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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGAATGGAAAAGTAGGTCATGTAAATCAAGCAAATAATATGTACCTGTTTCCTGGgttcgtgctcatttcttagtcattactaatttatgggctattcctagactgtcattaaattcatatagaactttgttgtctataattcag

Basic information

species Vitis vinifera
transcript Vv15s0046g03670.t01
intron # 15
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv15s0046g03670.t01 (Vitis vinifera), 5'ss of exon 15
lower sequence: LOC_Os10g35960.2 (Oryza sativa), 5'ss of exon 15
GGAATGGAAAAGTAGGTCATGTAAATCAAGCAAATAATATGTACCTGTTTCCTGGgttcgtgctcatttcttagtcattactaatttatgggctattcctagactgtcattaaattcatatagaactttgttgtctataattcag
| ||||| | |  |||  | |  ||||||||||| |||||||| |||||||||||||  |    |  || |   | |     || |  | |  | ||  |    | | || |  ||  | |         || | ||||||||||
GCAATGGTAGACAAGGGTACGCTAATCAAGCAAACAATATGTATCTGTTTCCTGGgtatgacaactgttatagcttaccttgaaatgcttgtttttttttccttttttat-atgttattctgatggacgtttctgtataattcag

upper sequence: Vv15s0046g03670.t01 (Vitis vinifera), 5'ss of exon 15
lower sequence: GLYMA03G01680.1 (Glycine max), 5'ss of exon 15
GGAATGGAAAAGTAGGTCATGTAAATCAAGCAAATAATATGTACCTGTTTCCTGGgttcgtgctcatttcttagtcattactaatttatgggctattccta--gactg--tcattaaattcatatagaactttgttgtcta--taattcag-----
| ||||||||||| |||||||||||||||||||| || |||||||| || || ||||  |   |   | ||| ||   ||     || ||   ||| |||     |||  | ||||   | |  ||  |  || | || ||  |  ||||      
GTAATGGAAAAGTGGGTCATGTAAATCAAGCAAACAACATGTACCTCTTCCCAGGgtagggtttatctccttggtttgtatattcttctgaattatacctgtcagctgaattattagtgtaacttactaacttctagtttaactttttcattccag

upper sequence: Vv15s0046g03670.t01 (Vitis vinifera), 5'ss of exon 15
lower sequence: GLYMA18G46340.1 (Glycine max), 5'ss of exon 15
GGAATGGAAAAGTAGGTCATGTAAATCAAGCAAATAATATGTACCTGTTTCCTGGgttcgtgctcatttcttagtcattactaatttatgggctattcctagactgtcattaaattcatatagaactttgttgtctataattcag-----
| |||||| |||| || |||||||||||||| || || |||||||||||||| ||||  |    | ||| |   | || | |  || | ||   || || |  | ||    | |||   ||| |  | |   | | | | ||||      
GAAATGGAGAAGTTGGCCATGTAAATCAAGCCAACAACATGTACCTGTTTCCAGGgtaggcatgcctttgtggcttat-attttttcacggatcatgcc-actcagtggaaacattggcata-atttctaccg-caacatttcatttcag

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|110414200|gb|EC980027.1|EC980027
EST:     GGAAAAGTAGGCCATGTAAATCAAGCAAATAATATGTACCTGTTTCCTGG                         GATTGGTTTGGGGACTCTTCTCGCAGGTGCTCATTTTATTTCAGATGGCAT
genomic: GGAAAAGTAGGTCATGTAAATCAAGCAAATAATATGTACCTGTTTCCTGGgttcgtgctc ... tataattcagGATTGGTTTGGGGACTCTTCTCGCAGGTGCTCATTTTATTTCAGATGGCAT
EST: gi|110699700|gb|EE076930.1|EE076930
EST:     GGAAAAGTACGTCATGTAAATCAAGCAAATAATATGTACCTGTTTCCTGG                         GATTGGTTTGGGGACTCTTCTCGCAGGTGCTCATTTTATTTCAGATGGCAT
genomic: GGAAAAGTAGGTCATGTAAATCAAGCAAATAATATGTACCTGTTTCCTGGgttcgtgctc ... tataattcagGATTGGTTTGGGGACTCTTCTCGCAGGTGCTCATTTTATTTCAGATGGCAT
EST: gi|33404797|gb|CF210424.1|CF210424
EST:     GGAAAAGTAGGTCATGTAAATCAAGCAAATAATATGTACCTGTTTCCTGG                         GATTNGTTTGGGGACTCTTCTCGC
genomic: GGAAAAGTAGGTCATGTAAATCAAGCAAATAATATGTACCTGTTTCCTGGgttcgtgctc ... tataattcagGATTGGTTTGGGGACTCTTCTCGC
EST: gi|33404880|gb|CF210507.1|CF210507
EST:     GGAAAAGTAGGTCATGTAAATCAAGCAAATAATATGTACCTGTTTCCTGG                         GATTGGTTTGGGGACTCTTCTCGCAGGTGCTCATTTTATTTCAGATGGCAT
genomic: GGAAAAGTAGGTCATGTAAATCAAGCAAATAATATGTACCTGTTTCCTGGgttcgtgctc ... tataattcagGATTGGTTTGGGGACTCTTCTCGCAGGTGCTCATTTTATTTCAGATGGCAT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGAATGGAAAAGTAGGTCATGTAAATCAAGCAAATAATATGTACCTGTTTCCTGGgttcgtgctcatttcttagtcattactaatttatgggctattcctagactgtcattaaattcatatagaactttgttgtctataattcag

- - - - - - - - - - - - -  AAGCAA