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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...caaatgcgcatgtctgatagtgacatagtgtgaatcagactaataaggtattgaatttgcatttttctggttcttttaactcttttgcttccaattgcagCTTGCTACCAACACCTTGGAACGGGTTGCGCCGCTTACACATGCAGTTGGAAATGTGTTGAAGCGAGTTTTTGTCATTGGATTCTCCATTGTTATATTCG

Basic information

species Vitis vinifera
transcript Vv01s0011g00600.t01
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv01s0011g00600.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: PP1S450_17V6.1 (Physcomitrella patens), 3'ss of exon 9
caaatgcgcatgtctgatagtgacatagtgtgaatcagactaataaggtattga-atttgcatttttctggttcttttaactcttttgcttccaattgcagCTTGCTACCAACACCTTGGAACGGGTTGCGCCGCTTACACATGCAGTTGGAAATGTGTTGAAGCGAGTTTTTGTCATTGGATTCTCCATTGTTATATTCG
  |  | |   |  |||  | |  |   ||  |    |  | ||    | |||     |    || | |        |||   ||  | |      |||||||||||| |||||| |||||| ||||||| || || || ||||| || || || |||||||||||||| ||||| || || |||||||| ||  | ||||
tgatagtgtg-gaatgagggggcgagtttgccaggaggcgtcatggaatgttggtggcttttgttgtgtaagagaagtaagagttgcggtgggttgtgcagCTTGCTAACAACACATTGGAAAGGGTTGCTCCCCTGACTCATGCCGTGGGGAACGTGTTGAAGCGAGTGTTTGTGATCGGGTTCTCCATCGTGGTGTTCG
















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|34362742|gb|CF404327.1|CF404327
EST:     ATCTGTACAATCAG                         CTTGCTACCAACACCTTGGAACGGGTTGCGCCGCTTACACATGCAGTTGGA
genomic: ATCTGTACAATCAGgtaagccaca ... ccaattgcagCTTGCTACCAACACCTTGGAACGGGTTGCGCCGCTTACACATGCAGTTGGA
EST: gi|71884544|gb|DT033599.1|DT033599
EST:     TTTTGTCTGATCTATTTTGGATTGGAATGTTTTACCATCTGTACAATCAG                         CTTGCTACCAACACCTTGGAACGGGTTGCGCCGCTTACACATGCAGTTGGA
genomic: TTTTGTCTGATCTATTTTGGATTGGAATGTTTTACCATCTGTACAATCAGgtaagccaca ... ccaattgcagCTTGCTACCAACACCTTGGAACGGGTTGCGCCGCTTACACATGCAGTTGGA
EST: gi|110365764|gb|EC929197.1|EC929197
EST:     TTTTGTCTGATCTATTTTGGATTGGAATGTTTTACCATCTGTACAATCAG                         CTTGCTACCAACACCTTGGAACGGGTTGCGCCGCTTACACATGCAGTTGGA
genomic: TTTTGTCTGATCTATTTTGGATTGGAATGTTTTACCATCTGTACAATCAGgtaagccaca ... ccaattgcagCTTGCTACCAACACCTTGGAACGGGTTGCGCCGCTTACACATGCAGTTGGA
EST: gi|351034668|gb|FQ458025.1|FQ458025
EST:     TTTTGTCTGATCTATTTTGGATTGGAATGTTTTACCATCTGTACAATCAG                         CTTGCTACCAACACCTTGGAACGGGTTGCGCCGCTTACACATGCAGTTGGA
genomic: TTTTGTCTGATCTATTTTGGATTGGAATGTTTTACCATCTGTACAATCAGgtaagccaca ... ccaattgcagCTTGCTACCAACACCTTGGAACGGGTTGCGCCGCTTACACATGCAGTTGGA
EST: gi|22012480|gb|BQ797514.1|BQ797514
EST:     TTTTGTCTGATCTATTTTGGATTGGAATGTTTTACCATCTGTACAATCAG                         CTTGCTACCAACACCTTGGAACGGGTTGCGCCGCTTACACATGCAGTTGGA
genomic: TTTTGTCTGATCTATTTTGGATTGGAATGTTTTACCATCTGTACAATCAGgtaagccaca ... ccaattgcagCTTGCTACCAACACCTTGGAACGGGTTGCGCCGCTTACACATGCAGTTGGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aggtattgaatttgcatttttctggttcttttaactcttttgcttccaattgcagCTTGCTACCAACACCTTGGAACGGGTTGCGCCGCTTACACATGCAGTTGGAAATGTGTTGAAGCGAGTTTTTGTCATTGGATTCTCCATTGTTATATTCG
                            ttttaac  putative branch site (score: 2)
                         ttcttttaactctttt  CT-rich tract
                         ttcttttaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
caaatgcgcatgtctgatagtgacatagtgtgaatcagactaataaggtattgaatttgcatttttctggttcttttaactcttttgcttccaattgcagCTTGCTACCAACACCTTGGAACGGGTTGCGCCGCTTACACATGCAGTTGGAAATGTGTTGAAGCGAGTTTTTGTCATTGGATTCTCCATTGTTATATTCG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
caaatgc
- - - -gcatgtc
- - - - - - - - - - - - - - - - aatcaga
- - - - - - - - - - - - - - - - - - - - -aataagg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cttttgc