGGCAGAAGGAGATCGATGATTGGCTGCCCATTTCTTCCTCCAGGAATGCAAAATGGTGGTATTCAGCATTCCACAATGTTA------
    |    |  |       |   |||| |   ||     | | | |    ||| || ||||| |    | | | || || ||| ||||| | || ||      ||||  |||||||  |  ||  ||| |   || ||||| ||||| || ||| ||||    ||||||| |||||||||||||||||| |||||||||||||      
tagcatattactcttgtttgagtgaatttatggcattatattataata--tatgtagcttgaaatggaagctcatttaatttgttgtttgttgataaa------atag-
















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|161719199|gb|FC065732.1|FC065732
EST:     ATTTTCGAAGTTGCAGTGCAGCCATGGGAACCCAAGGTCCACCCACCAGT                         ATAGATGAAAAATTAGCAAGGCAGAAGGAGATCGATGATTGGCTGCCCATT
genomic: ATTTTCGAAGTTGCAGTGCAGCCATGGGAACCCAAGGTCCACCCACCAGTgtgagtttcc ... tcaatggcagATAGATGAAAAATTAGCAAGGCAGAAGGAGATCGATGATTGGCTGCCCATT
EST: gi|161707654|gb|FC057408.1|FC057408
EST:     ATTTTCGAAGTTGCAGTGCAGCCATGGGAACCCAAGGTCCACCCACCAGT                         ATAGATGAAAAATTAGCAAGGCAGAAGGAGATCGATGATTGGCTGCCCATT
genomic: ATTTTCGAAGTTGCAGTGCAGCCATGGGAACCCAAGGTCCACCCACCAGTgtgagtttcc ... tcaatggcagATAGATGAAAAATTAGCAAGGCAGAAGGAGATCGATGATTGGCTGCCCATT
EST: gi|161718440|gb|FC067297.1|FC067297
EST:     ATTTTCGAAGTTGCAGTGCAGCCATGGGAACCCAAGGTCCACCCACCAG-                         -T--ATGAAAAATTAGCAAGGCAGAAGGAGATCGATGATTGGCTGCCCATT
genomic: ATTTTCGAAGTTGCAGTGCAGCCATGGGAACCCAAGGTCCACCCACCAGTgtgagtttcc ... tcaatggcagATAGATGAAAAATTAGCAAGGCAGAAGGAGATCGATGATTGGCTGCCCATT
EST: gi|161717137|gb|FC066560.1|FC066560
EST:     ATTTTCGAAGTTGCAGTGCAGCCATGGGAACCCAAGGTCCACCCACCAGT                         ATAGATGAAAAATTAGCAAGGCAGAAGGAGATCGATGATTGGCTGCCCATT
genomic: ATTTTCGAAGTTGCAGTGCAGCCATGGGAACCCAAGGTCCACCCACCAGTgtgagtttcc ... tcaatggcagATAGATGAAAAATTAGCAAGGCAGAAGGAGATCGATGATTGGCTGCCCATT
EST: gi|110724165|gb|EE099752.1|EE099752
EST:     ATTTTCGAAGTTGCAGTGCAGCCATGGGAACCCAAGGTCCACCCACCAGT                         ATAGATGAAAAATTAGCAAGGCAGAAGGAGATCGACGATTGGTTGCCCATT
genomic: ATTTTCGAAGTTGCAGTGCAGCCATGGGAACCCAAGGTCCACCCACCAGTgtgagtttcc ... tcaatggcagATAGATGAAAAATTAGCAAGGCAGAAGGAGATCGATGATTGGCTGCCCATT
EST: gi|110703326|gb|EE080072.1|EE080072
EST:     ATTTTCGAAGTTGCAGTGCAGCCATGGGAACCCAAGGTCCACCCACCAGT                         ATAGATGAAAAATTAGCAAGGCAGAAGGAGATCGACGATTGGTTGCCCATT
genomic: ATTTTCGAAGTTGCAGTGCAGCCATGGGAACCCAAGGTCCACCCACCAGTgtgagtttcc ... tcaatggcagATAGATGAAAAATTAGCAAGGCAGAAGGAGATCGATGATTGGCTGCCCATT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gccatggagattgaattttctgtaaattgatgtgtcgtttgataatcaatggcagATAGATGAAAAATTAGCAAGGCAGAAGGAGATCGATGATTGGCTGCCCATTTCTTCCTCCAGGAATGCAAAATGGTGGTATTCAGCATTCCACAATGTTA
             aattttctgtaaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aaacccaaccaaaaaaaataaaattgaaaacaagtcttgagagtcgccatggagattgaattttctgtaaattgatgtgtcgtttgataatcaatggcagATAGATGAAAAATTAGCAAGGCAGAAGGAGATCGATGATTGGCTGCCCATTTCTTCCTCCAGGAATGCAAAATGGTGGTATTCAGCATTCCACAATGTTA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - ccaacca
- - - - - aaaaaaa
- - - - - - - - - -aaaattg
- - - - - - - - - - aaattga
- - - - - - - - - - - - - aaaacaa
- - - - - - - - - - - - - - - - - - - - - - - ccatgga