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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAGATGTCCATTGAACTAAGTTTGGAAGATGTGAAGAAGGTTGCTTTACACTATGGATTTCAAATGGAGgtaatctcaatccacatgttttatgttgtcttgcatctgtatacaacgacatgaaattgtaattggacttagttcatgaattacag

Basic information

species Vitis vinifera
transcript Vv18s0041g00100.t01
intron # 16
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv18s0041g00100.t01 (Vitis vinifera), 5'ss of exon 16
lower sequence: LOC_Os05g43560.1 (Oryza sativa), 5'ss of exon 16
GAGATGTCCATTGAACTAAGTTTGGAAGATGTGAAGAAGGTTGCTTTACACTATGGATTTCAAATGGAGgtaa---tctc-----aatccacatgttttatgttgtctt----gcatctgtatacaacg-acatgaaattgta-attggacttagttcatgaattacag
|| ||||| |||||||| ||||||||||||||||| |  |||||||  || |||||||||   |||||||| |   | |      ||   | | |||||  | | |  |    | | ||  | || | | | ||| |  || | | || ||  |     || |||    
GATATGTCTATTGAACTGAGTTTGGAAGATGTGAAAAGAGTTGCTTACCATTATGGATTTGTGATGGAGgtgagtgttttgcaaaaaaaaaaaagttttgggctataattgaggaaactccaaactatgcatatgcatatgcatagtgcaccaatacgttggatttgta

upper sequence: Vv18s0041g00100.t01 (Vitis vinifera), 5'ss of exon 16
lower sequence: GLYMA20G16030.1 (Glycine max), 5'ss of exon 16
GAGATGTCCATTGAACTAAGTTTGGAAGATGTGAAGAAGGTTGCTTTACACTATGGATTTCAAATGGAGgtaatctcaatccacatgttttatgttgtcttgcatctgtatacaacgacatgaaattgtaattggac--ttagttcatgaattacag
|| |||||||||||| | |||||||||||||| |||| ||| || ||||| ||||||||| || | |||||||||||  | ||  | ||  ||  || | ||  |   | ||           |||  || ||| |   |  | |||||  || |||
GAAATGTCCATTGAATTGAGTTTGGAAGATGTTAAGAGGGTCGCATTACATTATGGATTTGAATTAGAGgtaatctc--ttcattttttgaataatgccctgttttaat-tatgcaagtgactaatcatatttgcattatctggtcatgggttgcag

upper sequence: Vv18s0041g00100.t01 (Vitis vinifera), 5'ss of exon 16
lower sequence: GLYMA13G10730.1 (Glycine max), 5'ss of exon 18
GAGATGTCCATTGAACTAAGTTTGGAAGATGTGAAGAAGGTTGCTTTACACTATGGATTTCAAATGGAGgtaatctcaatccacatgttttatgttgtcttgcatctgtatacaacgacatgaaattgtaattggacttagttcatgaattacag
|| |||||||||||| | |||||||||||||| |||| |||||| || || ||||||||| || | |||||||||||  |    |   |   |    | || | | || |    || |     | ||| | |   |  | || ||||  || |||
GAAATGTCCATTGAATTGAGTTTGGAAGATGTTAAGAGGGTTGCATTTCATTATGGATTTGAATTTGAGgtaatctctttttggacaat--gtcccattttacttatgcaagtgactaatcatatttgcatt---atctggt-catgggttgcag

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|34549600|gb|CF517832.1|CF517832
EST:     GTTTGGAAGATGTGAAGAAGGTTGCTTTACACTATGGATTTCAAATGGAG                         AAAGAAAGGACCATTGAGACGACCTACACAACGAATCCTCGATCCATGATG
genomic: GTTTGGAAGATGTGAAGAAGGTTGCTTTACACTATGGATTTCAAATGGAGgtaatctcaa ... tgaattacagAAAGAAAGGACCATTGAGACGACCTACACAACGAATCCTCGATCCATGATG
EST: gi|22014156|gb|BQ799190.1|BQ799190
EST:     GTTTGGAAGATGTGAAGAAGGTTGCTTTACACTATGGATTTCAAATGGAG                         AAAGAAAGGACCATTGAGACGACCTACACAACGAATCCTCGATCCATGATG
genomic: GTTTGGAAGATGTGAAGAAGGTTGCTTTACACTATGGATTTCAAATGGAGgtaatctcaa ... tgaattacagAAAGAAAGGACCATTGAGACGACCTACACAACGAATCCTCGATCCATGATG
EST: gi|30127173|gb|CB912512.1|CB912512
EST:     GTGGGGAAGATGTGAAGAAGGTTGCTTTACACTATGGATTTCAAATGGAG                         AAAGAAAGGACCATTGAGACGACCTACACAACGAATCCTCGATCCATGATG
genomic: GTTTGGAAGATGTGAAGAAGGTTGCTTTACACTATGGATTTCAAATGGAGgtaatctcaa ... tgaattacagAAAGAAAGGACCATTGAGACGACCTACACAACGAATCCTCGATCCATGATG
EST: gi|27585306|gb|CB008001.1|CB008001
EST:     GTTTGGAAGATGTGAAGAAGGTTGCTTTACACTATGGATTTCAAATGGAG                         AAAGAAAGGACCATTGAGACGACCTACACAACGAATCCTCGATCCATGATG
genomic: GTTTGGAAGATGTGAAGAAGGTTGCTTTACACTATGGATTTCAAATGGAGgtaatctcaa ... tgaattacagAAAGAAAGGACCATTGAGACGACCTACACAACGAATCCTCGATCCATGATG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAGATGTCCATTGAACTAAGTTTGGAAGATGTGAAGAAGGTTGCTTTACACTATGGATTTCAAATGGAGgtaatctcaatccacatgttttatgttgtcttgcatctgtatacaacgacatgaaattgtaattggacttagttcatgaattacag

- - - - - - - - - - - TGGAAG
- - - - - - - - - - -  GGAAGA
- - - - - - - - - - - -  AAGATG
- - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - -  AAGAAG