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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatcatctttaaatcatcgttgtcgtcatcccactctttgtctctgtggaaaggcagtaagttcattgagaaaattttctttatgtcttgctttgcagCACTCCTCAGATAAACACTTGGACATCAGATTGGGTCAAGTTTTATGCAGAGCATAGATTGGGTTATCAGCTGAAATTGGCATTAGACCAGTATGGAGAT

Basic information

species Vitis vinifera
transcript Vv15s0048g01810.t01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv15s0048g01810.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA03G01960.1 (Glycine max), 3'ss of exon 5
-------------------------------------------------------------------------------------------gtatcatct--ttaaatcatcgttgtc--gtcatcccactctttgtctctgtggaaaggcagtaagttcattgagaaaattttctttatgtcttgctttgcagCACTCCTCAGATAAACACTTGGACATCAGATTGGGTCAAGTTTTATGCAGAGCATAGATTGGGTTATCAGCTGAAATTGGCATTAGACCAGTATGGAGAT
                                                                                           || | | ||    |  |  |  |||||  |  ||  ||    |  ||| | ||         |    | | |    || |    | | | | ||    || |||||||| ||  ||||||| ||| |||||||||||||  | ||||||| |||||||||||||||||| ||| |||| |||||||||||||||||||| || 
gtttaatgcaccttcatcatgaaagttatcattgttgttgtaattgttattgttatcatttatcatgagttcttgactctttcttctttccgttttacctaggcatgtgctacttgtcaggatatatcagctatcatcttt-tgtttgtttgttcgaattagtttctaattacgttatgtatattatgctgtagCACTCCACAAGTAAACACCTGGTCATCAGATTGGGTTCAATTTTATGGAGAGCATAGATTGGGTTACCAGTTGAAGTTGGCATTAGACCAGTATGGTGAC
















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|28966833|gb|CB345866.1|CB345866
EST:     GGAAAATCTGAAAAAGGATTTGGGTTTGATGTTGATAATACCATAGGCAG                         CACTCCTCAGATAAACACTTGGACATCAGATTGGGTCAAGTTTTATGCAGA
genomic: GGAAAATCTGAAAAAGGATTTGGGTTTGATGTTGATAATACCATAGGCAGgtatcatctt ... tgctttgcagCACTCCTCAGATAAACACTTGGACATCAGATTGGGTCAAGTTTTATGCAGA
EST: gi|351033360|gb|FQ446592.1|FQ446592
EST:     GGAAAATCTGAAAAAGGATTTGGGTTTGATGTTGATAATACCATAGGCAG                         TACTCCTCAGATAAACACTTGGACATCAGATTGGGTCAAGTTTTATGCAGA
genomic: GGAAAATCTGAAAAAGGATTTGGGTTTGATGTTGATAATACCATAGGCAGgtatcatctt ... tgctttgcagCACTCCTCAGATAAACACTTGGACATCAGATTGGGTCAAGTTTTATGCAGA
EST: gi|30320371|gb|CD003633.1|CD003633
EST:     GGAAAATTTGAAAAAGGATTTGGGTTTGATGTTGATAATACCATAGGCAG                         CACTCCTCAGATAAACACTTGGACATCAGATTGGGTCAAGTTTTATGCAGA
genomic: GGAAAATCTGAAAAAGGATTTGGGTTTGATGTTGATAATACCATAGGCAGgtatcatctt ... tgctttgcagCACTCCTCAGATAAACACTTGGACATCAGATTGGGTCAAGTTTTATGCAGA
EST: gi|351044742|gb|FQ448996.1|FQ448996
EST:     GGAAAATCTGAAAAAGGATTTGGGTTTGATGTTGATAATACCATAGGCAG                         TACTCCTCAGATAAACACTTGGACATCAGATTGGGTCAAGTTTTATGCAGA
genomic: GGAAAATCTGAAAAAGGATTTGGGTTTGATGTTGATAATACCATAGGCAGgtatcatctt ... tgctttgcagCACTCCTCAGATAAACACTTGGACATCAGATTGGGTCAAGTTTTATGCAGA
EST: gi|18458320|gb|BM436598.1|BM436598
EST:     GGAAAATCTGAAAAAGGATTTGGGTTTGATGTTGATAATACCATAGGCAG                         CACTCCTCAGATAAACACTTGGACATCAGATTGGGTCAAGTTTTATGCAGA
genomic: GGAAAATCTGAAAAAGGATTTGGGTTTGATGTTGATAATACCATAGGCAGgtatcatctt ... tgctttgcagCACTCCTCAGATAAACACTTGGACATCAGATTGGGTCAAGTTTTATGCAGA
EST: gi|351013105|gb|FQ424810.1|FQ424810
EST:     GGAAAATCTGAAAAAGGATTTGGGTTTGATGTTGATAATACCATAGGCAG                         TACTCCTCAAATAAACACTTGGACATCAGATTGGGTCAAGTTTTATGCAGA
genomic: GGAAAATCTGAAAAAGGATTTGGGTTTGATGTTGATAATACCATAGGCAGgtatcatctt ... tgctttgcagCACTCCTCAGATAAACACTTGGACATCAGATTGGGTCAAGTTTTATGCAGA
EST: gi|110713565|gb|EE089595.1|EE089595
EST:     GGAAAATCTGAAAAAGGATTTGGGTTTGATGTTGATAATACCATAGGCAG                         CACTCCTCAGATAAACACTTGGACATCAGATTGGGTCAAGTTTTATGCAGA
genomic: GGAAAATCTGAAAAAGGATTTGGGTTTGATGTTGATAATACCATAGGCAGgtatcatctt ... tgctttgcagCACTCCTCAGATAAACACTTGGACATCAGATTGGGTCAAGTTTTATGCAGA
EST: gi|71881177|gb|DT030232.1|DT030232
EST:     GGAAAATCTGAAAAAGGATTTGGGTTTGATGTTGATAATACCATAGGCAG                         CACTCCTCAGATAAACACTTGGACATCAGATTGGGTCAAGTTTTATGCAGA
genomic: GGAAAATCTGAAAAAGGATTTGGGTTTGATGTTGATAATACCATAGGCAGgtatcatctt ... tgctttgcagCACTCCTCAGATAAACACTTGGACATCAGATTGGGTCAAGTTTTATGCAGA
EST: gi|28966778|gb|CB345811.1|CB345811
EST:     GGAAAATCTGAAAAAGGATTTGGGTTTGATGTTGATAATACCATAGGCAG                         CACTCCTCAGATAAACACTTGGACATCAGATTGGGTCAAGTTTTATGCAGA
genomic: GGAAAATCTGAAAAAGGATTTGGGTTTGATGTTGATAATACCATAGGCAGgtatcatctt ... tgctttgcagCACTCCTCAGATAAACACTTGGACATCAGATTGGGTCAAGTTTTATGCAGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctgtggaaaggcagtaagttcattgagaaaattttctttatgtcttgctttgcagCACTCCTCAGATAAACACTTGGACATCAGATTGGGTCAAGTTTTATGCAGAGCATAGATTGGGTTATCAGCTGAAATTGGCATTAGACCAGTATGGAGAT
                               ttttctttatgtctt  CT-rich tract
                         agaaaattttctttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatcatctttaaatcatcgttgtcgtcatcccactctttgtctctgtggaaaggcagtaagttcattgagaaaattttctttatgtcttgctttgcagCACTCCTCAGATAAACACTTGGACATCAGATTGGGTCAAGTTTTATGCAGAGCATAGATTGGGTTATCAGCTGAAATTGGCATTAGACCAGTATGGAGAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAT