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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGCGGTGTCAGACAACATTTTGATCTCATTGGAGAACCCTGCATGGCTTATTGCTATGGCCAACATGTTCGTGGTCATCCATGTTATTGGAAGCTATCAGgtgctgtcccaaacccccctaattcagtcgtctcaaatctttcctccaactcatggttttgtgtgccttcatgcag

Basic information

species Vitis vinifera
transcript Vv14s0171g00400.t01
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv14s0171g00400.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: GLYMA19G24520.1 (Glycine max), 5'ss of exon 3
TGCGGTGTCAGACAACATTTTGATCTCATTGGAGAACCCTGCATGGCTTATTGCTATGGCCAACATGTTCGTGGTCATCCATGTTATTGGAAGCTATCAGgtgctgtcccaaaccccc----ctaattcagtcgtctcaaatctttcctccaactcatggt-tttgtgtgccttcatgcag---------------------
| | ||   ||| |||||| | |||   || ||||| ||   |||||||||||| ||||| |||||||| || || |||||||||||||| || |||||||||   | |     | |     || ||  |      || ||| ||  |      |||      |   ||||  |   | |                      
TTCTGTTGAAGATAACATTCTCATCAGTTTAGAGAAACCAAAATGGCTTATTGCAATGGCTAACATGTTTGTTGTGATCCATGTTATTGGTAGTTATCAGgtgaaattcagtttctcttactcttatctaaaaccttctaattttaacattggttcaaaaaactaaagtgctctagagtaactcttttttttgttgatgtag

upper sequence: Vv14s0171g00400.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: GLYMA16G06750.1 (Glycine max), 5'ss of exon 3
TGCGGTGTCAGACAACATTTTGATCTCATTGGAGAACCCTGCATGGCTTATTGCTATGGCCAACATGTTCGTGGTCATCCATGTTATTGGAAGCTATCAGgtgctgtcccaaacccccctaat----tcagtcgtctcaaatctttcc---tccaac-tcatggttttgtgtgccttcatgcag--------------------------------------------
| | ||   ||| |||||| | |||   || ||||| ||   |||||||||||| ||||| || ||||| || || ||||||||||||||||| |||||||||   | | |    | | || |    ||  |  ||  ||| | ||     |  | | |||   |||  | |   ||||   |                                             
TACAGTTGAAGATAACATTCTCATCAGTTTAGAGAAACCAAAATGGCTTATTGCAATGGCTAATATGTTTGTTGTGATCCATGTTATTGGAAGTTATCAGgtgaaattc-agtttctcttactcttgtccattatccaaaacccttttgattttagcatcaccctttctttttggttcaaaaaacagaagtcatcaagagtaactcttttttttttttttttttgtag

upper sequence: Vv14s0171g00400.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: GLYMA19G22590.1 (Glycine max), 5'ss of exon 4
TGCGGTGTCAGACAACATTTTGATCTCATTGGAGAACCCTGCATGGCTTATTGCTATGGCCAACATGTTCGTGGTCATCCATGTTATTGGAAGCTATCAGgtgctgtccca--------aacccccctaattcagtcgtctcaaatcttt---cctccaactcatggttttgtgtgccttcatgcag-------------
|| |||        ||||  | ||||| |||||||| ||  | ||||||||||| ||||| ||| |||| || || || ||||| ||||||||||||||||||   | | |        |  |    || || |  | | |    | | |    ||| || | |   | |||| ||  ||| |  |              
TGAGGTTGATTCTGACATCCTCATCTCTTTGGAGAAACCAACTTGGCTTATTGCAATGGCTAACTTGTTTGTTGTTATTCATGTAATTGGAAGCTATCAGgtgaaattcaatttatcttattctttatagttgatacttttttcttttataagactcaaatttaaaatattgtctgatttcttttataagattcaattta

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|161712409|gb|FC061714.1|FC061714
EST:     TTGCTATGGCCAACATGTTCGTGGTCATCCATGTTATTGGAAGCTATCAG                         ATTTATGCTATGCCAGTGTTTGATATGATAGAAACTGTCTTGGTAAAGAAA
genomic: TTGCTATGGCCAACATGTTCGTGGTCATCCATGTTATTGGAAGCTATCAGgtgctgtccc ... cttcatgcagATTTATGCTATGCCAGTGTTTGATATGATAGAAACTGTCTTGGTAAAGAAA
EST: gi|32248067|gb|CD713886.1|CD713886
EST:     TTGCTATGGCCAACATGTTCGTGGTCATCCATGTTATTGGAAGCTATCAA                         ATTTATGCTATGCCAGTGTTTGATA
genomic: TTGCTATGGCCAACATGTTCGTGGTCATCCATGTTATTGGAAGCTATCAGgtgctgtccc ... cttcatgcagATTTATGCTATGCCAGTGTTTGATA
EST: gi|110700407|gb|EE078411.1|EE078411
EST:     TTGCTATGGCCAACATGTTCGTGGTCATCCATGTTATTGGAAGCTATCAG                         ATTTATGCTATGCCAGTGTTTGATATGATAGAAACTGTCTTGGTAAAGAAA
genomic: TTGCTATGGCCAACATGTTCGTGGTCATCCATGTTATTGGAAGCTATCAGgtgctgtccc ... cttcatgcagATTTATGCTATGCCAGTGTTTGATATGATAGAAACTGTCTTGGTAAAGAAA
EST: gi|32247418|gb|CD713237.1|CD713237
EST:     TTGCTATGGCCAACATGTTCGTGGTCATCCATGTTATTGGAAGCTATCAG                         ATTTATGCTATGCCAGTG
genomic: TTGCTATGGCCAACATGTTCGTGGTCATCCATGTTATTGGAAGCTATCAGgtgctgtccc ... cttcatgcagATTTATGCTATGCCAGTG
EST: gi|161716023|gb|FC069114.1|FC069114
EST:     TTGCTATGGCCAACATGTTCGTGGTCATCCATGTTATTGGAAGCTATCAG                         ATTTATGCTATGCCAGTGTTTGATATGATAGAAACTGTCTTGGTAAAGAAA
genomic: TTGCTATGGCCAACATGTTCGTGGTCATCCATGTTATTGGAAGCTATCAGgtgctgtccc ... cttcatgcagATTTATGCTATGCCAGTGTTTGATATGATAGAAACTGTCTTGGTAAAGAAA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGCGGTGTCAGACAACATTTTGATCTCATTGGAGAACCCTGCATGGCTTATTGCTATGGCCAACATGTTCGTGGTCATCCATGTTATTGGAAGCTATCAGgtgctgtcccaaacccccctaattcagtcgtctcaaatctttcctccaactcatggttttgtgtgccttcatgcag

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