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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tttcttgaaatgaggaataaggtctgcattctcatggttttctgtaacacccttcctcattttgattgttgacagtttatttctaatattatttttgtagCTCCAATATTGGAATCTGGAAGTTTTCCTCCTTCTTTAGACGAGGCTTTGATTTTGAAG

Basic information

species Vitis vinifera
transcript Vv07s0031g01600.t01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv07s0031g01600.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA08G14980.1 (Glycine max), 3'ss of exon 1
---tttcttgaaatgaggaataaggtctgcattctcatggttttctgtaacacccttcctcattttgattgttgacagtttatttctaatattatttttgtagCTCCAATATTGGAATCTGGAAGTTTTCCTCCTTCTTTAGACGAGGCTTTGATTTTGAAG
    |   | |     ||| |  | |||   |||| |  |  |     ||   |  | |  ||||||| | || |||  ||||| ||||| || ||||||||||| |||||||||||||||||||| ||| | || || | || || |   ||||| | |||
agtatggattatgcctggagtg-gatctagtttcttactggataaaacaagtgc--tgccaattttgaatttttacatattattcctaattttgtttttgtagCTTCAATATTGGAATCTGGAAGTGTTCGTGCTCCTCTTGATGAAGAGCTGATTCTAAAG
















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|71857264|gb|DT006319.1|DT006319
EST:     GCAAAAACATGTTGCGTTGGAGGCTTCTGGTTCTTACAGAAATTTTCCAG                         CTCCAATATTGGAATCTGGAAGTTTTCCTCCTTCTTTAGACGAGGCTTTGA
genomic: GCAAAAACATGTTGCGTTGGAGGCTTCTGGTTCTTACAGAAATTTTCCAGgtaattatga ... atttttgtagCTCCAATATTGGAATCTGGAAGTTTTCCTCCTTCTTTAGACGAGGCTTTGA
EST: gi|18458639|gb|BM436917.1|BM436917
EST:     GCAAAAACATGTTGCGTTGGAGGCTTCTGGTTCTTACAGAAATTTTCCAG                         CTCCAATATTGGAATCTGGAAGTTTTCCTCCTTCTTTAGACGAGGCTTTGA
genomic: GCAAAAACATGTTGCGTTGGAGGCTTCTGGTTCTTACAGAAATTTTCCAGgtaattatga ... atttttgtagCTCCAATATTGGAATCTGGAAGTTTTCCTCCTTCTTTAGACGAGGCTTTGA
EST: gi|55778155|gb|AJ862939.1|AJ862939
EST:     GCAAAAACATGTTGCGTTGGAGGCTTCTGGTTCTTACAGAAATTTTCCAG                         CTCCAATATTGGAATCTGGAAGTTTTCCTCCTTCTTTAGATGAGGCTTTGA
genomic: GCAAAAACATGTTGCGTTGGAGGCTTCTGGTTCTTACAGAAATTTTCCAGgtaattatga ... atttttgtagCTCCAATATTGGAATCTGGAAGTTTTCCTCCTTCTTTAGACGAGGCTTTGA
EST: gi|110709925|gb|EE085812.1|EE085812
EST:     GCAAAAACATGTTGCGTTGGAGGCTTCTGGTTCTTACAGAAATTTTCCAG                         CTCCAATATTGGAATCTGGAAGTTTTCCTCCTTCTTTAGACGAGGCTTTGA
genomic: GCAAAAACATGTTGCGTTGGAGGCTTCTGGTTCTTACAGAAATTTTCCAGgtaattatga ... atttttgtagCTCCAATATTGGAATCTGGAAGTTTTCCTCCTTCTTTAGACGAGGCTTTGA
EST: gi|110713219|gb|EE088948.1|EE088948
EST:     GCAAAAACATGTTGCGTTGGAGGCTTCTGGTTCTTACAGAAATTTTCCAG                         CTCCAATATTGGAATCTGGAAGTTTTCCTCCTTCTTTAGACGAGGCTTTGA
genomic: GCAAAAACATGTTGCGTTGGAGGCTTCTGGTTCTTACAGAAATTTTCCAGgtaattatga ... atttttgtagCTCCAATATTGGAATCTGGAAGTTTTCCTCCTTCTTTAGACGAGGCTTTGA
EST: gi|349832444|gb|FQ421005.1|FQ421005
EST:     GCAAAAACATGTTGCGTTGGAGGCTTCTGGTTCTTACAGAAATTTTCCAG                         CTCCAATATTGGAATCTGGAAGTTTTCCTCCTTCTTTAGACGAGGCTTTGA
genomic: GCAAAAACATGTTGCGTTGGAGGCTTCTGGTTCTTACAGAAATTTTCCAGgtaattatga ... atttttgtagCTCCAATATTGGAATCTGGAAGTTTTCCTCCTTCTTTAGACGAGGCTTTGA
EST: gi|161718354|gb|FC065013.1|FC065013
EST:     GCAAAAACATGTTGCGTTGGAGGCTTCTGGTTCTTACAGAAATTTTCCAG                         CTCCAATATTGGAATCTGGAAGTTTTCCTCCTTCTTTAGACGAGGCTTTGA
genomic: GCAAAAACATGTTGCGTTGGAGGCTTCTGGTTCTTACAGAAATTTTCCAGgtaattatga ... atttttgtagCTCCAATATTGGAATCTGGAAGTTTTCCTCCTTCTTTAGACGAGGCTTTGA
EST: gi|110708701|gb|EE086542.1|EE086542
EST:     GCAAAAACATGTTGCGTTGGAGGCTTCTGGTTCTTACAGAAATTTTCCAG                         CTCCAATATTGGAATCTGGAAGTTTTCCTCCTTCTTTAGACGAGGCTTTGA
genomic: GCAAAAACATGTTGCGTTGGAGGCTTCTGGTTCTTACAGAAATTTTCCAGgtaattatga ... atttttgtagCTCCAATATTGGAATCTGGAAGTTTTCCTCCTTCTTTAGACGAGGCTTTGA
EST: gi|294966086|gb|GW837453.1|GW837453
EST:     GCAAAAACATGTTGCGTTGGAGGCTTCTGGTTCTTACAGAAATTTTCCAG                         CTCCAATATTGGAATCTGGAAGTTTTCCTCCTTCTTTAGACGAGGCTTTGA
genomic: GCAAAAACATGTTGCGTTGGAGGCTTCTGGTTCTTACAGAAATTTTCCAGgtaattatga ... atttttgtagCTCCAATATTGGAATCTGGAAGTTTTCCTCCTTCTTTAGACGAGGCTTTGA
EST: gi|71874768|gb|DT023823.1|DT023823
EST:     GCAAAAACATGTTGCGTTGGAGGCTTCTGGTTCTTACAGAAATTTTCCAG                         CTCCAATATTGGAATCTGGAAGTTTTCCTCCTTCTTTAGACGAGGCTTTGA
genomic: GCAAAAACATGTTGCGTTGGAGGCTTCTGGTTCTTACAGAAATTTTCCAGgtaattatga ... atttttgtagCTCCAATATTGGAATCTGGAAGTTTTCCTCCTTCTTTAGACGAGGCTTTGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aacacccttcctcattttgattgttgacagtttatttctaatattatttttgtagCTCCAATATTGGAATCTGGAAGTTTTCCTCCTTCTTTAGACGAGGCTTTGATTTTGAAG
                                   ttctaat  putative branch site (score: 2)
                                           ttattttt  CT-rich tract
                       ttgacagtttatttct  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tttcttgaaatgaggaataaggtctgcattctcatggttttctgtaacacccttcctcattttgattgttgacagtttatttctaatattatttttgtagCTCCAATATTGGAATCTGGAAGTTTTCCTCCTTCTTTAGACGAGGCTTTGATTTTGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - gaaatga
- - - - - - -ggaataa
- - - - - - - - - - - - -gcattct
- - - - - - - - - - - - - - - - catggtt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgttgac