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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCACTCAGCTGGATATTCTGGGGCTTTGGCAAATCCTCTTTTAGCTCCAGAATCTGCAATAAACAGATTAGACAGCACAATTTTGGAGGAGTTTGTTGCTgtaagttgtaaagaatgtattagaccaatttgttttgcaaaccatattactttacagtgtccatttttctggatcttttgtgttcttaagcggtggattggcttgggcatttcag

Basic information

species Vitis vinifera
transcript Vv11s0016g02870.t01
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv11s0016g02870.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: GLYMA05G36040.1 (Glycine max), 5'ss of exon 4
TCACTCAGCTGGATATTCTGGGGCTTTGGCAAATCCTCTTTTAGCTCCAGAATCTGCAATAAACAGATTAGACAGCACAATTTTGGAGGAGTTTGTTGCTgtaagttgtaaagaatgtattagaccaatttgttttgcaaaccatattactttacagtgtc-catttttctggatcttttgt-----gttcttaagcggtggatt--ggcttgggcatttcag---------
||| || ||||| | |||||| || ||||||||||||||||||||| ||||||| ||| |||| ||| || | || |||||| |||||||||||||||||||||||  | |  | |    |  |    ||  ||    |    |||    || |  || || ||  |||   |||  ||| |     |||||| | |  |    |  | |||   | |||  |         
TCATTCTGCTGGTTTTTCTGGTGCCTTGGCAAATCCTCTTTTAGCTTCAGAATCAGCAGTAAATAGACTAAATAGTACAATTCTGGAGGAGTTTGTTGCTgtaagtcttcataattaatctttatatgttacttaattatttaatacgtgttcattgtctctcaaatttaaagattctttataagatgttctttacctttcttataagacttatacttttatgaaacatcag

upper sequence: Vv11s0016g02870.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: GLYMA08G03580.1 (Glycine max), 5'ss of exon 3
TCACTCAGCTGGATATTCTGGGGCTTTGGCAAATCCTCTTTTAGCTCCAGAATCTGCAATAAACAGATTAGACAGCACAATTTTGGAGGAGTTTGTTGCTgtaagttgtaaagaatg----tattagaccaatttgttttgcaaaccatattactttacagtgtccatttttctggatcttttgt-----gttcttaagcggtggatt--ggcttgggcatttcag---------
||| || ||||| | |||||| || ||||||||||||||||||||| ||||||| ||  |||| ||| || |  | |||||| |||||||||||||||||||||||  | || | |     |  || |  | ||  ||    ||  | | ||  |||    | || |  |||   ||| |||| |     |||||| | |  |    |  | ||||  | |||  |         
TCATTCTGCTGGTTTTTCTGGTGCCTTGGCAAATCCTCTTTTAGCTTCAGAATCAGCTCTAAATAGACTAAATGGTACAATTCTGGAGGAGTTTGTTGCTgtaagtcttcaaaattaatctttatatattacttaattacttaatacgtgttcatttgtc-tctcaaaatttaaagattttttataagatgttcttcacctttcttataagacttgaacttttatgaaacatcag
















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|32247970|gb|CD713789.1|CD713789
EST:     AATCTGCAATAAACAGATTAGACAGCACAATTTTGGAGGAGTTTGTTGCT                         TTAAATTATACTGCTCCTCGGATGGTACTTGCGGCTTCTGGGGTTGAACAT
genomic: AATCTGCAATAAACAGATTAGACAGCACAATTTTGGAGGAGTTTGTTGCTgtaagttgta ... ggcatttcagTTAAATTATACTGCTCCTCGGATGGTACTTGCGGCTTCTGGGGTTGAACAT
EST: gi|71879335|gb|DT028390.1|DT028390
EST:     AATCTGCAATAAACAAATTAGACAGCACAATTTTGGAGGAGTTTGTTGCT                         TTAAATTATACTGCTCCTCGGATGGTACTTGCGGCTTCTGGGGTTGAACAT
genomic: AATCTGCAATAAACAGATTAGACAGCACAATTTTGGAGGAGTTTGTTGCTgtaagttgta ... ggcatttcagTTAAATTATACTGCTCCTCGGATGGTACTTGCGGCTTCTGGGGTTGAACAT
EST: gi|71879768|gb|DT028823.1|DT028823
EST:     AATCTGCAATAAACAAATTAGACAGCACAATTTTGGAGGAGTTTGTTGCT                         TTAAATTATACTGCTCCTCGGATGGTACTTGCGGCTTCTGGGGTTGAACAT
genomic: AATCTGCAATAAACAGATTAGACAGCACAATTTTGGAGGAGTTTGTTGCTgtaagttgta ... ggcatttcagTTAAATTATACTGCTCCTCGGATGGTACTTGCGGCTTCTGGGGTTGAACAT
EST: gi|71878964|gb|DT028019.1|DT028019
EST:     AATCTGCAATAAACAAATTAGACAGCACAATTTTGGAGGAGTTTGTTGCT                         TTAAATTATACTGCTCCTCGGATGGTACTTGCGGCTTCTGGGGTTGAACAT
genomic: AATCTGCAATAAACAGATTAGACAGCACAATTTTGGAGGAGTTTGTTGCTgtaagttgta ... ggcatttcagTTAAATTATACTGCTCCTCGGATGGTACTTGCGGCTTCTGGGGTTGAACAT
EST: gi|77587546|gb|DV222937.1|DV222937
EST:     AATCTGCAATAAACAAATTAGACAGCACAATTTTGGAGGAGTTTGTTGCT                         TTAAATTATACTGCTCCTCGGATGGTACTTGCGGCTTCTGGGGTTGAACAT
genomic: AATCTGCAATAAACAGATTAGACAGCACAATTTTGGAGGAGTTTGTTGCTgtaagttgta ... ggcatttcagTTAAATTATACTGCTCCTCGGATGGTACTTGCGGCTTCTGGGGTTGAACAT
EST: gi|32268962|gb|CD718121.1|CD718121
EST:     AATCTGCAATAAACAGATTAGACAGCACAATTTTGGAGGAGTTTGTTGCT                         TTAAATTATACTGCTCCTCGGATGGTACTTGCGGCTTCTGGGGTTGAACAT
genomic: AATCTGCAATAAACAGATTAGACAGCACAATTTTGGAGGAGTTTGTTGCTgtaagttgta ... ggcatttcagTTAAATTATACTGCTCCTCGGATGGTACTTGCGGCTTCTGGGGTTGAACAT
EST: gi|46917512|gb|CN546841.1|CN546841
EST:     AATCTGCAATAAACAAATTAGACAGCACAATTTTGGAGGAGTTTGTTGCT                         TTAAATTATACTGCTCCTCGGATGGTACTTGCGGCTTCTGGGGTTGAACA
genomic: AATCTGCAATAAACAGATTAGACAGCACAATTTTGGAGGAGTTTGTTGCTgtaagttgta ... ggcatttcagTTAAATTATACTGCTCCTCGGATGGTACTTGCGGCTTCTGGGGTTGAACA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TCACTCAGCTGGATATTCTGGGGCTTTGGCAAATCCTCTTTTAGCTCCAGAATCTGCAATAAACAGATTAGACAGCACAATTTTGGAGGAGTTTGTTGCTgtaagttgtaaagaatgtattagaccaatttgttttgcaaaccatattactttacagtgtccatttttctggatcttttgtgttcttaagcggtggattggcttgggcatttcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG