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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttgaaatccatcttgattcattggatttttctcatcccatattgcatttgcctccaacaagaaaacaatgtcctcatcagtttcttcttaattgctgcagATATCAAGGTTGATCTATACAAATTCCGGTAATGCTATTCTGGCATTAGCATCAAATGCCATTCATTTTCTTTGGAAGTGGCAGCGCAATGATCGTAATT

Basic information

species Vitis vinifera
transcript Vv09s0002g08370.t01
intron # 18
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv09s0002g08370.t01 (Vitis vinifera), 3'ss of exon 18
lower sequence: GLYMA08G22910.2 (Glycine max), 3'ss of exon 19
-------ttgaaatccatcttgattcattggatttttctca---tcccatattgcatttgcctccaacaagaaaacaatgtcctcatcagtttcttcttaattgctgcagATATCAAGGTTGATCTATACAAATTCCGGTAATGCTATTCTGGCATTAGCATCAAATGCCATTCATTTTCTTTGGAAGTGGCAGCGCAATGATCGTAATT
       |||||||     |||      |  ||| || | |   | |  |  | || |   |||||  |   |||   |||  | ||  | ||  | || |      ||||||||||||||||| ||||||||||| ||||||||||||||||||||||||||||||||||||||  | || ||||| |||||||| ||||| ||||| |
ctgataattgaaataatgattggacaccttcattcttttaaggtttctctggttcactcctctccatgactgaaat--tgttgtgat--gctttattttga------cagATATCAAGGTTGATATATACAAATTCAGGTAATGCTATTCTGGCATTAGCATCAAATGCCATTCACCTGCTCTGGAAATGGCAGCGAAATGAGCGTAACT

upper sequence: Vv09s0002g08370.t01 (Vitis vinifera), 3'ss of exon 18
lower sequence: GLYMA07G03180.1 (Glycine max), 3'ss of exon 17
-------ttgaaatccatcttgattcattggatttttctca---tcccatattgcatttgcctccaacaagaaaacaatgtcctcatcagtttcttcttaattgctgcagATATCAAGGTTGATCTATACAAATTCCGGTAATGCTATTCTGGCATTAGCATCAAATGCCATTCATTTTCTTTGGAAGTGGCAGCGCAATGATCGTAATT
       ||||| |   | |||      |  ||| ||   |   | |  |  | || ||  |||||  |   |||   |||  | ||  ||||  | || |      ||||||||||||||||| ||||||||||| ||||||||||||||||||||||||||||||||||||||  | || ||||| |||||||| ||||| ||||| |
ctgataattgaagtaattattggacaccttcattcttgcaaggtttctctggttcacttctctccatgactgaaat--tgttgtgat--gttttattttga------cagATATCAAGGTTGATATATACAAATTCAGGTAATGCTATTCTGGCATTAGCATCAAATGCCATTCACCTACTCTGGAAATGGCAGCGAAATGAGCGTAACT

upper sequence: Vv09s0002g08370.t01 (Vitis vinifera), 3'ss of exon 18
lower sequence: GLYMA15G00880.1 (Glycine max), 3'ss of exon 18
-ttgaaatccatctt---gattcattggatttttctcatcccatattgcatttgcctccaacaagaaaacaatgtcctcatcagtttcttcttaattgctgcagATATCAAGGTTGATCTATACAAATTCCGGTAATGCTATTCTGGCATTAGCATCAAATGCCATTCATTTTCTTTGGAAGTGGCAGCGCAATGATCGTAATT
  ||||  | || ||    |  |||   ||||   || |   |  |   |    ||||||| |  ||||   ||| || || |    | ||||  ||    ||||||||||||||||| ||||| ||||| ||||||||||| ||||||||||| ||||||||||||||| | || ||||| |||||||| ||||| |||||||
gatgaatactatgttaagaacacatcaaatttccttcttgtaacctgatacc--cctccaaaactaaaat--tgttctgattatccgcatctttgttatgacagATATCAAGGTTGATATATACTAATTCAGGTAATGCTATCCTGGCATTAGCTTCAAATGCCATTCATCTGCTCTGGAAATGGCAGCGAAATGACCGTAATT

upper sequence: Vv09s0002g08370.t01 (Vitis vinifera), 3'ss of exon 18
lower sequence: GLYMA13G44420.2 (Glycine max), 3'ss of exon 19
ttgaaatccatcttgat----tcattggatttttctcatcccatattgcatttgcctccaacaagaaaacaatgtcctcatcagtttcttcttaattgctgcagATATCAAGGTTGATCTATACAAATTCCGGTAATGCTATTCTGGCATTAGCATCAAATGCCATTCATTTTCTTTGGAAGTGGCAGCGCAATGATCGTAATT
 ||||  | || || |      ||||| ||||   || |   |  |   |     |||||| |  ||||   ||| || || |    | ||||  ||    ||||||||||||||||| ||||| ||||| ||||||||||| ||||| ||||| ||||||||||||||| | || ||||| |||||||| ||||| |||||||
-tgaatactatgttaagaccaccattgaatttccttcttgtaacctgataccc-tctccaaaactaaaat--tgttctgattatccgcatctttgttatgacagATATCAAGGTTGATATATACTAATTCAGGTAATGCTATCCTGGCGTTAGCTTCAAATGCCATTCATCTGCTCTGGAAATGGCAGCGAAATGACCGTAATT

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|71861393|gb|DT010448.1|DT010448
EST:     CGTCGCAGTGTCGGTCATTGAGGCTTCAAGAAAACTTGAGAATAACAAAG                         ATATCAAGGTTGATCTATACAAATTCCGGTAATGCTATTCTGGCATTAGCA
genomic: CGTCGCAGTGTCGGTCATTGAGGCTTCAAGAAAACTTGAGAATAACAAAGgtatgttatt ... attgctgcagATATCAAGGTTGATCTATACAAATTCCGGTAATGCTATTCTGGCATTAGCA
EST: gi|71862780|gb|DT011835.1|DT011835
EST:     CGTCGCAGTGTCGGTCATTGAGGCTTCAAGAAAACTTGAGAATAACAAAG                         ATATCAAGGTTGATCTATACAAATTCCGGTAATGCTATTCTGGCATTAGCA
genomic: CGTCGCAGTGTCGGTCATTGAGGCTTCAAGAAAACTTGAGAATAACAAAGgtatgttatt ... attgctgcagATATCAAGGTTGATCTATACAAATTCCGGTAATGCTATTCTGGCATTAGCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atttgcctccaacaagaaaacaatgtcctcatcagtttcttcttaattgctgcagATATCAAGGTTGATCTATACAAATTCCGGTAATGCTATTCTGGCATTAGCATCAAATGCCATTCATTTTCTTTGGAAGTGGCAGCGCAATGATCGTAATT
                                        tcttaat  putative branch site (score: 3)
                                       ttcttaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttgaaatccatcttgattcattggatttttctcatcccatattgcatttgcctccaacaagaaaacaatgtcctcatcagtttcttcttaattgctgcagATATCAAGGTTGATCTATACAAATTCCGGTAATGCTATTCTGGCATTAGCATCAAATGCCATTCATTTTCTTTGGAAGTGGCAGCGCAATGATCGTAATT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- -aaatcca
- - - - - - - - - - - - - - - -tcatccc
- - - - - - - - - - - - - - - - - - - - - -gcatttg
- - - - - - - - - - - - - - - - - - - - - - - - - cctccaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - aagaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cctcatc