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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aaaagacaagggtatctcagagcaggcgttaatctgtgctttgtcaaattagtagatattttccattctttgtccttctcacataaacttttgcaaacagTATTAATCATGAGTACAAGGAGTGGGATGAGAAGAACCCTCAGTTGGCAACATGCAATGCAAATACCAAAAATTTGATTCAAAGTACCACTGTCCCACAA

Basic information

species Vitis vinifera
transcript Vv09s0002g02140.t01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv09s0002g02140.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA08G20640.1 (Glycine max), 3'ss of exon 5
aaaagacaagggtatctcagagcaggcgttaatctgtgctt--tgtcaaattagtagatattttccattctttgtccttctcacataaacttt-----tgcaaacagTATTAATCATGAGTACAAGGAGTGGGATGAGAAGAACCCTCAGTTGGCAACATGCAATGCAAATACCAAAAATTTGATTCAAAGTACCACTGTCCCACAA
     |     | | ||    |  |   ||  |   || ||  | |||||| | |   || | |  |||||  ||| |||| | || |||| |     || ||||||||| |||||||| |||||||||||| |||| ||||| || ||| |  |||||||||||  | ||||||| |||||||| ||| |||  ||||||||||||
-----aattaagcacctgtatgttgtatttctttcttgtttgatttcaaatgactgcttagtgtgtattct--gtctttctgatatgaactctgtaactgtaaacagTATAAATCATGAATACAAGGAGTGGAATGACAAGAATCCACAGGTAACAACATGCAATAAAGATACCAAGAATTTGATGCAAGGTAGTACTGTCCCACAA

upper sequence: Vv09s0002g02140.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA07G01240.1 (Glycine max), 3'ss of exon 5
-aaaagacaagggtatctcagagcaggcgttaatctgtgctttgtcaaattagtagatattttccattctttgtccttctcacataaacttt-----tgcaaacagTATTAATCATGAGTACAAGGAGTGGGATGAGAAGAACCCTCAGTTGGCAACATGCAATGCAAATACCAAAAATTTGATTCAAAGTACCACTGTCCCACAA
 | ||  |||  |||| |   |     | ||  | | || |||  ||||| | |   ||   |   ||||  ||| |||| | || |||| |     || ||||||||| ||||| || |||||||||||| |||| ||||| || ||| |  |||||||||||  | ||||||| |||||||| ||| |||  ||||||||||||
aataaagcaactgtatgttgtattt--ctttcttgtttgattt--caaatgactgcttaaggtgtgttct--gtctttcttatatgaactctgtaactgtaaacagTATAAATCACGAATACAAGGAGTGGAATGACAAGAATCCACAGGTAACAACATGCAATAAAGATACCAAGAATTTGATGCAAGGTAGTACTGTCCCACAA
















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|161705906|gb|FC054812.1|FC054812
EST:     CCTGAGACTGATTCTGCTCGAATTGTTGGGTTTGAGGTTTCTCCAAACAG                         TATTAATCATGAGTACAAGGAGTGGGATGAGAAGAACCCTCAGTTGGCAAC
genomic: CCTGAGACTGATTCTGCTCGAATTGTTGGGTTTGAGGTTACTCCAAACAGgttctgtaac ... ttgcaaacagTATTAATCATGAGTACAAGGAGTGGGATGAGAAGAACCCTCAGTTGGCAAC
EST: gi|110691298|gb|EE069240.1|EE069240
EST:     CCTGAGACTGATTCTGCTCGAATTGTTGGGTTTGAGGTTTCTCCAAACAG                         TATTAATCATGAGTACAAGGAGTGGGATGAGAAGAACCCTCAGTTGGCAAC
genomic: CCTGAGACTGATTCTGCTCGAATTGTTGGGTTTGAGGTTACTCCAAACAGgttctgtaac ... ttgcaaacagTATTAATCATGAGTACAAGGAGTGGGATGAGAAGAACCCTCAGTTGGCAAC
EST: gi|110719001|gb|EE096474.1|EE096474
EST:     CCTGAGACTGATTCTGCTCGAATTGTTGGGTTTGAGGTTTCTCCAAACAG                         TATTAATCATGAGTACAAGGAGTGGGATGAGAAGAACCCTCAGTTGGCAAC
genomic: CCTGAGACTGATTCTGCTCGAATTGTTGGGTTTGAGGTTACTCCAAACAGgttctgtaac ... ttgcaaacagTATTAATCATGAGTACAAGGAGTGGGATGAGAAGAACCCTCAGTTGGCAAC
EST: gi|351033128|gb|FQ446481.1|FQ446481
EST:     CCTGAGACTGATTCTGCTCGAATTGTTGGGTTTGAGGTTACTCCAAACAG                         TATTAATCATGAGTACAAGGAGTGGGATGAGAAGAACCCTCAGTTGGCAAC
genomic: CCTGAGACTGATTCTGCTCGAATTGTTGGGTTTGAGGTTACTCCAAACAGgttctgtaac ... ttgcaaacagTATTAATCATGAGTACAAGGAGTGGGATGAGAAGAACCCTCAGTTGGCAAC
EST: gi|351030399|gb|FQ432337.1|FQ432337
EST:     CCTGAGACTGATTCTGCTCGAATTGTTGGGTTTGAGGTTACTCCNAACAG                         TATTAATCATGAGTACAAGGAGTGGGATGAGAAGAACCCTCAGTTGGCAAC
genomic: CCTGAGACTGATTCTGCTCGAATTGTTGGGTTTGAGGTTACTCCAAACAGgttctgtaac ... ttgcaaacagTATTAATCATGAGTACAAGGAGTGGGATGAGAAGAACCCTCAGTTGGCAAC
EST: gi|349833072|gb|FQ416450.1|FQ416450
EST:     CCTGAGACTGATTCTGCTCAAATTGTTGGGTTTGAGGTTACTCCAAACAG                         TATTAATCATGAGTACAAGGAGTGGGATGAGAAGAACCCTCAGTTGGCAAC
genomic: CCTGAGACTGATTCTGCTCGAATTGTTGGGTTTGAGGTTACTCCAAACAGgttctgtaac ... ttgcaaacagTATTAATCATGAGTACAAGGAGTGGGATGAGAAGAACCCTCAGTTGGCAAC
EST: gi|34546863|gb|CF515095.1|CF515095
EST:     CCTGAGACTGATTCTGCTCGAATTGTTGGGTTTGAGGTTTCTCCAAACAG                         TATTAATCATGAGTACAAGGAGTGGGATGAGAAGAACCCTCAGTTGGCAAC
genomic: CCTGAGACTGATTCTGCTCGAATTGTTGGGTTTGAGGTTACTCCAAACAGgttctgtaac ... ttgcaaacagTATTAATCATGAGTACAAGGAGTGGGATGAGAAGAACCCTCAGTTGGCAAC
EST: gi|161713929|gb|FC062883.1|FC062883
EST:     CCTGAGACTGATTCTGCTCGA-TTGTTGGGTTTGAGGTTTCTCCAA-CAG                         TATTAATCATGAG-ACAAGGAGTGG-ATGAGAA-AACCCTC-GTTGGCA-C
genomic: CCTGAGACTGATTCTGCTCGAATTGTTGGGTTTGAGGTTACTCCAAACAGgttctgtaac ... ttgcaaacagTATTAATCATGAGTACAAGGAGTGGGATGAGAAGAACCCTCAGTTGGCAAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaattagtagatattttccattctttgtccttctcacataaacttttgcaaacagTATTAATCATGAGTACAAGGAGTGGGATGAGAAGAACCCTCAGTTGGCAACATGCAATGCAAATACCAAAAATTTGATTCAAAGTACCACTGTCCCACAA
                              ttctcac  putative branch site (score: 2)
                                          cttttgc  putative PPT
       tagatatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aaaagacaagggtatctcagagcaggcgttaatctgtgctttgtcaaattagtagatattttccattctttgtccttctcacataaacttttgcaaacagTATTAATCATGAGTACAAGGAGTGGGATGAGAAGAACCCTCAGTTGGCAACATGCAATGCAAATACCAAAAATTTGATTCAAAGTACCACTGTCCCACAA

aaaagac
- - - - - - - - - - -gcaggcg
- - - - - - - - - - - - - - - - - - tgctttg
- - - - - - - - - - - - - - - - - - - - - - caaatta
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cataaac