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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaggatgcaaatccttcttggttaacatcttcatctgtctctttctgattttgtttctcttcctaactcttgttgtctgttcaaacctgtttgttaagcgagctctgtccatctttgccttgaaataacaaatatctttctccccctttttgtagGTCCAAGCTCTCAAAGATTTTTTCAACATGCTTTCAAAT

Basic information

species Vitis vinifera
transcript Vv04s0023g00140.t01
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv04s0023g00140.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: AT4G27650.1 (Arabidopsis thaliana), 3'ss of exon 13
-------------------------gtaggatgcaaatcctt--cttggttaacatcttcatctgtctctttctgattttgtttctcttcctaactcttgttgtctgttcaaacctgtttgttaagc-gagctct----gtccatctttgcc-ttgaaataacaaatatctttctccccctttttgtagGTCCAAGCTCTCAAAGATTTTTTCAACATGCTTTCAAAT
                          |    |||  || |    || ||||| | |     ||    |      ||  |    |   | |  |    ||  || || || |   || |    | ||  | |||||     |  | ||||| | |  |  ||||  || |   | | ||    | |||||||| |||||||||| ||||||  |||||||||||||| |
gtgatttagaatgttgcctatatttttgaattgctcattcgaaactgggttagcttgaaagtcacaattcacacgaactcaaataagtcctcactgttttgtggcttttgatctctatcatctgagttgtgctcttgaaatgtacctttgtcatctacctaactgatgtgaatttgcc----tatgtagGTCAAAGCTCTCAATGATTTTCACAACATGCTTTCAACT
















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|110359983|gb|EC922418.1|EC922418
EST:     ATGCACCAAATGTGATGAACATGATAAAGGATACAAAAGCAGCACAAGAG                         GTCCAAGCTCTCAAAGATTTTTTCAACATGCTTTCAAAT
genomic: ATGCACCAAATGTGATGAACATGATAAAGGATACAAAAGCAGCACAAGAGgtaggatgca ... ctttttgtagGTCCAAGCTCTCAAAGATTTTTTCAACATGCTTTCAAAT
EST: gi|110356881|gb|EC920025.1|EC920025
EST:     ATGCACCAAATGTGATGAACATGATAAAGGATACAAAAGCAGCACAAGAG                         GTCCAAGCTCTCAAAGANNNNNNNCA-CATGCTTTTCAA-T
genomic: ATGCACCAAATGTGATGAACATGATAAAGGATACAAAAGCAGCACAAGAGgtaggatgca ... ctttttgtagGTCCAAGCTCTCAAAGATTTTTT-CAACATGCTTT-CAAAT
EST: gi|110357696|gb|EC921371.1|EC921371
EST:     ATGCACCAAATGTGATGAACATGATAAAGGATACAAAAGCAGCACAAGAG                         GTCCAAGCTCTCAAAGATTTTTTCAACATGCTTTCAAAT
genomic: ATGCACCAAATGTGATGAACATGATAAAGGATACAAAAGCAGCACAAGAGgtaggatgca ... ctttttgtagGTCCAAGCTCTCAAAGATTTTTTCAACATGCTTTCAAAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agctctgtccatctttgccttgaaataacaaatatctttctccccctttttgtagGTCCAAGCTCTCAAAGATTTTTTCAACATGCTTTCAAAT
                      aaataac  putative branch site (score: 2)
                                tatctttctccccctt  putative PPT
                      aaataacaaatatctt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaggatgcaaatccttcttggttaacatcttcatctgtctctttctgattttgtttctcttcctaactcttgttgtctgttcaaacctgtttgttaagcgagctctgtccatctttgccttgaaataacaaatatctttctccccctttttgtagGTCCAAGCTCTCAAAGATTTTTTCAACATGCTTTCAAAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAAGCT