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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aaaagcattttttttggggggggtcaaatattgcttattctaacttgatcacaaatgatattctgtcgatggtactaaaatgaattttcttctctttcagGATGGAAAGTGCGATGTGCTGAGTACTTCCCTTATTCAGCATACTTTGAGGGTAGGTGCAGCTCTGCCATCTCCAAATCATCTGAACACCAGATCTGCAA

Basic information

species Vitis vinifera
transcript Vv09s0002g05110.t01
intron # 27
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv09s0002g05110.t01 (Vitis vinifera), 3'ss of exon 27
lower sequence: GLYMA08G22180.1 (Glycine max), 3'ss of exon 25
---aaaagcattttttttggggggggtcaaat----attgcttattctaacttgatcacaaatgatattctgtcgatggtactaaaatgaattttcttctctttcagGATGGAAAGTGCGATGTGCTGAGTACTTCCCTTATTCAGCATACTTTGAGGGTAGGTGCAGCTCTGCCATCTCCAAATCATCTGAACACCAGATCTGCAA
   |   |   | || ||||      |   ||    ||| |||||| | | || ||      | ||| |   ||        | | || |||| | |  |||| |||||||||| ||||| ||||| ||||||||||| |||||  |||||||||||||  |   ||||||||||    |||| ||  |     | ||| |  | ||
tctatgtgtgctgttcttggtttatttttcattccgatttcttatttttatttaatttattgtaatagtgcatca-------tgagattaattctatattcttgcagGATGGAAGGTGCGTTGTGCAGAGTACTTCCCATATTCTACATACTTTGAGGGATGCCACAGCTCTGCCTCTCCCAACTCGGCCTTCAATCAGTTACGTAA

upper sequence: Vv09s0002g05110.t01 (Vitis vinifera), 3'ss of exon 27
lower sequence: GLYMA07G03850.1 (Glycine max), 3'ss of exon 25
-aaaagcattttttttggggggggtcaaatattgcttattctaacttgatcacaaatgatattctgtcgatg-gtactaaaatgaattttcttctctttcagGATGGAAAGTGCGATGTGCTGAGTACTTCCCTTATTCAGCATACTTTGAGGGTAGGTGCAGCTCTGCCATCTCCAAATCATCTGAACACCAGATCTGCAA
 ||    || || ||   |   | |     ||| |   |||||| ||      ||||  | || |     ||  |    | || |||| | | ||||| |||||||||| ||||| ||||| ||||| ||||| |||||  |||||||||||||  |   ||||||||||    |||| ||  |       ||| |  | ||
taattctatgttgttctcgattgatttttcattccaatttctaatttatattaaaat--ttttgtaatagtgcatcacgagattaattctatactcttgcagGATGGAAGGTGCGTTGTGCAGAGTATTTCCCATATTCTACATACTTTGAGGGATGCCACAGCTCTGCCTCTCCCAACTCGGCCTTCAGTCAGTTACGTAA
















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|110361255|gb|EC924715.1|EC924715
EST:     AGTCCACAAACTGCTAGGGACAGCTTTGGTTGACTGCGATGCTGCATCGA                         GATGGAAAGTGCGATGTGCTGAGTACTTCCCTTATTCAGCATACTTTGAGG
genomic: AGTCCACAAACTGCTAGGGACAGCTTTGGTTGACTGCAATGCTGCATCGAgtaagttctg ... tctctttcagGATGGAAAGTGCGATGTGCTGAGTACTTCCCTTATTCAGCATACTTTGAGG
EST: gi|37187269|gb|CF606622.1|CF606622
EST:     AGTCCACAAACTGCTAGGGACAGCTTTGGTTGACTGCGATGCTGCATCGA                         GATGGAAAGTGCGATGTGCTGAGTACTTCCCTTATTCAGCATACTTTGAGG
genomic: AGTCCACAAACTGCTAGGGACAGCTTTGGTTGACTGCAATGCTGCATCGAgtaagttctg ... tctctttcagGATGGAAAGTGCGATGTGCTGAGTACTTCCCTTATTCAGCATACTTTGAGG
EST: gi|351056596|gb|FQ442424.1|FQ442424
EST:     AGTCCACAAACTGCTAGGGACAGCTTTGGTTGACTGCAATGCTGCATCGA                         GATGGAAAGTGCGATGTGCTGAGTACTTCCCTTATTCAGCATACTTTGAGG
genomic: AGTCCACAAACTGCTAGGGACAGCTTTGGTTGACTGCAATGCTGCATCGAgtaagttctg ... tctctttcagGATGGAAAGTGCGATGTGCTGAGTACTTCCCTTATTCAGCATACTTTGAGG
EST: gi|110692108|gb|EE070978.1|EE070978
EST:     AGTCCACAAACTGCTAGGGACAGCTTTGGTTGACTGCGATGCTGCATCGA                         GATGGAAAGTGCGATGTGCTGAGTACTTCCCTTATTCAGCATACTTTGAGG
genomic: AGTCCACAAACTGCTAGGGACAGCTTTGGTTGACTGCAATGCTGCATCGAgtaagttctg ... tctctttcagGATGGAAAGTGCGATGTGCTGAGTACTTCCCTTATTCAGCATACTTTGAGG
EST: gi|110361532|gb|EC925013.1|EC925013
EST:     AGTCCACAAACTGCTAGGGACAGCTTTGGTTGACTGCAATGCTGCATCGA                         GATGGAAAGTGCGATGTGCTGAGTACTTCCCTTATTCAGCATACTTTGAGG
genomic: AGTCCACAAACTGCTAGGGACAGCTTTGGTTGACTGCAATGCTGCATCGAgtaagttctg ... tctctttcagGATGGAAAGTGCGATGTGCTGAGTACTTCCCTTATTCAGCATACTTTGAGG
EST: gi|110700342|gb|EE078274.1|EE078274
EST:     AGTCCACAAACTGCTAGGGACAGCTTTGGTTGACTGCGATGCTGCATCGA                         GATGGAAAGTGCGATGTGCTGAGTACTTCCCTTATTCAGCATACTTTGAGG
genomic: AGTCCACAAACTGCTAGGGACAGCTTTGGTTGACTGCAATGCTGCATCGAgtaagttctg ... tctctttcagGATGGAAAGTGCGATGTGCTGAGTACTTCCCTTATTCAGCATACTTTGAGG
EST: gi|110385151|gb|EC949648.1|EC949648
EST:     AGTCCACAAACTGCTAGGGACAGCTTTGGTTGACTGCGATGCTGCATCGA                         GATGGAAAGTGCGATGTGCTGAGTACTTCCCTTATTCAGCATACTTTGAGG
genomic: AGTCCACAAACTGCTAGGGACAGCTTTGGTTGACTGCAATGCTGCATCGAgtaagttctg ... tctctttcagGATGGAAAGTGCGATGTGCTGAGTACTTCCCTTATTCAGCATACTTTGAGG
EST: gi|110715995|gb|EE090587.1|EE090587
EST:     AGTCCACAAACTGCTAGGGACAGCTTTGGTTGACTGCGATGCTGCATCGA                         GATGGAAAGTGCGATGTGCTGAGTACTTCCCTTATTCAGCATACTTTGAGG
genomic: AGTCCACAAACTGCTAGGGACAGCTTTGGTTGACTGCAATGCTGCATCGAgtaagttctg ... tctctttcagGATGGAAAGTGCGATGTGCTGAGTACTTCCCTTATTCAGCATACTTTGAGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgatcacaaatgatattctgtcgatggtactaaaatgaattttcttctctttcagGATGGAAAGTGCGATGTGCTGAGTACTTCCCTTATTCAGCATACTTTGAGGGTAGGTGCAGCTCTGCCATCTCCAAATCATCTGAACACCAGATCTGCAA
                           tactaaa  putative branch site (score: 1)
                                       ttttcttctctttc  putative PPT
                           tactaaaatgaatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aaaagcattttttttggggggggtcaaatattgcttattctaacttgatcacaaatgatattctgtcgatggtactaaaatgaattttcttctctttcagGATGGAAAGTGCGATGTGCTGAGTACTTCCCTTATTCAGCATACTTTGAGGGTAGGTGCAGCTCTGCCATCTCCAAATCATCTGAACACCAGATCTGCAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTC
aaaagca
- - - - - - - -ggggggg
- - - - - - - - - - - - caaatat
- - - - - - - - - - - - - - - - - - - - - - - - -cacaaat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ttctgtc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaatgaa