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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aaaggaagctggttttccatttttttttatgtattctgttgacagttttgttgattattgacaatggtattcctatttctttctattttctctggtgcagATTTGAGCAGTATGTAGATTATGCTCTTGATGTTCCAATGTACTTTGTCTATCGGAAGAAGAAGTATATTGACTGTACTGGAATGTCCTTCCGG

Basic information

species Vitis vinifera
transcript Vv02s0025g03530.t01
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv02s0025g03530.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: LOC_Os07g27790.1 (Oryza sativa), 3'ss of exon 9
---------------------------------------------------aaaggaagctggttttccattttttttt------atgtattctgttgacagttttgttgattat-tgacaatggtattcctatttctttctattttctctggtgcagATTTGAGCAGTATGTAGATTATGCTCTTGATGTTCCAATGTACTTTGTCTATCGGAAGAAGAAGTATATTGACTGTACTGGAATGTCCTTCCGG
                                                      | ||  || ||    |  |  ||||      |  |||| |    |     |    | ||   ||  | ||  ||||  |||    | | ||| || || ||||| |||||||  ||||| || |||||  | ||||| || ||||| ||||||||||| || |||||||| |||||||||||||||||||| || |||
gttagtatatataatttcataccattcgaccctcttcccccacccagaacactggcaatttgattgaagacctcattttggccaaagatattttacacatgaaatgaaggtttccatgttactgaaattctgattatagtttgttt-ctttgatgcagGTTTGAGCGATATGTGGACTATGCATTAGATGTCCCGATGTATTTTGTCTATCGAAATAAGAAGTACATTGACTGTACTGGAATGTCATTTCGG

upper sequence: Vv02s0025g03530.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: LOC_Os05g03820.3 (Oryza sativa), 3'ss of exon 9
-------------------------------------------------------aaaggaagctggttttccatttttttttatg-tattctgttgacagttttgttgattattgacaatggtattcctatttctttctattttctctggtgcagATTTGAGCAGTATGTAGATTATGCTCTTGATGTTCCAATGTACTTTGTCTATCGGAAGAAGAAGTATATTGACTGTACTGGAATGTCCTTCCGG
                                                       || |  |          ||||||     | | |||| | |  |     |    | ||      ||  | | | ||  || |   |  ||||| || |||||||||||||  ||||| || || ||  | ||| | || ||||| ||||||||||| || |||||||| |||||||||||||||||||| || |||
gttagtatctataattcataccattcgaccctcttcccccacccagaacactggcaatgtgattgaaaacctcattttggccaaagatattttatacatgaaatgaaggtttccatgtaactgaaattctgattatagttcgtttctttgatgcagATTTGAGCGATATGTGGACTACGCATTAGATATCCCGATGTATTTTGTCTATCGTAATAAGAAGTACATTGACTGTACTGGAATGTCATTTCGG

upper sequence: Vv02s0025g03530.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GRMZM2G020096_T01 (Zea mays), 3'ss of exon 8
--------------aaaggaagctggttttccatttt--tttttatgtattctgttgacagttttgtt--------gattattgacaatggta----ttcctatttctttctattttctctggtgcagATTTGAGCAGTATGTAGATTATGCTCTTGATGTTCCAATGTACTTTGTCTATCGGAAGAAGAAGTATATTGACTGTACTGGAATGTCCTTCCGG
                |     |   |   |||  ||   |   |   |||   ||||  | ||  ||           | ||  |||||  |     ||||| || |   |  |||    ||||||| |||||||| ||||| ||||||||  | ||||| || ||||| ||||| || || || || |||||||||||||| || |||||||| || |||
gttagcatttcttttgaactccccactcccccaccttgagtgccagtaatttgattgattgcttcattctctttaaagatgttttcaatgtgaaagcatcctaattatagtttcttttgggggtgcagGTTTGAGCAATATGTGGATTATGCATTAGATGTCCCCATGTATTTTGTGTACCGAAATAATAAGTATATTGACTGCACCGGAATGTCATTTCGG

upper sequence: Vv02s0025g03530.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GLYMA05G37850.3 (Glycine max), 3'ss of exon 9
aaaggaagctggttttccatttttttttatgtattctgttgacagttttgttgattatt--gacaatggtattcctatttctttctatt--ttctctggt-gcagATTTGAGCAGTATGTAGATTATGCTCTTGATGTTCCAATGTACTTTGTCTATCGGAAGAAGAAGTATATTGACTGTACTGGAATGTCCTTCCGG
         |   ||||  |||||||  |  | |     ||| | ||      || | |  |  ||| || || |  ||| |||||  |   | |||| | |||| |||||||| ||||| |||||||||||||||||||| ||||| |||||||||||||| || |  ||||| ||||| ||||||| | ||||| ||
-----tgaattcctttctttttttttacaattttatcaatgatatttcatgcaatgacttggttaattgtttttcactttttttcttctaactttctgattgcagGTTTGAGCAATATGTTGATTATGCTCTTGATGTTCCTATGTATTTTGTCTATCGGAAAAACAGATATATCGACTGCACTGGAAAGACCTTCAGG

upper sequence: Vv02s0025g03530.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GLYMA08G01750.1 (Glycine max), 3'ss of exon 9
aaaggaagctggttttccatttttttttatgtattctgttgacagttttgttgattattgacaatggtattcctattt---ctttctattttct------ctggt-gcagATTTGAGCAGTATGTAGATTATGCTCTTGATGTTCCAATGTACTTTGTCTATCGGAAGAAGAAGTATATTGACTGTACTGGAATGTCCTTCCGG
        |   || |    |||||||||   ||| | |  |   | || |     | ||||   | | ||  | |||   |||| | | ||||      ||| | |||| ||| |||||||||| |||||||| ||||||||||| ||||| ||||||||||||||  | |  ||||| ||||||||||||| | ||||| ||
--------ccctttcttttattttttttaca-attttatcaattatatt-tcatgcaatgacttggtttttttttttttcactttttttcttctaactttctgattgcagGTTTCAGCAGTATGTTGATTATGCACTTGATGTTCCTATGTATTTTGTCTATCGGAAACACAGATATATCGACTGTACTGGAAAGACCTTCAGG

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|22009546|gb|BQ794580.1|BQ794580
EST:     GATAATAACCGTACTGGCATGCTTCCTTTTGTTTTTGATGGCTCCTTTGG                         A-TTGAGCAGTATGTAGATTATGCTCTTGATGTTCCAATGTACTTTGTCTA
genomic: GATAATAACCGTACTGGCATGCTTCCTTTTGTTTTTGATGGCTCCTTTGGgtaagtttat ... tctggtgcagATTTGAGCAGTATGTAGATTATGCTCTTGATGTTCCAATGTACTTTGTCTA
EST: gi|30300777|gb|CB977571.1|CB977571
EST:     GATAATAACCGTACTGGCATGCTTCCTTTTGTTTTTGATGGCTCCTTTGG                         ATTTGAGCAGTATGTAGATTATGCTCTTGATGTTCCAATGTACTTTGTCTA
genomic: GATAATAACCGTACTGGCATGCTTCCTTTTGTTTTTGATGGCTCCTTTGGgtaagtttat ... tctggtgcagATTTGAGCAGTATGTAGATTATGCTCTTGATGTTCCAATGTACTTTGTCTA
EST: gi|110428549|gb|EC995024.1|EC995024
EST:     GATAATAACCGTACTGGCATGCTTCCTTTTGTTTTTGATGGCTCCTTTGG                         ATTTGAGCAGTATGTAGATTATGCTCTTGATGTTCCAATGTACTTTGTCTA
genomic: GATAATAACCGTACTGGCATGCTTCCTTTTGTTTTTGATGGCTCCTTTGGgtaagtttat ... tctggtgcagATTTGAGCAGTATGTAGATTATGCTCTTGATGTTCCAATGTACTTTGTCTA
EST: gi|110725594|gb|EE102275.1|EE102275
EST:     CTTCCTTTTGTTTTTGATGGCTCCTTTGG                         ATTTGAGCAGTATGTAGATTATGCTCTTGATGTTCCAATGTACTTTGTCTA
genomic: CTTCCTTTTGTTTTTGATGGCTCCTTTGGgtaagtttat ... tctggtgcagATTTGAGCAGTATGTAGATTATGCTCTTGATGTTCCAATGTACTTTGTCTA
EST: gi|30132095|gb|CB917434.1|CB917434
EST:     GATAATAACCGTACTGGCATGCTTCCTTTTGTTTTTGATGGCTCCTTTGG                         ATTTGAGCAGTATGTAGATTATGCTCTTGATGTTCCNATGTACTTTGTCTA
genomic: GATAATAACCGTACTGGCATGCTTCCTTTTGTTTTTGATGGCTCCTTTGGgtaagtttat ... tctggtgcagATTTGAGCAGTATGTAGATTATGCTCTTGATGTTCCAATGTACTTTGTCTA
EST: gi|22009504|gb|BQ794538.1|BQ794538
EST:     GATAATAACCGTACTGGCATGCTTCC-TTTGTTTTTGATGGCTCCTTTGG                         ATTTGAGCAGTATGTAGATTATGCTCTTGATGTTCCAATGTACTTTGTCTA
genomic: GATAATAACCGTACTGGCATGCTTCCTTTTGTTTTTGATGGCTCCTTTGGgtaagtttat ... tctggtgcagATTTGAGCAGTATGTAGATTATGCTCTTGATGTTCCAATGTACTTTGTCTA
EST: gi|27586164|gb|CB008859.1|CB008859
EST:     GATAATAACCGTACTGGCATGCTTCCTTTTGTTTTTGATGGCTCCTTTGG                         ATTTGAGCAGTATGTAGATTATGCTCTTGATGTTCCAATGTACTTTGTCTA
genomic: GATAATAACCGTACTGGCATGCTTCCTTTTGTTTTTGATGGCTCCTTTGGgtaagtttat ... tctggtgcagATTTGAGCAGTATGTAGATTATGCTCTTGATGTTCCAATGTACTTTGTCTA
EST: gi|32246359|gb|CD712178.1|CD712178
EST:     GAT-ATAACCGTACTGGCATGC-TCCTTTTG-TTTTGATGGCTCCTTT-G                         ATTTGAGCAGTATGTAGATTATGCTCTTGATGTTCCAATGTACTTTGTCTA
genomic: GATAATAACCGTACTGGCATGCTTCCTTTTGTTTTTGATGGCTCCTTTGGgtaagtttat ... tctggtgcagATTTGAGCAGTATGTAGATTATGCTCTTGATGTTCCAATGTACTTTGTCTA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttgttgattattgacaatggtattcctatttctttctattttctctggtgcagATTTGAGCAGTATGTAGATTATGCTCTTGATGTTCCAATGTACTTTGTCTATCGGAAGAAGAAGTATATTGACTGTACTGGAATGTCCTTCCGG
          tattgac  putative branch site (score: 2)
                      tattcctatttctttc  putative PPT
                            tatttctttctatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aaaggaagctggttttccatttttttttatgtattctgttgacagttttgttgattattgacaatggtattcctatttctttctattttctctggtgcagATTTGAGCAGTATGTAGATTATGCTCTTGATGTTCCAATGTACTTTGTCTATCGGAAGAAGAAGTATATTGACTGTACTGGAATGTCCTTCCGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGT
aaaggaa
- - - - - - - - ccatttt
- - - - - - - - - - - - - - - - - - tgttgac