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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cgctagatgcatttttcatctcttcattcataaccaattctcctttgacattcatactgacagatggttctatgcattatcaatgtttactgttttatagATGTGAACGAATGCAAGGACAAGGTTGCCTGCAATTGTCCAGAGTGCAAATGCAAGAATACCTGGGGAAGTTATGAGTGCAGCTGCAGTGGCAATTTATT

Basic information

species Vitis vinifera
transcript Vv08s0058g01360.t01
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv08s0058g01360.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: LOC_Os12g02390.1 (Oryza sativa), 3'ss of exon 9
------------------------------cgctagatgcatttttcatctc--------ttcattcataaccaattctcctttgacattcatactgacagatggttctatgcat--tatcaatgtttactgttttat---agATGTGAACGAATGCAAGGACAAGGTTGCCTGCAATTGTCCAGAGTGCAAATGCAAGAATACCTGGGGAAGTTATGAGTGCAGCTGCAGTGGCAATTTATT
                               | | |||| | ||  ||||          |  | |  ||   || | ||  |||  || ||  ||    |     |  |  | |  ||   ||||  | | ||||||   |||| |  | ||||||||||| | |  ||| ||| | ||    || || ||||||||||| || |||||||| ||||||||| | |||||||||   ||  |
gtaagaatcgatttgtgaaccctgttcagctgttggatgtacttgccatcctgcaaagcttgtagttttagtgaaatatcacttgcaatacacccttgttgtgcacttgaccccttgtactgatgtgaaatattttatgaaagATATTGATGAATGCAAGGAAAGGACTGCATGCCAGTGCAAGGAATGTAAATGCAAGAACACATGGGGAAGCTATGAGTGCGGTTGCAGTGGCGGCTTGCT

upper sequence: Vv08s0058g01360.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GLYMA07G14800.1 (Glycine max), 3'ss of exon 9
---cgctagatgcat-ttttcatctcttcattcataaccaattctcctttgacattcatactgacagatggttctatgcattatcaatgtttactgttttatagATGTGAACGAATGCAAGGACAAGGTTGCCTGCAATTGTCCAGAGTGCAAATGCAAGAATACCTGGGGAAGTTATGAGTGCAGCTGCAGTGGCAATTTATT
   |  |    | ||  ||  || |  ||||  |||   |  | | ||   |   | | |  |     |   |||    ||| |   | || | | | || |||||||| | || ||||| || ||  | |  ||| | || ||||||||| ||||||| |||||||||||||||||||| ||||  || ||||   |||| ||
gaactttttcagaatgcttgaatgtgatcat--atagttagctattctgcaaatctgacaaggtttttt--ctcttaatatttttcgttttgattatgttgtagATGTGGATGAGTGCAAAGAGAAATTGGTGTGCCAGTGCCCAGAGTGCCAATGCAAAAATACCTGGGGAAGTTATGAATGCACGTGTAGTGATGATTTGTT

upper sequence: Vv08s0058g01360.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GLYMA03G00510.1 (Glycine max), 3'ss of exon 9
cgctagatgcatttttcatctcttcattcataaccaattctcctttgacattcata-ctgaca-gatggttctat---gcattatcaatgtttactgttttatagATGTGAACGAATGCAAGGACAAGGTTGCCTGCAATTGTCCAGAGTGCAAATGCAAGAATACCTGGGGAAGTTATGAGTGCAGCTGCAGTGGCAATTTATT
     ||    |||   |   ||| | |   | || |   |    |    | || | |||||| |||  ||         |||    || || | | | || |||| ||| | || ||||| || ||  | || ||| | || ||||||||| ||||||| |||||||||||||||||||| |||   || ||||    ||| ||
-----gaactttttcagaatgcttgaatgtgatcctacagttagctattctgcaaatctgacaagattttttcgcttaatatttctcattttgattatgttgtagACGTGGATGAGTGCAAAGAGAAATTGGCGTGCCAGTGCCCAGAGTGCCAATGCAAAAATACCTGGGGAAGTTATGAATGCTCATGTAGTGATGGTTTGTT

upper sequence: Vv08s0058g01360.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GLYMA18G44580.1 (Glycine max), 3'ss of exon 9
--------------------------------------------------------------------------------------------------cgctagatgcatttttcatctcttcattcataaccaattctcct-ttgacattcatactgacagatgg--ttctatgcattatcaatgtttactgttttatagATGTGAACGAATGCAAGGACAAGGTTGCCTGCAATTGTCCAGAGTGCAAATGCAAGAATACCTGGGGAAGTTATGAGTGCAGCTGCAGTGGCAATTTATT
                                                                                                     |  ||    ||  |||  || || |  | |  | |  | || ||  |  |  ||   | |  | |  || | | ||||     |  | | | | ||  |||| |  | || ||||| || ||    |||||  | || ||||  ||||||||||| || |||||||||||||| |||||||  ||||   |   ||| | 
ggtacttgctgccctaaatttagtgattgttgtagtattcggtgaatggcaaacacaaatcagatagagctacttctgttagtggattaatgctgaggaattgaatttgattcacattcctgcagttgttattagtcatgctattagccattctagaaatatgttggcttttctacatttcttcttctgattatgttgcaGATATTGATGAGTGCAAAGAGAAAACAGCCTGTCAATGCCCAGGTTGCAAATGCAAAAACACCTGGGGAAGTTACGAGTGCAAATGCAAAAGTGGTTTGT-

upper sequence: Vv08s0058g01360.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: AT3G52850.1 (Arabidopsis thaliana), 3'ss of exon 9
cgctagatgcatttttcatc-tcttcattcataa---ccaattctcctttgacattcatactgacagatggttctatgcattatcaatgtttactgttttatagATGTGAACGAATGCAAGGACAAGGTTGCCTGCAATTGTCCAGAGTGCAAATGCAAGAATACCTGGGGAAGTTATGAGTGCAGCTGCAGTGGCAATTTATT
    ||  | |||||| ||  |  ||| ||| |      |  ||    || |   ||| | |  || ||   |      ||| |     || | ||| |||  |||||| |||| ||||| || ||    |  ||| | || |||||||| ||||| || || || |||||||||||||| |||||||||||   |  |||  |
tatcagtggaattttttattgtactcaatcaaagaagtgagatcattgttaaacgtcaaatt--caaattcataatcatattcttttgattgaatgtgtta--gATGTGGACGAGTGCAAAGAAAAAACGGTGTGCCAGTGCCCAGAGTGTAAATGTAAAAACACTTGGGGAAGTTATGAATGCAGCTGCAGCAACGGTTTGCT

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|27579549|gb|CB002244.1|CB002244
EST:     GATTCAAGGGAGATGGAGTCAAAACTTGTGAAG                         ATGTGAACGAATGCAAGGACAAGGTTGCCTGCAATTGTCCAGAGTGCAAAT
genomic: GATTCAAGGGAGATGGAGTCAAAACTTGTGAAGgtactgcatt ... tgttttatagATGTGAACGAATGCAAGGACAAGGTTGCCTGCAATTGTCCAGAGTGCAAAT
EST: gi|33405593|gb|CF211220.1|CF211220
EST:     TTGCCAATGCCCACAGGGATTCAAGGGAGATGGAGTCAAAACTTGTGAAG                         ATGTGAACGAATGCAAGGACAAGGTTGCCTGCAATTGTCCAGAGTGCAAAT
genomic: TTGCCAATGCCCACAGGGATTCAAGGGAGATGGAGTCAAAACTTGTGAAGgtactgcatt ... tgttttatagATGTGAACGAATGCAAGGACAAGGTTGCCTGCAATTGTCCAGAGTGCAAAT
EST: gi|29781753|gb|CB346482.2|CB346482
EST:     TTGCCAATGCCCACAGGGATTCAAGGGAGATGGAGTCAAAACTTGTGAAG                         ATGTGAACGAATGCAAGGACAAGGTTGCCTGCAATTGTCCAGAGTGCAAAT
genomic: TTGCCAATGCCCACAGGGATTCAAGGGAGATGGAGTCAAAACTTGTGAAGgtactgcatt ... tgttttatagATGTGAACGAATGCAAGGACAAGGTTGCCTGCAATTGTCCAGAGTGCAAAT
EST: gi|33405675|gb|CF211302.1|CF211302
EST:     TTGCCAATGCCCACAGGGATTCAAGGGAGATGGAGTCAAAACTTGTGAAG                         ATGTGAACGAATGCAAGGACAAGGTTGCCTGCAATTGTCCAGAGTGCAAAT
genomic: TTGCCAATGCCCACAGGGATTCAAGGGAGATGGAGTCAAAACTTGTGAAGgtactgcatt ... tgttttatagATGTGAACGAATGCAAGGACAAGGTTGCCTGCAATTGTCCAGAGTGCAAAT
EST: gi|22014493|gb|BQ799527.1|BQ799527
EST:     TTGCCAATGCCCACAGGGATTCAAGGGAGATGGAGTCAAAACTTGTGAAG                         ATGTGAACGAATGCAAGGACAAGGTTGCCTGCAATTGTCCAGAGTGCAAAT
genomic: TTGCCAATGCCCACAGGGATTCAAGGGAGATGGAGTCAAAACTTGTGAAGgtactgcatt ... tgttttatagATGTGAACGAATGCAAGGACAAGGTTGCCTGCAATTGTCCAGAGTGCAAAT
EST: gi|110390350|gb|EC955254.1|EC955254
EST:     TTGCCAATGCCCACAGGGATTCAAGGGAGATGGAGTCAAAACTTGTGAAG                         ATGTGAACGAATGCAAGGACAAGGTTGCCTGCAATTGTCCAGAGTGCAAAT
genomic: TTGCCAATGCCCACAGGGATTCAAGGGAGATGGAGTCAAAACTTGTGAAGgtactgcatt ... tgttttatagATGTGAACGAATGCAAGGACAAGGTTGCCTGCAATTGTCCAGAGTGCAAAT
EST: gi|30255039|gb|CB971486.1|CB971486
EST:     TTGCCAATGCCCACAGGGATTCAAGGGAGATGGAGTCAAAACTTGTGAAG                         ATGTGAACGAATGCAAGGACAAGGTTGCCTGCAATTGTCCAGAGTGCAAAT
genomic: TTGCCAATGCCCACAGGGATTCAAGGGAGATGGAGTCAAAACTTGTGAAGgtactgcatt ... tgttttatagATGTGAACGAATGCAAGGACAAGGTTGCCTGCAATTGTCCAGAGTGCAAAT
EST: gi|110404060|gb|EC970018.1|EC970018
EST:     CAAGGGAGATGGAGTCAAAACTTGTGAAG                         ATGTGAACGAATGCAAGGACAAGGTTGCCTGCAATTGTCCAGAGTGCAAAT
genomic: CAAGGGAGATGGAGTCAAAACTTGTGAAGgtactgcatt ... tgttttatagATGTGAACGAATGCAAGGACAAGGTTGCCTGCAATTGTCCAGAGTGCAAAT
EST: gi|71875647|gb|DT024702.1|DT024702
EST:     TTGCCAATGCCCACAGGGATTCAAGGGAGATGGAGTCAAAACTTGTGAAG                         ATGTGAACGAATGCAAGGACAAGGTTGCCTGCAATTGTCCAGAGTGCAAAT
genomic: TTGCCAATGCCCACAGGGATTCAAGGGAGATGGAGTCAAAACTTGTGAAGgtactgcatt ... tgttttatagATGTGAACGAATGCAAGGACAAGGTTGCCTGCAATTGTCCAGAGTGCAAAT
EST: gi|110390265|gb|EC955167.1|EC955167
EST:     TTGCCAATGCCCACAGGGATTCAAGGGAGATGGAGTCAAAACTTGTGAAG                         ATGTGAACGAATGCAAGGACAAGGTTGCCTGCAATTGTCCAGAGTGCAAAT
genomic: TTGCCAATGCCCACAGGGATTCAAGGGAGATGGAGTCAAAACTTGTGAAGgtactgcatt ... tgttttatagATGTGAACGAATGCAAGGACAAGGTTGCCTGCAATTGTCCAGAGTGCAAAT
EST: gi|110371604|gb|EC935716.1|EC935716
EST:     TTGCCAATGCCCACAGGGATTCAAGGGAGATGGAGTCAAAACTTGTGAAG                         ATGTGAACGAATGCAAGGACAAGGTTGCCTGCAATTGTCCAGAGTGCAAAT
genomic: TTGCCAATGCCCACAGGGATTCAAGGGAGATGGAGTCAAAACTTGTGAAGgtactgcatt ... tgttttatagATGTGAACGAATGCAAGGACAAGGTTGCCTGCAATTGTCCAGAGTGCAAAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgacattcatactgacagatggttctatgcattatcaatgtttactgttttatagATGTGAACGAATGCAAGGACAAGGTTGCCTGCAATTGTCCAGAGTGCAAATGCAAGAATACCTGGGGAAGTTATGAGTGCAGCTGCAGTGGCAATTTATT
         tactgac  putative branch site (score: 1)
                                            ctgtttt  putative PPT
                              attatcaatgttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cgctagatgcatttttcatctcttcattcataaccaattctcctttgacattcatactgacagatggttctatgcattatcaatgtttactgttttatagATGTGAACGAATGCAAGGACAAGGTTGCCTGCAATTGTCCAGAGTGCAAATGCAAGAATACCTGGGGAAGTTATGAGTGCAGCTGCAGTGGCAATTTATT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG
- - -gatgcat
- - - - - - - -tcatctc
- - - - - - - - - - - -tcattca
- - - - - - - - - - - - cattcat
- - - - - - - - - - - - - - - taaccaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cagatgg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctatgca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - caatgtt