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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aaggaccctggataggaacacaatcatattttcaatgtcatatgtaattattgatatggaggtgcagagcaattaatcccagtttttattgttattttagGTTGGGAATAGGATTATTAGGAAAAGGATCCATGTGCGGGTGGAACATGTTCAACCATCAAGGTGCAGGGAAGAATTTAAACTGAGGAAAATTCGGAACG

Basic information

species Vitis vinifera
transcript Vv01s0150g00520.t01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv01s0150g00520.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: LOC_Os10g32820.1 (Oryza sativa), 3'ss of exon 1
-aaggaccctggataggaacacaatcatattttcaatgtcat-atgtaattattgatatggaggtgcagagcaattaatcccagtttttattgttattttagGTTGGGAATAGGATTATTAGGAAAAGGATCCATGTGCGGGTGGAACATGTTCAACCATCAAGGTGCAGGGAAGAATTTAAACTGAGGAAAATTCGGAACG
 | |     ||   ||  |       || |  ||   |  || || ||||| |||| ||   |   | |    | | ||     || ||| | |  |  |||||||||||  | ||||| ||||| ||||||||||| || ||||| ||||| || ||||| |||||||  || || ||    |||||||| ||   |||||
catgtgtaatgttcagtcatgtggatatgtagtcttcgggattatttaatttttgaaatcatgtatctgttttactgattgt--ttgttaatctcttggtagGTTGGGAACCGCATTATCAGGAAGAGGATCCATGTCCGTGTGGAGCATGTGCAGCCATCCAGGTGCACTGAGGAGTTCCGCCTGAGGAAGATCAAGAACG
















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|110426957|gb|EC993386.1|EC993386
EST:     AGGTCTGGAACGTCACCAAGCGTGCCATAGGCGTTGAAGTCAACAAACAG                         GTTGGGAATAGGATTATTAGGAAAAGGATCCATGTGCGGGTGGAACATGTT
genomic: AGGTCTGGAACGTCACCAAGCGTGCCATAGGCGTTGAAGTCAACAAACAGgcatctctct ... gttattttagGTTGGGAATAGGATTATTAGGAAAAGGATCCATGTGCGGGTGGAACATGTT
EST: gi|71873760|gb|DT022815.1|DT022815
EST:     AGGTCTGGAACGTCACCAAGCGTGCCATAGGCGTTGAAGTCAACAAACAG                         GTTGGGAATAGGATTATTAGGAAAAGGATCCATGTGCGGGTGGAACATGTT
genomic: AGGTCTGGAACGTCACCAAGCGTGCCATAGGCGTTGAAGTCAACAAACAGgcatctctct ... gttattttagGTTGGGAATAGGATTATTAGGAAAAGGATCCATGTGCGGGTGGAACATGTT
EST: gi|294964295|gb|GW838098.1|GW838098
EST:     AGGTCTGGAACGTCACCAAGCGTGCCATAGGCGTTGAAGTCAACAAACAG                         GTTGGGAATAGGATTATTAGGAAAAGGATCCATGTGCGGGTGGAAC
genomic: AGGTCTGGAACGTCACCAAGCGTGCCATAGGCGTTGAAGTCAACAAACAGgcatctctct ... gttattttagGTTGGGAATAGGATTATTAGGAAAAGGATCCATGTGCGGGTGGAAC
EST: gi|110727044|gb|EE103385.1|EE103385
EST:     AGGTCTGGAACGTCACCAAGCGTGCCATAGGCGTTGAAGTCAACAAACAG                         GTTGGGAATAGGATTATTAGGAAAAGGATCCATGTGCGGGTGGAACATGTT
genomic: AGGTCTGGAACGTCACCAAGCGTGCCATAGGCGTTGAAGTCAACAAACAGgcatctctct ... gttattttagGTTGGGAATAGGATTATTAGGAAAAGGATCCATGTGCGGGTGGAACATGTT
EST: gi|110709448|gb|EE084915.1|EE084915
EST:     AGGTCTGGAACGTCACCAAGCGTGCCATAGGCGTTGAAGTCAACAAACAG                         GTTGGGAATAGGATTATTAGGAAAAGGATCCATGTGCGGGTGGAACATGTT
genomic: AGGTCTGGAACGTCACCAAGCGTGCCATAGGCGTTGAAGTCAACAAACAGgcatctctct ... gttattttagGTTGGGAATAGGATTATTAGGAAAAGGATCCATGTGCGGGTGGAACATGTT
EST: gi|34416787|gb|CF415541.1|CF415541
EST:     AGGTCTGGAACGTCACCAAGCGTGCCATAGGCGTTGAAGTCAACAAACAG                         GTTGGGAATAGGATTATTAGGAAAAGGATCCATGTGCGGGTGGAACATGTT
genomic: AGGTCTGGAACGTCACCAAGCGTGCCATAGGCGTTGAAGTCAACAAACAGgcatctctct ... gttattttagGTTGGGAATAGGATTATTAGGAAAAGGATCCATGTGCGGGTGGAACATGTT
EST: gi|110390647|gb|EC955567.1|EC955567
EST:     AGGTCTGGAACGTCACCAAGCGTGCCATAGGCGTTGAAGTCAACAAACAG                         GTTGGGAATAGGATTATTAGGAAAAGGATCCATGTGCGGGTGGAACATGTT
genomic: AGGTCTGGAACGTCACCAAGCGTGCCATAGGCGTTGAAGTCAACAAACAGgcatctctct ... gttattttagGTTGGGAATAGGATTATTAGGAAAAGGATCCATGTGCGGGTGGAACATGTT
EST: gi|110418929|gb|EC985113.1|EC985113
EST:     AGGTCTGGAACGTCACCAAGCGTGCCATAGGCGTTGAAGTCAACAAACAG                         GTTGGGAATAGGATTATTAGGAAAAGGATCCATGTGCGGGTGGAACATGTT
genomic: AGGTCTGGAACGTCACCAAGCGTGCCATAGGCGTTGAAGTCAACAAACAGgcatctctct ... gttattttagGTTGGGAATAGGATTATTAGGAAAAGGATCCATGTGCGGGTGGAACATGTT
EST: gi|28967426|gb|CB346459.1|CB346459
EST:     AGGTCTGGAACGTCACCAAGCGTGCCATAGGCGTTGAAGTCAACAAACAG                         GTTGGGAATAGGATTATTAGGAAAAGGATCCATGTGCGGGTGGAACATGTT
genomic: AGGTCTGGAACGTCACCAAGCGTGCCATAGGCGTTGAAGTCAACAAACAGgcatctctct ... gttattttagGTTGGGAATAGGATTATTAGGAAAAGGATCCATGTGCGGGTGGAACATGTT
EST: gi|34319300|gb|CF372054.1|CF372054
EST:     GCGTGCCATAGGCGTTGAAGTCAACAAACAG                         GTTGGGAATAGGATTATTAGGAAAAGGATCCATGTGCGGGTGGAACATGTT
genomic: GCGTGCCATAGGCGTTGAAGTCAACAAACAGgcatctctct ... gttattttagGTTGGGAATAGGATTATTAGGAAAAGGATCCATGTGCGGGTGGAACATGTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aattattgatatggaggtgcagagcaattaatcccagtttttattgttattttagGTTGGGAATAGGATTATTAGGAAAAGGATCCATGTGCGGGTGGAACATGTTCAACCATCAAGGTGCAGGGAAGAATTTAAACTGAGGAAAATTCGGAACG
                         aattaat  putative branch site (score: 3)
                                              ttatttt  putative PPT
                                   agtttttattgttatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aaggaccctggataggaacacaatcatattttcaatgtcatatgtaattattgatatggaggtgcagagcaattaatcccagtttttattgttattttagGTTGGGAATAGGATTATTAGGAAAAGGATCCATGTGCGGGTGGAACATGTTCAACCATCAAGGTGCAGGGAAGAATTTAAACTGAGGAAAATTCGGAACG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - -ccctgga
- - - - - - - - - cacaatc
- - - - - - - - - - - - - - - - caatgtc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -ggaggtg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aatccca