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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgaaatactgaagttgattgcttctttatataatatctggagcataaatgtctaaaagttagttttatgtcgcatccgctaactgactttttattcacagATGATGCTGTTTCTGGTGGAATTCGTTCTTGGATTGCAACTGGAAGAAAAG

Basic information

species Vitis vinifera
transcript Vv01s0137g00630.t01
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv01s0137g00630.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: GLYMA14G05450.1 (Glycine max), 3'ss of exon 11
gtgaaatactgaagttgattgct-tctttatataatatctggagcataaatgtctaaaagttagttttatgtcgc-atccgctaac-tgacttt-ttattca--cagATGATGCTGTTTCTGGTGGAATTCGTTCTTGGATTGCAACTGGAAGAAAAG
|| |||    | |    |  | | ||| |||  |  ||    |       | | |  || |||  ||||||| |  |||   ||     ||||    | |||  ||| ||| | |  | ||  | | ||||| |||||||||||||||||||||||||
gtaaaaattagtaccaaaaagttatctctatgcagaattattaatgc---tatttctaattta--tttatgttgttatctaatagtgcaacttcaccaatcatgcagCTGAAGGTTATCCTAATCGGATTCGATCTTGGATTGCAACTGGAAGAAAAG
















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|37189209|gb|CF608558.1|CF608558
EST:     CCTTTTAAACAGTCATTCTGGTCTATGTGCAACTGTGAATGCGGTGCAAG                         ATGATGCTGTTTCTGGTGGAATTCGTTCTTGGATTGCAACTGGAAGA
genomic: CCTTTTAAACAGTCATTCTGGTCTATGTGCAACTGTGAATGCGGTGCAAGgtgaaatact ... ttattcacagATGATGCTGTTTCTGGTGGAATTCGTTCTTGGATTGCAACTGGAAGA
EST: gi|32245921|gb|CD711740.1|CD711740
EST:     CCTTTTAAACAGTCATTCTGGTCTATGTGCAACTGTGAATGCGGTGCAAG                         ATGATGCTGTTTCTGGTGGAATTCGTTCTTGGATTGCAACTGGAAGAAAAG
genomic: CCTTTTAAACAGTCATTCTGGTCTATGTGCAACTGTGAATGCGGTGCAAGgtgaaatact ... ttattcacagATGATGCTGTTTCTGGTGGAATTCGTTCTTGGATTGCAACTGGAAGAAAAG
EST: gi|18459504|gb|BM437782.1|BM437782
EST:     CCTTTTAAACAGTCATTCTGGTCTATGTGCAACTGTGAATGCGGTGCAAG                         ATGATGCTGTTTCTGGTGGAATTCGTTCTTGGATTGCAACTGGAAGAAAAG
genomic: CCTTTTAAACAGTCATTCTGGTCTATGTGCAACTGTGAATGCGGTGCAAGgtgaaatact ... ttattcacagATGATGCTGTTTCTGGTGGAATTCGTTCTTGGATTGCAACTGGAAGAAAAG
EST: gi|37189485|gb|CF608834.1|CF608834
EST:     CCTTTTAAACAGTCATTCTGGTCTATGTGCAACTGTGAATGCGGTGCAAG                         ATGATGCTGTTTCTGGTGGAATTCGTTCTTGGATTGCAACTGGAAG
genomic: CCTTTTAAACAGTCATTCTGGTCTATGTGCAACTGTGAATGCGGTGCAAGgtgaaatact ... ttattcacagATGATGCTGTTTCTGGTGGAATTCGTTCTTGGATTGCAACTGGAAG
EST: gi|110380121|gb|EC945365.1|EC945365
EST:     CCTTTTAAACAGTCATTCTGGTCTATGTGCAACTGTGAATGCGGTGCAAG                         ATGATGCTGTTTCTGGTGGAATTCGTTCTTGGATTGCAACTGGAAGAAAAG
genomic: CCTTTTAAACAGTCATTCTGGTCTATGTGCAACTGTGAATGCGGTGCAAGgtgaaatact ... ttattcacagATGATGCTGTTTCTGGTGGAATTCGTTCTTGGATTGCAACTGGAAGAAAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaatgtctaaaagttagttttatgtcgcatccgctaactgactttttattcacagATGATGCTGTTTCTGGTGGAATTCGTTCTTGGATTGCAACTGGAAGAAAAG
                                   aactgac  putative branch site (score: 2)
                                         ctttttattc  CT-rich tract
       taaaagttagttttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgaaatactgaagttgattgcttctttatataatatctggagcataaatgtctaaaagttagttttatgtcgcatccgctaactgactttttattcacagATGATGCTGTTTCTGGTGGAATTCGTTCTTGGATTGCAACTGGAAGAAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA