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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttccttttctctaccctttctttattaccatttggctgtgacccattttttcacctccaccaagagaaaaagcatggaataacttattgacctctgaaagctactcgtctgattttgtgatttttaaattgttcttggcagTTGAAAGGTTTTGAGTTTGTCAAAGCAGTTCACCTTGACCCTGTGCCATTTGATATGGAACGTGACCTGATCACTCCAACATATAAGAAGAAGAGGCCCC

Basic information

species Vitis vinifera
transcript Vv02s0025g01410.t01
intron # 17
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv02s0025g01410.t01 (Vitis vinifera), 3'ss of exon 17
lower sequence: LOC_Os01g46750.4 (Oryza sativa), 3'ss of exon 14
gttccttttctctaccctttctttattaccatttggctgtgacccattttttcacctccaccaagagaaaaagcatggaataacttattgacctctgaaagctactcgtctgattttgtgatttttaaattgttcttggcagTTGAAAGGTTTTGAGTTTGTCAAAGCAGTTCACCTTGACCCTGTGCCATTTGATATGGAACGTGACCTGATCACTCCAACATATAAGAAGAAGAGGCCCC
                         | |   ||||  | |  |    |||||   |   |     |   ||    |   |||  | |      || |   ||| ||    | | |   | | |||  |  |  | ||| ||| | ||||||||||| ||  | || || || || ||||| || ||||||||||| ||||| |||||  |||| |||||||||||||| |||||| | || |
------------------------gtaatattttgattattgcttgcttttttttcctgaaaggaaattaatctcttctatatatcacgtttgtccgcttgctccta--ttaactccttaactttctacgtacttttg-cagCTCAAAGGTTTTGAATTCATAAAGGCTGTACATCTTGAACCAGTGCCATTTGACATGGACCGTGATTTGATTACTCCAACATATAAAAAGAAGCGCCCTC

upper sequence: Vv02s0025g01410.t01 (Vitis vinifera), 3'ss of exon 17
lower sequence: GLYMA01G43470.2 (Glycine max), 3'ss of exon 17
gttccttttctctaccctttctttattaccatttggctgtgacccattttttcacctccaccaagagaaaa-agcatggaataacttattgacctctgaaagctactcgtctgattttgtgatttttaaattgttcttggcagTTGAAAGGTTTTGAGTTTGTCAAAGCAGTTCACCTTGACCCTGTGCCATTTGATATGGAACGTGACCTGATCACTCCAACATATAAGAAGAAGAGGCCCC
                                           |   | || |||       ||  ||    | | |  |   |    ||    |   |  ||   || |     ||||||   |    || ||  ||||||||||||||||||||||||| | |||||||||||||||||| |  | |||||||| |||||||||||||| |||||||||||||| |||||||||||||| |
------------------------------------------tctggtcttgcactggttttaaatgatcttatcctatatgtaaacgtttttgtacaagtgcatttcctgaagctttgtgggatgatgat-gtatttggcagTTGAAAGGTTTTGAGTTTATAAAAGCAGTTCACCTTGACTCAATTCCATTTGACATGGAACGTGACCTTATCACTCCAACATACAAGAAGAAGAGGCCAC

upper sequence: Vv02s0025g01410.t01 (Vitis vinifera), 3'ss of exon 17
lower sequence: GLYMA05G36910.1 (Glycine max), 3'ss of exon 17
gttccttttctctaccctttctttattaccatttggctgtgacccattttttcacctccaccaagagaaaaagcatggaataacttattgacctctgaaagctactcgtctgattttgtgatttttaaattgttcttggcagTTGAAAGGTTTTGAGTTTGTCAAAGCAGTTCACCTTGACCCTGTGCCATTTGATATGGAACGTGACCTGATCACTCCAACATATAAGAAGAAGAGGCCCC
                                     | | |    |  ||  |  ||  |    | | | |       |||  | | |||       |||||  |  |  |||  ||    |  ||| |||||  || ||||||||||||||||||||| | ||||| ||||| |||||||| || |||||||| ||||||||||  || || |||||||||| |||||||||||| ||| 
---------------------------------accttattatatgtgcttgtatgtctgctggtatatatatatatatatatataaatgat-----gaagct--ttatgcgatcctgattatagtaatttgtt--tgtcagTTGAAAGGTTTTGAGTTTATTAAAGCTGTTCATCTTGACCCAGTTCCATTTGACATGGAACGTGGTCTTATGACTCCAACATTTAAGAAGAAGAGACCCG

upper sequence: Vv02s0025g01410.t01 (Vitis vinifera), 3'ss of exon 17
lower sequence: PP1S108_163V6.1 (Physcomitrella patens), 3'ss of exon 17
gttccttttctctaccctttctttattaccatttggctgtgacccattttttcacctccaccaagagaaaaagcatggaataacttattgacctctgaaagctactcgtctgatt-ttgtgatttttaaattgttcttggcagTTGAAAGGTTTTGAGTTTGTCAAAGCAGTTCACCTTGACCCTGTGCCATTTGATATGGAACGTGACCTGATCACTCCAACATATAAGAAGAAGAGGCCCC
                               ||| |  ||||   || |    |  ||  | |||     | |||| | |    |  | |  ||||  ||           ||||  |  | |  |  | |  ||| | |||| | | ||| ||||||||  |||||| ||| |   | || |||   |||||||||||||| || ||||||||||||||||| || |||   ||  | || |
------------------------------gttttg--gtgaagtatgtaaagatttctgcaaagttgtca-gcattgcacttgtagtcgttctctataaa----------gattactaagctcctcgattcattcattgcagGTAAGAGGATTTGAGTTCATCAAAGGAGTGCTGTTAGATCCTCAACCATTTGATATGGAGCGCGACCTGATCACTCCAACTTACAAGCTCAAACGACCGC

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|30125801|gb|CB911140.1|CB911140
EST:     CAAAAGAATACATACTTGGAGAGCTCTCAAAGATTGGGAAGGAGAAAAAG                         TTGAAAGGTTTTGAGTTTGTCAAAGCAGTTCACCTTGACCCTGTGCCATTT
genomic: CAAAAGAATACATACTTGGAGAGCTCTCAAAGATTGGGAAGGAGAAAAAGgttccttttc ... ttcttggcagTTGAAAGGTTTTGAGTTTGTCAAAGCAGTTCACCTTGACCCTGTGCCATTT
EST: gi|110375957|gb|EC940989.1|EC940989
EST:     CAAAAGAATACATACTTGGAGAGCTCTCAAAGATTGGGAAGGAGAAAAAG                         TTGAAAGGTTTTGAGTTTGTCAAAGCAGTTCACCTTGACCCTGTGCCATTT
genomic: CAAAAGAATACATACTTGGAGAGCTCTCAAAGATTGGGAAGGAGAAAAAGgttccttttc ... ttcttggcagTTGAAAGGTTTTGAGTTTGTCAAAGCAGTTCACCTTGACCCTGTGCCATTT
EST: gi|27580341|gb|CB003036.1|CB003036
EST:     CAAAAGAATACATACTTGGAGAGCTCTCAAAGATTGGGAAGGAGAAAAAG                         TTGAAAGGTTTTGAGTTTGTCAAAGCAGTTCACCTTGACCCTGTGCCATTT
genomic: CAAAAGAATACATACTTGGAGAGCTCTCAAAGATTGGGAAGGAGAAAAAGgttccttttc ... ttcttggcagTTGAAAGGTTTTGAGTTTGTCAAAGCAGTTCACCTTGACCCTGTGCCATTT
EST: gi|352781554|gb|FQ468398.1|FQ468398
EST:     CAAAAGAATACATACTTGGAGAGCTCTCAAAGATTGGGAAGGAGAAAAAG                         TTGAAAGGTTTTGAGTTTGTCAAAGCAGTTCACCTTGACCCTGTGCCATTT
genomic: CAAAAGAATACATACTTGGAGAGCTCTCAAAGATTGGGAAGGAGAAAAAGgttccttttc ... ttcttggcagTTGAAAGGTTTTGAGTTTGTCAAAGCAGTTCACCTTGACCCTGTGCCATTT
EST: gi|32245315|gb|CD711134.1|CD711134
EST:     CAAAAGAATACATACTTGGAGAGCTCTCAAAGATTGGGAAGGAGAAAAAG                         TTGAAAGGTTTTGAGTTTGTCAAAGCAGTTCACCTTGACCCTGTGCCATTT
genomic: CAAAAGAATACATACTTGGAGAGCTCTCAAAGATTGGGAAGGAGAAAAAGgttccttttc ... ttcttggcagTTGAAAGGTTTTGAGTTTGTCAAAGCAGTTCACCTTGACCCTGTGCCATTT
EST: gi|27755362|gb|CB036117.1|CB036117
EST:     CAAAAGAATACATACTTGGAGAGCTCTCAAAGATTGGGAAGGAGAAAAAG                         TTGAAAGGTTTTGAGTTTGTCAAAGCAGTTCACCTTGACCCTGTGCCATTT
genomic: CAAAAGAATACATACTTGGAGAGCTCTCAAAGATTGGGAAGGAGAAAAAGgttccttttc ... ttcttggcagTTGAAAGGTTTTGAGTTTGTCAAAGCAGTTCACCTTGACCCTGTGCCATTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgacctctgaaagctactcgtctgattttgtgatttttaaattgttcttggcagTTGAAAGGTTTTGAGTTTGTCAAAGCAGTTCACCTTGACCCTGTGCCATTTGATATGGAACGTGACCTGATCACTCCAACATATAAGAAGAAGAGGCCCC
                                          ttgttctt  CT-rich tract
                         attttgtgatttttaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttccttttctctaccctttctttattaccatttggctgtgacccattttttcacctccaccaagagaaaaagcatggaataacttattgacctctgaaagctactcgtctgattttgtgatttttaaattgttcttggcagTTGAAAGGTTTTGAGTTTGTCAAAGCAGTTCACCTTGACCCTGTGCCATTTGATATGGAACGTGACCTGATCACTCCAACATATAAGAAGAAGAGGCCCC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG