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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTAACCTGCTAAGGGCCTTTGCCACTGGAGGTTATGCTGCGATGCAGAGAGTCACCCAGTGGAATCTTGATTTTGCCGAGCACAGCGAGCAGGGAGATAGgtaatttgctattttattcaggacctaacttgtctaatatttttgagttgaaagtaaaaaggcataaaattgatattggggattttctatgaaattctga...

Basic information

species Vitis vinifera
transcript Vv00s0391g00070.t01
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv00s0391g00070.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: EFJ08096 (Selaginella moellendorffii), 5'ss of exon 2
TTAACCTGCTAAGGGCCTTTGCCACTGGAGGTTATGCTGCGATGCAGAGAGTCACCCAGTGGAATCTTGATTTTGCCGAGCACAGCGAGCAGGGAGATAGgtaatttgctattttattcaggacctaacttgtctaatatttttgagttgaaagtaaaaaggcataaaattgatattggggattttctatgaaattctga
| ||| ||||  |  | |||||||| ||||||||||| || ||||| |||||||| |||||||| || |||||  ||    |||| || || || |  |||||       |  |  ||  |  | |        |  ||  ||||  |     ||  |  |         |    || | | |  | |       || | 
TCAACTTGCTGCGATCTTTTGCCACGGGAGGTTATGCCGCCATGCAAAGAGTCACTCAGTGGAACCTGGATTTCACCTCCGACAGTGAACAAGGTGGAAGgtacgggaaaacatccttgcgtccattttggactttttacctttggttgatttgtcgagtgctcgtttgcttgctttcgtggtcatttccagttctcagg

upper sequence: Vv00s0391g00070.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: EFJ24698 (Selaginella moellendorffii), 5'ss of exon 2
TTAACCTGCTAAGGGCCTTTGCCACTGGAGGTTATGCTGCGATGCAGAGAGTCACCCAGTGGAATCTTGATTTTGCCGAGCACAGCGAGCAGGGAGATAGgtaatttgctattttattcaggacctaacttgtctaatatttttgagttgaaagtaaaaaggcataaaattgatattggggattttctatgaaattctga
| ||| ||||  |  | |||||||| ||||||||||| || ||||| |||||||| |||||||| || |||||  ||    |||| || ||||| |  |||||       |  |  ||  |  | |        |  ||  | ||  |     ||  |  |         |    || | | |  | |       || | 
TCAACTTGCTGCGATCTTTTGCCACGGGAGGTTATGCCGCCATGCAAAGAGTCACTCAGTGGAACCTCGATTTCACCTCCGACAGTGAACAGGGTGGAAGgtacgggaaaacatccttgcgtgcattttggactttttacctgtggttgatttgtcgagtgctcgtttgcttgctttcgtggtcatttccagttctcagg
















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|27587008|gb|CB009703.1|CB009703
EST:     GTCACCCAGTGGAATCTTGATTTTGCCGAGCACAGCGAGCAGGGAGATAG                         GTACCAGGAACTGGCTCACCGAGTTGATGAGGCCTTAGGATTTATGTCTGC
genomic: GTCACCCAGTGGAATCTTGATTTTGCCGAGCACAGCGAGCAGGGAGATAGgtaatttgct ... tgttcaatagGTACCAGGAACTGGCTCACCGAGTTGATGAGGCCTTAGGATTTATGTCTGC
EST: gi|110693008|gb|EE068861.1|EE068861
EST:     GTCACCCAGTGGAATCTTGATTTTGCCGAGCACAGCGAGCAGGGAGATAG                         GTACCAGGAACTGGCTCACCGAGTTGACGAGGCCTTAGGATTTATGTCTGC
genomic: GTCACCCAGTGGAATCTTGATTTTGCCGAGCACAGCGAGCAGGGAGATAGgtaatttgct ... tgttcaatagGTACCAGGAACTGGCTCACCGAGTTGATGAGGCCTTAGGATTTATGTCTGC
EST: gi|71855694|gb|DT004749.1|DT004749
EST:     GTCACCCAGTGGAATCTTGATTTTGCCGAGCACAGCGAGCAGGGAGATAG                         GTACCAGGAACTGGCTCACCGAGTTGACGAGGCCTTAGGATTTATGTCTGC
genomic: GTCACCCAGTGGAATCTTGATTTTGCCGAGCACAGCGAGCAGGGAGATAGgtaatttgct ... tgttcaatagGTACCAGGAACTGGCTCACCGAGTTGATGAGGCCTTAGGATTTATGTCTGC
EST: gi|161706002|gb|FC056706.1|FC056706
EST:     GTCACCCAGTGGAATCTTGATTTTGCCGAGCACAGCGAGCAGGGAGATAG                         GTACCAGGAACTGGCTCACCGAGTTGACGAGGCCTTAGGATTTATGTCTGC
genomic: GTCACCCAGTGGAATCTTGATTTTGCCGAGCACAGCGAGCAGGGAGATAGgtaatttgct ... tgttcaatagGTACCAGGAACTGGCTCACCGAGTTGATGAGGCCTTAGGATTTATGTCTGC
EST: gi|27581082|gb|CB003777.1|CB003777
EST:     GTCACCCAGTGGAATCTTGATTTTGCCGAGCACAGCGAGCAGGGAGATAG                         GTACCAGGAACTGGCTCACCGAGTTGATGAGGCCTTAGGATTTATGTCTGC
genomic: GTCACCCAGTGGAATCTTGATTTTGCCGAGCACAGCGAGCAGGGAGATAGgtaatttgct ... tgttcaatagGTACCAGGAACTGGCTCACCGAGTTGATGAGGCCTTAGGATTTATGTCTGC
EST: gi|18458715|gb|BM436993.1|BM436993
EST:     GTCACCCAGTGGAATCTTGATTTTGCCGAGCACAGCGAGCAGGGAGATAG                         GTACCAGGAACTGGCTCACCGAGTTGATGAGGCCTTAGGATTTATGTCTGC
genomic: GTCACCCAGTGGAATCTTGATTTTGCCGAGCACAGCGAGCAGGGAGATAGgtaatttgct ... tgttcaatagGTACCAGGAACTGGCTCACCGAGTTGATGAGGCCTTAGGATTTATGTCTGC
EST: gi|71871506|gb|DT020561.1|DT020561
EST:     GTCACCCAGTGGAATCTTGATTTTGCCGAGCACAGCGAGCAGGGAGATAG                         GTACCAGGAACTGGCTCACCGAGTTGACGAGGCCTTAGGATTTATGTCTGC
genomic: GTCACCCAGTGGAATCTTGATTTTGCCGAGCACAGCGAGCAGGGAGATAGgtaatttgct ... tgttcaatagGTACCAGGAACTGGCTCACCGAGTTGATGAGGCCTTAGGATTTATGTCTGC
EST: gi|37187911|gb|CF607262.1|CF607262
EST:     GTCACCCAGTGGAATCTTGATTTTGCCGAGCACAGCGAGCAGGGAGATAG                         GTACCAGGAACTGGCTCACCGAGTTGATGAGGCCTTAGGATTTATGTCTGC
genomic: GTCACCCAGTGGAATCTTGATTTTGCCGAGCACAGCGAGCAGGGAGATAGgtaatttgct ... tgttcaatagGTACCAGGAACTGGCTCACCGAGTTGATGAGGCCTTAGGATTTATGTCTGC
EST: gi|110688800|gb|EE067768.1|EE067768
EST:     GTCACCCAGTGGAATCTTGATTTTGCCGAGCACAGCGAGCAGGGAGATAG                         GTACCAGGAACTGGCTCACCGAGTTGACGAGGCCTTAGGATTTATGTCTGC
genomic: GTCACCCAGTGGAATCTTGATTTTGCCGAGCACAGCGAGCAGGGAGATAGgtaatttgct ... tgttcaatagGTACCAGGAACTGGCTCACCGAGTTGATGAGGCCTTAGGATTTATGTCTGC
EST: gi|110361608|gb|EC925094.1|EC925094
EST:     GCCGAGCACAGCGAGCAGGGAGATAG                         GTACCAGGAACTGGCTCACCGAGTTGACGAGGCCTTAGGATTTATGTCTGC
genomic: GCCGAGCACAGCGAGCAGGGAGATAGgtaatttgct ... tgttcaatagGTACCAGGAACTGGCTCACCGAGTTGATGAGGCCTTAGGATTTATGTCTGC
EST: gi|161713267|gb|FC063081.1|FC063081
EST:     GTCACCCAGTGGAATCTTGATTTTGCCGAGCACAGCGAGCAGGGAGATAG                         GTACCAGGAACTGGCTCACCGAGTTGACGAGGCCTTAGGATTTATGTCTGC
genomic: GTCACCCAGTGGAATCTTGATTTTGCCGAGCACAGCGAGCAGGGAGATAGgtaatttgct ... tgttcaatagGTACCAGGAACTGGCTCACCGAGTTGATGAGGCCTTAGGATTTATGTCTGC
EST: gi|110712271|gb|EE089704.1|EE089704
EST:     GTCACCCAGTGGAATCTTGATTTTGCCGAGCACAGCGAGCAGGGAGATAG                         GTACCAGGAACTGGCTCACCGAGTTGACGAGGCCTTAGGATTTATGTCTGC
genomic: GTCACCCAGTGGAATCTTGATTTTGCCGAGCACAGCGAGCAGGGAGATAGgtaatttgct ... tgttcaatagGTACCAGGAACTGGCTCACCGAGTTGATGAGGCCTTAGGATTTATGTCTGC
EST: gi|161721625|gb|FC070835.1|FC070835
EST:     GTCACCCAGTGGAATCTTGATTTTGCCGAGCACAGCGAGCAGGGAGATAG                         GTACCAGGAACTGGCTCACCGAGTTGACGAGGCCTTAGGATTTATGTCTGC
genomic: GTCACCCAGTGGAATCTTGATTTTGCCGAGCACAGCGAGCAGGGAGATAGgtaatttgct ... tgttcaatagGTACCAGGAACTGGCTCACCGAGTTGATGAGGCCTTAGGATTTATGTCTGC
EST: gi|110703030|gb|EE079517.1|EE079517
EST:     GTCACCCAGTGGAATCTTGATTTTGCCGAGCACAGCGAGCAGGGAGATAG                         GTACCAGGAACTGGCTCACCGAGTTGACGAGGCCTTAGGATTTATGTCTGC
genomic: GTCACCCAGTGGAATCTTGATTTTGCCGAGCACAGCGAGCAGGGAGATAGgtaatttgct ... tgttcaatagGTACCAGGAACTGGCTCACCGAGTTGATGAGGCCTTAGGATTTATGTCTGC
EST: gi|110692039|gb|EE070829.1|EE070829
EST:     GTCACCCAGTGGAATCTTGATTTTGCCGAGCACAGCGAGCAGGGAGATAG                         GTACCAGGAACTGGCTCACCGAGTTGACGAGGCCTTAGGATTTATGTCTGC
genomic: GTCACCCAGTGGAATCTTGATTTTGCCGAGCACAGCGAGCAGGGAGATAGgtaatttgct ... tgttcaatagGTACCAGGAACTGGCTCACCGAGTTGATGAGGCCTTAGGATTTATGTCTGC
EST: gi|156738155|gb|EV242276.1|EV242276
EST:     GTCACCCAGTGGAATCTTGATTTTGCCGAGCACAGCGAGCAGGGAGATAG                         GTACCAGGAACTGGCTCACCGAGTTGACGAGGCCTTAGGATTTATGTCTGC
genomic: GTCACCCAGTGGAATCTTGATTTTGCCGAGCACAGCGAGCAGGGAGATAGgtaatttgct ... tgttcaatagGTACCAGGAACTGGCTCACCGAGTTGATGAGGCCTTAGGATTTATGTCTGC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTAACCTGCTAAGGGCCTTTGCCACTGGAGGTTATGCTGCGATGCAGAGAGTCACCCAGTGGAATCTTGATTTTGCCGAGCACAGCGAGCAGGGAGATAGgtaatttgctattttattcaggacctaacttgtctaatatttttgagttgaaagtaaaaaggcataaaattgatattggggattttctatgaaattctga

- - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gtaaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaattga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tatgaaa