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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...taaagtgggcaatgactacaagggagggagtgcgccgttacaacttatatggtcaacatgtatgatgctgaccatttgaattcattaatggttgctgcagGGATACTTTGATGAGCATCGCTAAGCACTATGAAACTGGAGAAACACTACCTGAAGATGTGTATTTGAAACTTGTTGCAGCAAGGACTTTTCGTGCCGGG

Basic information

species Vitis vinifera
transcript Vv00s0211g00060.t01
intron # 14
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv00s0211g00060.t01 (Vitis vinifera), 3'ss of exon 14
lower sequence: AT5G65620.1 (Arabidopsis thaliana), 3'ss of exon 11
taaagtgggcaatgactacaagggagggagtgcgccgttacaacttatatggtcaacatgtatgatgctgaccatttgaattcattaatggttgctgcagGGATACTTTGATGAGCATCGCTAAGCACTATGAAACTGGAGAAACACTACCTGAAGATGTGTATTTGAAACTTGTTGCAGCAAGGACTTTTCGTGCCGGG
  || | ||   | | | | ||| ||      ||  |||||  | | | || |  |||    | |||   |  ||  |  ||    | || | | | |||||| ||||| |||||||| |||||||| || ||||| ||||||||||| || || || || ||   ||||||  | || ||||| || || ||||| |||
gtaatttggagttcatttccaggcagaat---cgatgttacctcgt-tgtgatttacaaa-gtaatgtgaa--atgagcgttatgaattgctggtttcagGGACACTTTAATGAGCATTGCTAAGCATTACGAAACAGGAGAAACACTCCCAGAGGAAGTATACAAGAAACTCCTGGCCGCAAGAACATTCCGTGCAGGG
















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|26263230|gb|CA814293.1|CA814293
EST:     TCATGGAAAATTGGTGTTACCACAG                         GGATACTTTGATGAGCATCGCTAAGCACTATGAAACTGGAGAAACACTACC
genomic: TCATGGAAAATTGGTGTTACCACAGgtacttttct ... gttgctgcagGGATACTTTGATGAGCATCGCTAAGCACTATGAAACTGGAGAAACACTACC
EST: gi|33408872|gb|CF214499.1|CF214499
EST:     GATGCTGTTGAATTACCTTCTCAATTCATGGAAAATTGGTGTTACCACAG                         GGATACTTTGATGAGCATCGCTAAGCACTATGAAACTGGAGAAACACTACC
genomic: GATGCTGTTGAATTACCTTCTCAATTCATGGAAAATTGGTGTTACCACAGgtacttttct ... gttgctgcagGGATACTTTGATGAGCATCGCTAAGCACTATGAAACTGGAGAAACACTACC
EST: gi|71887581|gb|DT036636.1|DT036636
EST:     ATGCTGTTGAATTACCTTCTCAATTCATGGAAAATTGGTG-TACCCACAG                         GGATACTTTGATGAGCATCGCTAAGCACTATGAAACTGGAGAAACACTAC
genomic: ATGCTGTTGAATTACCTTCTCAATTCATGGAAAATTGGTGTTA-CCACAGgtacttttct ... gttgctgcagGGATACTTTGATGAGCATCGCTAAGCACTATGAAACTGGAGAAACACTAC
EST: gi|77579724|gb|DV218723.1|DV218723
EST:     GATGCTGTTGAATTACCTTCTCAATTCATGGAAAATTGGTGTTACCACAG                         GGATACTTTGATGAGCATCGCTAAGCACTATGAAACTGGAGAAACACTACC
genomic: GATGCTGTTGAATTACCTTCTCAATTCATGGAAAATTGGTGTTACCACAGgtacttttct ... gttgctgcagGGATACTTTGATGAGCATCGCTAAGCACTATGAAACTGGAGAAACACTACC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatatggtcaacatgtatgatgctgaccatttgaattcattaatggttgctgcagGGATACTTTGATGAGCATCGCTAAGCACTATGAAACTGGAGAAACACTACCTGAAGATGTGTATTTGAAACTTGTTGCAGCAAGGACTTTTCGTGCCGGG
                            atttgaattcattaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
taaagtgggcaatgactacaagggagggagtgcgccgttacaacttatatggtcaacatgtatgatgctgaccatttgaattcattaatggttgctgcagGGATACTTTGATGAGCATCGCTAAGCACTATGAAACTGGAGAAACACTACCTGAAGATGTGTATTTGAAACTTGTTGCAGCAAGGACTTTTCGTGCCGGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - gcaatga
- - - - - - - - - - -gggaggg
- - - - - - - - - - - - - - - - - - - - - - - - - - -caacatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctgacca