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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GACGTCGGAAGAATTGAGTATTGGGAAAATCAAGTTCAAGGCCTTCGATTTGGGAGGTCATCAGATTGCTCGCAGAGTCTGGAAGGATTACTATGCCAAAgtatggaatttctctggtatctgttagtcatttggttaatatttctttattcgtctagattgtatgttgatgttattggttatgatatagaatttggcta...

Basic information

species Vitis vinifera
transcript Vv07s0005g01330.t01
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv07s0005g01330.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: PP1S183_17V6.1 (Physcomitrella patens), 5'ss of exon 2
GACGTCGGAAGAATTGAGTATTGGGAAAATCAAGTTCAAGGCCTTCGATTTGGGAGGTCATCAGATTGCTCGCAGAGTCTGGAAGGATTACTATGCCAAAgtatggaatttct--ctggtatctgttagtcatttg-gttaatatttctttattcgtctagattgtatgt-tgatgttattggttatgatatagaatttggcta
 || ||||| || |||||||| || |||||||||||||| || || ||| |||| ||||| ||||| ||  |  |||| ||||||||||| |||||||| || |  ||| |||   |     |  |   |  | || || |  | | |   |||  |  |      | || |  |  ||| ||||  ||||    || | | | 
TACTTCGGAGGAGTTGAGTATCGGAAAAATCAAGTTCAAAGCATTTGATCTGGGTGGTCACCAGATCGCCAGGCGAGTGTGGAAGGATTATTATGCCAAGgt-tacaatctctacttatggaccctcccttttgtgcgtcagcagtgcgagattgattgaaggatcacgtctagttctatgggtt--gataagagatgtagat-

upper sequence: Vv07s0005g01330.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: EFJ35155 (Selaginella moellendorffii), 5'ss of exon 2
GACGTCGGAAGAATTGAGTATTGGGAAAATCAAGTTCAAGGCCTTCGATTTGGGAGGTCATCAGATTGCTCGCAGAGTCTGGAAGGATTACTATGCCAAAgtatggaatttctctggtatctgtt---agtcatttggttaatattt----ctttattcgtctagattgtatgttgatgttattggttatgata-tagaatttggcta--------------------------------------------------------------------------------------------
 || || || ||  | || ||    || ||||| ||||||||||||||| |||| ||||| ||||| || ||  | || |||||||| ||||||||||| || ||  | |  ||||  |  | ||   | ||   || ||    |||    |  |  |     | |   | | ||  | || |||    || |  |   | | | | |                                                                                            
AACATCCGAGGAGCTAAGCATCAACAAGATCAAATTCAAGGCCTTCGATCTGGGGGGTCACCAGATCGCGCGACGCGTGTGGAAGGACTACTATGCCAAGgtttgacactcatctgagaattctttcgaatccaatgctttgcctttgaagcgatgctttggcaaaagttctttttgttttcttgccagtggtggtttgactggacgacttgttctagatctagttgctaacgatgttttgtcacaaactcgtcagatgatctgactggattccatggcttgtttactttgatcatccag

upper sequence: Vv07s0005g01330.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: EFJ16976 (Selaginella moellendorffii), 5'ss of exon 2
GACGTCGGAAGAATTGAGTATTGGGAAAATCAAGTTCAAGGCCTTCGATTTGGGAGGTCATCAGATTGCTCGCAGAGTCTGGAAGGATTACTATGCCAAAgtatggaatttctctggtatctgttagtcatttggttaatatttctttattcgtctagattgtatgttgatgttattggttatgatatagaatttggcta
||| ||||| ||  |||| || || || ||||||||||| || || |||||||||||||| ||||| |||||  | ||||||||||| ||||| ||||| || ||       |||    |||||  ||  || ||| || | |     | |  |   | || | | ||  | || |||| |||   |             
GACCTCGGAGGAGCTGAGCATCGGCAAGATCAAGTTCAAAGCGTTTGATTTGGGAGGTCACCAGATCGCTCGTCGCGTCTGGAAGGACTACTACGCCAAGgtttgtgggaaatct----tctgt--gttcttgggtgaaaactatagcactaatt--gtttctctttttttttttttggctatacaag------------

upper sequence: Vv07s0005g01330.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: EFJ24104 (Selaginella moellendorffii), 5'ss of exon 2
GACGTCGGAAGAATTGAGTATTGGGAAAATCAAGTTCAAGGCCTTCGATTTGGGAGGTCATCAGATTGCTCGCAGAGTCTGGAAGGATTACTATGCCAAAgtatggaatttctctggta--tctgttagtcatttggttaatatttct--ttattcgtctagattgtatgttgatgttattggttatgatatagaatttggcta
 || || || ||  | || ||    || ||||| ||||||||||||||| |||| ||||| ||||| || ||  | || |||||||| ||||||||||| ||  |  | |  ||||  |  ||| |||    ||||  |    |||||  | |  |  || | ||| ||  | |  || ||  || | ||  |    | |    
AACATCCGAGGAGCTAAGCATCAACAAGATCAAATTCAAGGCCTTCGATCTGGGGGGTCACCAGATCGCGCGACGCGTGTGGAAGGACTACTATGCCAAGgttggacactcatctgagaattcttttatgtgtttgccttggttttctactcaaactccttgcttgaatcgttac-ttgttctttcttatcaaatgctcgt---

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|27583160|gb|CB005855.1|CB005855
EST:     TGGGAGGGCATCAGATTGCTCGCAGAGTCTGGAAGGATTACTATGCCAAA                         GTGGATGCTGTAGTGTACCTGGTGGATGCCTATGATAAGGAGAGGTTTGCA
genomic: TGGGAGGTCATCAGATTGCTCGCAGAGTCTGGAAGGATTACTATGCCAAAgtatggaatt ... actgttacagGTGGATGCTGTCGTGTACCTGGTGGATGCCTATGATAAGGAGAGGTTTGCA
EST: gi|71855570|gb|DT004625.1|DT004625
EST:     TGGGAGGGCATCAGATTGCTCGCAGAGTCTGGAAGGATTACTATGCCAAA                         GTGGATGCTGTCGTGTACCTG
genomic: TGGGAGGTCATCAGATTGCTCGCAGAGTCTGGAAGGATTACTATGCCAAAgtatggaatt ... actgttacagGTGGATGCTGTCGTGTACCTG
EST: gi|110366810|gb|EC930728.1|EC930728
EST:     TGGGAGGGCATCAGATTGCTCGCAGAGTCTGGAAGGATTACTATGCCAAA                         GTGGATGCTGTCGTGTACCTGGTGGATGCCTATGATAAGGAGAGGTTTGCA
genomic: TGGGAGGTCATCAGATTGCTCGCAGAGTCTGGAAGGATTACTATGCCAAAgtatggaatt ... actgttacagGTGGATGCTGTCGTGTACCTGGTGGATGCCTATGATAAGGAGAGGTTTGCA
EST: gi|110731766|gb|EE106466.1|EE106466
EST:     TGGGAGGGCATCAGATTGCTCGCAGAGTCTGGAAGGATTACTATGCCAAA                         GTGGATGCTGTCGTGTACCTGGTGGATGCCTATGATAAGGAGAGGTTTGCA
genomic: TGGGAGGTCATCAGATTGCTCGCAGAGTCTGGAAGGATTACTATGCCAAAgtatggaatt ... actgttacagGTGGATGCTGTCGTGTACCTGGTGGATGCCTATGATAAGGAGAGGTTTGCA
EST: gi|110385025|gb|EC949507.1|EC949507
EST:     TGGGAGGGCATCAGATTGCTCGCAGAGTCTGGAAGGATTACTATGCCAAA                         GTGGATGCTGTCGTGTACCTGGTGGATGCCTATGATAAGGAGAGGTTTGCA
genomic: TGGGAGGTCATCAGATTGCTCGCAGAGTCTGGAAGGATTACTATGCCAAAgtatggaatt ... actgttacagGTGGATGCTGTCGTGTACCTGGTGGATGCCTATGATAAGGAGAGGTTTGCA
EST: gi|110410149|gb|EC975826.1|EC975826
EST:     TGGGAGGGCATCAGATTGCTCGCAGAGTCTGGAAGGATTACTATGCCAAA                         GTGGATGCTGTAGTGTACCTGGTGGATGCCTATGATAAGGAGAGGTTTGCA
genomic: TGGGAGGTCATCAGATTGCTCGCAGAGTCTGGAAGGATTACTATGCCAAAgtatggaatt ... actgttacagGTGGATGCTGTCGTGTACCTGGTGGATGCCTATGATAAGGAGAGGTTTGCA
EST: gi|71889308|gb|DT038363.1|DT038363
EST:     TGGGAGGGCATCAGATTGCTCGCAGAGTCTGGAAGGATTACTATGCCAAA                         GTGGATGCTGTCGTGTACCTGGTGGATGCCTATGATAAGGAGAGGTTTGCA
genomic: TGGGAGGTCATCAGATTGCTCGCAGAGTCTGGAAGGATTACTATGCCAAAgtatggaatt ... actgttacagGTGGATGCTGTCGTGTACCTGGTGGATGCCTATGATAAGGAGAGGTTTGCA
EST: gi|161715468|gb|FC067086.1|FC067086
EST:     TGGGAGGGCATCAGATTGCTCGCAGAGTCTGGAAGGATTACTATGCCAAA                         GTGGATGCTGTCGTGTACCTGGTGGATGCCTATGATAAGGAGAGGTTTGCA
genomic: TGGGAGGTCATCAGATTGCTCGCAGAGTCTGGAAGGATTACTATGCCAAAgtatggaatt ... actgttacagGTGGATGCTGTCGTGTACCTGGTGGATGCCTATGATAAGGAGAGGTTTGCA
EST: gi|161721274|gb|FC069688.1|FC069688
EST:     TGGGAGGGCATCAGATTGCTCGCAGAGTCTGGAAGGATTACTATGCCAAA                         GTGGATGCTGTCGTGTACCTGGTGGATGCCTATGATAAGGAGAGGTTTGCA
genomic: TGGGAGGTCATCAGATTGCTCGCAGAGTCTGGAAGGATTACTATGCCAAAgtatggaatt ... actgttacagGTGGATGCTGTCGTGTACCTGGTGGATGCCTATGATAAGGAGAGGTTTGCA
EST: gi|110705664|gb|EE082774.1|EE082774
EST:     TGGGAGGGCATCAGATTGCTCGCAGAGTCTGGAAGGATTACTATGCCAAA                         GTGGATGCTGTCGTGTACCTGGTGGATGCCTATGATAAGGAGAGGTTTGCA
genomic: TGGGAGGTCATCAGATTGCTCGCAGAGTCTGGAAGGATTACTATGCCAAAgtatggaatt ... actgttacagGTGGATGCTGTCGTGTACCTGGTGGATGCCTATGATAAGGAGAGGTTTGCA
EST: gi|110420203|gb|EC986468.1|EC986468
EST:     TGGGAGGGCATCAGATTGCTCGCAGAGTCTGGAAGGATTACTATGCCAAA                         GTGGATGCTGTAGTGTACCTGGTGGATGCCTATGATAAGGAGAGGTTTGCA
genomic: TGGGAGGTCATCAGATTGCTCGCAGAGTCTGGAAGGATTACTATGCCAAAgtatggaatt ... actgttacagGTGGATGCTGTCGTGTACCTGGTGGATGCCTATGATAAGGAGAGGTTTGCA
EST: gi|30297283|gb|CB974077.1|CB974077
EST:     TGGGAGGGCATCAGATTGCTCGCAGAGTCTGGAAGGATTACTATGCCAAA                         GTGGATGCTGTCGTGTACCTGGTGGATGCCTATGATAAGGAGAGGTTTGCA
genomic: TGGGAGGTCATCAGATTGCTCGCAGAGTCTGGAAGGATTACTATGCCAAAgtatggaatt ... actgttacagGTGGATGCTGTCGTGTACCTGGTGGATGCCTATGATAAGGAGAGGTTTGCA
EST: gi|294964945|gb|GW838748.1|GW838748
EST:     TGGGAGGGCATCAGATTGCTCGCAGAGTCTGGAAGGATTACTATGCCAAA                         GTGGATGCTGTCGTGTACCTGGTGGATGCCTATGATAAGGAGAGGTTTGCA
genomic: TGGGAGGTCATCAGATTGCTCGCAGAGTCTGGAAGGATTACTATGCCAAAgtatggaatt ... actgttacagGTGGATGCTGTCGTGTACCTGGTGGATGCCTATGATAAGGAGAGGTTTGCA
EST: gi|110393443|gb|EC958683.1|EC958683
EST:     TGGGAGGGCATCAGATTGCTCGCAGAGTCTGGAAGGATTACTATGCCAAA                         GTGGATGCTGTCGTGTACCTGGTGGATGCCTATGATAAGGAGAGGTTTGCA
genomic: TGGGAGGTCATCAGATTGCTCGCAGAGTCTGGAAGGATTACTATGCCAAAgtatggaatt ... actgttacagGTGGATGCTGTCGTGTACCTGGTGGATGCCTATGATAAGGAGAGGTTTGCA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GACGTCGGAAGAATTGAGTATTGGGAAAATCAAGTTCAAGGCCTTCGATTTGGGAGGTCATCAGATTGCTCGCAGAGTCTGGAAGGATTACTATGCCAAAgtatggaatttctctggtatctgttagtcatttggttaatatttctttattcgtctagattgtatgttgatgttattggttatgatatagaatttggcta

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG