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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtatgtcactgatgcatgctatcttatccataaaatgtgaagcaaggcttcatgctcattaaatgtttgttgatcttgtacattaatgttgtatctgcagTTCTCACCCACATCAGAGCATTTATTACTTGCCTATGGGCGTCGCCATAATTCACTTCTCAAAAGTATTGTCATTGATGGGGAGACAACAGTGCCTATTT

Basic information

species Vitis vinifera
transcript Vv05s0077g00140.t01
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv05s0077g00140.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: LOC_Os09g12550.1 (Oryza sativa), 3'ss of exon 11
-gtatgtcactgatgcatgctatcttatccataaaatgtgaagcaaggcttcatgctcattaaatgtttgttgatcttgtacattaatgttgtat-ctgcagTTCTCACCCACATCAGAGCATTTATTACTTGCCTATGGGCGTCGCCATAATTCACTTCTCAAAAGTATTGTCATTGATGGGGAGACAACAGTGCCTATTT
   |      || || |   |    ||    | |    | ||    ||  | ||| | ||   |  | ||||   | || |   || | || |   |||||||| ||||| |||||||||||  || |||| || ||||| ||||| ||||| |||||||| |   | ||| |||| |||||  |||| ||| | ||| | |
ctaacccttttggtggacaattctgtagttctgatcatttaattttggactgatg-tgatatgaaatctgttctgcatg-atgatatttttattcgctgcagTTTTCACCTACATCAGAGCACATACTACTGGCATATGGTCGTCGTCATAACTCACTTCTGAGGGGCATTTTCATGGATGGCAAGACCACAATCCCTGTGT
















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|30129161|gb|CB914500.1|CB914500
EST:     CATTGTTTAACTTCAATTCAG                         TTCTCACCCACATCAGAGCATTTATTACTTGCCTATGGGCGTCGCCATAAT
genomic: CATTGTTTAACTTCAATCCAGgtcagctgct ... gtatctgcagTTCTCACCCACATCAGAGCATTTATTACTTGCCTATGGGCGTCGCCATAAT
EST: gi|30125879|gb|CB911218.1|CB911218
EST:     CATTGTTTAACTTCAATTCAG                         TTCTCACCCACATCAGAGCATTTATTACTTGCCTATGGGCGTCGCCATAAT
genomic: CATTGTTTAACTTCAATCCAGgtcagctgct ... gtatctgcagTTCTCACCCACATCAGAGCATTTATTACTTGCCTATGGGCGTCGCCATAAT
EST: gi|32457197|gb|CD798371.1|CD798371
EST:     CTTTTGCGTCACGAGCAATACGAGCTGCTCATTGTTTAACTTCAATTCAG                         TTCTCACCCACATCAGAGCATTTATTACTTGCCTATGGGCGTCGCCATAAT
genomic: C--TTGCGTCACGAGCAATACGAGCTGCTCATTGTTTAACTTCAATCCAGgtcagctgct ... gtatctgcagTTCTCACCCACATCAGAGCATTTATTACTTGCCTATGGGCGTCGCCATAAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggcttcatgctcattaaatgtttgttgatcttgtacattaatgttgtatctgcagTTCTCACCCACATCAGAGCATTTATTACTTGCCTATGGGCGTCGCCATAATTCACTTCTCAAAAGTATTGTCATTGATGGGGAGACAACAGTGCCTATTT
                                   cattaat  putative branch site (score: 3)
            attaaatgtttgtt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgtcactgatgcatgctatcttatccataaaatgtgaagcaaggcttcatgctcattaaatgtttgttgatcttgtacattaatgttgtatctgcagTTCTCACCCACATCAGAGCATTTATTACTTGCCTATGGGCGTCGCCATAATTCACTTCTCAAAAGTATTGTCATTGATGGGGAGACAACAGTGCCTATTT

gtatgtc
- - - - - - -gcatgct
- - - - - - - - - - - - - -ccataaa
- - - - - - - - - - - - - - - - - - - gaagcaa
- - - - - - - - - - - - - - - - - - - - - - - - - catgctc