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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cagaaatagaagggaagcgtgaccctgtaattgtgtgaaccattccttctgtttcagtgggttcataactgcaaagttttctcttgtcattgaactacagATTGATGGATGTTAAACAAAGCCTGAATAAGGAAGGGAAAACGGTTCTGTACTTGGTGTTTGAGTATATGGACACTGATCTTAAGAAGTATATCCGAAGC

Basic information

species Vitis vinifera
transcript Vv18s0122g00550.t01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv18s0122g00550.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA07G07640.1 (Glycine max), 3'ss of exon 1
-cagaaatagaagggaagcgtgaccctgtaattgtgtgaaccattccttctgtttcagtgggttcataactgcaaagttttctcttgtcattgaactacagATTGATGGATGTTAAACAAAGCCTGAATAAGGAAGGGAAAACGGTTCTGTACTTGGTGTTTGAGTATATGGACACTGATCTTAAGAAGTATATCCGAAGC
  |   |   || |  ||  |     | | |||||   ||     |||| | ||||  ||   ||||  ||  || | ||| |    |||||   | |||| || |||||||| || ||| ||| ||| ||||||||||| || ||  ||||||||||||||||||| |||||||| ||||| ||||| |  |||||   |
gtattcaccaaatgttagtttcttggttttattgt---aatgtaaccttttctttctttgaaatcat--ctttaatggttttt----tcatt---ccacagCTTAATGGATGTGAAGCAAGGCCAGAACAAGGAAGGGAAGACAGTGTTGTACTTGGTGTTTGAGTACATGGACACCGATCTCAAGAAATTCATCCGCTCC

upper sequence: Vv18s0122g00550.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: PP1S127_92V6.1 (Physcomitrella patens), 3'ss of exon 1
cagaaatagaagggaagcgtgaccctgtaattgtgtgaaccattccttctgtttcagtgggttcataactgcaa---agttttctcttgtcattga--actacagATTGATGGATGTTAAACAAAGCCTGAATAAGGAAGGGAAAACGGTTCTGTACTTGGTGTTTGAGTATATGGACACTGATCTTAAGAAGTATATCCGAAGC----
       |  | |     | | | || |   |  ||   | ||| | |       |||| |   |||   |  |   || |  ||||| |   ||   ||| |||  |  |    ||  | ||   | |  | || |  || ||  |  | || |||||||| ||||| |||||||||||||||||||||||||||||  ||       
---tgccatgaagtttatg-ggctctatttcta-gtctccaatttcgtaatcactagtgtggctatagaggtcattcagataactcttatgggtgttcactccagGCTACTTTGCGTGGAGCA---CGTCGAGAAAGGCGGCAAGCCCATGCTCTACTTGGTCTTTGAATATATGGACACTGATCTTAAGAAGTATATT-GACTTGCAC
















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|351046614|gb|FQ453230.1|FQ453230
EST:     CGTGAGGTCTCCTTGCTTCGCATGTTATCCCGAGATCCCCATGTCGTCAG                         ATTGATGGATGTTAAACAAAGCCTGAATAAGGAAGGGAAAACGGTTCTGTA
genomic: CGTGAGGTCTCCTTGCTTCGCATGTTATCCCGAGATCCCCATGTCGTCAGgtcttcttta ... tgaactacagATTGATGGATGTTAAACAAAGCCTGAATAAGGAAGGGAAAACGGTTCTGTA
EST: gi|351056035|gb|FQ453496.1|FQ453496
EST:     CGTGAGGTCTCCTTGCTTCGCATGTTATCCCGAGATCCCCATGTCGTCAG                         ATTGATGGATGTTAAACAAAGCCTGAATAAGGAAGGGAAAACGGTTCTGTA
genomic: CGTGAGGTCTCCTTGCTTCGCATGTTATCCCGAGATCCCCATGTCGTCAGgtcttcttta ... tgaactacagATTGATGGATGTTAAACAAAGCCTGAATAAGGAAGGGAAAACGGTTCTGTA
EST: gi|110426132|gb|EC992529.1|EC992529
EST:     CGTGAGGTCTCCTTGCTTCGCATGTTATCCCGAGATCCCCATGTCGTCAG                         ATTGATGGATGTTAAACAAAGCCTGAATAAGGAAGGGAAAACGGTTCTGTA
genomic: CGTGAGGTCTCCTTGCTTCGCATGTTATCCCGAGATCCCCATGTCGTCAGgtcttcttta ... tgaactacagATTGATGGATGTTAAACAAAGCCTGAATAAGGAAGGGAAAACGGTTCTGTA
EST: gi|352795715|gb|FQ480303.1|FQ480303
EST:     CGTGAGGTCTCCTTGCTTCGCATGTTATCCCGAGATCCCCATGTCGTCAG                         ATTGATGGATGTTAAACAAAGCCTGAATAAGGAAGGGAAAACGGTTCTGTA
genomic: CGTGAGGTCTCCTTGCTTCGCATGTTATCCCGAGATCCCCATGTCGTCAGgtcttcttta ... tgaactacagATTGATGGATGTTAAACAAAGCCTGAATAAGGAAGGGAAAACGGTTCTGTA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttctgtttcagtgggttcataactgcaaagttttctcttgtcattgaactacagATTGATGGATGTTAAACAAAGCCTGAATAAGGAAGGGAAAACGGTTCTGTACTTGGTGTTTGAGTATATGGACACTGATCTTAAGAAGTATATCCGAAGC
                 tcataac  putative branch site (score: 2)
                               ttttctcttgtcatt  putative PPT
                           aaagtttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cagaaatagaagggaagcgtgaccctgtaattgtgtgaaccattccttctgtttcagtgggttcataactgcaaagttttctcttgtcattgaactacagATTGATGGATGTTAAACAAAGCCTGAATAAGGAAGGGAAAACGGTTCTGTACTTGGTGTTTGAGTATATGGACACTGATCTTAAGAAGTATATCCGAAGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGT
- - aatagaa
- - - - - - - - - - -accctgt
- - - - - - - - - - - - - - - -tgtgtga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - gtgggtt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctgcaaa